Global Methane Hub Wikipedia - User contributions [en]

Lachnospiraceae bacterium NK3A20

2026-11-08T20:59:23Z

Mahoneykurpe: /* Genome */

== 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:
|New Zealand, isolated by Nikki Kenters [1]
|-
|Sequenced by:
|Sam Mahoney-Kurpe
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==
{| class="wikitable"
|+
! colspan="2" |Genome characteristics
|-
|Contigs
|1
|-
|size (bp)
|3,001,182
|-
|GC %
|54.2
|-
|CDS
|2513
|-
|rRNA
|9
|-
|tRNA
|46
|-
|CRISPR
|1
|}

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Methylated motif
!Percent methylated
|-
|C(6mA)YCNNNNNTGG
|99.1
|-
|CC(6mA)NNNNNGRTG
|99.2
|-
|C(5mC)GG
|76.5
|}

== 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.

Aristaeella lactis WTE2008T

2026-11-08T20:49:26Z

Mahoneykurpe: /* Genome */

== Introduction ==
''Aristaeella lactis'' WTE2008T (DSM 112788, JCM 34734) was isolated from rumen contents of a dairy cow grazing a ryegrass pasture in New Zealand [1]. WTE2008 ferments a variety of substrates including the plant cell wall polysaccharides xylan and pectin, forming acetate, lactate, ethanol and hydrogen as end products [2].

NCBI: Aristaeella lactis

Risk Group: 1

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|New Zealand, isolated by Samantha J. Noel [1]
|-
|Sequenced by:
|Sam Mahoney-Kurpe
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==
{| class="wikitable"
|+
! colspan="2" |Genome characteristics
|-
|Contigs
|1
|-
|size (bp)
|3,442,562
|-
|GC %
|53.5
|-
|CDS
|3022
|-
|rRNA
|10
|-
|tRNA
|48
|-
|CRISPR
|0
|}

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==
{| class="wikitable"
|+
!Methylated motif
!Percent methylated
|-
|CCAAA(6mA)
|95.7
|-
|A(5mC)GGG
|96.1
|-
|C(5mC)CGT
|76.8
|}

== 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] Mahoney-Kurpe SC, Palevich N, Noel SJ, Gagic D, Biggs PJ, Soni P, Reid PM, Koike S, Kobayashi Y, Janssen PH, Attwood GT, Moon CD. 2023. ''Aristaeella hokkaidonensis'' gen. nov. sp. nov. and ''Aristaeella lactis'' sp. nov., two rumen bacterial species of a novel proposed family, ''Aristaeellaceae'' fam. nov. Int J Syst Evol Microbiol 73:005831.

Aristaeella hokkaidonensis R-7T

2026-11-08T20:30:33Z

Mahoneykurpe: /* Genome */

== Introduction ==
''Aristaeella hokkaidonensis'' R-7T (DSM 112795, JCM 34733) was isolated from serial dilutions of the cellulose-adherent fraction from incubations of crystalline cellulose with rumen contents collected from a sheep fed a 9:1 forage-concentrate diet in Hokkaido, Japan. R-7 ferments a range of substrates including the plant cell wall polysaccharides xylan and pectin, though despite its apparent adherence, not crystalline cellulose. R-7 forms acetate, hydrogen, ethanol, and lactate as fermentation end products [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 ==
{| class="wikitable"
|+
! colspan="2" |Genome characteristics
|-
|Contigs
|1
|-
|size (bp)
|3,390,520
|-
|GC %
|53.0
|-
|CDS
|2966
|-
|rRNA
|9
|-
|tRNA
|49
|-
|CRISPR
|0
|}

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Methylated motif
!Percent methylated
|-
|(6mA)CGNNNNNTGC
|98.0
|-
|GC(6mA)NNNNNCGT
|92.7
|-
|TGG(6mA)NNNNNNTRC
|99.8
|-
|GY(6mA)NNNNNNTCCA
|93.3
|-
|CCAAA(6mA)
|97.1
|}

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==
[1] Mahoney-Kurpe SC, Palevich N, Noel SJ, Gagic D, Biggs PJ, Soni P, Reid PM, Koike S, Kobayashi Y, Janssen PH, Attwood GT, Moon CD. 2023. ''Aristaeella hokkaidonensis'' gen. nov. sp. nov. and ''Aristaeella lactis'' sp. nov., two rumen bacterial species of a novel proposed family, ''Aristaeellaceae'' fam. nov. Int J Syst Evol Microbiol 73:005831.

Sharpea azabuensis KH1P5

2026-11-08T20:00:31Z

Mahoneykurpe: /* Genome */

[[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

== 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 ==
{| class="wikitable"
|+
! colspan="2" |Genome characteristics
|-
|Contigs
|1
|-
|size (bp)
|2,465,508
|-
|GC %
|37.5
|-
|CDS
|2364
|-
|rRNA
|16
|-
|tRNA
|66
|-
|CRISPR
|2
|}
[[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. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

KH1P5 also grows well on M2G medium at 39 °C, with 10 ml cultures reaching stationary phase after 6-7 h at optical densities of ~4-5. Cells of KH1P5 form long chains.

[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

== 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)
|-
|carbenicillin
|5
|-
|chloramphenicol
|0.38
|-
|clarithromycin
|25
|-
|erythromycin
|1
|-
|kanamycin
|insensitive
|-
|spectinomycin
|96
|-
|tetracycline
|0.23
|-
|thiamphenicol
|5
|}

== 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.

Aristaeella lactis WTE2008T

2026-11-02T07:38:43Z

Mahoneykurpe: /* Introduction*/

== Introduction ==
''Aristaeella lactis'' WTE2008T (DSM 112788, JCM 34734) was isolated from rumen contents of a dairy cow grazing a ryegrass pasture in New Zealand [1]. WTE2008 ferments a variety of substrates including the plant cell wall polysaccharides xylan and pectin, forming acetate, lactate, ethanol and hydrogen as end products [2].

NCBI: Aristaeella lactis

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 ==
{| class="wikitable"
|+
!Methylated motif
!Percent methylated
|-
|CCAAA(6mA)
|95.7
|-
|A(5mC)GGG
|96.1
|-
|C(5mC)CGT
|76.8
|}

== 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] Mahoney-Kurpe SC, Palevich N, Noel SJ, Gagic D, Biggs PJ, Soni P, Reid PM, Koike S, Kobayashi Y, Janssen PH, Attwood GT, Moon CD. 2023. ''Aristaeella hokkaidonensis'' gen. nov. sp. nov. and ''Aristaeella lactis'' sp. nov., two rumen bacterial species of a novel proposed family, ''Aristaeellaceae'' fam. nov. Int J Syst Evol Microbiol 73:005831.

Selenomonas ruminantium PC18

2026-11-02T04:22:22Z

Mahoneykurpe: /* Methylating E. coli Strains */

== 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 ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==
''E. coli'' strain AG22287 has been developed by ORNL to match the methylome of PC 18.

== Culturing Conditions ==
PC 18 grows very well in M2G medium, reaching OD >2.5 within ~3-5 h. PC 18 also grows well on M2G agar plates, with a plating efficiency of ~70%.

== Antibiotic MIC Tests ==
{| class="wikitable"
|+
!antibiotic
!concentration (μg/ml)
|-
|carbenicillin
|5
|-
|clarithromycin
|50
|-
|tetracycline
|insensitive
|-
|thiamphenicol
|1
|}

== Protocols ==

== Transformation Results ==

== 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.

Aristaeella lactis WTE2008T

2026-11-02T04:07:30Z

Mahoneykurpe: /* Methylome */

== Introduction ==

== 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 ==
{| class="wikitable"
|+
!Methylated motif
!Percent methylated
|-
|CCAAA(6mA)
|95.7
|-
|A(5mC)GGG
|96.1
|-
|C(5mC)CGT
|76.8
|}

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==

Aristaeella hokkaidonensis R-7T

2026-11-02T03:58:35Z

Mahoneykurpe: /* Methylome */

== Introduction ==

== 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 ==
{| class="wikitable"
|+
!Methylated motif
!Percent methylated
|-
|(6mA)CGNNNNNTGC
|98.0
|-
|GC(6mA)NNNNNCGT
|92.7
|-
|TGG(6mA)NNNNNNTRC
|99.8
|-
|GY(6mA)NNNNNNTCCA
|93.3
|-
|CCAAA(6mA)
|97.1
|}

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==

Lachnospiraceae bacterium NK3A20

2026-11-02T03:42:57Z

Mahoneykurpe: /* Methylome */

== 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 ==
{| class="wikitable"
|+
!Methylated motif
!Percent methylated
|-
|C(6mA)YCNNNNNTGG
|99.1
|-
|CC(6mA)NNNNNGRTG
|99.2
|-
|C(5mC)GG
|76.5
|}

== 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.

Eubacterium maltosivorans SA11

2026-11-01T00:39:12Z

Mahoneykurpe: /* Protocols */

== 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 ==
SA11 grows well in M2G medium, with cultures reaching optical densities >2.5 after ~8 hours. Cells have a tendency to aggregate into clumps becoming more pronounced later in growth, complicating efforts to calculate plating efficiency. However, SA11 seems to plate relatively well on M2GSC agar (1.5% w/v) permitting selection of transformant colonies on this medium.

== Antimicrobial MIC Tests ==
{| class="wikitable"
|+
!antibiotic
!MIC (μg/ml)
|-
|carbenicillin
|50
|-
|clarithromycin
|5
|-
|tetracycline
|5
|-
|thiamphenicol
|5
|}
add here

== Protocols ==

* [[Eubacterium maltosivorans SA11 transformation protocol (BSI)]]

== 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.

Eubacterium maltosivorans SA11

2026-10-30T08:13:40Z

Mahoneykurpe: /* Culturing Conditions */

== 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 ==
SA11 grows well in M2G medium, with cultures reaching optical densities >2.5 after ~8 hours. Cells have a tendency to aggregate into clumps becoming more pronounced later in growth, complicating efforts to calculate plating efficiency. However, SA11 seems to plate relatively well on M2GSC agar (1.5% w/v) permitting selection of transformant colonies on this medium.

== Antimicrobial MIC Tests ==
{| class="wikitable"
|+
!antibiotic
!MIC (μg/ml)
|-
|carbenicillin
|50
|-
|clarithromycin
|5
|-
|tetracycline
|5
|-
|thiamphenicol
|5
|}
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.

Eubacterium maltosivorans SA11

2026-10-30T08:09:33Z

Mahoneykurpe: /* Culturing Conditions */

== 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 ==
SA11 grows well in M2G medium, with cultures reaching optical densities >2.5 after ~8 hours. Cells have a tendency to aggregate into clumps becoming more pronounced at later growth stages, complicating efforts to calculate plating efficiency. However, SA11 seems to plate relatively well on M2GSC agar (1.5% w/v) permitting selection of transformant colonies on this medium.

== Antimicrobial MIC Tests ==
{| class="wikitable"
|+
!antibiotic
!MIC (μg/ml)
|-
|carbenicillin
|50
|-
|clarithromycin
|5
|-
|tetracycline
|5
|-
|thiamphenicol
|5
|}
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.

Eubacterium maltosivorans SA11

2026-10-30T08:08:00Z

Mahoneykurpe: /* Culturing Conditions */

== 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 ==
SA11 grows well in M2G medium, with cultures reaching optical densities >2.5 after ~8 hours. Cells have a tendency to aggregate into clumps becoming more pronounced at later growth stages, complicating efforts to calculate plating efficiency. However, SA11 seems to plate relatively well on M2GSC agar (1.5% w/v) permitting successful selection of transformant colonies on this medium.

== Antimicrobial MIC Tests ==
{| class="wikitable"
|+
!antibiotic
!MIC (μg/ml)
|-
|carbenicillin
|50
|-
|clarithromycin
|5
|-
|tetracycline
|5
|-
|thiamphenicol
|5
|}
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.

Eubacterium maltosivorans SA11

2026-10-30T08:06:50Z

Mahoneykurpe: /* Culturing Conditions */

== 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 ==
SA11 grows well in M2G medium, with cultures reaching optical densities >2.5 after ~8 hours. Cells have a tendency to aggregate into clumps becoming more pronounced at later growth stages, complicating efforts to calculate plating efficiencies. However, SA11 seems to plate relatively well on M2GSC agar (1.5% w/v) permitting successful selection of transformant colonies on this medium.

== Antimicrobial MIC Tests ==
{| class="wikitable"
|+
!antibiotic
!MIC (μg/ml)
|-
|carbenicillin
|50
|-
|clarithromycin
|5
|-
|tetracycline
|5
|-
|thiamphenicol
|5
|}
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.

Eubacterium maltosivorans SA11 transformation protocol (BSI)

2026-10-30T08:00:20Z

Mahoneykurpe: Created page with "Based on protocol for ''E. limosum'' described in Sanford & Woolston (2022) [1], with some adjustments made based on results from initial electroporation tests which gave a transformation efficiency of approx. 6,000 CFU/µg in a best attempt. === '''Electrocompetent cell preparation''' === # Grow six 10 ml SA11 cultures (or upscale as required) to early log phase (OD ~0.5) # Cool cultures on ice for 20 min. # Bring cultures into chamber on ice, pour 30 ml culture into..."

Based on protocol for ''E. limosum'' described in Sanford & Woolston (2022) [1], with some adjustments made based on results from initial electroporation tests which gave a transformation efficiency of approx. 6,000 CFU/µg in a best attempt.

=== '''Electrocompetent cell preparation''' ===

# Grow six 10 ml SA11 cultures (or upscale as required) to early log phase (OD ~0.5)
# Cool cultures on ice for 20 min.
# Bring cultures into chamber on ice, pour 30 ml culture into two O-ring sealed Oak Ridge centrifuge tubes, ensure lids are sealed tightly and remove from anaerobic chamber, keeping on ice.
# Centrifuge at 15,000 × ''g'' at 4 °C for 10 min.
# Bring tubes back into chamber and pour off culture supernatant and add 30 ml ice cold 270 mM sucrose buffer, gently resuspending with a ≥5 ml pipette tip.
# Repeat buffer wash and centrifugation steps under the same conditions, but also including 20% (v/v) glycerol in the wash buffer.
# Bring washed pellets back into chamber, decant supernatant and remove as much excess buffer as possible without disturbing pellet.
# Add 300 µl 270 mM sucrose/20% glycerol buffer and gently resuspend as minimally as needed.
# Dispense preferred volumes into chilled Kimax tubes ensuring lids are securely fastened before removing from chamber.
# Store aliquots at -80 °C for later use.

=== '''Electroporation''' ===

# Thaw electrocompetent cell aliquots on ice, bring into anaerobic chamber with pre-chilled 2 mm electroporation cuvettes, CO2 -filled Kimax tubes for recoveries, anaerobic M2GSC recovery medium, and pJIR750 plasmid DNA.
# Add 50 µl electrocompetent cells and 100-200 ng of pJIR750 plasmid to an electroporation cuvette, flick to mix and chill on ice for 3 min.
# Electroporate using the following settings: exponential decay, 2.5 kV, 400 Ω, 25 μF.
# Pipette 950 µl of M2GSC medium into the cuvette, mix gently and pipette into Kimax tube.
# Recover at 39 °C for six hours before plating 100 µl on M2GSC agar plates with 5 µg/ml thiamphenicol and incubate at 39 °C. Colonies usually form on the second day of incubation.

== External Links ==
Sanford PA, Woolston BM. 2022. Expanding the genetic engineering toolbox for the metabolically flexible acetogen ''Eubacterium limosum''. J Ind Microbiol Biotechnol 49: kuac019.

Selenomonas ruminantium PC18

2026-10-29T06:14:43Z

Mahoneykurpe:

== 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 ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== 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.

Lachnospiraceae bacterium NK3A20

2026-10-29T06:13:33Z

Mahoneykurpe: Created page with " == Introduction == == 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 Link..."

== Introduction ==

== 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 ==

Aristaeella lactis WTE2008T

2026-10-29T06:12:49Z

== Introduction ==

== 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 ==

Aristaeella hokkaidonensis R-7T

2026-10-29T06:11:59Z

== Introduction ==

== 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 ==

Sharpea azabuensis KH1P5

2026-10-26T09:42:18Z

Mahoneykurpe: /* Methylating E. coli Strains */

[[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

== 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. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

KH1P5 also grows well on M2G medium at 39 °C, with 10 ml cultures reaching stationary phase after 6-7 h at optical densities of ~4-5. Cells of KH1P5 form long chains.

[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

== 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)
|-
|carbenicillin
|5
|-
|chloramphenicol
|0.38
|-
|clarithromycin
|25
|-
|erythromycin
|1
|-
|kanamycin
|insensitive
|-
|spectinomycin
|96
|-
|tetracycline
|0.23
|-
|thiamphenicol
|5
|}

== 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.

Sharpea azabuensis KH1P5

2026-10-26T09:29:03Z

Mahoneykurpe: /* Culturing Conditions */

[[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

== 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. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

KH1P5 also grows well on M2G medium at 39 °C, with 10 ml cultures reaching stationary phase after 6-7 h at optical densities of ~5-6. Cells of KH1P5 grow as long poorly-defined chains.

[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

== 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)
|-
|carbenicillin
|5
|-
|chloramphenicol
|0.38
|-
|clarithromycin
|25
|-
|erythromycin
|1
|-
|kanamycin
|insensitive
|-
|spectinomycin
|96
|-
|tetracycline
|0.23
|-
|thiamphenicol
|5
|}

== 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.

Sharpea azabuensis KH1P5

2026-10-26T09:01:36Z

Mahoneykurpe: /* Culturing Conditions */

[[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

== 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. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

KH1P5 also grows well on M2G medium, with 10 ml cultures reaching stationary phase after 6-7 h at optical densities of ~5-6. Cells of KH1P5 grow as long poorly-defined chains.

[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

== 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)
|-
|carbenicillin
|5
|-
|chloramphenicol
|0.38
|-
|clarithromycin
|25
|-
|erythromycin
|1
|-
|kanamycin
|insensitive
|-
|spectinomycin
|96
|-
|tetracycline
|0.23
|-
|thiamphenicol
|5
|}

== 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.

Sharpea azabuensis KH1P5

2026-10-26T06:34:20Z

Mahoneykurpe: /* Culturing Conditions and Growth Characteristics */

[[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

== 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]] and M2G medium at 37-39 °C. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer. Cells of KH1P5 grow as long poorly-defined chains.

[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

== 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)
|-
|carbenicillin
|5
|-
|chloramphenicol
|0.38
|-
|clarithromycin
|25
|-
|erythromycin
|1
|-
|kanamycin
|insensitive
|-
|spectinomycin
|96
|-
|tetracycline
|0.23
|-
|thiamphenicol
|5
|}

== 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.

Sharpea azabuensis KH1P5

2026-10-23T02:56:32Z

Mahoneykurpe: /* Culturing Conditions and Growth Characteristics */

[[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

== 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 and Growth Characteristics ==
''S. azabuensis'' KH1P5 grows well in stock [[RCM]] at 37 °C. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

''S. azabuensis KH1P5'' also grows well in M2G medium at 39 °C, reaching stationary phase after approximately 6-7 h. Cells grow as long poorly-defined chains, preventing the use of direct cell counts to calculate plating efficiencies.

[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

== 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)
|-
|carbenicillin
|5
|-
|chloramphenicol
|0.38
|-
|clarithromycin
|25
|-
|erythromycin
|1
|-
|kanamycin
|insensitive
|-
|spectinomycin
|96
|-
|tetracycline
|0.23
|-
|thiamphenicol
|5
|}

== 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.

Sharpea azabuensis KH1P5

2026-10-23T02:51:01Z

Mahoneykurpe: /* Culturing Conditions and Growth Characteristics */

[[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

== 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 and Growth Characteristics ==
''S. azabuensis'' KH1P5 grows well in stock [[RCM]] at 37 °C. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

''S. azabuensis KH1P5'' also grows well in M2G medium at 39 °C, reaching stationary phase after approximately 6-7 h. Cells grow as long poorly-defined chains, preventing the use of direct cell counts to calculate plating efficiencies.

[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

== 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.

Sharpea azabuensis KH1P5

2026-10-23T02:22:36Z

Mahoneykurpe: /* Culturing Conditions and Growth Characteristics */

[[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

== 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 and Growth Characteristics ==
''S. azabuensis'' KH1P5 grows well in stock [[RCM]] at 37 °C. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

''S. azabuensis KH1P5'' also grows well in M2G medium at 39 °C, reaching stationary phase after approximately 6-7 h. Cells grow as long poorly-defined chains (to insert image), preventing the use of cell counting methods to calculate plating efficiencies.

[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of S. azabuensis KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

/
== 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.

Sharpea azabuensis KH1P5

2026-10-23T02:21:58Z

Mahoneykurpe: /* Culturing Conditions and Growth Characteristics */

[[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

== 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 and Growth Characteristics ==
''S. azabuensis'' KH1P5 grows well in stock [[RCM]] at 37 °C. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

''S. azabuensis KH1P5'' also grows well in M2G medium at 39 °C, reaching stationary phase after approximately 6-7 h. Cells grow as long poorly-defined chains (to insert image), preventing the use of cell counting methods to calculate plating efficiencies.
[[File:KH1P5 micrograph.jpg|thumb|Phase-contrast micrograph of S. azabuensis KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

== 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.

File:KH1P5 micrograph.jpg

2026-10-23T02:19:02Z

Mahoneykurpe:

Phase contrast microscopy image of S. azabuensis KH1P5

Eubacterium maltosivorans SA11

2026-10-23T00:37:42Z

Mahoneykurpe: /* Antimicrobial MIC Tests */

== 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 ==

== Antimicrobial MIC Tests ==
{| class="wikitable"
|+
!antibiotic
!MIC (μg/ml)
|-
|carbenicillin
|50
|-
|clarithromycin
|5
|-
|tetracycline
|5
|-
|thiamphenicol
|5
|}
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.

Sharpea azabuensis KH1P5

2026-10-22T21:06:51Z

Mahoneykurpe: /* Culturing Conditions */

[[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

== 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 and Growth Characteristics ==
''S. azabuensis'' KH1P5 grows well in stock [[RCM]] at 37 °C. However, the inclusion of agar in commercially made RCM causes the strain to produce 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. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.

''S. azabuensis KH1P5'' also grows well in M2G medium at 39 °C, reaching stationary phase after approximately 6-7 h. Cells grow as long poorly-defined chains (to insert image), preventing the use of cell counting methods to calculate plating efficiencies.

== 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.

Selenomonas ruminantium PC18

2026-10-20T06:24:50Z

Mahoneykurpe:

== Introduction ==

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

== Genome ==

Selenomonas ruminantium PC18

2026-10-19T22:55:21Z

Mahoneykurpe: Created page with "== Introduction =="

== Introduction ==

Sharpea azabuensis KH1P5

2026-10-19T22:52:52Z

Mahoneykurpe: /* Methylating E. coli Strains */

[[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 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 ==