Global Methane Hub Wikipedia - User contributions [en]

Methanobrevibacter wolinii SHT

2026-11-01T22:46:27Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Methanarmilla wolinii'' SHT'''

''Methanarmilla wolinii'' SHT (DSM 11976), formerly ''Methanobrevibacter wolinii'', is a hydrogenotrophic methanogen isolated from sheep faeces in the USA [1]. Characteristics of the culture have been described [1]. SH is the type strain of the species, and taxonomic revision resulted in the genus name being changed to ''Methanarmilla'' [2].

SH is the only isolate recorded for this species, but it is no longer available from DSMZ.

The draft genome for SH (2,041,814 bp) was generated through the Hungate1000 project with JGI [3]. Resequencing gave a genome of 2,067,659 bp. Analysis of the SH genome sequence has identified genes for alcohol and aldehyde dehydrogenases (HCBCBKED_00294-295) indicating that SH may be able to use alcohols as an alternative source of reducing potential for methanogenesis [4].

LPSN: ''Methanarmilla wolinii'' (Miller and Lin 2002) Protasov and Brune 2026.

NCBI: ''Methanobrevibacter wolinii''.

GTDB: ''Methanarmilla wolinii''.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Miller TL, Lin C. 2002. Description of ''Methanobrevibacter gottschalkii'' sp. nov., ''Methanobrevibacter thaueri'' sp. nov., ''Methanobrevibacter woesei'' sp. nov. and ''Methanobrevibacter wolinii'' sp. nov. Int J Syst Evol Microbiol 52: 819-822. doi. 10.1099/00207713-52-3-819.

[2] Protasov E, Shiratori M, Mies US, Kastle Silva J, Heimerl T, Platt K, Itoh T, Ohkuma M, Spring S, Oren A, Brune A. 2026. Taxonomic revision of the genus ''Methanobrevibacter'', description of ''Methanomonile shimae'' gen. nov. sp. nov., and proposal of ''Methanobrevibacteraceae'' fam. nov. Int J Syst Evol Microbiol 76: 7286. doi. 10.1099/ijsem.0.007286.

[3] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[4] Hoedt EC, Cuív PÓ, Evans PN, Smith WJ, McSweeney CS, Denman SE, Morrison M. 2016. Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids. ISME J 10: 2376-88. doi: 10.1038/ismej.2016.41.

Lachnospiraceae bacterium NK3A20

2026-11-01T20:44:56Z

Billkelleydonvis: /* Introduction */ and external links

== Introduction ==
'''''Lachnospiraceae'' bacterium NK3A20'''

''Lachnospiraceae'' bacterium NK3A20 was isolated from sheep rumen contents in NZ [1] and is a representative of one of the most abundant bacterial taxa found in the rumen [2]. NK3A20 has an extensive complement of glycosyl hydrolases and can ferment a wide range of carbohydrates. Acetate, butyrate and hydrogen are the main products from glucose fermentation, while acetate is the main product from galacturonic or glucuronic acid fermentation [3]. Like ''Butyrivibrio'' sp., NK3A20 has two distinct respiratory enzyme complexes, Rnf and Ech.

The draft genome for NK3A20 (2,958,954 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: Lachnospiraceae bacterium.

GTDB: CAG-791 sp900107575.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1]. Kenters N, Henderson G, Jeyanathan J, Kittelmann S, Janssen PH. 2011. Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium. J Microbiol Methods 84: 52-60. doi: 10.1016/j.mimet.2010.10.011.

[2] Henderson G, Cox F, Ganesh S, Jonker A, Young W, Global Rumen Census Collaborators, Janssen PH. 2015. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 5:14567. doi: 10.1038/srep14567.

[3] Kaminsky RA, Reid PM, Altermann E, Kenters N, Kelly WJ, Noel SJ, Attwood GT, Janssen PH. 2023. Rumen Lachnospiraceae isolate NK3A20 exhibits metabolic flexibility in response to substrate and coculture with a methanogen. Appl Environ Microbiol 89 :e0063423. doi: 10.1128/aem.00634-23.

[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Lachnospiraceae bacterium YSB2008

2026-11-01T20:43:05Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Lachnospiraceae'' bacterium YSB2008'''

''Lachnospiraceae'' bacterium YSB2008 (DSM 121616) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow B]. It has not been phenotypically characterized.

Group A3 [FeFe]-hydrogenases appear to be the primary catalysts of H2 production in ruminants. YSB2008 represents one of the uncharacterised cultured lineages that encodes group A3 [FeFe]-hydrogenases [2].

The draft genome for YSB2008 (2,686,267 bp) was generated through the Hungate1000 project with JGI [3].

NCBI: ''Lachnospiraceae'' bacterium.

GTDB: ''Eubacterium_Q'' sp000687655.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI. 2019. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME J 13: 2617-2632. doi: 10.1038/s41396-019-0464-2.

[3] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Lachnospiraceae bacterium NK4A136

2026-11-01T20:41:36Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Lachnospiraceae'' bacterium NK4A136'''

''Lachnospiraceae'' bacterium NK4A136 (DSM 121584) was isolated from sheep rumen contents in NZ [1]. It has not been phenotypically characterized. In GTDB NK4A136 is used as the name of an uncharacterized genus within the family ''Lachnospiraceae''.

The draft genome for NK4A136 (2,730,030 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: ''Lachnospiraceae'' bacterium.

GTDB: NK4A136 sp000687675.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1]. Kenters N, Henderson G, Jeyanathan J, Kittelmann S, Janssen PH. 2011. Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium. J Microbiol Methods 84: 52-60. doi: 10.1016/j.mimet.2010.10.011.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Lachnospiraceae bacterium ND2006

2026-10-30T03:22:11Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Lachnospiraceae'' bacterium ND2006'''

''Lachnospiraceae'' bacterium ND2006 (DSM 121559) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow D]. ND2006 is Gram negative, non-motile and can ferment a wide range of carbohydrates. Growth on glucose produced lactate with lower amounts of acetate, butyrate, formate and hydrogen. In GTDB ND2006 has been assigned to an uncharacterized genus (NK4A144) within the family ''Lachnospiraceae''.

The ND2006 genome encodes a CRISPR-Cas12a system (LbCas12a/LbCpf1) [2, 3] that has been widely used for gene editing.

The draft genome for ND2006 (3,945,387 bp) was generated through the Hungate1000 project with JGI [4].

NCBI: ''Lachnospiraceae'' bacterium.

GTDB: NK4A144 sp900114405.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK. 2016. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nat Biotechnol 34: 869-74. doi: 10.1038/nbt.3620.

[3] <nowiki>https://undark.org/2025/03/05/digital-genetic-data-ownership/</nowiki>

[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Lachnospiraceae bacterium FE2018

2026-10-30T03:20:31Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Lachnospiraceae'' bacterium FE2018'''

''Lachnospiraceae'' bacterium FE2018 was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow E]. It has not been phenotypically characterized, but the genome encodes a lactate utilization gene cluster. In GTDB FE2018 has been assigned to an uncharacterized genus (CADBRN01) within the family ''Lachnospiraceae''.

The draft genome for FE2018 (3,213,641 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: ''Lachnospiraceae'' bacterium.

GTDB: CADBRN01 sp000702845.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Lachnospiraceae bacterium FD2005

2026-10-30T03:19:13Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Lachnospiraceae'' bacterium FD2005'''

''Lachnospiraceae'' bacterium FD2005 was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow D]. It has not been phenotypically characterized. In GTDB FD2005 is used as the name of an uncharacterized genus within the family ''Lachnospiraceae''.

The draft genome for FD2005 (2,440,715 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: ''Lachnospiraceae'' bacterium.

GTDB: FD2005 sp000702525.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Lachnospiraceae bacterium AC2014

2026-10-30T03:17:54Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Lachnospiraceae'' bacterium AC2014'''

''Lachnospiraceae'' bacterium AC2014 (DSM 118844) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow C]. It has not been phenotypically characterized, but was identified as a strain of ''Agathobacter ruminis'', a carbohydrate-fermenting bacterium that produces butyrate, acetate, lactate and hydrogen [2].

The draft genome for AC2014 (2,760,118 bp) was generated through the Hungate1000 project with JGI [3].

NCBI: ''Lachnospiraceae'' bacterium.

GTDB: ''Roseburia ruminis''. AC2014 belongs in the same species group as the type strain of ''A. ruminis''/''R. ruminis'' (JK623, DSM 29029) [2].

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Rosero JA, Killer J, Sechovcova H, Mrazek J, Benada O, Fliegerova K, Havlik J, Kopecny J. 2016. Reclassification of ''Eubacterium rectale'' (Hauduroy et al. 1937) Prevot 1938 in a new genus ''Agathobacter'' gen. nov. as ''Agathobacter rectalis'' comb. nov., and description of ''Agathobacter ruminis'' sp. nov., isolated from the rumen contents of sheep and cows. Int J Syst Evol Microbiol 66: 768-773. doi: 10.1099/ijsem.0.000788.

[3] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Lachnospira multipara D32T

2026-10-30T03:16:20Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Lachnospira multipara'' D32T'''

''Lachnospira multipara'' D32T (DSM 3073) was isolated from bovine rumen contents, from an animal fed a ration of alfalfa hay and grain, in the USA [1]. D32 produces woolly colonies and ferments a range of carbohydrates producing acetate, formate, butyrate and ethanol along with CO2 and a small amount of hydrogen. ''Lachnospira multipara'' is regarded as one of the main rumen bacteria involved in pectin metabolism [2] and the D32 genome encodes pectin methylesterases predicted to produce methanol [3], a substrate for methylotrophic methanogens. D32 is the type species of the genus ''Lachnospira'' within the family ''Lachnospiraceae'' and the type stain of the ''L. multipara'' species [4].

The draft genome for D32 (2,871,860 bp) was generated through the Hungate1000 project with JGI [5]. It is likely that the D32 genome has a large plasmid that encodes Ech hydrogenase, hydrogenase maturation proteins and a cell-wall associated pectin methylesterase, similar to ''Butyrivibrio fibrisolvens'' D1.

LPSN: ''Lachnospira multipara'' corrig. Bryant and Small 1956.

NCBI: ''Lachnospira multipara''.

GTDB: ''Lachnospira multipara''.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Bryant MP, Small N. 1956. Characteristics of two new genera of anaerobic curved rods isolated from the rumen of cattle. J Bacteriol 72: 22-26. doi: 10.1128/jb.72.1.22-26.1956.

[2] Dehority BA. 1969. Pectin-fermenting bacteria isolated from the bovine rumen. J Bacteriol 99: 189-96. doi: 10.1128/jb.99.1.189-196.1969.

[3] Kelly WJ, Leahy SC, Kamke J, Soni P, Koike S, Mackie R, Seshadri R, Cook GM, Morales SE, Greening C, Attwood GT. 2019. Occurrence and expression of genes encoding methyl-compound production in rumen bacteria. Anim Microbiome 1: 15. doi: 10.1186/s42523-019-0016-0.

[4] <nowiki>https://bacdive.dsmz.de/strain/6359</nowiki>.

[5] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Lachnobacterium bovis AE2004

2026-10-30T03:14:30Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Lachnobacterium bovis'' AE2004'''

''Lachnobacterium bovis'' AE2004 (DSM 120349) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow E]. It has not been phenotypically characterized, but was identified as a strain of ''Lachnobacterium bovis'', a carbohydrate-fermenting bacterium that produces lactate and minor amounts of acetate and butyrate [2]. ''Lachnobacterium'' is a genus within the family ''Lachnospiraceae''.

The draft genome for AE2004 (2,844,447 bp) was generated through the Hungate1000 project with JGI [3].

NCBI: ''Lachnobacterium bovis.''

GTDB: ''Roseburia bovis_A''. AE2004 belongs to a different species group than the ''L. bovis''/''R. bovis'' type strain (YZ 87, DSM 14045) [2].

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Whitford MF, Yanke LJ, Forster RJ, Teather RM. ''Lachnobacterium bovis'' gen. nov., sp. nov., a novel bacterium isolated from the rumen and faeces of cattle. 2001. Int J Syst Evol Microbiol 51: 1977-1981. doi: 10.1099/00207713-51-6-1977.

[3] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Ruminococcus albus AD2013

2026-10-29T21:22:37Z

Billkelleydonvis: /* Strain history and information */

== Introduction ==

=== Strain characteristics and function in the rumen ===

=== Strain history and information ===
'''''Ruminococcus albus'' AD2013'''

''Ruminococcus albus'' AD2013 (DSM 115563) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow D]. AD2013 has not been phenotypically characterized but its genome encodes a broad range of carbohydrate active enzymes, as well as proteins containing dockerin and carbohydrate-binding domains. AD2013 is predicted to be cellulolytic, and to have similar metabolism to ''Ruminococcus albus'' 7.

The draft genome for AD2013 (4,234,989 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: ''Ruminococcus albus''/''Hominimerdicola alba''

GTDB: ''Hominimerdicola alba_A''. AD2013 belongs to a different species group than the type strain of ''H. alba'' (7, DSM 20455) [3].

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
| valign="top" |Strain origin:
| valign="top" |New Zealand
|-
| valign="top" |Isolated from:
| valign="top" |Cow rumen
|-
| valign="top" |Sequenced by:
| valign="top" |
|-
| valign="top" |Assembled by:
| valign="top" |William G. Alexander
|-
| valign="top" |Genome and methylome analysis by:
| valign="top" |
|-
| valign="top" |MIC and culturing conditions by:
| valign="top" |
|-
| valign="top" |Transformed by:
| valign="top" |
|}

== Genome ==
{| class="wikitable"
| colspan="2" valign="top" |''R. albus'' AD2013 Genome Summary
|-
| valign="top" |Sequencing method
| valign="top" |Oxford Nanopore
|-
| valign="top" |Contigs
| valign="top" |
|-
| valign="top" |Base pairs
| valign="top" |
|-
| valign="top" |CDSs
| valign="top" |
|-
| valign="top" |CRISPR
| valign="top" |
|-
| valign="top" |Genes
| valign="top" |
|-
| valign="top" |rRNA
| valign="top" |
|-
| valign="top" |tRNA
| valign="top" |
|-
| valign="top" |Miscellaneous RNA
| valign="top" |
|-
| valign="top" |Antimicrobial resistance genes
| valign="top" |
|}

== Methylome ==

=== Methylome analysis summary results ===
{| class="wikitable"
| colspan="2" |''R. albus'' AD2013 Methylome Summary
|-
| valign="top" |Isolation Motif
| valign="top" |% Motif Methylation
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|}

=== DefenseFinder Results ===
{| class="wikitable"
| colspan="2" valign="top" |''R. albus'' AD2013 DefenseFinder Results
|-
| valign="top" |DefenseFinder System
| valign="top" |# Found
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|}

=== Methylating ''Escherichia coli'' strains ===
''E. coli'' strain AGXXXXX engineered to carry methytransferases X, X, X for methylating plasmid DNA for ''R. albus'' AD2013.

== Culturing Conditions ==

== Antimicrobial Susceptibility ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[3] Hisatomi A, Ohkuma M, Sakamoto M. 2026. ''Hominimerdicola intestinalis'' sp. nov. and ''Ruminococcus sporogenes'' sp. nov., isolated from human faeces, and reclassification of ''Ruminococcus albus'' Hungate 1957 as ''Hominimerdicola alba'' comb. nov. Int J Syst Evol Microbiol 76: 7091. doi: 10.1099/ijsem.0.007091.

Ruminococcus sp. HUN007

2026-10-29T21:19:22Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Ruminococcaceae'' sp. HUN007'''

''Ruminococcaceae'' sp. HUN007 was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1]. HUN007 has not been phenotypically characterized but its genome encodes a broad range of carbohydrate active enzymes, many of which contain cohesion and dockerin domains. HUN007 is predicted to be cellulolytic and to produce a functional cellulosome but is distinct from ''R. flavefaciens''. In GTDB HUN007 is used as the name of a genus within the family ''Ruminococcaceae''.

The draft genome for HUN007 (4,207,177 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: ''Ruminococcus'' sp.

GTDB: HUN007 sp000712055.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Ruminococcus flavefaciens AE3010

2026-10-29T21:17:49Z

Billkelleydonvis: /* Introduction */ and external links

[[File:Image4.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus flavefaciens'' AE3010.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus flavefaciens''''' '''AE3010'''

''Ruminococcus flavefaciens'' AE3010 is an obligately anaerobic, fibrolytic bacterium isolated from the rumen of a cow in New Zealand and selected as a key reference genome for the global Hungate1000 project [1]. Exhibiting the core phenotypic traits of the species, AE3010 relies on the breakdown of complex structural polysaccharides for growth, utilizing an extensive array of highly conserved cohesin and dockerin modules to assemble its specialized cell-surface cellulosome [2].

''Ruminococcus flavefaciens'' AE3010 (DSM 115568) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [3, cow E]. AE3010 has not been phenotypically characterized but its genome encodes a broad range of carbohydrate active enzymes, many of which contain cohesion and dockerin domains. Like other rumen ''R. flavefaciens'' strains AE3010 is predicted to be cellulolytic and to produce a functional cellulosome [4].

The draft genome for AE3010 (3,705,946 bp) was generated through the Hungate1000 project with JGI [1].

NCBI: ''Ruminococcus flavefaciens''.

GTDB: ''Ruminococcus flavefaciens_D''. AE3010 belongs to a different species group than the type strain of ''R. flavefaciens'' (C94, ATCC 19208).

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|United States of America, Macike lab
|-
|Sequenced by:
|Makoto Adachi
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|Roy Rodriguez Carrero
|-
|MIC and Culturing Conditions by:
|Roy Rodriguez Carrero
|-
|Transformation by:
|
|}

== Genome ==
[[File:55RBRH 1 Rum E3010 1 circos.png|center|thumb|300x300px|Circos plot of ''R. flavefaciens'' AE3010. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
| valign="middle" |Motif
| valign="middle" |Percent methylated
|-
| valign="middle" |TGAA(6mA)T
| valign="middle" |99.49
|-
| valign="middle" |CTTG(6mA)YG
| valign="middle" |99.76
|-
| valign="middle" |CG(6mA)CC
| valign="middle" |97.15
|-
| valign="middle" |CACA(6mA)T
| valign="middle" |97.75
|}

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
''R. flavefaciens'' AE3010 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. falvefaciens'' AE3010 on M10 agar is close to 66%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.5
|-
|Chlorhamphenicol
|0.3
|-
|Erythromycin
|1.6
|-
|Gentamycin
|0.5
|-
|Kanamycin
|4.7
|-
|Streptomycin
|0.5
|-
|Tetracycline
|0.1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D, Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2018. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol 36:359–367.

[2] Minor CM, Takayesu A, Ha SM, Salwinski L, Sawaya MR, Pellegrini M, Clubb RT. 2024. A genomic analysis reveals the diversity of cellulosome displaying bacteria. Front Microbiol 15:1473396.

[3] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[4] Moraïs S, Winkler S, Zorea A, Levin L, Nagies FSP, Kapust N, Lamed E, Artan-Furman A, Bolam DN, Yadav MP, Bayer EA, Martin WF, Mizrahi I. 2024. Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans. Science 383(6688): eadj9223. doi: 10.1126/science.adj9223.

Ruminococcaceae bacterium AE2021

2026-10-29T21:14:46Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Saccharofermentans'' sp. AE2021'''

''Saccharofermentans'' sp. AE2021(DSM 122476) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow E]. AE2021 has not been phenotypically characterized. ''Saccharofermentans'' is one of the 14 genera regarded as part of the rumen core microbiome [2], and another ''Saccharofermentans'' strain (R-25) contributes to fibre digestion in the rumen with production of D-lactate [3].

The draft genome for AE3010 (3,083,950 bp) was generated through the Hungate1000 project with JGI [4].

NCBI: ''Ruminococcaceae'' bacterium.

GTDB: ''Saccharofermentans'' sp900176545.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Tovar-Herrera OE, Grinshpan I, Sorek G, Lybovits I, Levin L, Moraïs S, Mizrahi I. 2026. Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function. Nat Ecol Evol 10: 44-58. doi: 10.1038/s41559-025-02904-3.

[3] Fukuma N, Koike S, Kobayashi Y. 2012. Involvement of recently cultured group U2 bacterium in ruminal fiber digestion revealed by coculture with ''Fibrobacter succinogenes'' S85. FEMS Microbiol Lett 336: 17-25. doi: 10.1111/j.1574-6968.2012.02649.x.

[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Bacteroidales bacterium WCE2004

2026-10-28T23:05:00Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Bacteroidales'' bacterium WCE2004'''

''Bacteroidales'' bacterium WCE2004 was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow E]. It has not been phenotypically characterized but the genome encodes numerous glycosyl hydrolases suggesting a role in polysaccharide degradation. WCE2004 belongs in the proposed genus “''Candidatus'' Cryptobacteroides". In GTDB ''Cryptobacteroides'' is a genus within the unnamed family UBA932. These bacteria are abundant in the rumen (formerly referred to as the RC-9 gut group), but very few cultures have been isolated.

The draft genome for WCE2004 (2,322,854 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: ''Bacteroidales'' bacterium.

GTDB: ''Cryptobacteroides'' sp900167895.

Risk group: Not assigned.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Bacteroidales bacterium Ga6A1

2026-10-28T23:02:33Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Bacteroidaceae'' bacterium Ga6A1'''

''Bacteroidaceae'' bacterium Ga6A1 was isolated from bovine rumen contents using galacturonic acid-containing media in NZ [1]. It has not been phenotypically characterised, but the genome encodes numerous glycosyl hydrolases and polysaccharide lyases suggesting a role in polysaccharide degradation. In GTDB Ga6A1 is used as the name of a genus within the family ''Bacteroidaceae''.

The draft genome for Ga6A1 (3,848,685 bp) was generated through the Hungate1000 project with JGI [1].

NCBI: ''Bacteroides'' sp.

GTDB: Ga6A1 sp900102385.

Risk group: Not assigned.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

List of GMH Strains

2026-10-28T20:16:21Z

Billkelleydonvis: Changed genus name for M. wolinii

* [[Acetitomaculum ruminis 139BT|Acetitomaculum ruminis 139BT]]
* [[Acidaminococcus fermentans WCC6]]
* [[Anaerovibrio lipolyticus 5ST|Anaerovibrio lipolyticus 5ST]]
* [[Anaerovibrio lipolyticus LB2005]]
* [[Aristaeella hokkaidonensis R-7T|Aristaeella hokkaidonensis R-7T]]
* [[Aristaeella lactis WTE2008T|Aristaeella lactis WTE2008T]]
* [[Bacteroidales bacterium Ga6A1]]
* [[Bacteroidales bacterium WCE2004]]
* [[Ruminococcus productus B43]]
* [[Blautia schinkii BT|Blautia schinkii BT]]
* [[Butyrivibrio fibrisolvens D1T|Butyrivibrio fibrisolvens D1T]]
* [[Butyrivibrio fibrisolvens TB|''Butyrivibrio fibrisolvens'' TB]]
* [[Butyrivibrio hungatei MB2003|''Butyrivibrio hungatei'' MB2003]]
* [[Butyrivibrio proteoclasticus B316ᵀ|Butyrivibrio proteoclasticus B316T]]
* [[Clostridium aminophilum FT|Clostridium aminophilum FT]]
* [[Desulfotomaculum ruminis DLT|Desulfotomaculum ruminis DLT]]
* [[Desulfovibrio desulfuricans G11]]
* [[Desulfovibrio legallii KHC7]]
* [[Eubacterium callanderi NLAE-zl-G225]]
* [[Eubacterium limosum RF]]
* [[Eubacterium maltosivorans SA11]]
* [[Eubacterium sp. AB3007]]
* [[Fibrobacter succinogenes S85T|Fibrobacter succinogenes S85T]]
* [[Kandleria vitulina WCE2011]]
* [[Lachnobacterium bovis AE2004]]
* [[Lachnospira multipara D32T]]
* [[Lachnospiraceae bacterium AC2014]]
* [[Lachnospiraceae bacterium FD2005]]
* [[Lachnospiraceae bacterium FE2018]]
* [[Lachnospiraceae bacterium ND2006]]
* [[Lachnospiraceae bacterium NK3A20]]
* [[Lachnospiraceae bacterium NK4A136]]
* [[Lachnospiraceae bacterium YSB2008]]
* [[Ligilactobacillus ruminis WC1T17]]
* [[Megasphaera elsdenii LC1T|Megasphaera elsdenii LC1T]]
* [[Megasphaera elsdenii T81]]
* [[Methanobacterium bryantii YCM1|''Methanobacterium bryantii'' YCM1]]
* [[Methanobacterium formicicum BRM9|''Methanobacterium formicicum'' BRM9]]
* [[Methanobrevibacter boviskoreani AbM4|''Methanarmilla boviskoreani'' AbM4]]
* ''[[Methanobrevibacter boviskoreani JH1T|Methanarmilla]] [[Methanobrevibacter boviskoreani JH1T|boviskoreani]]'' [[Methanobrevibacter boviskoreani JH1T|JH1T]]
* [[Methanocatella gottschalkii HO|''Methanocatella gottschalkii'' HO]]
* [[Methanobrevibacter gottschalkii PG|''Methanocatella gottschalkii'' PG]]
* [[Methanocatella millerae SM9|''Methanocatella millerae'' SM9]]
* [[Methanobrevibacter millerae ZA-10T|''Methanocatella millerae'' ZA-10T]]
* [[Methanobrevibacter olleyae 1H5-1PT|''Methanobrevibacter olleyae'' 1H5-1PT]]
* [[Methanobrevibacter olleyae YLM1|''Methanobrevibacter olleyae'' YLM1]]
* [[Methanobrevibacter ruminantium M1T|''Methanobrevibacter ruminantium'' M1T]]
* [[Methanobrevibacter sp. D5]] - group 1 to check nomenclature
* [[Methanobrevibacter thaueri ISO4-G16|''Methanocatella thaueri'' G16]]
* [[Methanobrevibacter thaueri CWT|''Methanocatella thaueri'' CWT]]
* [[Methanobrevibacter woesei GST|''Methanocatella woesei'' GST]]
* [[Methanobrevibacter wolinii SHT|''Methanarmilla wolinii'' SHT]]
* [[Methanomassiliicoccales ISO4-G1|''Candidatus'' ''Methanoprimaticola sp.'' ISO4-G1]]
* ''[[Methanomassiliicoccales ISO4-H5|Methanomethylophilus sp.]]'' [[Methanomassiliicoccales ISO4-H5|ISO4-H5]]
* [[Methanomicrobium mobile 1T|''Methanomicrobium mobile'' 1T]]
* [[Methanosarcina barkeri CM1|''Methanosarcina barkeri'' CM1]]
* [[Methanosarcina thermophila Ms97|''Methanosarcina thermophila'' Ms97]]
* [[Methanosphaera sp. A4]] - group 1 to check nomenclature
* [[Methanosphaera sp. ISO3-F5*|''Methanosphaera sp.'' ISO3-F5*]]
* [[Olsenella sp. KH2P3]]
* [[Olsenella sp. KHGC19]]
* [[Peptostreptococcaceae bacterium VA2]]
* [[Porphyromonadaceae bacterium KH3R12]]
* [[Prevotella albensis M384T|Prevotella albensis M384T]]
* [[Prevotella brevis GA33T|Prevotella brevis GA33T]]
* [[Prevotella brevis P6B11]]
* [[Prevotella bryantii B14|''Prevotella bryanti''i B14]]
* [[Prevotella bryantii C21a|''Prevotella bryantii'' C21a]]
* [[Prevotella ruminicola 23T|''Prevotella ruminicola'' 23T]]
* [[Prevotella ruminicola KHP1]]
* [[Pseudobutyrivibrio ruminis A12-1T|Pseudobutyrivibrio ruminis A12-1T]]
* [[Pseudobutyrivibrio xylanivorans MA3014]]
* [[Ruminobacter amylophilus H18T|Ruminobacter amylophilus H18T]]
* [[Ruminococcaceae bacterium AE2021]]
* [[Ruminococcus albus 7|''Ruminococcus albus'' 7]]
* [[Ruminococcus albus 8|''Ruminococcus albus'' 8]]
* [[Ruminococcus albus AD2013]]
* [[Ruminococcus albus SY3]]
* [[Ruminococcus flavefaciens AE3010]]
* [[Ruminococcus flavefaciens 007c]]
* [[Ruminococcus flavefaciens 17]]
* [[Ruminococcus flavefaciens C94T|Ruminococcus flavefaciens C94T]]
* [[Ruminococcus flavefaciens FD-1]]
* [[Ruminococcus sp. HUN007]]
* [[Selenomonas bovis strain|Selenomonas bovis]] 8-14-1
* [[Selenomonas ruminantium AB3002]]
* [[Selenomonas ruminantium GA192|''Selenomonas ruminantium'' GA192T]]
* [[Selenomonas ruminantium HD4]]
* [[Selenomonas ruminantium PC18]]
* [[Selenomonas ruminantium subsp lactilytica TAM6421]]
* ''[[Sharpea azabuensis KH1P5|Sharpea azabuensis]]'' [[Sharpea azabuensis KH1P5|KH1P5]]
* [[Streptococcus bovis JB1]]
* [[Streptococcus equinus B315]]
* [[Succiniclasticum ruminis SE10T|Succiniclasticum ruminis SE10T]]
* [[Succinivibrio dextrinosolvens H5]]
* [[Terrisporobacter glycolicus KPPR-9]]

Streptococcus equinus B315

2026-10-28T19:51:07Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Streptococcus equinus'' B315'''

''Streptococcus equinus'' B315 was isolated from bovine rumen contents in NZ [1]. B315 is proteolytic, Gram positive, and able to ferment a wide range of carbohydrates. Its main fermentation product is lactate, together with succinate and acetate [1]. The B315 genome encodes two lantibiotic bacteriocin biosynthetic gene clusters.

The draft genome for B315 (1,786,673 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: ''Streptococcus equinus''.

GTDB: ''Streptococcus equinus''. B315 belongs to the same species group as the ''S. equinus'' type strain (DSM 20558).

Risk group: 2.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Attwood GT, Reilly K. 1995. Identification of proteolytic rumen bacteria isolated from New Zealand cattle. J Appl Bacteriol 79: 22-9. doi: 10.1111/j.1365-2672.1995.tb03119.x.

[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Olsenella sp. KHGC19

2026-10-28T19:48:29Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Olsenella'' sp. KHGC19'''

''Olsenella'' sp. KHGC19 (DSM 115844) was isolated from bovine rumen contents in NZ using KH medium which was supplemented with haemin and vitamin K [1]. KHGC19 is a non-motile, non-spore forming Gram positive, anaerobe which produces D-lactate as the main product from glucose fermentation. KHGC19 is a high G+C lactic acid bacterium and while originally identified as ''Olsenella'' it was subsequently assigned to the genus ''Parafannyhessea'' within the family ''Atopobiaceae'' [2]. However, its smaller genome size and repertoire of carbohydrate active enzymes is distinct from that for the type strain of ''Parafannyhessea umbonata'' (lac31, DSM 22620).

KHGC19 is of interest as it is one of the few rumen bacteria whose genome encodes the gene cluster for the enzyme choline trimethylamine lyase (CTMAL; EC:4.3.99.4) which generates trimethylamine a substrate for methylotrophic methanogens, especially members of the ''Methanomassiliicoccales'' [3]. In KHGC19, CTMAL is an enzyme complex composed of a catalytic choline utilisation polypeptide CutC, and an associated activating protein CutD, encoded by a 21 gene cluster that also contains genes encoding bacterial microcompartment proteins. A similar, slightly larger, CTMAL gene cluster is found in the type strain of ''Parafannyhessea umbonata''.

The draft genome for KHGC19 (2,057,956 bp) was generated through the Hungate1000 project with JGI [1].

NCBI: ''Parafannyhessea umbonata.''

GTDB: ''Olsenella_J umbonata_A.''

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[2] Zgheib R, Anani H, Meng MM, Mailhe M, Ricaboni D, Morand A, Caputo A, Traore SI, Fontanini A, Armstrong N, Raoult D, Fournier PE, 2021. New human-associated species of the family ''Atopobiaceae'' and proposal to reclassify members of the genus ''Olsenella''. Int J Syst Evol Microbiol 71. doi: 10.1099/ijsem.0.004819.

[3] Kelly WJ, Leahy SC, Kamke J, Soni P, Koike S, Mackie R, Seshadri R, Cook GM, Morales SE, Greening C, Attwood GT. 2019. Occurrence and expression of genes encoding methyl-compound production in rumen bacteria. Anim Microbiome 1: 15. doi: 10.1186/s42523-019-0016-0.

Olsenella sp. KH2P3

2026-10-28T19:43:35Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Tractidigestivibacter'' sp. KH2P3'''

''Tractidigestivibacter'' sp. KH2P3 was isolated from bovine rumen contents in NZ using KH medium which was supplemented with haemin and vitamin K [1]. KH2P3 is a non-motile, non-spore forming Gram positive, anaerobe which produces D-lactate as the main product from glucose fermentation. KH2P3 is a high G+C lactic acid bacterium and while originally identified as ''Olsenella'' it was subsequently assigned to the genus ''Tractidigestivibacter'' within the family ''Atopobiaceae'' [2].

''Tractidigestivibacter'' species encode glycyl radical enzyme (GRE) superfamily enzymes that catalyse reactions rarely found in other bacteria, such as aromatic amino acid decarboxylases that enable ''T. scatoligenes'' to produce skatole and p-cresol from tryptophan and tyrosine [3]. KH2P3 encodes two arylacetate decarboxylase gene clusters.

The draft genome for KH2P3 (2,421,020 bp) was generated through the Hungate1000 project with JGI [1].

NCBI: ''Olsenella'' sp.

GTDB: ''Tractidigestivibacter'' sp900119625

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|
|-
|Sequenced by:
|
|-
|Assembled by:
|
|-
|Methylome called by:
|
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[2] Zgheib R, Anani H, Meng MM, Mailhe M, Ricaboni D, Morand A, Caputo A, Traore SI, Fontanini A, Armstrong N, Raoult D, Fournier PE, 2021. New human-associated species of the family ''Atopobiaceae'' and proposal to reclassify members of the genus ''Olsenella''. Int J Syst Evol Microbiol 71. doi: 10.1099/ijsem.0.004819.

[3] Li X, Jensen RL, Højberg O, Canibe N, Jensen BB, 2015. ''Olsenella scatoligenes'' sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces. Int J Syst Evol Microbiol 65, 1227-1233. doi: 10.1099/ijs.0.000083.

Prevotella bryantii B14

2026-10-27T23:00:36Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Segatella bryantii'' B14'''

''Segatella bryantii'' B14 (DSM 11371), formerly ''Prevotella bryantii'', was isolated from rumen contents of a Holstein cow fed alfalfa hay in the USA [1]. It was originally named as ''Bacteroides ruminicola'' subsp. ''brevis'' and subsequently changed to ''Prevotella bryantii'' [2]. The strain was originally designated B14 but B14 is commonly used. B14 has been the focus of many studies and is able to ferment a wide range of carbohydrates [3, 4]. The genes involved in xylan degradation have been characterized [5].

Taxonomic analysis of the genus ''Prevotella'' lists B14 as the ''Segatella bryantii'' type strain [6]. However, NCBI now records B14 and C21a as belonging to the species ''Segatella baroniae'', although the reason for this is unclear.

Draft genome sequences are available for B14 (3.6 Mb) [7]. Resequencing indicates that ''Segatella bryantii'' strains (B14 and C21a) each have two replicons of ~2.5 and ~1.0 Mb. Two other sequenced ''P. bryantii'' cultures (TC1-1, TS1-5) have a similar genomic architecture suggesting this is a feature of this species.

The B14 genome encodes a large conjugative transposon [8] although this has not been characterized in detail or shown to be transferable. Based on the presence of a the traG gene (TIGR03783) large conjugative transposons may be encoded by other rumen ''Prevotella'' strains.

LPSN: ''Segatella bryantii'' (Avguštin et al. 1997) Hitch et al. 2023.

NCBI: ''Segatella baroniae''.

GTBD: ''Prevotella bryantii''.

Risk group: 2.

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|GTC(6mA)NNNNNRTC/G(6mA)YNNNNNTGAC
|75.00%/80.51%
|-
|GTHN(6mA)NCC
|76.99%
|-
|GTC(6mA)G
|71.12%
|-
|A(6mA)CNNNNNGGG/C(4mC)CNNNNNGTT
|82.78%/
|-
|GG(5mC)GT
|82.25%
|-
|A(5mC)GCC
|81.20%
|}

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Bryant MP, Small N, Bouma C, Chu H. 1958. ''Bacteroides ruminicola'' n. sp. and ''Succinimonas amylolytica''; the new genus and species. Species of succinic acid-producing anaerobic bacteria of the bovine rumen. J Bacteriol 76: 15-23. doi: 10.1128/jb.76.1.15-23.1958.

[2] Avgustin G, Wallace RJ, Flint HJ. 1997. Phenotypic diversity among ruminal isolates of ''Prevotella ruminicola'': proposal of ''Prevotella brevis'' sp. nov., ''Prevotella bryantii'' sp. nov., and ''Prevotella albensis'' sp. nov. and redefinition of ''Prevotella ruminicola''. Int J Syst Bacteriol 47: 284-8. doi: 10.1099/00207713-47-2-284.

[3] Accetto T, Avguštin G. 2019. The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut ''Prevotella'' species: A factor in their ubiquity? Syst Appl Microbiol 42: 107-116. doi: 10.1016/j.syapm.2018.10.001.

[4] <nowiki>https://bacdive.dsmz.de/strain/12536</nowiki>.

[5] Dodd D, Mackie RI, Cann IK. 2011. Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes. Mol Microbiol 79: 292-304. doi: 10.1111/j.1365-2958.2010.07473.x.

[6] Hitch TCA, Bisdorf K, Afrizal A, Riedel T, Overmann J, Strowig T, Clavel T. 2022. A taxonomic note on the genus ''Prevotella'': Description of four novel genera and emended description of the genera ''Hallella'' and ''Xylanibacter''. Syst Appl Microbiol 45: 126354. doi: 10.1016/j.syapm.2022.126354.

[7] Purushe J, Fouts DE, Morrison M, White BA, Mackie RI; North American Consortium for Rumen Bacteria; Coutinho PM, Henrissat B, Nelson KE. 2010. Comparative genome analysis of ''Prevotella ruminicola'' and ''Prevotella bryantii'': insights into their environmental niche. Microb Ecol 60: 721-9. doi: 10.1007/s00248-010-9692-8.

[8] Gorenc K, Accetto T, Avguštin G. 2012. Bioinformatic evidence and characterization of novel putative large conjugative transposons residing in genomes of genera ''Bacteroides'' and ''Prevotella''. Folia Microbiol (Praha) 57: 285-90. doi: 10.1007/s12223-012-0126-5.

Eubacterium callanderi NLAE-zl-G225

2026-10-27T01:24:30Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Eubacterium callanderi'' NLAE-zl-G225'''

''Eubacterium callanderi'' NLAE-zl-G225 was isolated from continuous culture enrichment of goat faecal samples in the USA [1]. NLAE-zl-G225 has not been phenotypically characterized but has a similar gene complement to E. maltosivorans SA11.

The draft genome for NLAE-zl-G225 (4,368,996 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: ''Eubacterium callanderi.''

GTDB: ''Eubacterium callanderi''. NLAE-zl-G225 belongs to the same species group as the ''E. callanderi'' type strain (FD, DSM 3662) [3].

Risk group: 1.

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Atherly T, Ziemer CJ. 2014. ''Bacteroides'' isolated from four mammalian hosts lack host-specific 16S rRNA gene phylogeny and carbon and nitrogen utilization patterns. Microbiologyopen 3: 225-38. doi: 10.1002/mbo3.159.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[3] Mountfort DO, Grant WD, Clarke R, Asher RA. 1988. ''Eubacterium callanderi'' sp. nov. that demethoxylates O-methoxylated aromatic acids to volatile fatty acids. Int J Syst Bacteriol 38: 254-258. doi: 10.1099/00207713-38-3-254.

List of GMH Strains

2026-10-27T00:51:19Z

Billkelleydonvis: Corrected spelling

* [[Acetitomaculum ruminis 139BT|Acetitomaculum ruminis 139BT]]
* [[Acidaminococcus fermentans WCC6]]
* [[Anaerovibrio lipolyticus 5ST|Anaerovibrio lipolyticus 5ST]]
* [[Anaerovibrio lipolyticus LB2005]]
* [[Aristaeella hokkaidonensis R-7T|Aristaeella hokkaidonensis R-7T]]
* [[Aristaeella lactis WTE2008T|Aristaeella lactis WTE2008T]]
* [[Bacteroidales bacterium Ga6A1]]
* [[Bacteroidales bacterium WCE2004]]
* [[Ruminococcus productus B43]]
* [[Blautia schinkii BT|Blautia schinkii BT]]
* [[Butyrivibrio fibrisolvens D1T|Butyrivibrio fibrisolvens D1T]]
* [[Butyrivibrio fibrisolvens TB|''Butyrivibrio fibrisolvens'' TB]]
* [[Butyrivibrio hungatei MB2003|''Butyrivibrio hungatei'' MB2003]]
* [[Butyrivibrio proteoclasticus B316ᵀ|Butyrivibrio proteoclasticus B316T]]
* [[Clostridium aminophilum FT|Clostridium aminophilum FT]]
* [[Desulfotomaculum ruminis DLT|Desulfotomaculum ruminis DLT]]
* [[Desulfovibrio desulfuricans G11]]
* [[Desulfovibrio legallii KHC7]]
* [[Eubacterium callanderi NLAE-zl-G225]]
* [[Eubacterium limosum RF]]
* [[Eubacterium maltosivorans SA11]]
* [[Eubacterium sp. AB3007]]
* [[Fibrobacter succinogenes S85T|Fibrobacter succinogenes S85T]]
* [[Kandleria vitulina WCE2011]]
* [[Lachnobacterium bovis AE2004]]
* [[Lachnospira multipara D32T]]
* [[Lachnospiraceae bacterium AC2014]]
* [[Lachnospiraceae bacterium FD2005]]
* [[Lachnospiraceae bacterium FE2018]]
* [[Lachnospiraceae bacterium ND2006]]
* [[Lachnospiraceae bacterium NK3A20]]
* [[Lachnospiraceae bacterium NK4A136]]
* [[Lachnospiraceae bacterium YSB2008]]
* [[Ligilactobacillus ruminis WC1T17]]
* [[Megasphaera elsdenii LC1T|Megasphaera elsdenii LC1T]]
* [[Megasphaera elsdenii T81]]
* [[Methanobacterium bryantii YCM1|''Methanobacterium bryantii'' YCM1]]
* [[Methanobacterium formicicum BRM9|''Methanobacterium formicicum'' BRM9]]
* [[Methanobrevibacter boviskoreani AbM4|''Methanarmilla boviskoreani'' AbM4]]
* ''[[Methanobrevibacter boviskoreani JH1T|Methanarmilla]] [[Methanobrevibacter boviskoreani JH1T|boviskoreani]]'' [[Methanobrevibacter boviskoreani JH1T|JH1T]]
* [[Methanocatella gottschalkii HO|''Methanocatella gottschalkii'' HO]]
* [[Methanobrevibacter gottschalkii PG|''Methanocatella gottschalkii'' PG]]
* [[Methanocatella millerae SM9|''Methanocatella millerae'' SM9]]
* [[Methanobrevibacter millerae ZA-10T|''Methanocatella millerae'' ZA-10T]]
* [[Methanobrevibacter olleyae 1H5-1PT|''Methanobrevibacter olleyae'' 1H5-1PT]]
* [[Methanobrevibacter olleyae YLM1|''Methanobrevibacter olleyae'' YLM1]]
* [[Methanobrevibacter ruminantium M1T|''Methanobrevibacter ruminantium'' M1T]]
* [[Methanobrevibacter sp. D5]] - group 1 to check nomenclature
* [[Methanobrevibacter thaueri ISO4-G16|''Methanocatella thaueri'' G16]]
* [[Methanobrevibacter thaueri CWT|''Methanocatella thaueri'' CWT]]
* [[Methanobrevibacter woesei GST|''Methanocatella woesei'' GST]]
* [[Methanobrevibacter wolinii SHT|''Methanobrevibacter wolinii'' SHT]]
* [[Methanomassiliicoccales ISO4-G1|''Candidatus'' ''Methanoprimaticola sp.'' ISO4-G1]]
* ''[[Methanomassiliicoccales ISO4-H5|Methanomethylophilus sp.]]'' [[Methanomassiliicoccales ISO4-H5|ISO4-H5]]
* [[Methanomicrobium mobile 1T|''Methanomicrobium mobile'' 1T]]
* [[Methanosarcina barkeri CM1|''Methanosarcina barkeri'' CM1]]
* [[Methanosarcina thermophila Ms97|''Methanosarcina thermophila'' Ms97]]
* [[Methanosphaera sp. A4]] - group 1 to check nomenclature
* [[Methanosphaera sp. ISO3-F5*|''Methanosphaera sp.'' ISO3-F5*]]
* [[Olsenella sp. KH2P3]]
* [[Olsenella sp. KHGC19]]
* [[Peptostreptococcaceae bacterium VA2]]
* [[Porphyromonadaceae bacterium KH3R12]]
* [[Prevotella albensis M384T|Prevotella albensis M384T]]
* [[Prevotella brevis GA33T|Prevotella brevis GA33T]]
* [[Prevotella brevis P6B11]]
* [[Prevotella bryantii B14|''Prevotella bryanti''i B14]]
* [[Prevotella bryantii C21a|''Prevotella bryantii'' C21a]]
* [[Prevotella ruminicola 23T|''Prevotella ruminicola'' 23T]]
* [[Prevotella ruminicola KHP1]]
* [[Pseudobutyrivibrio ruminis A12-1T|Pseudobutyrivibrio ruminis A12-1T]]
* [[Pseudobutyrivibrio xylanivorans MA3014]]
* [[Ruminobacter amylophilus H18T|Ruminobacter amylophilus H18T]]
* [[Ruminococcaceae bacterium AE2021]]
* [[Ruminococcus albus 7|''Ruminococcus albus'' 7]]
* [[Ruminococcus albus 8|''Ruminococcus albus'' 8]]
* [[Ruminococcus albus AD2013]]
* [[Ruminococcus albus SY3]]
* [[Ruminococcus flavefaciens AE3010]]
* [[Ruminococcus flavefaciens 007c]]
* [[Ruminococcus flavefaciens 17]]
* [[Ruminococcus flavefaciens C94T|Ruminococcus flavefaciens C94T]]
* [[Ruminococcus flavefaciens FD-1]]
* [[Ruminococcus sp. HUN007]]
* [[Selenomonas bovis strain|Selenomonas bovis]] 8-14-1
* [[Selenomonas ruminantium AB3002]]
* [[Selenomonas ruminantium GA192|''Selenomonas ruminantium'' GA192T]]
* [[Selenomonas ruminantium HD4]]
* [[Selenomonas ruminantium PC18]]
* [[Selenomonas ruminantium subsp lactilytica TAM6421]]
* ''[[Sharpea azabuensis KH1P5|Sharpea azabuensis]]'' [[Sharpea azabuensis KH1P5|KH1P5]]
* [[Streptococcus bovis JB1]]
* [[Streptococcus equinus B315]]
* [[Succiniclasticum ruminis SE10T|Succiniclasticum ruminis SE10T]]
* [[Succinivibrio dextrinosolvens H5]]
* [[Terrisporobacter glycolicus KPPR-9]]

List of GMH Strains

2026-10-27T00:49:12Z

Billkelleydonvis: Removed methanogen strains that are not available for the project

* [[Acetitomaculum ruminis 139BT|Acetitomaculum ruminis 139BT]]
* [[Acidaminococcus fermentans WCC6]]
* [[Anaerovibrio lipolyticus 5ST|Anaerivibrio lipolyticus 5ST]] (NB: do we really have an Anaerivibrio and an Anaerovibrio genus, or is one of these misspelled? Makoto: Yes we have (Illinois group). I fixed the missspell.)
* [[Anaerovibrio lipolyticus LB2005]]
* [[Aristaeella hokkaidonensis R-7T|Aristaeella hokkaidonensis R-7T]]
* [[Aristaeella lactis WTE2008T|Aristaeella lactis WTE2008T]]
* [[Bacteroidales bacterium Ga6A1]]
* [[Bacteroidales bacterium WCE2004]]
* [[Ruminococcus productus B43]]
* [[Blautia schinkii BT|Blautia schinkii BT]]
* [[Butyrivibrio fibrisolvens D1T|Butyrivibrio fibrisolvens D1T]]
* [[Butyrivibrio fibrisolvens TB|''Butyrivibrio fibrisolvens'' TB]]
* [[Butyrivibrio hungatei MB2003|''Butyrivibrio hungatei'' MB2003]]
* [[Butyrivibrio proteoclasticus B316ᵀ|Butyrivibrio proteoclasticus B316T]]
* [[Clostridium aminophilum FT|Clostridium aminophilum FT]]
* [[Desulfotomaculum ruminis DLT|Desulfotomaculum ruminis DLT]]
* [[Desulfovibrio desulfuricans G11]]
* [[Desulfovibrio legallii KHC7]]
* [[Eubacterium callanderi NLAE-zl-G225]]
* [[Eubacterium limosum RF]]
* [[Eubacterium maltosivorans SA11]]
* [[Eubacterium sp. AB3007]]
* [[Fibrobacter succinogenes S85T|Fibrobacter succinogenes S85T]]
* [[Kandleria vitulina WCE2011]]
* [[Lachnobacterium bovis AE2004]]
* [[Lachnospira multipara D32T]]
* [[Lachnospiraceae bacterium AC2014]]
* [[Lachnospiraceae bacterium FD2005]]
* [[Lachnospiraceae bacterium FE2018]]
* [[Lachnospiraceae bacterium ND2006]]
* [[Lachnospiraceae bacterium NK3A20]]
* [[Lachnospiraceae bacterium NK4A136]]
* [[Lachnospiraceae bacterium YSB2008]]
* [[Ligilactobacillus ruminis WC1T17]]
* [[Megasphaera elsdenii LC1T|Megasphaera elsdenii LC1T]]
* [[Megasphaera elsdenii T81]]
* [[Methanobacterium bryantii YCM1|''Methanobacterium bryantii'' YCM1]]
* [[Methanobacterium formicicum BRM9|''Methanobacterium formicicum'' BRM9]]
* [[Methanobrevibacter boviskoreani AbM4|''Methanarmilla boviskoreani'' AbM4]]
* ''[[Methanobrevibacter boviskoreani JH1T|Methanarmilla]] [[Methanobrevibacter boviskoreani JH1T|boviskoreani]]'' [[Methanobrevibacter boviskoreani JH1T|JH1T]]
* [[Methanocatella gottschalkii HO|''Methanocatella gottschalkii'' HO]]
* [[Methanobrevibacter gottschalkii PG|''Methanocatella gottschalkii'' PG]]
* [[Methanocatella millerae SM9|''Methanocatella millerae'' SM9]]
* [[Methanobrevibacter millerae ZA-10T|''Methanocatella millerae'' ZA-10T]]
* [[Methanobrevibacter olleyae 1H5-1PT|''Methanobrevibacter olleyae'' 1H5-1PT]]
* [[Methanobrevibacter olleyae YLM1|''Methanobrevibacter olleyae'' YLM1]]
* [[Methanobrevibacter ruminantium M1T|''Methanobrevibacter ruminantium'' M1T]]
* [[Methanobrevibacter sp. D5]] - group 1 to check nomenclature
* [[Methanobrevibacter thaueri ISO4-G16|''Methanocatella thaueri'' G16]]
* [[Methanobrevibacter thaueri CWT|''Methanocatella thaueri'' CWT]]
* [[Methanobrevibacter woesei GST|''Methanocatella woesei'' GST]]
* [[Methanobrevibacter wolinii SHT|''Methanobrevibacter wolinii'' SHT]]
* [[Methanomassiliicoccales ISO4-G1|''Candidatus'' ''Methanoprimaticola sp.'' ISO4-G1]]
* ''[[Methanomassiliicoccales ISO4-H5|Methanomethylophilus sp.]]'' [[Methanomassiliicoccales ISO4-H5|ISO4-H5]]
* [[Methanomicrobium mobile 1T|''Methanomicrobium mobile'' 1T]]
* [[Methanosarcina barkeri CM1|''Methanosarcina barkeri'' CM1]]
* [[Methanosarcina thermophila Ms97|''Methanosarcina thermophila'' Ms97]]
* [[Methanosphaera sp. A4]] - group 1 to check nomenclature
* [[Methanosphaera sp. ISO3-F5*|''Methanosphaera sp.'' ISO3-F5*]]
* [[Olsenella sp. KH2P3]]
* [[Olsenella sp. KHGC19]]
* [[Peptostreptococcaceae bacterium VA2]]
* [[Porphyromonadaceae bacterium KH3R12]]
* [[Prevotella albensis M384T|Prevotella albensis M384T]]
* [[Prevotella brevis GA33T|Prevotella brevis GA33T]]
* [[Prevotella brevis P6B11]]
* [[Prevotella bryantii B14|''Prevotella bryanti''i B14]]
* [[Prevotella bryantii C21a|''Prevotella bryantii'' C21a]]
* [[Prevotella ruminicola 23T|''Prevotella ruminicola'' 23T]]
* [[Prevotella ruminicola KHP1]]
* [[Pseudobutyrivibrio ruminis A12-1T|Pseudobutyrivibrio ruminis A12-1T]]
* [[Pseudobutyrivibrio xylanivorans MA3014]]
* [[Ruminobacter amylophilus H18T|Ruminobacter amylophilus H18T]]
* [[Ruminococcaceae bacterium AE2021]]
* [[Ruminococcus albus 7|''Ruminococcus albus'' 7]]
* [[Ruminococcus albus 8|''Ruminococcus albus'' 8]]
* [[Ruminococcus albus AD2013]]
* [[Ruminococcus albus SY3]]
* [[Ruminococcus flavefaciens AE3010]]
* [[Ruminococcus flavefaciens 007c]]
* [[Ruminococcus flavefaciens 17]]
* [[Ruminococcus flavefaciens C94T|Ruminococcus flavefaciens C94T]]
* [[Ruminococcus flavefaciens FD-1]]
* [[Ruminococcus sp. HUN007]]
* [[Selenomonas bovis strain|Selenomonas bovis]] 8-14-1
* [[Selenomonas ruminantium AB3002]]
* [[Selenomonas ruminantium GA192|''Selenomonas ruminantium'' GA192T]]
* [[Selenomonas ruminantium HD4]]
* [[Selenomonas ruminantium PC18]]
* [[Selenomonas ruminantium subsp lactilytica TAM6421]]
* ''[[Sharpea azabuensis KH1P5|Sharpea azabuensis]]'' [[Sharpea azabuensis KH1P5|KH1P5]]
* [[Streptococcus bovis JB1]]
* [[Streptococcus equinus B315]]
* [[Succiniclasticum ruminis SE10T|Succiniclasticum ruminis SE10T]]
* [[Succinivibrio dextrinosolvens H5]]
* [[Terrisporobacter glycolicus KPPR-9]]

Prevotella bryantii C21a

2026-10-27T00:42:16Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Segatella bryantii'' C21a'''

''Segatella bryantii'' C21a, formerly ''Prevotella bryantii'', was isolated from bovine rumen contents in NZ [1]. C21a is proteolytic, Gram negative, and able to ferment a wide range of carbohydrates. Its main fermentation product is lactate, together with succinate and acetate [1].

Taxonomic analysis of the genus ''Prevotella'' lists B14 as the ''S. bryantii'' type strain [2]. However, NCBI now records B14 and C21a as belonging to the species ''Segatella baroniae''.

The draft genome for C21a (3,249,285 bp) was generated through the Hungate1000 project with JGI [3].

NCBI: ''Segatella baroniae''.

GTBD: ''Prevotella bryantii''. C21a groups with the type strain of ''S. bryantii'' (B14, DSM 11371)

Risk group: 2.

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
{| class="wikitable"
|+
|'''Motif'''
!Percent methylated
|-
|ACGC(6mA)B
|98.66%
|-
|CAAG(6mA)T
|96.36%
|-
|
|
|}

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Attwood GT, Reilly K. 1995. Identification of proteolytic rumen bacteria isolated from New Zealand cattle. J Appl Bacteriol 79: 22-9. doi: 10.1111/j.1365-2672.1995.tb03119.x.

[2] Hitch TCA, Bisdorf K, Afrizal A, Riedel T, Overmann J, Strowig T, Clavel T. 2022. A taxonomic note on the genus ''Prevotella'': Description of four novel genera and emended description of the genera ''Hallella'' and ''Xylanibacter''. Syst Appl Microbiol 45: 126354. doi: 10.1016/j.syapm.2022.126354.

[3] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Prevotella ruminicola KHP1

2026-10-26T23:03:40Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Xylanibacter ruminicola'' KHP1'''

''Xylanibacter ruminicola'' KHP1, formerly ''Prevotella ruminicola'', was isolated from bovine rumen contents in NZ using KH medium which was supplemented with haemin and vitamin K [1]. It has been used in studies of propionate production [2] and polysaccharide utilization [3].

The KHP1 genome sequence consists of a 3,439,340 bp chromosome [2].

NCBI: ''Xylanibacter ruminicola''.

GTBD: ''Prevotella ruminicola''. KHP1 groups with the type strain of ''X. ruminicola'' (Bryant 23, DSM 19721).

Risk group: 2

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[2] Mahoney-Kurpe SC, Palevich N, Gagic D, Biggs PJ, Reid PM, Altshuler I, Pope PB, Attwood GT, Moon CD. 2024. Transcriptomic and proteomic changes associated with cobalamin-dependent propionate production by the rumen bacterium ''Xylanibacter ruminicola''. mSystems 9: e0086424. doi: 10.1128/msystems.00864-24.

[3] Murovec U, Accetto T. 2024. Transcriptomic analysis of polysaccharide utilization loci reveals substrate preferences in ruminal generalists ''Segatella bryantii'' TF1-3 and ''Xylanibacter ruminicola'' KHP1. BMC Genomics 25: 495. doi: 10.1186/s12864-024-10421-z.

Prevotella brevis P6B11

2026-10-26T22:41:18Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Xylanibacter brevis'' P6B11'''

''Xylanibacter brevis'' P6B11, formerly ''Prevotella brevis'', was isolated from bovine rumen contents using pectin-containing media in NZ [1]. It has not been phenotypically characterised.

The draft genome for P6B11 (3,216,972 bp) was generated through the Hungate1000 project with JGI [1].

NCBI: ''Xylanibacter brevis.''

GTBD: ''Prevotella brevis.'' P6B11 groups with the type strain of ''X. brevis'' (GA33, ATCC 19188).

Risk group: 2.

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Selenomonas ruminantium GA192

2026-10-26T21:58:25Z

Billkelleydonvis: Introduction and external links

Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae

== Introduction ==
'''''Pseudoselenomonas ruminantium'' GA192T'''

''Pseudoselenomonas ruminantium'' GA192T (DSM 2150) formerly ''Selenomonas ruminantium'' was isolated from bovine rumen contents from an animal fed fresh alfalfa in the USA [1]. GA192 is the type species of the genus ''Pseudoselenomonas'' within the family ''Selenomonadaceae'' and the type stain of the ''P. ruminantium'' species [2, 3]. GA192 is an anaerobic bacterium that ferments a broad range of carbohydrates and produces primarily propionate, lactate, and CO₂ [1, 2]. Lactate is not fermented [1], sulfate and fumarate but not nitrate are reduced.

The draft genome for GA192 (3,387,070 bp) was generated through the Hungate1000 project with JGI [4]. A20,067 bp plasmid has been predicted from the genome sequence.

LPSN: ''Pseudoselenomonas ruminantium'' (Certes 1889) Heng and Kittelmann 2026

NCBI: ''Pseudoselenomonas ruminantium''.

GTDB: ''Selenomonas_A ruminantium''.

Risk group: 1.

== Genome ==

== Methylome ==

{| class="wikitable"
|+ Methylome Motifs
|-
! motif !! # site methylated !! total sites !! % methylated
|-
| G(6mA)TC || Example || Example || Example
|-
| G(6mA)CNNNNNCTC/ G(6mA)GNNNNNGTC || Example || Example || Example
|-
| GA(6mA)YNNNNNAATC/ G(6mA)TTNNNNRTTC || Example || Example || Example
|-
| CC(6mA)GNNNNNTCG/ CG(6mA)NNNNNCTGG || Example || Example || Example
|-
| GA(6mA)GNNNNNCTC/ G(6mA)GNNNNNCTTC || Example || Example || Example
|-
| GA(6mA)CNNNNNACT/ (6mA)GTNNNNNGTTC || Example || Example || Example
|}

== ''E.coli'' methylation strain ==
Completed, AG22058

== Antibiotic MIC tests ==
==== MIC test strip result ====
{| class="wikitable"
|+ MIC test strip result
|-
! Antibiotic !! MIC
|-
| Ampicillin || 0.016ug/ml
|-
| Tetracycline || 0.094ug/ml
|-
| Trimethoprim || 8 ug/ml
|-
| Streptomycin || 2 ug/ml
|-
| Spectinomycin || 16ug/ml
|-
| Kanamycin || 3 ug/ml
|-
| Chloramphenicol || 0.5 ug/ml
|-
| Gentamicin || 2 ug/ml
|-
| Erythromycin || 0.2ug/ml
|}

== Defensefinder prediction ==
{| class="wikitable"
|+ Defense Systems
|-
! Type / Subtype !! Mechanism !! Note
|-
| PD-Lambda-1 (PD-Lambda-1) || ||
|-
| PrrC (PrrC) || ||
|-
| RM (RM_Type_IV) || ||
|-
| Abi2 (Abi2) || ||
|-
| VP1839 (VP1839) || ||
|-
| Wadjet (Wadjet_I) || || Lacks JetD (endonuclease)
|-
| Eleos (Eleos) || ||
|-
| Cas (CAS_Class1-Subtype-I-F) || ||
|-
| SspBCDE (SspBCDE) || || Lacks SspA & SspE (endonuclease)
|-
| Cas (CAS_Class1-Subtype-III-D) || ||
|-
| AbiD (AbiD) || ||
|-
| Mokosh (Mokosh_Type_I_B) || ||
|-
| VP1851 (VP1851) || ||
|-
| Cas (CAS_Cluster) || ||
|}

== External Links ==
[1] Bryant MP. 1956. The characteristics of strains of ''Selenomonas'' isolated from bovine rumen contents. J Bacteriol 72: 162-7. doi: 10.1128/jb.72.2.162-167.1956.

[2] Heng YC, Kittelmann S. 2026. Taxonomic reclassification and expansion of the family ''Selenomonadaceae''. Int J Syst Evol Microbiol 76: 7178. doi: 10.1099/ijsem.0.007178.

[3] <nowiki>https://bacdive.dsmz.de/strain/17156</nowiki>.

[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.e

Selenomonas ruminantium GA192

2026-10-26T21:55:51Z

Billkelleydonvis: introduction

Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae

== Introduction ==
'''Pseudoselenomonas ruminantium GA192T'''

Pseudoselenomonas ruminantium GA192T (DSM 2150) formerly Selenomonas ruminantium was isolated from bovine rumen contents from an animal fed fresh alfalfa in the USA [1]. GA192 is the type species of the genus Pseudoselenomonas within the family Selenomonadaceae and the type stain of the P. ruminantium species [2, 3]. GA192 is an anaerobic bacterium that ferments a broad range of carbohydrates and produces primarily propionate, lactate, and CO₂ [1, 2]. Lactate is not fermented [1], sulfate and fumarate but not nitrate are reduced.

The draft genome for GA192 (3,387,070 bp) was generated through the Hungate1000 project with JGI [4]. A20,067 bp plasmid has been predicted from the genome sequence.

LPSN: Pseudoselenomonas ruminantium (Certes 1889) Heng and Kittelmann 2026

NCBI: Pseudoselenomonas ruminantium.

GTDB: Selenomonas_A ruminantium.

Risk group: 1.

== Genome ==

== Methylome ==

{| class="wikitable"
|+ Methylome Motifs
|-
! motif !! # site methylated !! total sites !! % methylated
|-
| G(6mA)TC || Example || Example || Example
|-
| G(6mA)CNNNNNCTC/ G(6mA)GNNNNNGTC || Example || Example || Example
|-
| GA(6mA)YNNNNNAATC/ G(6mA)TTNNNNRTTC || Example || Example || Example
|-
| CC(6mA)GNNNNNTCG/ CG(6mA)NNNNNCTGG || Example || Example || Example
|-
| GA(6mA)GNNNNNCTC/ G(6mA)GNNNNNCTTC || Example || Example || Example
|-
| GA(6mA)CNNNNNACT/ (6mA)GTNNNNNGTTC || Example || Example || Example
|}

== ''E.coli'' methylation strain ==
Completed, AG22058

== Antibiotic MIC tests ==
==== MIC test strip result ====
{| class="wikitable"
|+ MIC test strip result
|-
! Antibiotic !! MIC
|-
| Ampicillin || 0.016ug/ml
|-
| Tetracycline || 0.094ug/ml
|-
| Trimethoprim || 8 ug/ml
|-
| Streptomycin || 2 ug/ml
|-
| Spectinomycin || 16ug/ml
|-
| Kanamycin || 3 ug/ml
|-
| Chloramphenicol || 0.5 ug/ml
|-
| Gentamicin || 2 ug/ml
|-
| Erythromycin || 0.2ug/ml
|}

== Defensefinder prediction ==
{| class="wikitable"
|+ Defense Systems
|-
! Type / Subtype !! Mechanism !! Note
|-
| PD-Lambda-1 (PD-Lambda-1) || ||
|-
| PrrC (PrrC) || ||
|-
| RM (RM_Type_IV) || ||
|-
| Abi2 (Abi2) || ||
|-
| VP1839 (VP1839) || ||
|-
| Wadjet (Wadjet_I) || || Lacks JetD (endonuclease)
|-
| Eleos (Eleos) || ||
|-
| Cas (CAS_Class1-Subtype-I-F) || ||
|-
| SspBCDE (SspBCDE) || || Lacks SspA & SspE (endonuclease)
|-
| Cas (CAS_Class1-Subtype-III-D) || ||
|-
| AbiD (AbiD) || ||
|-
| Mokosh (Mokosh_Type_I_B) || ||
|-
| VP1851 (VP1851) || ||
|-
| Cas (CAS_Cluster) || ||
|}

== External Links ==
[1] Bryant MP. 1956. The characteristics of strains of Selenomonas isolated from bovine rumen contents. J Bacteriol 72: 162-7. doi: 10.1128/jb.72.2.162-167.1956.

[2] Heng YC, Kittelmann S. 2026. Taxonomic reclassification and expansion of the family Selenomonadaceae. Int J Syst Evol Microbiol 76: 7178. doi: 10.1099/ijsem.0.007178.

[3] <nowiki>https://bacdive.dsmz.de/strain/17156</nowiki>.

[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.e

Selenomonas ruminantium GA192

2026-10-26T21:49:35Z

Billkelleydonvis: Introduction and external links

Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae

== Introduction ==
'''Pseudoselenomonas ruminantium GA192T'''

Pseudoselenomonas ruminantium GA192T (DSM 2150) formerly Selenomonas ruminantium was isolated from bovine rumen contents from an animal fed fresh alfalfa in the USA [1]. GA192 is the type species of the genus Pseudoselenomonas within the family Selenomonadaceae and the type stain of the P. ruminantium species [2, 3]. GA192 is an anaerobic bacterium that ferments a broad range of carbohydrates and produces primarily propionate, lactate, and CO₂ [1, 2]. Lactate is not fermented [1], sulfate and fumarate but not nitrate are reduced.

The draft genome for PC 18 (3,387,070 bp) was generated through the Hungate1000 project with JGI [4]. A20,067 bp plasmid has been predicted from the genome sequence.

LPSN: Pseudoselenomonas ruminantium (Certes 1889) Heng and Kittelmann 2026

NCBI: Pseudoselenomonas ruminantium.

GTDB: Selenomonas_A ruminantium.

Risk group: 1.

== Genome ==

== Methylome ==

{| class="wikitable"
|+ Methylome Motifs
|-
! motif !! # site methylated !! total sites !! % methylated
|-
| G(6mA)TC || Example || Example || Example
|-
| G(6mA)CNNNNNCTC/ G(6mA)GNNNNNGTC || Example || Example || Example
|-
| GA(6mA)YNNNNNAATC/ G(6mA)TTNNNNRTTC || Example || Example || Example
|-
| CC(6mA)GNNNNNTCG/ CG(6mA)NNNNNCTGG || Example || Example || Example
|-
| GA(6mA)GNNNNNCTC/ G(6mA)GNNNNNCTTC || Example || Example || Example
|-
| GA(6mA)CNNNNNACT/ (6mA)GTNNNNNGTTC || Example || Example || Example
|}

== ''E.coli'' methylation strain ==
Completed, AG22058

== Antibiotic MIC tests ==
==== MIC test strip result ====
{| class="wikitable"
|+ MIC test strip result
|-
! Antibiotic !! MIC
|-
| Ampicillin || 0.016ug/ml
|-
| Tetracycline || 0.094ug/ml
|-
| Trimethoprim || 8 ug/ml
|-
| Streptomycin || 2 ug/ml
|-
| Spectinomycin || 16ug/ml
|-
| Kanamycin || 3 ug/ml
|-
| Chloramphenicol || 0.5 ug/ml
|-
| Gentamicin || 2 ug/ml
|-
| Erythromycin || 0.2ug/ml
|}

== Defensefinder prediction ==
{| class="wikitable"
|+ Defense Systems
|-
! Type / Subtype !! Mechanism !! Note
|-
| PD-Lambda-1 (PD-Lambda-1) || ||
|-
| PrrC (PrrC) || ||
|-
| RM (RM_Type_IV) || ||
|-
| Abi2 (Abi2) || ||
|-
| VP1839 (VP1839) || ||
|-
| Wadjet (Wadjet_I) || || Lacks JetD (endonuclease)
|-
| Eleos (Eleos) || ||
|-
| Cas (CAS_Class1-Subtype-I-F) || ||
|-
| SspBCDE (SspBCDE) || || Lacks SspA & SspE (endonuclease)
|-
| Cas (CAS_Class1-Subtype-III-D) || ||
|-
| AbiD (AbiD) || ||
|-
| Mokosh (Mokosh_Type_I_B) || ||
|-
| VP1851 (VP1851) || ||
|-
| Cas (CAS_Cluster) || ||
|}

== External Links ==
[1] Bryant MP. 1956. The characteristics of strains of Selenomonas isolated from bovine rumen contents. J Bacteriol 72: 162-7. doi: 10.1128/jb.72.2.162-167.1956.

[2] Heng YC, Kittelmann S. 2026. Taxonomic reclassification and expansion of the family Selenomonadaceae. Int J Syst Evol Microbiol 76: 7178. doi: 10.1099/ijsem.0.007178.

[3] <nowiki>https://bacdive.dsmz.de/strain/17156</nowiki>.

[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.e

Selenomonas ruminantium PC18

2026-10-26T21:46:18Z

Billkelleydonvis: Introduction and external links

== Introduction ==

'''Pseudoselenomonas lactilytica PC 18T'''

Pseudoselenomonas lactilytica PC18T (DSM 2872), formerly Selenomonas ruminantium subsp. lactilytica was isolated from bovine rumen contents from an animal fed a grass pasture and grain mixture in the USA [1]. PC 18 is an anaerobic bacterium that ferments a broad range of carbohydrates and produces primarily propionate, lactate, and CO₂ [1, 2]. Lactate is fermented to propionate and acetate [1], and PC 18 can reduce nitrate, sulfate and fumarate. PC 18 is the type strain of the species [3].

Rumen metatranscriptomic and metagenomic studies have shown that in addition to methanogenesis there are other pathways of H2 use, including nitrate, sulfate, and fumarate reduction as well as homoacetogenesis [4]. Sulfate and nitrate are external electron acceptors that can be taken up from the environment and reduced to sulfide and ammonia, respectively, while fumarate is reduced to succinate followed by decarboxylation to propionate.

The draft genome for PC 18 (3,039,002 bp) was generated through the Hungate1000 project with JGI [5]. Resequencing gave a 3,074,662 genome consisting of a chromosome (2,979,598 bp) and two plasmids (76,524 bp and 18,540 bp).

LPSN: Pseudoselenomonas lactilytica (Bryant 1956) Heng and Kittelmann 2026.

NCBI: Pseudoselenomonas lactilytica.

GTDB: Selenomonas_A ruminantium_B.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin
|
|-
|Sequenced by
|
|-
|Assembled by
|
|-
|Methylome called by
|
|-
|MIC and culturing conditions by
|
|-
|Transformation by
|
|}

== Genome ==

== External Links ==
[1] Bryant MP. 1956. The characteristics of strains of Selenomonas isolated from bovine rumen contents. J Bacteriol 72: 162-7. doi: 10.1128/jb.72.2.162-167.1956.

[2] <nowiki>https://bacdive.dsmz.de/strain/17155</nowiki>.

[3] Heng YC, Kittelmann S. 2026. Taxonomic reclassification and expansion of the family Selenomonadaceae. Int J Syst Evol Microbiol 76: 7178. doi: 10.1099/ijsem.0.007178.

[4] Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI. 2019. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME J 13: 2617-2632. doi: 10.1038/s41396-019-0464-2.

[5] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

List of GMH Strains

2026-10-26T21:44:13Z

Billkelleydonvis: Strain designation

* [[Acetitomaculum ruminis 139BT|Acetitomaculum ruminis 139BT]]
* [[Acidaminococcus fermentans WCC6]]
* [[Anaerovibrio lipolyticus 5ST|Anaerivibrio lipolyticus 5ST]] (NB: do we really have an Anaerivibrio and an Anaerovibrio genus, or is one of these misspelled? Makoto: Yes we have (Illinois group). I fixed the missspell.)
* [[Anaerovibrio lipolyticus LB2005]]
* [[Aristaeella hokkaidonensis R-7T|Aristaeella hokkaidonensis R-7T]]
* [[Aristaeella lactis WTE2008T|Aristaeella lactis WTE2008T]]
* [[Bacteroidales bacterium Ga6A1]]
* [[Bacteroidales bacterium WCE2004]]
* [[Ruminococcus productus B43]]
* [[Blautia schinkii BT|Blautia schinkii BT]]
* [[Butyrivibrio fibrisolvens D1T|Butyrivibrio fibrisolvens D1T]]
* [[Butyrivibrio fibrisolvens TB|''Butyrivibrio fibrisolvens'' TB]]
* [[Butyrivibrio hungatei MB2003|''Butyrivibrio hungatei'' MB2003]]
* [[Butyrivibrio proteoclasticus B316ᵀ|Butyrivibrio proteoclasticus B316T]]
* [[Clostridium aminophilum FT|Clostridium aminophilum FT]]
* [[Desulfotomaculum ruminis DLT|Desulfotomaculum ruminis DLT]]
* [[Desulfovibrio desulfuricans G11]]
* [[Desulfovibrio legallii KHC7]]
* [[Eubacterium callanderi NLAE-zl-G225]]
* [[Eubacterium limosum RF]]
* [[Eubacterium maltosivorans SA11]]
* [[Eubacterium sp. AB3007]]
* [[Fibrobacter succinogenes S85T|Fibrobacter succinogenes S85T]]
* [[Kandleria vitulina WCE2011]]
* [[Lachnobacterium bovis AE2004]]
* [[Lachnospira multipara D32T]]
* [[Lachnospiraceae bacterium AC2014]]
* [[Lachnospiraceae bacterium FD2005]]
* [[Lachnospiraceae bacterium FE2018]]
* [[Lachnospiraceae bacterium ND2006]]
* [[Lachnospiraceae bacterium NK3A20]]
* [[Lachnospiraceae bacterium NK4A136]]
* [[Lachnospiraceae bacterium YSB2008]]
* [[Ligilactobacillus ruminis WC1T17]]
* [[Megasphaera elsdenii LC1T|Megasphaera elsdenii LC1T]]
* [[Megasphaera elsdenii T81]]
* [[Methanobacterium bryantii YCM1|''Methanobacterium bryantii'' YCM1]]
* [[Methanobacterium formicicum BRM9|''Methanobacterium formicicum'' BRM9]]
* [[Methanobrevibacter boviskoreani AbM4|''Methanarmilla boviskoreani'' AbM4]]
* ''[[Methanobrevibacter boviskoreani JH1T|Methanarmilla]] [[Methanobrevibacter boviskoreani JH1T|boviskoreani]]'' [[Methanobrevibacter boviskoreani JH1T|JH1T]]
* [[Methanocatella gottschalkii HO|''Methanocatella gottschalkii'' HO]]
* [[Methanobrevibacter gottschalkii PG|''Methanocatella gottschalkii'' PG]]
* [[Methanocatella millerae SM9|''Methanocatella millerae'' SM9]]
* [[Methanobrevibacter millerae ZA-10T|''Methanocatella millerae'' ZA-10T]]
* [[Methanobrevibacter olleyae 1H5-1PT|''Methanobrevibacter olleyae'' 1H5-1PT]]
* [[Methanobrevibacter olleyae YLM1|''Methanobrevibacter olleyae'' YLM1]]
* [[Methanobrevibacter ruminantium M1T|''Methanobrevibacter ruminantium'' M1T]]
* [[Methanobrevibacter ruminantium YE286|''Methanobrevibacter ruminantium'' YE286]]
* [[Methanobrevibacter sp. 87.7|''Methanarmilla sp.'' 87.7]]
* [[Methanobrevibacter sp. D5]] - group 1 to check nomenclature
* [[Methanobrevibacter sp. YE315|''Methanocatella sp.'' YE315]]
* [[Methanobrevibacter thaueri ISO4-G16|''Methanocatella thaueri'' ISO4-G16]]
* [[Methanobrevibacter thaueri CWT|''Methanocatella thaueri'' CWT]]
* [[Methanobrevibacter woesei GST|''Methanocatella woesei'' GST]]
* [[Methanobrevibacter wolinii SHT|''Methanobrevibacter wolinii'' SHT]]
* [[Methanomassiliicoccales BRNA1|''Methanomethylophilus sp.'' BRNA1]]
* [[Methanomassiliicoccales ISO4-G1|''Candidatus'' ''Methanoprimaticola sp.'' ISO4-G1]]
* [[Methanomassiliicoccales ISO4-G11]] - Group 1, do we have the ISO4-G11 strain? If I remember, we don't.
* ''[[Methanomassiliicoccales ISO4-H5|Methanomethylophilus sp.]]'' [[Methanomassiliicoccales ISO4-H5|ISO4-H5]]
* [[Methanomicrobium mobile 1T|''Methanomicrobium mobile'' 1T]]
* [[Methanosarcina barkeri CM1|''Methanosarcina barkeri'' CM1]]
* [[Methanosarcina thermophila Ms97|''Methanosarcina thermophila'' Ms97]]
* [[Methanosphaera sp. A4]] - group 1 to check nomenclature
* [[Methanosphaera sp. BMS|''Methanosphaera sp.'' BMS]]
* [[Methanosphaera sp. ISO3-F5*|''Methanosphaera sp.'' ISO3-F5*]]
* [[Methanosphaera sp. WGK6]] - group 1 to check nomenclature
* [[Olsenella sp. KH2P3]]
* [[Olsenella sp. KHGC19]]
* [[Peptostreptococcaceae bacterium VA2]]
* [[Porphyromonadaceae bacterium KH3R12]]
* [[Prevotella albensis M384T|Prevotella albensis M384T]]
* [[Prevotella brevis GA33T|Prevotella brevis GA33T]]
* [[Prevotella brevis P6B11]]
* [[Prevotella bryantii B14|''Prevotella bryanti''i B14]]
* [[Prevotella bryantii C21a|''Prevotella bryantii'' C21a]]
* [[Prevotella ruminicola 23T|''Prevotella ruminicola'' 23T]]
* [[Prevotella ruminicola KHP1]]
* [[Pseudobutyrivibrio ruminis A12-1T|Pseudobutyrivibrio ruminis A12-1T]]
* [[Pseudobutyrivibrio xylanivorans MA3014]]
* [[Ruminobacter amylophilus H18T|Ruminobacter amylophilus H18T]]
* [[Ruminococcaceae bacterium AE2021]]
* [[Ruminococcus albus 7|''Ruminococcus albus'' 7]]
* [[Ruminococcus albus 8|''Ruminococcus albus'' 8]]
* [[Ruminococcus albus AD2013]]
* [[Ruminococcus albus SY3]]
* [[Ruminococcus flavefaciens AE3010]]
* [[Ruminococcus flavefaciens 007c]]
* [[Ruminococcus flavefaciens 17]]
* [[Ruminococcus flavefaciens C94T|Ruminococcus flavefaciens C94T]]
* [[Ruminococcus flavefaciens FD-1]]
* [[Ruminococcus sp. HUN007]]
* [[Selenomonas bovis strain|Selenomonas bovis]] 8-14-1
* [[Selenomonas ruminantium AB3002]]
* [[Selenomonas ruminantium GA192|''Selenomonas ruminantium'' GA192T]]
* [[Selenomonas ruminantium HD4]]
* [[Selenomonas ruminantium PC18]]
* [[Selenomonas ruminantium subsp lactilytica TAM6421]]
* ''[[Sharpea azabuensis KH1P5|Sharpea azabuensis]]'' [[Sharpea azabuensis KH1P5|KH1P5]]
* [[Streptococcus bovis JB1]]
* [[Streptococcus equinus B315]]
* [[Succiniclasticum ruminis SE10T|Succiniclasticum ruminis SE10T]]
* [[Succinivibrio dextrinosolvens H5]]
* [[Terrisporobacter glycolicus KPPR-9]]

List of GMH Strains

2026-10-26T21:43:18Z

Billkelleydonvis: Strain designation

* [[Acetitomaculum ruminis 139BT|Acetitomaculum ruminis 139BT]]
* [[Acidaminococcus fermentans WCC6]]
* [[Anaerovibrio lipolyticus 5ST|Anaerivibrio lipolyticus 5ST]] (NB: do we really have an Anaerivibrio and an Anaerovibrio genus, or is one of these misspelled? Makoto: Yes we have (Illinois group). I fixed the missspell.)
* [[Anaerovibrio lipolyticus LB2005]]
* [[Aristaeella hokkaidonensis R-7T|Aristaeella hokkaidonensis R-7T]]
* [[Aristaeella lactis WTE2008T|Aristaeella lactis WTE2008T]]
* [[Bacteroidales bacterium Ga6A1]]
* [[Bacteroidales bacterium WCE2004]]
* [[Ruminococcus productus B43]]
* [[Blautia schinkii BT|Blautia schinkii BT]]
* [[Butyrivibrio fibrisolvens D1T|Butyrivibrio fibrisolvens D1T]]
* [[Butyrivibrio fibrisolvens TB|''Butyrivibrio fibrisolvens'' TB]]
* [[Butyrivibrio hungatei MB2003|''Butyrivibrio hungatei'' MB2003]]
* [[Butyrivibrio proteoclasticus B316ᵀ|Butyrivibrio proteoclasticus B316T]]
* [[Clostridium aminophilum FT|Clostridium aminophilum FT]]
* [[Desulfotomaculum ruminis DLT|Desulfotomaculum ruminis DLT]]
* [[Desulfovibrio desulfuricans G11]]
* [[Desulfovibrio legallii KHC7]]
* [[Eubacterium callanderi NLAE-zl-G225]]
* [[Eubacterium limosum RF]]
* [[Eubacterium maltosivorans SA11]]
* [[Eubacterium sp. AB3007]]
* [[Fibrobacter succinogenes S85T|Fibrobacter succinogenes S85T]]
* [[Kandleria vitulina WCE2011]]
* [[Lachnobacterium bovis AE2004]]
* [[Lachnospira multipara D32T]]
* [[Lachnospiraceae bacterium AC2014]]
* [[Lachnospiraceae bacterium FD2005]]
* [[Lachnospiraceae bacterium FE2018]]
* [[Lachnospiraceae bacterium ND2006]]
* [[Lachnospiraceae bacterium NK3A20]]
* [[Lachnospiraceae bacterium NK4A136]]
* [[Lachnospiraceae bacterium YSB2008]]
* [[Ligilactobacillus ruminis WC1T17]]
* [[Megasphaera elsdenii LC1T|Megasphaera elsdenii LC1T]]
* [[Megasphaera elsdenii T81]]
* [[Methanobacterium bryantii YCM1|''Methanobacterium bryantii'' YCM1]]
* [[Methanobacterium formicicum BRM9|''Methanobacterium formicicum'' BRM9]]
* [[Methanobrevibacter boviskoreani AbM4|''Methanarmilla boviskoreani'' AbM4]]
* ''[[Methanobrevibacter boviskoreani JH1T|Methanarmilla]] [[Methanobrevibacter boviskoreani JH1T|boviskoreani]]'' [[Methanobrevibacter boviskoreani JH1T|JH1T]]
* [[Methanocatella gottschalkii HO|''Methanocatella gottschalkii'' HO]]
* [[Methanobrevibacter gottschalkii PG|''Methanocatella gottschalkii'' PG]]
* [[Methanocatella millerae SM9|''Methanocatella millerae'' SM9]]
* [[Methanobrevibacter millerae ZA-10T|''Methanocatella millerae'' ZA-10T]]
* [[Methanobrevibacter olleyae 1H5-1PT|''Methanobrevibacter olleyae'' 1H5-1PT]]
* [[Methanobrevibacter olleyae YLM1|''Methanobrevibacter olleyae'' YLM1]]
* [[Methanobrevibacter ruminantium M1T|''Methanobrevibacter ruminantium'' M1T]]
* [[Methanobrevibacter ruminantium YE286|''Methanobrevibacter ruminantium'' YE286]]
* [[Methanobrevibacter sp. 87.7|''Methanarmilla sp.'' 87.7]]
* [[Methanobrevibacter sp. D5]] - group 1 to check nomenclature
* [[Methanobrevibacter sp. YE315|''Methanocatella sp.'' YE315]]
* [[Methanobrevibacter thaueri ISO4-G16|''Methanocatella thaueri'' ISO4-G16]]
* [[Methanobrevibacter thaueri CWT|''Methanocatella thaueri'' CWT]]
* [[Methanobrevibacter woesei GST|''Methanocatella woesei'' GST]]
* [[Methanobrevibacter wolinii SHT|''Methanobrevibacter wolinii'' SHT]]
* [[Methanomassiliicoccales BRNA1|''Methanomethylophilus sp.'' BRNA1]]
* [[Methanomassiliicoccales ISO4-G1|''Candidatus'' ''Methanoprimaticola sp.'' ISO4-G1]]
* [[Methanomassiliicoccales ISO4-G11]] - Group 1, do we have the ISO4-G11 strain? If I remember, we don't.
* ''[[Methanomassiliicoccales ISO4-H5|Methanomethylophilus sp.]]'' [[Methanomassiliicoccales ISO4-H5|ISO4-H5]]
* [[Methanomicrobium mobile 1T|''Methanomicrobium mobile'' 1T]]
* [[Methanosarcina barkeri CM1|''Methanosarcina barkeri'' CM1]]
* [[Methanosarcina thermophila Ms97|''Methanosarcina thermophila'' Ms97]]
* [[Methanosphaera sp. A4]] - group 1 to check nomenclature
* [[Methanosphaera sp. BMS|''Methanosphaera sp.'' BMS]]
* [[Methanosphaera sp. ISO3-F5*|''Methanosphaera sp.'' ISO3-F5*]]
* [[Methanosphaera sp. WGK6]] - group 1 to check nomenclature
* [[Olsenella sp. KH2P3]]
* [[Olsenella sp. KHGC19]]
* [[Peptostreptococcaceae bacterium VA2]]
* [[Porphyromonadaceae bacterium KH3R12]]
* [[Prevotella albensis M384T|Prevotella albensis M384T]]
* [[Prevotella brevis GA33T|Prevotella brevis GA33T]]
* [[Prevotella brevis P6B11]]
* [[Prevotella bryantii B14|''Prevotella bryanti''i B14]]
* [[Prevotella bryantii C21a|''Prevotella bryantii'' C21a]]
* [[Prevotella ruminicola 23T|''Prevotella ruminicola'' 23T]]
* [[Prevotella ruminicola KHP1]]
* [[Pseudobutyrivibrio ruminis A12-1T|Pseudobutyrivibrio ruminis A12-1T]]
* [[Pseudobutyrivibrio xylanivorans MA3014]]
* [[Ruminobacter amylophilus H18T|Ruminobacter amylophilus H18T]]
* [[Ruminococcaceae bacterium AE2021]]
* [[Ruminococcus albus 7|''Ruminococcus albus'' 7]]
* [[Ruminococcus albus 8|''Ruminococcus albus'' 8]]
* [[Ruminococcus albus AD2013]]
* [[Ruminococcus albus SY3]]
* [[Ruminococcus flavefaciens AE3010]]
* [[Ruminococcus flavefaciens 007c]]
* [[Ruminococcus flavefaciens 17]]
* [[Ruminococcus flavefaciens C94T|Ruminococcus flavefaciens C94T]]
* [[Ruminococcus flavefaciens FD-1]]
* [[Ruminococcus sp. HUN007]]
* [[Selenomonas bovis strain]] 8-14-1
* [[Selenomonas ruminantium AB3002]]
* [[Selenomonas ruminantium GA192|''Selenomonas ruminantium'' GA192T]]
* [[Selenomonas ruminantium HD4]]
* [[Selenomonas ruminantium PC18]]
* [[Selenomonas ruminantium subsp lactilytica TAM6421]]
* ''[[Sharpea azabuensis KH1P5|Sharpea azabuensis]]'' [[Sharpea azabuensis KH1P5|KH1P5]]
* [[Streptococcus bovis JB1]]
* [[Streptococcus equinus B315]]
* [[Succiniclasticum ruminis SE10T|Succiniclasticum ruminis SE10T]]
* [[Succinivibrio dextrinosolvens H5]]
* [[Terrisporobacter glycolicus KPPR-9]]

Selenomonas bovis strain

2026-10-26T21:38:33Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Dongibacter'' bovis 8-14-1'''

''Dongibacter'' bovis 8-14-1 formerly ''Selenomonas bovis'' was isolated from bovine rumen contents in Japan. The culture was provided by Dr Satoshi Koike for inclusion in the Hungate1000 genome sequencing project.

The draft genome for 8-14-1 (2,615,863 bp) was generated through the Hungate1000 project with JGI [1].

NCBI: ''Dongibacter bovis'' [2].

GTDB: ''Selenomonas_C bovis''

Risk group: 1.

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[2] Heng YC, Kittelmann S. 2026. Taxonomic reclassification and expansion of the family ''Selenomonadaceae''. Int J Syst Evol Microbiol 76: 7178. doi: 10.1099/ijsem.0.007178.

Selenomonas ruminantium HD4

2026-10-26T19:55:17Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Pseudoselenomonas ruminantium'' HD4'''

''Pseudoselenomonas ruminantium'' HD4 was isolated from bovine rumen contents in the USA [1] and characterised along with other ''Selenomonas'' strains [2]. HD4 is an anaerobic bacterium that ferments a broad range of carbohydrates and produces primarily propionate, and acetate. Lactate is fermented [2] and HD4 can reduce nitrate, sulfate and fumarate.

The draft genome for HD4 (3,116,786 bp) was generated through the Hungate1000 project with JGI [3]. A 4.8 kb plasmid has been reported from HD4 [4] and a 4,899 bp plasmid was predicted from the draft genome sequence. Resequencing gave a genome of 3,180,636 bp consisting of a 2,987,729 bp chromosome and a 192,907 bp plasmid.

NCBI: ''Pseudoselenomonas ruminantium''.

GTDB: ''Selenomonas_A ruminantium_D''. HD4 belongs in a different species group than the type strain of ''P. ruminantium'' (GA192, DSM 2150).

Risk group: 1.

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Huhtanen C N, Gall LS. 1953. Rumen organisms I. Curved rods and a related rod type. J Bacteriol 65, 548-553. doi: 10.1128/jb.65.5.548-553.1953.

[2] Bryant MP. 1956. The characteristics of strains of ''Selenomonas'' isolated from bovine rumen contents. J Bacteriol 72: 162-7. doi: 10.1128/jb.72.2.162-167.1956.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[4] Martin SA, Dean RG. 1989. Characterization of a plasmid from the ruminal bacterium ''Selenomonas ruminantium''. Appl Environ Microbiol 55: 3035–3038. doi: 10.1128/aem.55.12.3035-3038.1989.

Selenomonas ruminantium subsp lactilytica TAM6421

2026-10-26T19:52:40Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''''Pseudoselenomonas lactilytica'' TAM6421'''

''Pseudoselenomonas lactilytica'' TAM6421 formerly ''Selenomonas ruminantium'' subsp. ''lactilytica'' was isolated from sheep rumen contents in Japan [1]. Glucose, glycerol and lactate are fermented and propionate is produced.

The genome of TAM6421 (3,631,933 bp) consists of a chromosome (3,003,680 bp) and nine plasmids (285, 449 bp, 94,348 bp, 73,380 bp, 72, 893 bp, 35,182 bp, 29,913 bp, 29,781 bp, 4,693 bp and 2,614 bp) [2].

NCBI: ''Pseudoselenomonas lactilytica''.

GTDB: ''Selenomonas_A lactilytica''. TAM6421 belongs to a different species group than the P''. lactilytica'' type strain (PC 18, DSM 2872)

Risk group: 1.

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Kanegasaki S, Takahashi H. 1967. Function of growth factors for rumen microorganisms. I. Nutritional characteristics of ''Selenomonas ruminantium''. J Bacteriol 93: 456-463. doi: 10.1128/jb.93.1.456-463.1967.

[2] Kaneko J, Yamada-Narita S, Abe N, Onodera T, Kan E, Kojima S, Miyazaki T, Yamamoto Y, Oguchi A, Ankai A, Ichikawa N, Nakazawa H, Fukui S, Takahashi M, Yamazaki S, Fujita N, Kamio Y. 2015. Complete genome sequence of ''Selenomonas ruminantium'' subsp. ''lactilytica'' will accelerate further understanding of the nature of the class ''Negativicutes''. FEMS Microbiol Lett 362: fnv050. doi: 10.1093/femsle/fnv050.

Anaerovibrio lipolyticus 5ST

2026-10-22T21:16:44Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''Anaerovibrio lipolyticus 5ST'''

Anaerovibrio lipolyticus 5ST (DSM 3074) is an anaerobic Gram-negative bacterium isolated from sheep rumen contents in Scotland (UK) [1] and originally named Anaerovibrio lipolytica [3]. It is the type species of the genus Anaerovibrio within the family Selenomonadaceae and the type stain of the A. lipolyticus species [2]. Ribose, fructose and lactate were used as growth substrates and glycerol was fermented to propionate, and succinate [4]. It is regarded as one of the main lipolytic species in the rumen and lipases have been characterized [5].

A draft genome for A. lipolyticus 5S (2,781,134 bp) was generated by the JGI GEBA project.

LPSN: Anaerovibrio lipolyticus corrig. Hungate 1966

NCBI: Anaerovibrio lipolyticus

GTDB: Anaerovibrio lipolyticus

Risk group: 1

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hobson PN, Mann SO. 1961. The isolation of glycerol fermenting and lipolytic bacteria from the rumen of the sheep. J Gen Microbiol 25: 227–240. doi: 10.1099/00221287-25-2-227.

[2] <nowiki>https://bacdive.dsmz.de/strain/17117</nowiki>.

[3] Hungate RE. 1966. The rumen and its microbes. Academic Press, New York, USA.

[4] Prins RA, Lankhorst A, van der Meer P, Van Nevel CJ. 1975. Some characteristics of Anaerovibrio lipolytica a rumen lipolytic organism. Antonie Van Leeuwenhoek 41: 1-11. doi: 10.1007/BF02565031.

[5] Privé F, Kaderbhai NN, Girdwood S, Worgan HJ, Pinloche E, Scollan ND, Huws SA, Newbold CJ.2013. Identification and characterization of three novel lipases belonging to families II and V from Anaerovibrio lipolyticus 5ST. PLoS One 8 : e69076. doi: 10.1371/journal.pone.0069076.

Selenomonas ruminantium AB3002

2026-10-22T21:11:49Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''Selenomonas sp. AB3002'''

Selenomonas sp. AB3002 was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow B). AB3002 is an anaerobic bacterium that ferments a broad range of carbohydrates and produces primarily propionate, lactate, and CO₂. Lactate is not fermented, fumarate is reduced but nitrate and sulfate are not.

The draft genome for AB3002 (3,665,894 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: Selenomonas sp.

GTDB: Selenomonas_B ruminantium_A. With bacteria classified as Selenomonas_A renamed as Pseudoselenomonas it is likely that this organism will be assigned to a yet unnamed genus.

Risk group: 1.

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Anaerovibrio lipolyticus LB2005

2026-10-22T21:09:00Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''Anaerovibrio lipolyticus LB2005'''

Anaerovibrio lipolyticus LB2005 (DSM 115830) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow B). Its carbohydrate metabolism and fermentation end products have not been determined. LB2005 can metabolise lactate and the lactate utilization gene cluster has been identified from the genome sequence.

The draft genome for LB2005 (2,682,728 bp) was generated through the Hungate1000 project with JGI [2].

NCBI: Anaerovibrio lipolyticus

GTDB: Anaerovibrio lipolyticus_A. LB2005 belongs in a different species group than the type strain of A. lipolyticus (5S, DSM 3074).

Risk group: 1

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Selenomonas ruminantium PC18

2026-10-22T21:00:17Z

Billkelleydonvis: Introduction and external links

== Introduction ==

'''Pseudoselenomonas lactilytica PC 18T'''

Pseudoselenomonas lactilytica PC18T (DSM 2872), formerly Selenomonas ruminantium subsp. lactilytica was isolated from bovine rumen contents from an animal fed a grass pasture and grain mixture in the USA [1]. PC 18 is an anaerobic bacterium that ferments a broad range of carbohydrates and produces primarily propionate, lactate, and CO₂ [1, 2]. Lactate is fermented to propionate and acetate [1], and PC 18 can reduce nitrate, sulfate and fumarate. PC 18 is the type strain of the species.

Rumen metatranscriptomic and metagenomic studies have shown that in addition to methanogenesis there are other pathways of H2 use, including nitrate, sulfate, and fumarate reduction as well as homoacetogenesis [3]. Sulfate and nitrate are external electron acceptors that can be taken up from the environment and reduced to sulfide and ammonia, respectively, while fumarate is reduced to succinate followed by decarboxylation to propionate.

The draft genome for PC 18 (3,039,002 bp) was generated through the Hungate1000 project with JGI [4]. Resequencing gave a 3,074,662 genome consisting of a chromosome (2,979,598 bp) and two plasmids (76,524 bp and 18,540 bp).

LPSN: Pseudoselenomonas lactilytica (Bryant 1956) Heng and Kittelmann 2026.

NCBI: Pseudoselenomonas lactilytica.

GTDB: Selenomonas_A ruminantium_B.

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin
|
|-
|Sequenced by
|
|-
|Assembled by
|
|-
|Methylome called by
|
|-
|MIC and culturing conditions by
|
|-
|Transformation by
|
|}

== Genome ==

== External Links ==
[1] Bryant MP. 1956. The characteristics of strains of Selenomonas isolated from bovine rumen contents. J Bacteriol 72: 162-7. doi: 10.1128/jb.72.2.162-167.1956.
[2] <nowiki>https://bacdive.dsmz.de/strain/17155</nowiki>.

[3] Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI. 2019. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME J 13: 2617-2632. doi: 10.1038/s41396-019-0464-2.

[4] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

Selenomonas ruminantium PC18

2026-10-22T20:54:33Z

Billkelleydonvis: /* Introduction */

Eubacterium maltosivorans SA11

2026-10-21T00:56:17Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''Eubacterium maltosivorans SA11'''

Eubacterium maltosivorans SA11 (formerly Eubacterium limosum, and sheep acetogen SA11) was isolated from the rumen of a New Zealand sheep grazing fresh forage [1]. SA11 is a metabolically versatile bacterium able to grow on a wide variety of compounds including CO2/H2, formate, glucose, fructose, xylose, ribose, maltose, pyruvate, L-lactate, methanol, vanillate, syringate, and 3,4,5-trimethoxybenzoatehexoses. Acetate and butyrate are the main fermentation end products [2]. A feature of the SA11 genome is the presence of multiple copies of genes encoding trimethylamine methyltransferase family proteins (COG5598). SA11 has 39 genes in this category, but in most cases their substrate is not known. The genome contains a 55 kb prophage and genes required for the metabolism of 1,2 propanediol.

The SA11 genome consists of a single 4,150,332 bp circular chromosome [2].

LPSN: Eubacterium maltosivorans Feng et al. 2018

NCBI: Eubacterium maltosivorans

GTDB: Eubacterium maltosivorans. SA11 groups with the type strain of E. maltosivorans (Y1, DSM 105863) [3].

Risk group: 1

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Joblin KN. 1999. Ruminal acetogens and their potential to lower ruminant methane emissions. Aust J Agric Res 50:1307–13. doi: 10.1071/AR99004.

[2] Kelly WJ, Henderson G, Pacheco DM, Li D, Reilly K, Naylor GE, Janssen PH, Attwood GT, Altermann E, Leahy SC. 2016. The complete genome sequence of Eubacterium limosum SA11, a metabolically versatile rumen acetogen. Stand Genomic Sci 11: 26. doi: 10.1186/s40793-016-0147-9

[3] Feng Y, Stams AJM, Sanchez-Andrea I, de Vos WM. 2018. Eubacterium maltosivorans sp. nov., a novel human intestinal acetogenic and butyrogenic bacterium with a versatile metabolism. Int J Syst Evol Microbiol 68: 3546–3550. doi: 10.1099/ijsem.0.003028.

Ligilactobacillus ruminis WC1T17

2026-10-20T23:02:57Z

Billkelleydonvis: /* External Links */

== Introduction ==
[[File:Lruminis WC1T17 microscopy.png|thumb|Microscopy (100X) magnification image of ''Ligilactobacillus ruminis'' WC1T17 ]]

=== Strain characteristics and function in the rumen ===
''Ligilactobacillus ruminis'' WC1T17 is a Gram-positive, rod-shaped, aerotolerant anaerobic bacterium that typically grows in a single bacillus or diplo-bacillus cellular arrangement. ''Lactobacillus'' species are of increasing interest for methane mitigation research in ruminant animals as their metabolic network in the rumen can function as a hydrogen sink. ''Ligilactobacillus'' are lactic acid bacteria which ferment glucose in the rumen and produce lactate, this lactate can be utilized by syntrophic lactate utilizing bacteria to produce propionate, an important metabolite for the host animal, and this process also requires absorbs hydrogen thus reducing available substrate for methanogenesis. ''L. ruminis'' is of particular interest to the Global Methane Hub as it is the only known member of the ''Lactobacillus'' genus to be motile making it an attractive prospect for ruminant methane mitigation research as it is theoretically better suited to translocate to multiple niches within the rumen biome.

=== Strain history and information ===
''L. ruminis'' WC1T17 was isolated from the rumen of a healthy cow in Palmerston North, New Zealand by the Institute for Bioeconomy Science, formerly known as AgResearch. The strain contains a circular 1.9 Mb genome with no extrachromosomal elements such as plasmids. This strain can be readily cultured in MRS broth and on MRS agar plates under anaerobic conditions with an average doubling time of 40 minutes.
Minimum inhibitory concentration (MIC) screening of antibiotics and counter-selective agents in liquid media shows that the strain is sensitive to the following tested antibiotics: chloramphenicol, ampicillin, tetracycline, and streptomycin and the following counter-selective agents: 8-azehypoxanthine, 2-deoxy-d-galactose, 5-fluordeoxyuridine, and sucrose.

''L. ruminis'' WC1T17 is genetically tractable and has been successfully transformed via electroporation with the replicative shuttle vector pMTL89151. This vector confers resistance to chloramphenicol and contains the pAMB1 Gram-positive origin of replication machinery in addition to a multiple cloning sight for integration of reporter genes or biological payloads of interest.

Ligilactobacillus ruminis WC1T17 (DSM 115561) was isolated from bovine rumen contents in NZ using Wilkins-Chalgren Agar. It has not been phenotypically characterised.

The draft genome for WC1T17 (1,842,330 bp) was generated through the Hungate1000 project with JGI [1].

This species was formerly named as Lactobacillus ruminis [2].

NCBI: Ligilactobacillus ruminis

GTDB: Ligilactobacillus ruminis_A. WC1T17 belongs in a different species group than the type strain of L. ruminis (RF1, DSM 20403) [2]

Risk group: 1

== Global Methane Hub Metadata ==
{| class="wikitable"
| valign="top" |Strain origin:
| valign="top" |New Zealand1
|-
| valign="top" |Isolated from:
| valign="top" |Cow rumen
|-
| valign="top" |Sequenced by:
| valign="top" |Rhiannon Cecil2
|-
| valign="top" |Assembled by:
| valign="top" |William G. Alexander3
|-
| valign="top" |Genome and methylome analysis by:
| valign="top" |William G. Alexander3 & Ashley Hall2
|-
| valign="top" |MIC and culturing conditions by:
| valign="top" |Rhiannon Cecil & Ashley Howes2
|-
| valign="top" |Transformed by:
| valign="top" |Ashley Howes
|}
1Institute for Bioeconomy Science, Palmerston North, New Zealand. 2BiomEdit, Indianapolis, Indiana, United States. 3Oak Ridge National Lab, Oak Ridge, Tennessee, United States.

== Genome ==
{| class="wikitable"
| colspan="2" valign="top" |'''''L. ruminis'' WC1T17 Genome Summary'''
|-
| valign="top" |'''Sequencing method'''
| valign="top" |'''Oxford Nanopore'''
|-
| valign="top" |'''Contigs'''
| valign="top" |'''1'''
|-
| valign="top" |'''Base pairs'''
| valign="top" |'''1.9 Mb'''
|-
| valign="top" |'''CDSs'''
| valign="top" |'''1,830'''
|-
| valign="top" |'''CRISPR'''
| valign="top" |'''1'''
|-
| valign="top" |'''Genes'''
| valign="top" |'''1,952'''
|-
| valign="top" |'''rRNA'''
| valign="top" |'''19'''
|-
| valign="top" |'''tRNA'''
| valign="top" |'''73'''
|-
| valign="top" |'''Miscellaneous RNA'''
| valign="top" |'''29'''
|-
| valign="top" |'''Antimicrobial resistance genes'''
| valign="top" |'''None'''
|}

== Methylome ==

=== Methylome analysis summary results ===
{| class="wikitable"
| colspan="2" |''L. ruminis'' WC1T17 Methylome Summary
|-
| valign="top" |Isolation Motif
| valign="top" |% Motif Methylation
|-
| valign="top" |GTTGN(6mA)C
| valign="top" |99.13
|-
| valign="top" |CAC(6mA)G
| valign="top" |92.58
|-
| valign="top" |CAGR(6mA)G
| valign="top" |99.54
|}

=== DefenseFinder Results ===
{| class="wikitable"
| colspan="2" valign="top" |''L. ruminis'' WC1T17 DefenseFinder Results
|-
| valign="top" |DefenseFinder System
| valign="top" |# Found
|-
| valign="top" |Cas (Class I, Type I-E)
| valign="top" |1
|-
| valign="top" |RM Type III
| valign="top" |1
|-
| valign="top" |PD-T7-2
| valign="top" |1
|-
| valign="top" |RM Type IIG
| valign="top" |3
|}

=== Methylating ''Escherichia coli'' strains ===
''E. coli'' strain AGXXXXX engineered to carry methytransferases X, X, X for methylating plasmid DNA for ''L. ruminis'' WC1T17.

== Culturing Conditions ==
''L. ruminis'' WC1T17 can be readily cultured in MRS broth or agar plates under anaerobic conditions (75% N2, 5% H2, and 20% CO2) at 39°C for 12 – 48 hours of incubation. ''L. ruminis'' WC1T17 colonies typically form on MRS agar plates overnight and colonies inoculated from an agar plate or transferred from an active liquid culture will also grow overnight; however, when reviving from cryostock the strain takes ~48 hours to exhibit growth in broth. The strain will remain viable in liquid or solid medium for ~1 week at room temperature under anaerobic conditions. For long-tern storage 1mL of active culture with an OD600 >0.8 should be combined with anaerobic 50% glycerol to a final glycerol concentration of 25% in anaerobic screw-cap cryovials then stored at -80°C. Revival of cryostocked cells is achieved by transferring a small amount of the cryostock to either an MRS agar plate or to MRS broth followed by incubation under anaerobic conditions.

== Antimicrobial Susceptibility ==

== Transformation Results ==

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[2] Sharpe ME, Latham MJ, Garvie EI, Zirngibl J, Kandler O. 1973. Two new species of Lactobacillus isolated from the bovine rumen, Lactobacillus ruminis sp.nov. and Lactobacillus vitulinus sp.nov. J Gen Microbiol 77: 37-49. doi: 10.1099/00221287-77-1-37.

Ligilactobacillus ruminis WC1T17

2026-10-20T23:02:09Z

Billkelleydonvis: /* External Links */

== Introduction ==
[[File:Lruminis WC1T17 microscopy.png|thumb|Microscopy (100X) magnification image of ''Ligilactobacillus ruminis'' WC1T17 ]]

=== Strain characteristics and function in the rumen ===
''Ligilactobacillus ruminis'' WC1T17 is a Gram-positive, rod-shaped, aerotolerant anaerobic bacterium that typically grows in a single bacillus or diplo-bacillus cellular arrangement. ''Lactobacillus'' species are of increasing interest for methane mitigation research in ruminant animals as their metabolic network in the rumen can function as a hydrogen sink. ''Ligilactobacillus'' are lactic acid bacteria which ferment glucose in the rumen and produce lactate, this lactate can be utilized by syntrophic lactate utilizing bacteria to produce propionate, an important metabolite for the host animal, and this process also requires absorbs hydrogen thus reducing available substrate for methanogenesis. ''L. ruminis'' is of particular interest to the Global Methane Hub as it is the only known member of the ''Lactobacillus'' genus to be motile making it an attractive prospect for ruminant methane mitigation research as it is theoretically better suited to translocate to multiple niches within the rumen biome.

=== Strain history and information ===
''L. ruminis'' WC1T17 was isolated from the rumen of a healthy cow in Palmerston North, New Zealand by the Institute for Bioeconomy Science, formerly known as AgResearch. The strain contains a circular 1.9 Mb genome with no extrachromosomal elements such as plasmids. This strain can be readily cultured in MRS broth and on MRS agar plates under anaerobic conditions with an average doubling time of 40 minutes.
Minimum inhibitory concentration (MIC) screening of antibiotics and counter-selective agents in liquid media shows that the strain is sensitive to the following tested antibiotics: chloramphenicol, ampicillin, tetracycline, and streptomycin and the following counter-selective agents: 8-azehypoxanthine, 2-deoxy-d-galactose, 5-fluordeoxyuridine, and sucrose.

''L. ruminis'' WC1T17 is genetically tractable and has been successfully transformed via electroporation with the replicative shuttle vector pMTL89151. This vector confers resistance to chloramphenicol and contains the pAMB1 Gram-positive origin of replication machinery in addition to a multiple cloning sight for integration of reporter genes or biological payloads of interest.

Ligilactobacillus ruminis WC1T17 (DSM 115561) was isolated from bovine rumen contents in NZ using Wilkins-Chalgren Agar. It has not been phenotypically characterised.

The draft genome for WC1T17 (1,842,330 bp) was generated through the Hungate1000 project with JGI [1].

This species was formerly named as Lactobacillus ruminis [2].

NCBI: Ligilactobacillus ruminis

GTDB: Ligilactobacillus ruminis_A. WC1T17 belongs in a different species group than the type strain of L. ruminis (RF1, DSM 20403) [2]

Risk group: 1

== Global Methane Hub Metadata ==
{| class="wikitable"
| valign="top" |Strain origin:
| valign="top" |New Zealand1
|-
| valign="top" |Isolated from:
| valign="top" |Cow rumen
|-
| valign="top" |Sequenced by:
| valign="top" |Rhiannon Cecil2
|-
| valign="top" |Assembled by:
| valign="top" |William G. Alexander3
|-
| valign="top" |Genome and methylome analysis by:
| valign="top" |William G. Alexander3 & Ashley Hall2
|-
| valign="top" |MIC and culturing conditions by:
| valign="top" |Rhiannon Cecil & Ashley Howes2
|-
| valign="top" |Transformed by:
| valign="top" |Ashley Howes
|}
1Institute for Bioeconomy Science, Palmerston North, New Zealand. 2BiomEdit, Indianapolis, Indiana, United States. 3Oak Ridge National Lab, Oak Ridge, Tennessee, United States.

== Genome ==
{| class="wikitable"
| colspan="2" valign="top" |'''''L. ruminis'' WC1T17 Genome Summary'''
|-
| valign="top" |'''Sequencing method'''
| valign="top" |'''Oxford Nanopore'''
|-
| valign="top" |'''Contigs'''
| valign="top" |'''1'''
|-
| valign="top" |'''Base pairs'''
| valign="top" |'''1.9 Mb'''
|-
| valign="top" |'''CDSs'''
| valign="top" |'''1,830'''
|-
| valign="top" |'''CRISPR'''
| valign="top" |'''1'''
|-
| valign="top" |'''Genes'''
| valign="top" |'''1,952'''
|-
| valign="top" |'''rRNA'''
| valign="top" |'''19'''
|-
| valign="top" |'''tRNA'''
| valign="top" |'''73'''
|-
| valign="top" |'''Miscellaneous RNA'''
| valign="top" |'''29'''
|-
| valign="top" |'''Antimicrobial resistance genes'''
| valign="top" |'''None'''
|}

== Methylome ==

=== Methylome analysis summary results ===
{| class="wikitable"
| colspan="2" |''L. ruminis'' WC1T17 Methylome Summary
|-
| valign="top" |Isolation Motif
| valign="top" |% Motif Methylation
|-
| valign="top" |GTTGN(6mA)C
| valign="top" |99.13
|-
| valign="top" |CAC(6mA)G
| valign="top" |92.58
|-
| valign="top" |CAGR(6mA)G
| valign="top" |99.54
|}

=== DefenseFinder Results ===
{| class="wikitable"
| colspan="2" valign="top" |''L. ruminis'' WC1T17 DefenseFinder Results
|-
| valign="top" |DefenseFinder System
| valign="top" |# Found
|-
| valign="top" |Cas (Class I, Type I-E)
| valign="top" |1
|-
| valign="top" |RM Type III
| valign="top" |1
|-
| valign="top" |PD-T7-2
| valign="top" |1
|-
| valign="top" |RM Type IIG
| valign="top" |3
|}

=== Methylating ''Escherichia coli'' strains ===
''E. coli'' strain AGXXXXX engineered to carry methytransferases X, X, X for methylating plasmid DNA for ''L. ruminis'' WC1T17.

== Culturing Conditions ==
''L. ruminis'' WC1T17 can be readily cultured in MRS broth or agar plates under anaerobic conditions (75% N2, 5% H2, and 20% CO2) at 39°C for 12 – 48 hours of incubation. ''L. ruminis'' WC1T17 colonies typically form on MRS agar plates overnight and colonies inoculated from an agar plate or transferred from an active liquid culture will also grow overnight; however, when reviving from cryostock the strain takes ~48 hours to exhibit growth in broth. The strain will remain viable in liquid or solid medium for ~1 week at room temperature under anaerobic conditions. For long-tern storage 1mL of active culture with an OD600 >0.8 should be combined with anaerobic 50% glycerol to a final glycerol concentration of 25% in anaerobic screw-cap cryovials then stored at -80°C. Revival of cryostocked cells is achieved by transferring a small amount of the cryostock to either an MRS agar plate or to MRS broth followed by incubation under anaerobic conditions.

== Antimicrobial Susceptibility ==

== Transformation Results ==

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.
[2] Sharpe ME, Latham MJ, Garvie EI, Zirngibl J, Kandler O. 1973. Two new species of Lactobacillus isolated from the bovine rumen, Lactobacillus ruminis sp.nov. and Lactobacillus vitulinus sp.nov. J Gen Microbiol 77: 37-49. doi: 10.1099/00221287-77-1-37.

Ligilactobacillus ruminis WC1T17

2026-10-20T23:01:12Z

Billkelleydonvis: introduction

Pseudobutyrivibrio xylanivorans MA3014

2026-10-20T22:34:46Z

Billkelleydonvis: Introduction and external links

== Introduction ==
'''Pseudobutyrivibrio xylanivorans MA3014'''

Pseudobutyrivibrio xylanivorans MA3014 (DSM 120355) was isolated from the plant-adherent fraction of bovine rumen contents in NZ [1, cow A]. It ferments a range of carbohydrates [2] with butyrate, formate and lactate as the main fermentation end products.

The MA3014 genome (3,584,491 bp) consists of a chromosome (3,412,851 bp) and two plasmids (88,942 bp, and 82,698 bp) [2].

NCBI: Pseudobutyrivibrio xylanivorans.

GTBD: Pseudobutyrivibrio xylanivorans_A. Strain MA3014 belongs in a different species group than the type strain of P. xylanivorans (Mz5T, DSM 14809) [3].

Risk group: 1

== Global Methane Hub Metadata ==
add here

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Noel S. 2013. Cultivation and community composition analysis of plant-adherent rumen bacteria. PhD dissertation. Massey University, Palmerston North, New Zealand. <nowiki>https://mro.massey.ac.nz/server/api/core/bitstreams/bcfbe4cb-19a9-40c0-b5e8-61f9ddb90ce0/content</nowiki>.

[2] Palevich N, Maclean PH, Kelly WJ, Leahy SC, Rakonjac J, Attwood GT. 2020. Complete genome sequence of the polysaccharide-degrading rumen bacterium Pseudobutyrivibrio xylanivorans MA3014 reveals an incomplete glycolytic pathway. Genome Biol Evol 12: 1566-1572. doi: 10.1093/gbe/evaa165.

[3] Kopecny J, Zorec M, Mrazek J, Kobayashi Y, Marinsek-Logar R. 2003. Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen. Int J Syst Evol Microbiol 53: 201–9. doi: 10.1099/ijs.0.02345-0.

Pseudobutyrivibrio ruminis A12-1T

2026-10-20T22:31:55Z

Billkelleydonvis: /* External Links */

== Introduction ==
'''Pseudobutyrivibrio ruminis A12-1T'''

Pseudobutyrivibrio ruminis A12-1T (DSM 9787) was isolated from bovine rumen contents in Sweden [1]. It stains Gram negative and ferments a range of carbohydrates producing butyrate, formate and lactate. It is the type species of the genus Pseudobutyrivibrio within the family Lachnospiraceae and the type stain of the P. ruminis species [2]

The draft genome for A12-1 (3,020,378 bp) was generated through the Hungate1000 project with JGI [3].

As with Butyrivibrio species A12-1has two distinct respiratory enzyme complexes, Rnf and Ech, which couple with two ATP synthases in separate chemiosmotic circuits and impact energy conservation in these organisms [4].

LPSN: Pseudobutyrivibrio ruminis van Gylswyk et al. 1996

NCBI: Pseudobutyrivibrio ruminis.

GTBD: Pseudobutyrivibrio ruminis.

Risk group: 1

=== Strain characteristics and function in the rumen ===

=== Strain history and information ===

== Global Methane Hub Metadata ==
{| class="wikitable"
| valign="top" |Strain origin:
| valign="top" |Sweden
|-
| valign="top" |Isolated from:
| valign="top" |Cow rumen
|-
| valign="top" |Sequenced by:
| valign="top" |
|-
| valign="top" |Assembled by:
| valign="top" |William G. Alexander
|-
| valign="top" |Genome and methylome analysis by:
| valign="top" |
|-
| valign="top" |MIC and culturing conditions by:
| valign="top" |
|-
| valign="top" |Transformed by:
| valign="top" |
|}

== Genome ==
{| class="wikitable"
| colspan="2" valign="top" |''P. ruminis'' A12-1T Genome Summary
|-
| valign="top" |Sequencing method
| valign="top" |Oxford Nanopore
|-
| valign="top" |Contigs
| valign="top" |
|-
| valign="top" |Base pairs
| valign="top" |
|-
| valign="top" |CDSs
| valign="top" |
|-
| valign="top" |CRISPR
| valign="top" |
|-
| valign="top" |Genes
| valign="top" |
|-
| valign="top" |rRNA
| valign="top" |
|-
| valign="top" |tRNA
| valign="top" |
|-
| valign="top" |Miscellaneous RNA
| valign="top" |
|-
| valign="top" |Antimicrobial resistance genes
| valign="top" |
|}

== Methylome ==

=== Methylome analysis summary results ===
{| class="wikitable"
| colspan="2" |''P. ruminis'' A12-1T Methylome Summary
|-
| valign="top" |Isolation Motif
| valign="top" |% Motif Methylation
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|}

=== DefenseFinder Results ===
{| class="wikitable"
| colspan="2" valign="top" |''P. ruminis'' A12-1T DefenseFinder Results
|-
| valign="top" |DefenseFinder System
| valign="top" |# Found
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|}

=== Methylating ''Escherichia coli'' strains ===
''E. coli'' strain AGXXXXX engineered to carry methytransferases X, X, X for methylating plasmid DNA for ''P. ruminis'' A12-1T.

== Culturing Conditions ==

== Antimicrobial Susceptibility ==

== Transformation Results ==

== External Links ==
[1] van Gylswyk NO, Hippe H, Rainey FA. 1996. Pseudobutyrivibrio ruminis gen. nov., sp. nov., a butyrate-producing bacterium from the rumen that closely resembles Butyrivibrio fibrisolvens in phenotype. Int. J. Syst. Bacteriol 46: 559-563. doi: 10.1099/00207713-46-2-559

[2] https://bacdive.dsmz.de/strain/6362

[3] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[4] Schoelmerich MC, Katsyv A, Dönig J, Hackmann TJ, Müller V. 2020. Energy conservation involving 2 respiratory circuits. Proc Natl Acad Sci U S A 117: 1167-1173. doi: 10.1073/pnas.1914939117.

Pseudobutyrivibrio ruminis A12-1T

2026-10-20T22:31:01Z

Billkelleydonvis: /* External Links */

== Introduction ==
'''Pseudobutyrivibrio ruminis A12-1T'''

Pseudobutyrivibrio ruminis A12-1T (DSM 9787) was isolated from bovine rumen contents in Sweden [1]. It stains Gram negative and ferments a range of carbohydrates producing butyrate, formate and lactate. It is the type species of the genus Pseudobutyrivibrio within the family Lachnospiraceae and the type stain of the P. ruminis species [2]

The draft genome for A12-1 (3,020,378 bp) was generated through the Hungate1000 project with JGI [3].

As with Butyrivibrio species A12-1has two distinct respiratory enzyme complexes, Rnf and Ech, which couple with two ATP synthases in separate chemiosmotic circuits and impact energy conservation in these organisms [4].

LPSN: Pseudobutyrivibrio ruminis van Gylswyk et al. 1996

NCBI: Pseudobutyrivibrio ruminis.

GTBD: Pseudobutyrivibrio ruminis.

Risk group: 1

=== Strain characteristics and function in the rumen ===

=== Strain history and information ===

== Global Methane Hub Metadata ==
{| class="wikitable"
| valign="top" |Strain origin:
| valign="top" |Sweden
|-
| valign="top" |Isolated from:
| valign="top" |Cow rumen
|-
| valign="top" |Sequenced by:
| valign="top" |
|-
| valign="top" |Assembled by:
| valign="top" |William G. Alexander
|-
| valign="top" |Genome and methylome analysis by:
| valign="top" |
|-
| valign="top" |MIC and culturing conditions by:
| valign="top" |
|-
| valign="top" |Transformed by:
| valign="top" |
|}

== Genome ==
{| class="wikitable"
| colspan="2" valign="top" |''P. ruminis'' A12-1T Genome Summary
|-
| valign="top" |Sequencing method
| valign="top" |Oxford Nanopore
|-
| valign="top" |Contigs
| valign="top" |
|-
| valign="top" |Base pairs
| valign="top" |
|-
| valign="top" |CDSs
| valign="top" |
|-
| valign="top" |CRISPR
| valign="top" |
|-
| valign="top" |Genes
| valign="top" |
|-
| valign="top" |rRNA
| valign="top" |
|-
| valign="top" |tRNA
| valign="top" |
|-
| valign="top" |Miscellaneous RNA
| valign="top" |
|-
| valign="top" |Antimicrobial resistance genes
| valign="top" |
|}

== Methylome ==

=== Methylome analysis summary results ===
{| class="wikitable"
| colspan="2" |''P. ruminis'' A12-1T Methylome Summary
|-
| valign="top" |Isolation Motif
| valign="top" |% Motif Methylation
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|}

=== DefenseFinder Results ===
{| class="wikitable"
| colspan="2" valign="top" |''P. ruminis'' A12-1T DefenseFinder Results
|-
| valign="top" |DefenseFinder System
| valign="top" |# Found
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|-
| valign="top" |
| valign="top" |
|}

=== Methylating ''Escherichia coli'' strains ===
''E. coli'' strain AGXXXXX engineered to carry methytransferases X, X, X for methylating plasmid DNA for ''P. ruminis'' A12-1T.

== Culturing Conditions ==

== Antimicrobial Susceptibility ==

== Transformation Results ==

== External Links ==
[1] van Gylswyk NO, Hippe H, Rainey FA. 1996. Pseudobutyrivibrio ruminis gen. nov., sp. nov., a butyrate-producing bacterium from the rumen that closely resembles Butyrivibrio fibrisolvens in phenotype. Int. J. Syst. Bacteriol 46: 559-563. doi: 10.1099/00207713-46-2-559
[2] https://bacdive.dsmz.de/strain/6362
[3] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.
[4] Schoelmerich MC, Katsyv A, Dönig J, Hackmann TJ, Müller V. 2020. Energy conservation involving 2 respiratory circuits. Proc Natl Acad Sci U S A 117: 1167-1173. doi: 10.1073/pnas.1914939117.

Pseudobutyrivibrio ruminis A12-1T

2026-10-20T22:30:03Z

Billkelleydonvis: /* Introduction */

Sharpea azabuensis KH1P5

2026-10-20T22:27:39Z

Billkelleydonvis: /* Introduction */

[[File:Sabu tube.png|thumb|''S. azabuensis'' KH1P5 in liquid culture exhibiting its dense layer of EPS. Source: Dr. Roy Rodriguez Carrero|346x346px]]

== Introduction ==
'''Sharpea azabuensis KH1P5'''

Sharpea azabuensis KH1P5 was isolated from bovine rumen contents in NZ using KH medium which was supplemented with haemin and vitamin K [1]. KH1P5 ferments glucose, fructose, galactose, cellobiose, sucrose, lactose and raffinose with D-lactate as the main fermentation product together with small amounts of acetate, formate and ethanol [2]. It is a member of the family Coprobacillaceae.

Sharpea and Kandleria were identified as key bacteria associated with the S-type (Sharpea-enriched) bacterial community, one of the two low-CH4 community types in rumen samples from sheep that differed in the amount of CH4 formed per unit of feed consumed when these sheep were fed pelletized lucerne [3]. A metagenomic and metatranscriptomic study conducted by Kamke et al. [4] confirmed that the relative abundance of Sharpea spp. was greater in a group of low-CH4 emitting sheep than in their high-CH4 emitting flock mates. It was hypothesized that lactate produced by these bacteria is further converted to butyrate by Megasphaera spp., resulting in lower CH4 emissions.

The draft genome for KH1P5 (2,329,465 bp) was generated through the Hungate1000 project with JGI [1]. Resequencing gave a single chromosome of 2,465,508 bp.

LPSN: ''Sharpea azabuensis'' Morita ''et al.'' 2008

NCBI: Sharpea azabuensis.

GTDB: Sharpea azabuensis. KH1P5 groups with the type strain (ST18, DSM 18934) [5]

Risk group: 1

''[[Sharpea azabuensis]]'' KH1P5 is a high-interest microbe to the Global Methane Hub. It produces a thick, mucoidal layer of [[wikipedia:Extracellular_polymeric_substance|extracellular polymeric substance (EPS)]] that requires [[Sharpea azabuensis KH1P5#Protocols|removal via washing]] with chelating agents and detergent before work with the culture.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|New Zealand, Kelly Lab
|-
|Sequenced by:
|Sam Mahoney Kurpe
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|Roy Rodriguez Carrero
|-
|MIC and Culturing Conditions by:
|Roy Rodriguez Carrero
|-
|Transformation by:
|Roy Rodriguez Carrero
|}

== Genome ==
[[File:S azabuensis circos.png|Circos plot of ''S. azabuensis'' KH1P5. Source: Dr. William G. Alexander|center|thumb]]

== DefenseFinder Results ==

== Methylome ==
While ''S. azabuensis'' KH1P5 possesses two putative Type II restriction endonucleases, no methylation is detectable in the isolate. Also, these two genes do not methylate in ''E. coli'' strains, suggesting that they're vestigial defense systems.

== Methylating E. coli Strains ==
Use a strain of ''E. coli'' that lacks dam, dcm, and hsdRMS, such as AG5589.

== Culturing Conditions ==
''S. azabuensis'' KH1P5 grows well in stock [[RCM]] at 37 °C.

== Antibiotic MIC Tests ==
[[File:Sabu MIC.png|left|thumb|MIC tests of ''S. azabuensis''. Source: Dr. Roy Rodriguez Carrero]]
{| class="wikitable"
!antibiotic
!concentration (ug/mL)
|-
|chloramphenicol
|0.38
|-
|erythromycin
|1
|-
|kanamycin
|insensitive
|-
|spectinomycin
|96
|-
|tetracycline
|0.23
|}

== Protocols ==

* [[Removal of extracellular material via chelation washing]]

== Transformation Results ==

== External Links ==
[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; Hungate1000 project collaborators; Perry R, Henderson G, Creevey CJ, Terrapon N, Lapebie P, Drula E, Lombard V, Rubin E, Kyrpides NC, Henrissat B, Woyke T, Ivanova NN, Kelly WJ. 2019. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nature Biotechnol 36: 359-367. doi: 10.1038/nbt.4110.

[2] Kumar S, Treloar BP, Teh KH, McKenzie CM, Henderson G, Attwood GT, Waters SM, Patchett ML, Janssen PH. 2018. Sharpea and Kandleria are lactic acid producing rumen bacteria that do not change their fermentation products when co-cultured with a methanogen. Anaerobe 54: 31-38. doi: 10.1016/j.anaerobe.2018.07.008.

[3] Kittelmann S, Pinares-Patiño CS, Seedorf H, Kirk MR, Ganesh S, McEwan JC, Janssen PH. 2014. Two different bacterial community types are linked with the low-methane emission trait in sheep. PLoS One 9: e103171. doi: 10.1371/journal.pone.0103171.

[4] Kamke J, Kittelmann S, Soni P, Li Y, Tavendale M, Ganesh S, Janssen PH, Shi W, Froula J, Rubin EM, Attwood GT. 2016. Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome 4: 56. doi: 10.1186/s40168-016-0201-2.

[5] Morita H, Shiratori C, Murakami M, Takami H, Toh H, Kato Y, Nakajima F, Takagi M, Akita H, Masaoka T, Hattori M. 2008. Sharpea azabuensis gen. nov., sp. nov., a Gram-positive, strictly anaerobic bacterium isolated from the faeces of thoroughbred horses. Int J Syst Evol Microbiol 58: 2682-2686 doi: 10.1099/ijs.0.65543-0.