Global Methane Hub Wikipedia - User contributions [en]

Anaerovibrio lipolyticus 5ST

2026-10-30T18:41:16Z

Madachi: /* Global Methane Hub Metadata */

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

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

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

LPSN: Anaerovibrio lipolyticus corrig. Hungate 1966

NCBI: Anaerovibrio lipolyticus

GTDB: Anaerovibrio lipolyticus

Risk group: 1

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|DSMZ
|-
|Sequenced by:
|Makoto Adachi
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|
|-
|MIC and Culturing Conditions by:
|
|-
|Transformation by:
|
|}

== Genome ==
[[File:NVJKVF 1 1 1 circos.png|center|thumb|301x301px|Circos plot of ''A. lipolyticus'' 5ST. Source: Makoto Adachi]]

== DefenseFinder Results ==
add here

== Methylome ==
{| class="wikitable"
|'''Motif'''
|'''Percent methylated'''
|-
|G(6mA)TC
| align="right" |99.94
|-
|GATGA(6mA)
| align="right" |100
|-
|GAA(6mA)CC
| align="right" |98.2
|-
|GCCC(6mA)G
| align="right" |98.78
|-
|G(6mA)CNNNNNTAAC
| align="right" |100
|-
|GTT(6mA)NNNNNGTC
| align="right" |93.96
|-
|G(6mA)GNNNNCTAA
| align="right" |98.89
|-
|TT(6mA)GNNNNCTC
| align="right" |85.56
|-
|CAG(4mC)TG
| align="right" |96.22
|}

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

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

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

Anaerovibrio lipolyticus 5ST

2026-10-30T18:39:31Z

Madachi:

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

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

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

LPSN: Anaerovibrio lipolyticus corrig. Hungate 1966

NCBI: Anaerovibrio lipolyticus

GTDB: Anaerovibrio lipolyticus

Risk group: 1

== Global Methane Hub Metadata ==
add here

== Genome ==
[[File:NVJKVF 1 1 1 circos.png|center|thumb|301x301px|Circos plot of ''A. lipolyticus'' 5ST. Source: Makoto Adachi]]

== DefenseFinder Results ==
add here

== Methylome ==
{| class="wikitable"
|'''Motif'''
|'''Percent methylated'''
|-
|G(6mA)TC
| align="right" |99.94
|-
|GATGA(6mA)
| align="right" |100
|-
|GAA(6mA)CC
| align="right" |98.2
|-
|GCCC(6mA)G
| align="right" |98.78
|-
|G(6mA)CNNNNNTAAC
| align="right" |100
|-
|GTT(6mA)NNNNNGTC
| align="right" |93.96
|-
|G(6mA)GNNNNCTAA
| align="right" |98.89
|-
|TT(6mA)GNNNNCTC
| align="right" |85.56
|-
|CAG(4mC)TG
| align="right" |96.22
|}

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

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

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

File:NVJKVF 1 1 1 circos.png

2026-10-30T18:37:26Z

Madachi:

Selenomonas ruminantium HD4

2026-10-30T18:23:50Z

Madachi: /* Global Methane Hub Metadata */

[[File:Image1-9.png|thumb|350x350px|Scanning electron microscopic image of ''Selenomonas ruminantium'' HD4.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

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

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

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

NCBI: ''Pseudoselenomonas ruminantium''.

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

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|Origin:
|United States of America, Mackie lab
|-
|Sequenced by:
|Add here
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|Jill Walton
|-
|MIC and Culturing Conditions by:
|Makoto Adachi
|-
|Transformation by:
|
|}

== Genome ==
[[File:8YPGLC 1 S.rum HD4 1 circos.png|center|thumb|300x300px|Circos plot of ''Selenomonas ruminantium'' HD4. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|'''Motif'''
|'''Percent methylated'''
|-
|GTC(6mA)NNNNNNNTGG
| align="right" |87.64
|-
|CC(6mA)NNNNNNNTGAC
| align="right" |96.03
|-
|AC(6mA)YNNNNNNTGAY
| align="right" |97.49
|-
|RA(6mA)CNNNNNNNTAYG
| align="right" |95.97
|-
|CRT(6mA)NNNNNNNGTTY
| align="right" |89.93
|-
|RTC(6mA)NNNNNNRTGT
| align="right" |87.72
|-
|TC(4mC)ATG
| align="right" |70.48
|-
|TC(4mC)AT
| align="right" |58.71
|}

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

== Culturing Conditions ==
''S. ruminantium'' HD4 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''S. ruminantium'' HD4 on M10 agar is close to 96%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using [[M2GSC Medium|M2GSC]] liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|10.39
|-
|Chlorhamphenicol
|0.98
|-
|Erythromycin
|40
|-
|Gentamycin
|40.4
|-
|Kanamycin
|72.13
|-
|Streptomycin
|Resistance > 200
|-
|Tetracycline
|1.78
|}

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

Selenomonas ruminantium GA192

2026-10-30T18:23:18Z

Madachi:

[[File:Image1-8.png|thumb|350x350px|Scanning electron microscopic image of ''Selenomonas ruminantium'' GA192T.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]
Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae

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

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

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

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

NCBI: ''Pseudoselenomonas ruminantium''.

GTDB: ''Selenomonas_A ruminantium''.

Risk group: 1.

== Genome ==
[[File:55RBRH 2 Sel GA-192 1 circos.png|center|thumb|300x300px|Circos plot of ''S. ruminantium'' GA192T. Source: Makoto Adachi]]

== DefenseFinder Results ==
== Methylome ==

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

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

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

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

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

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

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

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

File:55RBRH 2 Sel GA-192 1 circos.png

2026-10-30T18:21:29Z

Madachi:

Ruminococcus flavefaciens AE3010

2026-10-30T18:18:47Z

Madachi: /* Global Methane Hub Metadata */

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

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

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

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

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

NCBI: ''Ruminococcus flavefaciens''.

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

Risk group: 1.

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

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

== DefenseFinder Results ==

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

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

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

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

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

Ruminococcus flavefaciens FD-1

2026-10-30T18:17:47Z

Madachi: /* Global Methane Hub Metadata */

[[File:Image3.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus flavefaciens'' FD-1.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus flavefaciens''''' '''FD-1'''

''Ruminococcus flavefaciens'' FD-1 is a strictly anaerobic bacterium isolated from the bovine rumen by Marvin P. Bryant in 1953. This bacterium is known to deconstruct lignocellulose efficiently using cellulosomes, which are highly modular enzymatic complexes [1]. The efficient degradation of lignocellulose by strain FD-1 results in the production of volatile fatty acids that are absorbed across the rumen epithelium, directly supporting the metabolic and energetic requirements of the ruminant host. Furthermore, the hydrogen evolved during its fermentation process is utilized by syntrophic methanogens, linking the robust fibrolytic activity of FD-1 to ruminal methanogenesis. The extensive genetic and structural mapping of ''R. flavefaciens'' FD-1 has established it as a critical benchmark strain for understanding the molecular assembly of bacterial cellulosomes and exploring biotechnological applications in lignocellulose bioconversion.

LPSN: ''Ruminococcus flavefaciens'' Sijpesteijn 1948

NCBI: ''Ruminococcus flavefaciens'' FD-1

GTDB: ''Ruminococcus flavefaciens''

Risk group: 1

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

== Genome ==
[[File:MRGXBF 2 FD1 2 1 circos.png|center|thumb|300x300px|Circos plot of ''R. flavefaciens'' FD-1. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|Motif
|Percent methylated
|-
|GA(6mA)GG
| align="right" |99.08
|-
|TGAA(6mA)T
| align="right" |80.83
|-
|GC(6mA)YNNNNNTCG
| align="right" |95.53
|-
|(6mA)CGNNNNNNTCAA
| align="right" |96.06
|-
|CGCC(6mA)G
| align="right" |89.77
|-
|CCN(6mA)CC
| align="right" |93.94
|-
|TTG(6mA)NNNNNNCGT
| align="right" |98.13
|-
|GTA(6mA)NNNNNGRTA
| align="right" |97.72
|-
|CG(6mA)NNNNNRTGC
| align="right" |98.68
|-
|T(6mA)YCNNNNNTTAC
| align="right" |92.71
|-
|CACA(6mA)TW
| align="right" |77.18
|-
|SAG(5mC)TS
| align="right" |81.6
|-
|GGN(5mC)C
| align="right" |47.52
|}

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

== Culturing Conditions ==
''R. flavefaciens'' FD-1 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. falvefaciens'' FD-1 on M10 agar is close to 72%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using [[M2GSC Medium|M2GSC]] liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.13
|-
|Chlorhamphenicol
|1.8
|-
|Erythromycin
|1.7
|-
|Gentamycin
|0.5
|-
|Kanamycin
|Resistance (>200)
|-
|Streptomycin
|0.1
|-
|Tetracycline
|0.1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Moraïs S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CMGA, Bayer EA. 2017. Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. Sci Rep 7:42355.

Ruminococcus albus 8

2026-10-30T18:17:03Z

Madachi: /* Global Methane Hub Metadata */

[[File:Image2.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 8.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''8'''

''Ruminococcus albus'' 8 is an obligately anaerobic, fibrolytic bacterium originally isolated from the rumen of an alfalfa-fed cow by Marvin P. Bryant.

While ''R. albus'' 8 shares core phenotypic characteristics with other strains, genomic and transcriptomic analyses indicate that it exhibits a specialized ecological preference for hemicellulose and xylan degradation over highly crystalline cellulose, distinguishing it from the highly cellulolytic ''R. albus'' 7 [1]. The strain secretes multiple endoxylanases and utilizes a unique phosphoketolase pathway for the rapid catabolism of pentose sugars, producing acetate, ethanol, formate, and hydrogen [2]. In the rumen, ''R. albus'' 8 contributes to the energy acquisition of the host animal through the production of volatile fatty acids, while acting in syntrophy with methanogenic archaea by providing the hydrogen necessary for enteric methane production.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus'' 8

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:2N52CS 1 R8 1 circos.png|center|thumb|300x300px|Circos plot of ''R. albus'' 8. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
!Motif
!Percent methylated
|-
|G(6mA)TCC
|99.53
|-
|GG(6mA)TC
|99.93
|-
|GG(6mA)GG
|98.88
|-
|GNC(6mA)YNNNNNNCCT
|97.47
|-
|(6mA)GGNNNNNNRTGNC
|99.28
|-
|G(6mA)TNNNNCTCA
|98.36
|-
|TG(6mA)GNNNNATC
|97.64
|-
|A(5mC)GGG
|97.16
|-
|C(5mC)CGT
|87.25
|-
|G(5mC)CTCC
|85.17
|}

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

== Culturing Conditions ==
''R. albus'' 8 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 8 on M10 agar is close to 89%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using [[M2GSC Medium|M2GSC]] liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.1
|-
|Chlorhamphenicol
|Resistance (>200)
|-
|Erythromycin
|0.1
|-
|Gentamycin
|0.1
|-
|Kanamycin
|0.6
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Kwon I. 2016. Comparative whole genome transcriptional responses of ''Ruminococcus albus'' strain 7 and 8: a case for specialization and niche differentiation. Ph.D. dissertation. University of Illinois at Urbana-Champaign, Urbana, IL.

[2] Moon YH, Iakiviak M, Bauer S, Mackie RI, Cann IKO. 2011. Biochemical analyses of multiple endoxylanases from the rumen bacterium Ruminococcus albus 8 and their synergistic activities with accessory hemicellulose-degrading enzymes. Appl Environ Microbiol 77:5157–5169.

Ruminococcus albus 7

2026-10-30T18:16:02Z

Madachi: /* Methylome */

[[File:Image1.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 7.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''7 (DSM 20455 ATCC 272107 JCM 14654)'''

''Ruminococcus albus'' 7 is an obligately anaerobic, Gram-positive bacterium first isolated from the bovine rumen by Robert Edward Hungate in 1951 [1]. This strain primarily utilizes plant-derived carbohydrates, such as cellulose, xylan, and cellobiose, as fermentation substrates, and produces ethanol and CO2 as it primary fermentation end products, along with relatively law amount of acetate [2].

This bacterium have high cellolytic ability and play a key roll for initial fiber degradation in rumen. Additioally, the production of H2 during fermentation by ''R. albus'', providing electrons for CO₂ reduction and methane production by methanogenic archaea [3]. Consequently, understanding the metabolic pathways and symbiotic relationships of ''R. albus'' 7 is essential for ongoing research aimed at mitigating enteric methane emissions from livestock.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus''

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:Image.png|thumb|center|Circos plot of ''R. albus'' 7. Source: Makoto Adachi|300x300px]]
== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|99.9
|-
|GCGC(6mA)G
|96.79
|-
|CAG(6mA)KC
|99.54
|-
|CTYR(6mA)G
|83.68
|-
|C(6mA)GNNNNNNNTTYG/

CRA(6mA)NNNNNNNCTG
|96/99.89
|-
|G(6mA)STC
|98.94
|-
|GAGG(6mA)G
|97.58
|-
|G(5mC)WGC
|84.64
|-
|GGN(5mC)C
|72.94
|-
|CTC(4mC)TC
|95.86
|}

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

== Culturing Conditions ==
''R. albus'' 7 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 7 on M10 agar is close to 100%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using [[M2GSC Medium|M2GSC]] liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|2.92
|-
|Chlorhamphenicol
|0.08
|-
|Erythromycin
|1.79
|-
|Gentamycin
|4.67
|-
|Kanamycin
|5.77
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1.0
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289–311.

[2] Pavlostathis SG, Miller TL, Wolin MJ. 1988. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus. Appl Environ Microbiol 54:2655–2659.

[3] Kim NK, Koike S, Kelly W, Attwood GT, Cook GM, Cann I, Mackie RI. 2026. Transcriptomic and metabolic analyses of interspecies hydrogen and electron transfer during syntrophic growth of Ruminococcus albus 7 with four different hydrogen-utilizing Methanobrevibacter strains. Anim Microbiome <nowiki>https://doi.org/10.1186/s42523-026-00644-8</nowiki>.

Ruminococcus albus 7

2026-10-30T18:11:16Z

Madachi: /* Global Methane Hub Metadata */

[[File:Image1.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 7.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''7 (DSM 20455 ATCC 272107 JCM 14654)'''

''Ruminococcus albus'' 7 is an obligately anaerobic, Gram-positive bacterium first isolated from the bovine rumen by Robert Edward Hungate in 1951 [1]. This strain primarily utilizes plant-derived carbohydrates, such as cellulose, xylan, and cellobiose, as fermentation substrates, and produces ethanol and CO2 as it primary fermentation end products, along with relatively law amount of acetate [2].

This bacterium have high cellolytic ability and play a key roll for initial fiber degradation in rumen. Additioally, the production of H2 during fermentation by ''R. albus'', providing electrons for CO₂ reduction and methane production by methanogenic archaea [3]. Consequently, understanding the metabolic pathways and symbiotic relationships of ''R. albus'' 7 is essential for ongoing research aimed at mitigating enteric methane emissions from livestock.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus''

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:Image.png|thumb|center|Circos plot of ''R. albus'' 7. Source: Makoto Adachi|300x300px]]
== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|
|-
|GCGC(6mA)G
|
|-
|CAG(6mA)KC
|
|-
|CTYR(6mA)G
|
|-
|C(6mA)GNNNNNNNTTYG/

CRA(6mA)NNNNNNNCTG
|
|-
|G(6mA)STC
|
|-
|GAGG(6mA)G
|
|-
|G(5mC)WGC
|
|-
|GGN(5mC)C
|
|-
|CTC(4mC)TC
|
|}

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

== Culturing Conditions ==
''R. albus'' 7 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 7 on M10 agar is close to 100%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|2.92
|-
|Chlorhamphenicol
|0.08
|-
|Erythromycin
|1.79
|-
|Gentamycin
|4.67
|-
|Kanamycin
|5.77
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1.0
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289–311.

[2] Pavlostathis SG, Miller TL, Wolin MJ. 1988. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus. Appl Environ Microbiol 54:2655–2659.

[3] Kim NK, Koike S, Kelly W, Attwood GT, Cook GM, Cann I, Mackie RI. 2026. Transcriptomic and metabolic analyses of interspecies hydrogen and electron transfer during syntrophic growth of Ruminococcus albus 7 with four different hydrogen-utilizing Methanobrevibacter strains. Anim Microbiome <nowiki>https://doi.org/10.1186/s42523-026-00644-8</nowiki>.

Ruminococcus albus 7

2026-10-30T18:10:16Z

Madachi: /* Introduction */

[[File:Image1.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 7.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''7 (DSM 20455 ATCC 272107 JCM 14654)'''

''Ruminococcus albus'' 7 is an obligately anaerobic, Gram-positive bacterium first isolated from the bovine rumen by Robert Edward Hungate in 1951 [1]. This strain primarily utilizes plant-derived carbohydrates, such as cellulose, xylan, and cellobiose, as fermentation substrates, and produces ethanol and CO2 as it primary fermentation end products, along with relatively law amount of acetate [2].

This bacterium have high cellolytic ability and play a key roll for initial fiber degradation in rumen. Additioally, the production of H2 during fermentation by ''R. albus'', providing electrons for CO₂ reduction and methane production by methanogenic archaea [3]. Consequently, understanding the metabolic pathways and symbiotic relationships of ''R. albus'' 7 is essential for ongoing research aimed at mitigating enteric methane emissions from livestock.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus''

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:Image.png|thumb|center|Circos plot of ''R. albus'' 7. Source: Makoto Adachi|300x300px]]
== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|
|-
|GCGC(6mA)G
|
|-
|CAG(6mA)KC
|
|-
|CTYR(6mA)G
|
|-
|C(6mA)GNNNNNNNTTYG/

CRA(6mA)NNNNNNNCTG
|
|-
|G(6mA)STC
|
|-
|GAGG(6mA)G
|
|-
|G(5mC)WGC
|
|-
|GGN(5mC)C
|
|-
|CTC(4mC)TC
|
|}

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

== Culturing Conditions ==
''R. albus'' 7 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 7 on M10 agar is close to 100%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|2.92
|-
|Chlorhamphenicol
|0.08
|-
|Erythromycin
|1.79
|-
|Gentamycin
|4.67
|-
|Kanamycin
|5.77
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1.0
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289–311.

[2] Pavlostathis SG, Miller TL, Wolin MJ. 1988. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus. Appl Environ Microbiol 54:2655–2659.

[3] Kim NK, Koike S, Kelly W, Attwood GT, Cook GM, Cann I, Mackie RI. 2026. Transcriptomic and metabolic analyses of interspecies hydrogen and electron transfer during syntrophic growth of Ruminococcus albus 7 with four different hydrogen-utilizing Methanobrevibacter strains. Anim Microbiome <nowiki>https://doi.org/10.1186/s42523-026-00644-8</nowiki>.

M2GSC Medium

2026-10-30T17:11:29Z

Madachi: /* Method */

== Description ==
M2GSC medium is based on a modified M2 medium [1] supplemented with glucose, soluble starch, cellobiose, and rumen fluid in an anaerobic broth.

== Recipe ==
'''M2GSC medium composition'''
{| class="wikitable"
|Bacto casitone
| align="right" |10 g
|-
|Bacto yeast extract
| align="right" |2.5 g
|-
|NaHCO3
| align="right" |4 g
|-
|Glucose
| align="right" |2 g
|-
|Soluble starch
| align="right" |2 g
|-
|Cellobiose
| align="right" |2 g
|-
|Rumen fluid (spun)
| align="right" |300 ml
|-
|Mineral solution 1
| align="right" |150 ml
|-
|Mineral solution 2
| align="right" |150 ml
|-
|Resazurin (0.1%)
| align="right" |1 ml
|-
|Cysteine HCl
| align="right" |1 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

'''Mineral solution 1'''
{| class="wikitable"
|K2HPO4
| align="right" |3 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

'''Mineral solution 2'''
{| class="wikitable"
|NaCl
| align="right" |6 g
|-
|KH2PO4
| align="right" |3 g
|-
|(NH4)2SO4
| align="right" |6 g
|-
|CaCl2.2H2O
| align="right" |0.6 g
|-
|MgSO4.7H2O
| align="right" |0.6 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

== Direction ==

* Weigh all ingredients as listed into a Pyrex conical glass flask, with the exception of cysteine.
* Add mineral solutions, rumen fluid, resazurin and water.
* Microwave flask on high until rapidly boiling.
* Remove flask from microwave and bubble with a gentle stream of CO2 until cool. Slowly add cysteine and then flush headspace only as bubble can change pH.
* Dispense M2GSC medium in 9.5 ml volumes into CO2 flushed Hungate tubes.
* Butyl rubber stoppers should be placed in the neck of tubes while withdrawing the CO2 sparger and the tubes sealed with screw caps.
* Autoclave tubes at 121ºC for 15 min. on same day as prepared.

== Notes ==
Note: for rumen fluid

# Thaw once-spun (10,000 g for 20 min) rumen fluid and bubble with N2 (100%) for 20 minutes.
# Autoclave under N2 at 121⁰C for 20 minutes in a high pressure Schott bottle to inactivate viruses, etc. The anoxic conditions are to limit the formation of unwanted oxidation products. Allow to cool.
# Freeze at -80⁰C for 2 hours or -20⁰C overnight.
# Spin at 10,000 G for 20 minutes.

== Sources ==

[1] Hobson PN. (1969). Rumen bacteria. In: Methods in Microbiology, vol 3B. Academic Press, pp. 133–149.

M10 Medium

2026-10-30T17:11:08Z

Madachi: /* Method */

== Description ==
M10 is a medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria [1].
== Recipe ==
{| class="wikitable"
|+
!Component
!Percentage in mediuma
|-
|Glucose
|0.05
|-
|Cellobiose
|0.05
|-
|Soluble Starch
|0.05
|-
|Minerals (v/v)b
|3.75
|-
|Na2S·9H2O
|0.025
|-
|Cystein·HCl·H2O
|0.025
|-
|Resazurin
|0.001
|-
|Na2CO3
|0.4
|-
|Trypticase
|0.2
|-
|Yeast extract
|0.05
|-
|Volatile fatty acids (v/v)c
|0.31
|-
|Hemin
|0.0001
|}
a Weight/ volume unless otherwise indicated.

b Except for K2HPO4, which was prepared separately, the minerals were prepared as a common stock solution. The final mineral concentrations in the medium were as follows: KH2PO4, 1.3 X 10-3 M; NaCl, 7.6 X 10-4 M; (NH)2SO4, 3.4 X 10-3 M; K2HPO4, 1.7 X 10-3 M; Ca(Cl)2, 4.1 X 10-4 M; MgSO4·7H20, 3.8 X 10-4 M.

c The volatile fatty acid mixture used was the following: acetic, 17 ml (2.9 X 10-2 M); propionic, 6ml (8.0 X 10-3 M); butyric, 4 ml (4.3 X 10-3 M); isobutyric, 1 ml (1.1 X 10-3 M); n-valeric, isovaleric, and DL-α-methylbutyric, 1 ml each (9 X 10-4 M). The figures in parentheses indicate the final concentration of each acid when 0.31 ml of mixture was placed in a final medium volume of 100 ml.
== Direction ==
Mix all the components in distilled water except Na2CO3 and Cystein·HCl·H2O. Boil the medium, then cool it immediately in an ice bath while bubuling with 100% CO2. Add appropirate amount of Na2CO3 and Cystein·HCl·H2O, once the medium is cooled. Adjust th pH to 6.7-6.8 by addition of NaOH. Aliquot the medium, and autoclave at 121 °C for 20 minutes.

== Notes ==

== Sources ==

[1] Caldwell DR, Bryant MP. 1966. Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Appl Microbiol 14:794–801.

Ruminococcus albus 7

2026-10-29T22:20:34Z

Madachi: /* Introduction */

[[File:Image1.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 7.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''7 (DSM 20455 ATCC 27210 7 JCM 14654)'''

''Ruminococcus albus'' 7 is an obligately anaerobic, Gram-positive bacterium first isolated from the bovine rumen by Robert Edward Hungate in 1951 [1]. This strain primarily utilizes plant-derived carbohydrates, such as cellulose, xylan, and cellobiose, as fermentation substrates, and produces ethanol and CO2 as it primary fermentation end products, along with relatively law amount of acetate [2].

This bacterium have high cellolytic ability and play a key roll for initial fiber degradation in rumen. Additioally, the production of H2 during fermentation by ''R. albus'', providing electrons for CO₂ reduction and methane production by methanogenic archaea [3]. Consequently, understanding the metabolic pathways and symbiotic relationships of ''R. albus'' 7 is essential for ongoing research aimed at mitigating enteric methane emissions from livestock.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus''

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:Image.png|thumb|center|Circos plot of ''R. albus'' 7. Source: Makoto Adachi|300x300px]]
== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|
|-
|GCGC(6mA)G
|
|-
|CAG(6mA)KC
|
|-
|CTYR(6mA)G
|
|-
|C(6mA)GNNNNNNNTTYG/

CRA(6mA)NNNNNNNCTG
|
|-
|G(6mA)STC
|
|-
|GAGG(6mA)G
|
|-
|G(5mC)WGC
|
|-
|GGN(5mC)C
|
|-
|CTC(4mC)TC
|
|}

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

== Culturing Conditions ==
''R. albus'' 7 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 7 on M10 agar is close to 100%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|2.92
|-
|Chlorhamphenicol
|0.08
|-
|Erythromycin
|1.79
|-
|Gentamycin
|4.67
|-
|Kanamycin
|5.77
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1.0
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289–311.

[2] Pavlostathis SG, Miller TL, Wolin MJ. 1988. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus. Appl Environ Microbiol 54:2655–2659.

[3] Kim NK, Koike S, Kelly W, Attwood GT, Cook GM, Cann I, Mackie RI. 2026. Transcriptomic and metabolic analyses of interspecies hydrogen and electron transfer during syntrophic growth of Ruminococcus albus 7 with four different hydrogen-utilizing Methanobrevibacter strains. Anim Microbiome <nowiki>https://doi.org/10.1186/s42523-026-00644-8</nowiki>.

Ruminococcus albus 7

2026-10-29T22:19:39Z

Madachi: /* Introduction */

[[File:Image1.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 7.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''7 (DSM 20455 ATCC 27210 7 JCM 14654)'''

''Ruminococcus albus'' (strain 7) is an obligately anaerobic, Gram-positive bacterium first isolated from the bovine rumen by Robert Edward Hungate in 1951 [1]. This strain primarily utilizes plant-derived carbohydrates, such as cellulose, xylan, and cellobiose, as fermentation substrates, and produces ethanol and CO2 as it primary fermentation end products, along with relatively law amount of acetate [2].

This bacterium have high cellolytic ability and play a key roll for initial fiber degradation in rumen. Additioally, the production of H2 during fermentation by ''R. albus'', providing electrons for CO₂ reduction and methane production by methanogenic archaea [3]. Consequently, understanding the metabolic pathways and symbiotic relationships of ''R. albus'' 7 is essential for ongoing research aimed at mitigating enteric methane emissions from livestock.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus''

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:Image.png|thumb|center|Circos plot of ''R. albus'' 7. Source: Makoto Adachi|300x300px]]
== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|
|-
|GCGC(6mA)G
|
|-
|CAG(6mA)KC
|
|-
|CTYR(6mA)G
|
|-
|C(6mA)GNNNNNNNTTYG/

CRA(6mA)NNNNNNNCTG
|
|-
|G(6mA)STC
|
|-
|GAGG(6mA)G
|
|-
|G(5mC)WGC
|
|-
|GGN(5mC)C
|
|-
|CTC(4mC)TC
|
|}

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

== Culturing Conditions ==
''R. albus'' 7 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 7 on M10 agar is close to 100%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|2.92
|-
|Chlorhamphenicol
|0.08
|-
|Erythromycin
|1.79
|-
|Gentamycin
|4.67
|-
|Kanamycin
|5.77
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1.0
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289–311.

[2] Pavlostathis SG, Miller TL, Wolin MJ. 1988. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus. Appl Environ Microbiol 54:2655–2659.

[3] Kim NK, Koike S, Kelly W, Attwood GT, Cook GM, Cann I, Mackie RI. 2026. Transcriptomic and metabolic analyses of interspecies hydrogen and electron transfer during syntrophic growth of Ruminococcus albus 7 with four different hydrogen-utilizing Methanobrevibacter strains. Anim Microbiome <nowiki>https://doi.org/10.1186/s42523-026-00644-8</nowiki>.

M10 Medium

2026-10-29T22:18:07Z

Madachi: /* Method */

== Description ==
M10 is a medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria [1].
== Recipe ==
{| class="wikitable"
|+
!Component
!Percentage in mediuma
|-
|Glucose
|0.05
|-
|Cellobiose
|0.05
|-
|Soluble Starch
|0.05
|-
|Minerals (v/v)b
|3.75
|-
|Na2S·9H2O
|0.025
|-
|Cystein·HCl·H2O
|0.025
|-
|Resazurin
|0.001
|-
|Na2CO3
|0.4
|-
|Trypticase
|0.2
|-
|Yeast extract
|0.05
|-
|Volatile fatty acids (v/v)c
|0.31
|-
|Hemin
|0.0001
|}
a Weight/ volume unless otherwise indicated.

b Except for K2HPO4, which was prepared separately, the minerals were prepared as a common stock solution. The final mineral concentrations in the medium were as follows: KH2PO4, 1.3 X 10-3 M; NaCl, 7.6 X 10-4 M; (NH)2SO4, 3.4 X 10-3 M; K2HPO4, 1.7 X 10-3 M; Ca(Cl)2, 4.1 X 10-4 M; MgSO4·7H20, 3.8 X 10-4 M.

c The volatile fatty acid mixture used was the following: acetic, 17 ml (2.9 X 10-2 M); propionic, 6ml (8.0 X 10-3 M); butyric, 4 ml (4.3 X 10-3 M); isobutyric, 1 ml (1.1 X 10-3 M); n-valeric, isovaleric, and DL-α-methylbutyric, 1 ml each (9 X 10-4 M). The figures in parentheses indicate the final concentration of each acid when 0.31 ml of mixture was placed in a final medium volume of 100 ml.
== Method ==
Mix all the components in distilled water except Na2CO3 and Cystein·HCl·H2O. Boil the medium, then cool it immediately in an ice bath while bubuling with 100% CO2. Add appropirate amount of Na2CO3 and Cystein·HCl·H2O, once the medium is cooled. Adjust th pH to 6.7-6.8 by addition of NaOH. Aliquot the medium, and autoclave at 121 °C for 20 minutes.

== Notes ==

== Sources ==

[1] Caldwell DR, Bryant MP. 1966. Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Appl Microbiol 14:794–801.

Selenomonas ruminantium HD4

2026-10-29T22:14:39Z

Madachi: /* Culturing Conditions */

[[File:Image1-9.png|thumb|350x350px|Scanning electron microscopic image of ''Selenomonas ruminantium'' HD4.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

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

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

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

NCBI: ''Pseudoselenomonas ruminantium''.

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

Risk group: 1.

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

== Genome ==
[[File:8YPGLC 1 S.rum HD4 1 circos.png|center|thumb|300x300px|Circos plot of ''Selenomonas ruminantium'' HD4. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|'''Motif'''
|'''Percent methylated'''
|-
|GTC(6mA)NNNNNNNTGG
| align="right" |87.64
|-
|CC(6mA)NNNNNNNTGAC
| align="right" |96.03
|-
|AC(6mA)YNNNNNNTGAY
| align="right" |97.49
|-
|RA(6mA)CNNNNNNNTAYG
| align="right" |95.97
|-
|CRT(6mA)NNNNNNNGTTY
| align="right" |89.93
|-
|RTC(6mA)NNNNNNRTGT
| align="right" |87.72
|-
|TC(4mC)ATG
| align="right" |70.48
|-
|TC(4mC)AT
| align="right" |58.71
|}

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

== Culturing Conditions ==
''S. ruminantium'' HD4 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''S. ruminantium'' HD4 on M10 agar is close to 96%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|10.39
|-
|Chlorhamphenicol
|0.98
|-
|Erythromycin
|40
|-
|Gentamycin
|40.4
|-
|Kanamycin
|72.13
|-
|Streptomycin
|Resistance > 200
|-
|Tetracycline
|1.78
|}

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

Ruminococcus flavefaciens FD-1

2026-10-29T22:14:17Z

Madachi: /* Culturing Conditions */

[[File:Image3.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus flavefaciens'' FD-1.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus flavefaciens''''' '''FD-1'''

''Ruminococcus flavefaciens'' FD-1 is a strictly anaerobic bacterium isolated from the bovine rumen by Marvin P. Bryant in 1953. This bacterium is known to deconstruct lignocellulose efficiently using cellulosomes, which are highly modular enzymatic complexes [1]. The efficient degradation of lignocellulose by strain FD-1 results in the production of volatile fatty acids that are absorbed across the rumen epithelium, directly supporting the metabolic and energetic requirements of the ruminant host. Furthermore, the hydrogen evolved during its fermentation process is utilized by syntrophic methanogens, linking the robust fibrolytic activity of FD-1 to ruminal methanogenesis. The extensive genetic and structural mapping of ''R. flavefaciens'' FD-1 has established it as a critical benchmark strain for understanding the molecular assembly of bacterial cellulosomes and exploring biotechnological applications in lignocellulose bioconversion.

LPSN: ''Ruminococcus flavefaciens'' Sijpesteijn 1948

NCBI: ''Ruminococcus flavefaciens'' FD-1

GTDB: ''Ruminococcus flavefaciens''

Risk group: 1

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

== Genome ==
[[File:MRGXBF 2 FD1 2 1 circos.png|center|thumb|300x300px|Circos plot of ''R. flavefaciens'' FD-1. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|Motif
|Percent methylated
|-
|GA(6mA)GG
| align="right" |99.08
|-
|TGAA(6mA)T
| align="right" |80.83
|-
|GC(6mA)YNNNNNTCG
| align="right" |95.53
|-
|(6mA)CGNNNNNNTCAA
| align="right" |96.06
|-
|CGCC(6mA)G
| align="right" |89.77
|-
|CCN(6mA)CC
| align="right" |93.94
|-
|TTG(6mA)NNNNNNCGT
| align="right" |98.13
|-
|GTA(6mA)NNNNNGRTA
| align="right" |97.72
|-
|CG(6mA)NNNNNRTGC
| align="right" |98.68
|-
|T(6mA)YCNNNNNTTAC
| align="right" |92.71
|-
|CACA(6mA)TW
| align="right" |77.18
|-
|SAG(5mC)TS
| align="right" |81.6
|-
|GGN(5mC)C
| align="right" |47.52
|}

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

== Culturing Conditions ==
''R. flavefaciens'' FD-1 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. falvefaciens'' FD-1 on M10 agar is close to 72%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.13
|-
|Chlorhamphenicol
|1.8
|-
|Erythromycin
|1.7
|-
|Gentamycin
|0.5
|-
|Kanamycin
|Resistance (>200)
|-
|Streptomycin
|0.1
|-
|Tetracycline
|0.1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Moraïs S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CMGA, Bayer EA. 2017. Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. Sci Rep 7:42355.

Ruminococcus flavefaciens AE3010

2026-10-29T22:13:56Z

Madachi: /* Culturing Conditions */

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

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

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

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

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

NCBI: ''Ruminococcus flavefaciens''.

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

Risk group: 1.

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

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

== DefenseFinder Results ==

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

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

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

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

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

Ruminococcus albus 8

2026-10-29T22:11:25Z

Madachi: /* Culturing Conditions */

[[File:Image2.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 8.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''8'''

''Ruminococcus albus'' 8 is an obligately anaerobic, fibrolytic bacterium originally isolated from the rumen of an alfalfa-fed cow by Marvin P. Bryant.

While ''R. albus'' 8 shares core phenotypic characteristics with other strains, genomic and transcriptomic analyses indicate that it exhibits a specialized ecological preference for hemicellulose and xylan degradation over highly crystalline cellulose, distinguishing it from the highly cellulolytic ''R. albus'' 7 [1]. The strain secretes multiple endoxylanases and utilizes a unique phosphoketolase pathway for the rapid catabolism of pentose sugars, producing acetate, ethanol, formate, and hydrogen [2]. In the rumen, ''R. albus'' 8 contributes to the energy acquisition of the host animal through the production of volatile fatty acids, while acting in syntrophy with methanogenic archaea by providing the hydrogen necessary for enteric methane production.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus'' 8

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:2N52CS 1 R8 1 circos.png|center|thumb|300x300px|Circos plot of ''R. albus'' 8. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
!Motif
!Percent methylated
|-
|G(6mA)TCC
|99.53
|-
|GG(6mA)TC
|99.93
|-
|GG(6mA)GG
|98.88
|-
|GNC(6mA)YNNNNNNCCT
|97.47
|-
|(6mA)GGNNNNNNRTGNC
|99.28
|-
|G(6mA)TNNNNCTCA
|98.36
|-
|TG(6mA)GNNNNATC
|97.64
|-
|A(5mC)GGG
|97.16
|-
|C(5mC)CGT
|87.25
|-
|G(5mC)CTCC
|85.17
|}

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

== Culturing Conditions ==
''R. albus'' 8 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 8 on M10 agar is close to 89%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.1
|-
|Chlorhamphenicol
|Resistance (>200)
|-
|Erythromycin
|0.1
|-
|Gentamycin
|0.1
|-
|Kanamycin
|0.6
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Kwon I. 2016. Comparative whole genome transcriptional responses of ''Ruminococcus albus'' strain 7 and 8: a case for specialization and niche differentiation. Ph.D. dissertation. University of Illinois at Urbana-Champaign, Urbana, IL.

[2] Moon YH, Iakiviak M, Bauer S, Mackie RI, Cann IKO. 2011. Biochemical analyses of multiple endoxylanases from the rumen bacterium Ruminococcus albus 8 and their synergistic activities with accessory hemicellulose-degrading enzymes. Appl Environ Microbiol 77:5157–5169.

Ruminococcus albus 7

2026-10-29T22:10:42Z

Madachi: /* Culturing Conditions */

[[File:Image1.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 7.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''7'''

''Ruminococcus albus'' (strain 7) is an obligately anaerobic, Gram-positive bacterium first isolated from the bovine rumen by Robert Edward Hungate in 1951 [1]. This strain primarily utilizes plant-derived carbohydrates, such as cellulose, xylan, and cellobiose, as fermentation substrates, and produces ethanol and CO2 as it primary fermentation end products, along with relatively law amount of acetate [2].

This bacterium have high cellolytic ability and play a key roll for initial fiber degradation in rumen. Additioally, the production of H2 during fermentation by ''R. albus'', providing electrons for CO₂ reduction and methane production by methanogenic archaea [3]. Consequently, understanding the metabolic pathways and symbiotic relationships of ''R. albus'' 7 is essential for ongoing research aimed at mitigating enteric methane emissions from livestock.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus''

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:Image.png|thumb|center|Circos plot of ''R. albus'' 7. Source: Makoto Adachi|300x300px]]
== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|
|-
|GCGC(6mA)G
|
|-
|CAG(6mA)KC
|
|-
|CTYR(6mA)G
|
|-
|C(6mA)GNNNNNNNTTYG/

CRA(6mA)NNNNNNNCTG
|
|-
|G(6mA)STC
|
|-
|GAGG(6mA)G
|
|-
|G(5mC)WGC
|
|-
|GGN(5mC)C
|
|-
|CTC(4mC)TC
|
|}

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

== Culturing Conditions ==
''R. albus'' 7 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 7 on M10 agar is close to 100%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|2.92
|-
|Chlorhamphenicol
|0.08
|-
|Erythromycin
|1.79
|-
|Gentamycin
|4.67
|-
|Kanamycin
|5.77
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1.0
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289–311.

[2] Pavlostathis SG, Miller TL, Wolin MJ. 1988. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus. Appl Environ Microbiol 54:2655–2659.

[3] Kim NK, Koike S, Kelly W, Attwood GT, Cook GM, Cann I, Mackie RI. 2026. Transcriptomic and metabolic analyses of interspecies hydrogen and electron transfer during syntrophic growth of Ruminococcus albus 7 with four different hydrogen-utilizing Methanobrevibacter strains. Anim Microbiome <nowiki>https://doi.org/10.1186/s42523-026-00644-8</nowiki>.

M2GSC Medium

2026-10-29T22:09:38Z

Madachi: /* Method */

== Description ==
M2GSC medium is based on a modified M2 medium [1] supplemented with glucose, soluble starch, cellobiose, and rumen fluid in an anaerobic broth.

== Recipe ==
'''M2GSC medium composition'''
{| class="wikitable"
|Bacto casitone
| align="right" |10 g
|-
|Bacto yeast extract
| align="right" |2.5 g
|-
|NaHCO3
| align="right" |4 g
|-
|Glucose
| align="right" |2 g
|-
|Soluble starch
| align="right" |2 g
|-
|Cellobiose
| align="right" |2 g
|-
|Rumen fluid (spun)
| align="right" |300 ml
|-
|Mineral solution 1
| align="right" |150 ml
|-
|Mineral solution 2
| align="right" |150 ml
|-
|Resazurin (0.1%)
| align="right" |1 ml
|-
|Cysteine HCl
| align="right" |1 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

'''Mineral solution 1'''
{| class="wikitable"
|K2HPO4
| align="right" |3 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

'''Mineral solution 2'''
{| class="wikitable"
|NaCl
| align="right" |6 g
|-
|KH2PO4
| align="right" |3 g
|-
|(NH4)2SO4
| align="right" |6 g
|-
|CaCl2.2H2O
| align="right" |0.6 g
|-
|MgSO4.7H2O
| align="right" |0.6 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

== Method ==

* Weigh all ingredients as listed into a Pyrex conical glass flask, with the exception of cysteine.
* Add mineral solutions, rumen fluid, resazurin and water.
* Microwave flask on high until rapidly boiling.
* Remove flask from microwave and bubble with a gentle stream of CO2 until cool. Slowly add cysteine and then flush headspace only as bubble can change pH.
* Dispense M2GSC medium in 9.5 ml volumes into CO2 flushed Hungate tubes.
* Butyl rubber stoppers should be placed in the neck of tubes while withdrawing the CO2 sparger and the tubes sealed with screw caps.
* Autoclave tubes at 121ºC for 15 min. on same day as prepared.

== Notes ==
Note: for rumen fluid

# Thaw once-spun (10,000 g for 20 min) rumen fluid and bubble with N2 (100%) for 20 minutes.
# Autoclave under N2 at 121⁰C for 20 minutes in a high pressure Schott bottle to inactivate viruses, etc. The anoxic conditions are to limit the formation of unwanted oxidation products. Allow to cool.
# Freeze at -80⁰C for 2 hours or -20⁰C overnight.
# Spin at 10,000 G for 20 minutes.

== Sources ==

[1] Hobson PN. (1969). Rumen bacteria. In: Methods in Microbiology, vol 3B. Academic Press, pp. 133–149.

M10 Medium

2026-10-29T22:09:16Z

Madachi: /* Sources */

== Description ==
M10 is a medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria [1].
== Recipe ==
{| class="wikitable"
|+
!Component
!Percentage in mediuma
|-
|Glucose
|0.05
|-
|Cellobiose
|0.05
|-
|Soluble Starch
|0.05
|-
|Minerals (v/v)b
|3.75
|-
|Na2S·9H2O
|0.025
|-
|Cystein·HCl·H2O
|0.025
|-
|Resazurin
|0.001
|-
|Na2CO3
|0.4
|-
|Trypticase
|0.2
|-
|Yeast extract
|0.05
|-
|Volatile fatty acids (v/v)c
|0.31
|-
|Hemin
|0.0001
|}
a Weight/ volume unless otherwise indicated.

b Except for K2HPO4, which was prepared separately, the minerals were prepared as a common stock solution. The final mineral concentrations in the medium were as follows: KH2PO4, 1.3 X 10-3 M; NaCl, 7.6 X 10-4 M; (NH)2SO4, 3.4 X 10-3 M; K2HPO4, 1.7 X 10-3 M; Ca(Cl)2, 4.1 X 10-4 M; MgSO4·7H20, 3.8 X 10-4 M.

c The volatile fatty acid mixture used was the following: acetic, 17 ml (2.9 X 10-2 M); propionic, 6ml (8.0 X 10-3 M); butyric, 4 ml (4.3 X 10-3 M); isobutyric, 1 ml (1.1 X 10-3 M); n-valeric, isovaleric, and DL-α-methylbutyric, 1 ml each (9 X 10-4 M). The figures in parentheses indicate the final concentration of each acid when 0.31 ml of mixture was placed in a final medium volume of 100 ml.
=== Method ===
Mix all the components in distilled water except Na2CO3 and Cystein·HCl·H2O. Boil the medium, then cool it immediately in an ice bath while bubuling with 100% CO2. Add appropirate amount of Na2CO3 and Cystein·HCl·H2O, once the medium is cooled. Adjust th pH to 6.7-6.8 by addition of NaOH. Aliquot the medium, and autoclave at 121 °C for 20 minutes.

== Notes ==

== Sources ==

[1] Caldwell DR, Bryant MP. 1966. Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Appl Microbiol 14:794–801.

M2GSC Medium

2026-10-29T22:08:49Z

Madachi: /* Method */

== Description ==
M2GSC medium is based on a modified M2 medium [1] supplemented with glucose, soluble starch, cellobiose, and rumen fluid in an anaerobic broth.

== Recipe ==
'''M2GSC medium composition'''
{| class="wikitable"
|Bacto casitone
| align="right" |10 g
|-
|Bacto yeast extract
| align="right" |2.5 g
|-
|NaHCO3
| align="right" |4 g
|-
|Glucose
| align="right" |2 g
|-
|Soluble starch
| align="right" |2 g
|-
|Cellobiose
| align="right" |2 g
|-
|Rumen fluid (spun)
| align="right" |300 ml
|-
|Mineral solution 1
| align="right" |150 ml
|-
|Mineral solution 2
| align="right" |150 ml
|-
|Resazurin (0.1%)
| align="right" |1 ml
|-
|Cysteine HCl
| align="right" |1 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

'''Mineral solution 1'''
{| class="wikitable"
|K2HPO4
| align="right" |3 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

'''Mineral solution 2'''
{| class="wikitable"
|NaCl
| align="right" |6 g
|-
|KH2PO4
| align="right" |3 g
|-
|(NH4)2SO4
| align="right" |6 g
|-
|CaCl2.2H2O
| align="right" |0.6 g
|-
|MgSO4.7H2O
| align="right" |0.6 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

== Method ==
Weigh all ingredients as listed into a Pyrex conical glass flask, with the exception of cysteine.

Add mineral solutions, rumen fluid, resazurin and water.

Microwave flask on high until rapidly boiling.

Remove flask from microwave and bubble with a gentle stream of CO2 until cool. Slowly add cysteine and then flush headspace only as bubble can change pH.

Dispense M2GSC medium in 9.5 ml volumes into CO2 flushed Hungate tubes.

Butyl rubber stoppers should be placed in the neck of tubes while withdrawing the CO2 sparger and the tubes sealed with screw caps.

Autoclave tubes at 121ºC for 15 min. on same day as prepared.

== Notes ==
Note: for rumen fluid

# Thaw once-spun (10,000 g for 20 min) rumen fluid and bubble with N2 (100%) for 20 minutes.
# Autoclave under N2 at 121⁰C for 20 minutes in a high pressure Schott bottle to inactivate viruses, etc. The anoxic conditions are to limit the formation of unwanted oxidation products. Allow to cool.
# Freeze at -80⁰C for 2 hours or -20⁰C overnight.
# Spin at 10,000 G for 20 minutes.

== Sources ==

[1] Hobson PN. (1969). Rumen bacteria. In: Methods in Microbiology, vol 3B. Academic Press, pp. 133–149.

M2GSC Medium

2026-10-29T22:08:27Z

Madachi: /* Recipe */

== Description ==
M2GSC medium is based on a modified M2 medium [1] supplemented with glucose, soluble starch, cellobiose, and rumen fluid in an anaerobic broth.

== Recipe ==
'''M2GSC medium composition'''
{| class="wikitable"
|Bacto casitone
| align="right" |10 g
|-
|Bacto yeast extract
| align="right" |2.5 g
|-
|NaHCO3
| align="right" |4 g
|-
|Glucose
| align="right" |2 g
|-
|Soluble starch
| align="right" |2 g
|-
|Cellobiose
| align="right" |2 g
|-
|Rumen fluid (spun)
| align="right" |300 ml
|-
|Mineral solution 1
| align="right" |150 ml
|-
|Mineral solution 2
| align="right" |150 ml
|-
|Resazurin (0.1%)
| align="right" |1 ml
|-
|Cysteine HCl
| align="right" |1 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

'''Mineral solution 1'''
{| class="wikitable"
|K2HPO4
| align="right" |3 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

'''Mineral solution 2'''
{| class="wikitable"
|NaCl
| align="right" |6 g
|-
|KH2PO4
| align="right" |3 g
|-
|(NH4)2SO4
| align="right" |6 g
|-
|CaCl2.2H2O
| align="right" |0.6 g
|-
|MgSO4.7H2O
| align="right" |0.6 g
|-
| colspan="2" |Add distilled H2O to 1 L
|}

== Method ==
Weigh all ingredients as listed into a Pyrex conical glass flask, with the exception of cysteine.

Add mineral solutions, rumen fluid, resazurin and water.

Microwave flask on high until rapidly boiling

Remove flask from microwave and bubble with a gentle stream of CO2 until cool. Slowly add cysteine and then flush headspace only as bubble can change pH.

Dispense M2GSC medium in 9.5 ml volumes into CO2 flushed Hungate tubes.

Butyl rubber stoppers should be placed in the neck of tubes while withdrawing the CO2 sparger and the tubes sealed with screw caps.

Autoclave tubes at 121ºC for 15 min. on same day as prepared.

== Notes ==
Note: for rumen fluid

# Thaw once-spun (10,000 g for 20 min) rumen fluid and bubble with N2 (100%) for 20 minutes.
# Autoclave under N2 at 121⁰C for 20 minutes in a high pressure Schott bottle to inactivate viruses, etc. The anoxic conditions are to limit the formation of unwanted oxidation products. Allow to cool.
# Freeze at -80⁰C for 2 hours or -20⁰C overnight.
# Spin at 10,000 G for 20 minutes.

== Sources ==

[1] Hobson PN. (1969). Rumen bacteria. In: Methods in Microbiology, vol 3B. Academic Press, pp. 133–149.

M10 Medium

2026-10-29T22:05:18Z

Madachi:

== Description ==
M10 is a medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria [1].
== Recipe ==
{| class="wikitable"
|+
!Component
!Percentage in mediuma
|-
|Glucose
|0.05
|-
|Cellobiose
|0.05
|-
|Soluble Starch
|0.05
|-
|Minerals (v/v)b
|3.75
|-
|Na2S·9H2O
|0.025
|-
|Cystein·HCl·H2O
|0.025
|-
|Resazurin
|0.001
|-
|Na2CO3
|0.4
|-
|Trypticase
|0.2
|-
|Yeast extract
|0.05
|-
|Volatile fatty acids (v/v)c
|0.31
|-
|Hemin
|0.0001
|}
a Weight/ volume unless otherwise indicated.

b Except for K2HPO4, which was prepared separately, the minerals were prepared as a common stock solution. The final mineral concentrations in the medium were as follows: KH2PO4, 1.3 X 10-3 M; NaCl, 7.6 X 10-4 M; (NH)2SO4, 3.4 X 10-3 M; K2HPO4, 1.7 X 10-3 M; Ca(Cl)2, 4.1 X 10-4 M; MgSO4·7H20, 3.8 X 10-4 M.

c The volatile fatty acid mixture used was the following: acetic, 17 ml (2.9 X 10-2 M); propionic, 6ml (8.0 X 10-3 M); butyric, 4 ml (4.3 X 10-3 M); isobutyric, 1 ml (1.1 X 10-3 M); n-valeric, isovaleric, and DL-α-methylbutyric, 1 ml each (9 X 10-4 M). The figures in parentheses indicate the final concentration of each acid when 0.31 ml of mixture was placed in a final medium volume of 100 ml.
=== Method ===
Mix all the components in distilled water except Na2CO3 and Cystein·HCl·H2O. Boil the medium, then cool it immediately in an ice bath while bubuling with 100% CO2. Add appropirate amount of Na2CO3 and Cystein·HCl·H2O, once the medium is cooled. Adjust th pH to 6.7-6.8 by addition of NaOH. Aliquot the medium, and autoclave at 121 °C for 20 minutes.

== Notes ==

== Sources ==

[1] Hobson PN. (1969). Rumen bacteria. In: ''Methods in Microbiology'', vol 3B. Academic Press, pp. 133–149.

M2GSC Medium

2026-10-29T21:44:44Z

Madachi:

== Description ==
add here

== Recipe ==
add here

== Direction ==
add here

== Notes ==
add here

== Sources ==

M2GSC Medium

2026-10-29T21:43:44Z

Madachi: Created page with " == Description == == Recipe == === Directions === == Notes == == Sources == [1] Caldwell DR, Bryant MP. 1966. Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Appl Microbiol 14:794–801."

== Description ==

== Recipe ==

=== Directions ===

== Notes ==

== Sources ==
[1] Caldwell DR, Bryant MP. 1966. Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Appl Microbiol 14:794–801.

Ruminococcus flavefaciens FD-1

2026-10-29T21:31:29Z

Madachi: /* Introduction */

[[File:Image3.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus flavefaciens'' FD-1.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus flavefaciens''''' '''FD-1'''

''Ruminococcus flavefaciens'' FD-1 is a strictly anaerobic bacterium isolated from the bovine rumen by Marvin P. Bryant in 1953. This bacterium is known to deconstruct lignocellulose efficiently using cellulosomes, which are highly modular enzymatic complexes [1]. The efficient degradation of lignocellulose by strain FD-1 results in the production of volatile fatty acids that are absorbed across the rumen epithelium, directly supporting the metabolic and energetic requirements of the ruminant host. Furthermore, the hydrogen evolved during its fermentation process is utilized by syntrophic methanogens, linking the robust fibrolytic activity of FD-1 to ruminal methanogenesis. The extensive genetic and structural mapping of ''R. flavefaciens'' FD-1 has established it as a critical benchmark strain for understanding the molecular assembly of bacterial cellulosomes and exploring biotechnological applications in lignocellulose bioconversion.

LPSN: ''Ruminococcus flavefaciens'' Sijpesteijn 1948

NCBI: ''Ruminococcus flavefaciens'' FD-1

GTDB: ''Ruminococcus flavefaciens''

Risk group: 1

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

== Genome ==
[[File:MRGXBF 2 FD1 2 1 circos.png|center|thumb|300x300px|Circos plot of ''R. flavefaciens'' FD-1. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|Motif
|Percent methylated
|-
|GA(6mA)GG
| align="right" |99.08
|-
|TGAA(6mA)T
| align="right" |80.83
|-
|GC(6mA)YNNNNNTCG
| align="right" |95.53
|-
|(6mA)CGNNNNNNTCAA
| align="right" |96.06
|-
|CGCC(6mA)G
| align="right" |89.77
|-
|CCN(6mA)CC
| align="right" |93.94
|-
|TTG(6mA)NNNNNNCGT
| align="right" |98.13
|-
|GTA(6mA)NNNNNGRTA
| align="right" |97.72
|-
|CG(6mA)NNNNNRTGC
| align="right" |98.68
|-
|T(6mA)YCNNNNNTTAC
| align="right" |92.71
|-
|CACA(6mA)TW
| align="right" |77.18
|-
|SAG(5mC)TS
| align="right" |81.6
|-
|GGN(5mC)C
| align="right" |47.52
|}

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

== Culturing Conditions ==
''R. flavefaciens'' FD-1 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. falvefaciens'' FD-1 on M10 agar is close to 72%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.13
|-
|Chlorhamphenicol
|1.8
|-
|Erythromycin
|1.7
|-
|Gentamycin
|0.5
|-
|Kanamycin
|Resistance (>200)
|-
|Streptomycin
|0.1
|-
|Tetracycline
|0.1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Moraïs S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CMGA, Bayer EA. 2017. Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. Sci Rep 7:42355.

Ruminococcus albus 8

2026-10-29T21:29:40Z

Madachi: /* Introduction */

[[File:Image2.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 8.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''8'''

''Ruminococcus albus'' 8 is an obligately anaerobic, fibrolytic bacterium originally isolated from the rumen of an alfalfa-fed cow by Marvin P. Bryant.

While ''R. albus'' 8 shares core phenotypic characteristics with other strains, genomic and transcriptomic analyses indicate that it exhibits a specialized ecological preference for hemicellulose and xylan degradation over highly crystalline cellulose, distinguishing it from the highly cellulolytic ''R. albus'' 7 [1]. The strain secretes multiple endoxylanases and utilizes a unique phosphoketolase pathway for the rapid catabolism of pentose sugars, producing acetate, ethanol, formate, and hydrogen [2]. In the rumen, ''R. albus'' 8 contributes to the energy acquisition of the host animal through the production of volatile fatty acids, while acting in syntrophy with methanogenic archaea by providing the hydrogen necessary for enteric methane production.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus'' 8

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:2N52CS 1 R8 1 circos.png|center|thumb|300x300px|Circos plot of ''R. albus'' 8. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
!Motif
!Percent methylated
|-
|G(6mA)TCC
|99.53
|-
|GG(6mA)TC
|99.93
|-
|GG(6mA)GG
|98.88
|-
|GNC(6mA)YNNNNNNCCT
|97.47
|-
|(6mA)GGNNNNNNRTGNC
|99.28
|-
|G(6mA)TNNNNCTCA
|98.36
|-
|TG(6mA)GNNNNATC
|97.64
|-
|A(5mC)GGG
|97.16
|-
|C(5mC)CGT
|87.25
|-
|G(5mC)CTCC
|85.17
|}

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

== Culturing Conditions ==
''R. albus'' 8 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 8 on M10 agar is close to 89%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.1
|-
|Chlorhamphenicol
|Resistance (>200)
|-
|Erythromycin
|0.1
|-
|Gentamycin
|0.1
|-
|Kanamycin
|0.6
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Kwon I. 2016. Comparative whole genome transcriptional responses of ''Ruminococcus albus'' strain 7 and 8: a case for specialization and niche differentiation. Ph.D. dissertation. University of Illinois at Urbana-Champaign, Urbana, IL.

[2] Moon YH, Iakiviak M, Bauer S, Mackie RI, Cann IKO. 2011. Biochemical analyses of multiple endoxylanases from the rumen bacterium Ruminococcus albus 8 and their synergistic activities with accessory hemicellulose-degrading enzymes. Appl Environ Microbiol 77:5157–5169.

Ruminococcus albus 7

2026-10-29T19:04:36Z

Madachi: /* Introduction */

[[File:Image1.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 7.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''7'''

''Ruminococcus albus'' (strain 7) is an obligately anaerobic, Gram-positive bacterium first isolated from the bovine rumen by Robert Edward Hungate in 1951 [1]. This strain primarily utilizes plant-derived carbohydrates, such as cellulose, xylan, and cellobiose, as fermentation substrates, and produces ethanol and CO2 as it primary fermentation end products, along with relatively law amount of acetate [2].

This bacterium have high cellolytic ability and play a key roll for initial fiber degradation in rumen. Additioally, the production of H2 during fermentation by ''R. albus'', providing electrons for CO₂ reduction and methane production by methanogenic archaea [3]. Consequently, understanding the metabolic pathways and symbiotic relationships of ''R. albus'' 7 is essential for ongoing research aimed at mitigating enteric methane emissions from livestock.

LPSN: ''Ruminococcus albus'' Hungate 1957

NCBI: ''Ruminococcus albus''

GTDB: ''Ruminococcus albus''

Risk group: 1

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

== Genome ==
[[File:Image.png|thumb|center|Circos plot of ''R. albus'' 7. Source: Makoto Adachi|300x300px]]
== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|
|-
|GCGC(6mA)G
|
|-
|CAG(6mA)KC
|
|-
|CTYR(6mA)G
|
|-
|C(6mA)GNNNNNNNTTYG/

CRA(6mA)NNNNNNNCTG
|
|-
|G(6mA)STC
|
|-
|GAGG(6mA)G
|
|-
|G(5mC)WGC
|
|-
|GGN(5mC)C
|
|-
|CTC(4mC)TC
|
|}

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

== Culturing Conditions ==
''R. albus'' 7 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 7 on M10 agar is close to 100%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|2.92
|-
|Chlorhamphenicol
|0.08
|-
|Erythromycin
|1.79
|-
|Gentamycin
|4.67
|-
|Kanamycin
|5.77
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1.0
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289–311.

[2] Pavlostathis SG, Miller TL, Wolin MJ. 1988. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus. Appl Environ Microbiol 54:2655–2659.

[3] Kim NK, Koike S, Kelly W, Attwood GT, Cook GM, Cann I, Mackie RI. 2026. Transcriptomic and metabolic analyses of interspecies hydrogen and electron transfer during syntrophic growth of Ruminococcus albus 7 with four different hydrogen-utilizing Methanobrevibacter strains. Anim Microbiome <nowiki>https://doi.org/10.1186/s42523-026-00644-8</nowiki>.

Selenomonas ruminantium GA192

2026-10-29T18:34:20Z

Madachi:

[[File:Image1-8.png|thumb|350x350px|Scanning electron microscopic image of ''Selenomonas ruminantium'' GA192T.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]
Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae

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

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

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

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

NCBI: ''Pseudoselenomonas ruminantium''.

GTDB: ''Selenomonas_A ruminantium''.

Risk group: 1.

== Genome ==

== Methylome ==

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

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

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

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

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

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

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

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

File:Image1-8.png

2026-10-29T18:33:02Z

Madachi:

Selenomonas ruminantium GA192

2026-10-29T17:19:03Z

Madachi: /* MIC test strip result */

Bacillota (firmicutes)- Negativicutes - Selenomonadales - Selenomonadaceae

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

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

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

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

NCBI: ''Pseudoselenomonas ruminantium''.

GTDB: ''Selenomonas_A ruminantium''.

Risk group: 1.

== Genome ==

== Methylome ==

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

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

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

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

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

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

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

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

Selenomonas ruminantium HD4

2026-10-29T17:17:52Z

Madachi: /* Methylome */

[[File:Image1-9.png|thumb|350x350px|Scanning electron microscopic image of ''Selenomonas ruminantium'' HD4.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

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

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

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

NCBI: ''Pseudoselenomonas ruminantium''.

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

Risk group: 1.

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

== Genome ==
[[File:8YPGLC 1 S.rum HD4 1 circos.png|center|thumb|300x300px|Circos plot of ''Selenomonas ruminantium'' HD4. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|'''Motif'''
|'''Percent methylated'''
|-
|GTC(6mA)NNNNNNNTGG
| align="right" |87.64
|-
|CC(6mA)NNNNNNNTGAC
| align="right" |96.03
|-
|AC(6mA)YNNNNNNTGAY
| align="right" |97.49
|-
|RA(6mA)CNNNNNNNTAYG
| align="right" |95.97
|-
|CRT(6mA)NNNNNNNGTTY
| align="right" |89.93
|-
|RTC(6mA)NNNNNNRTGT
| align="right" |87.72
|-
|TC(4mC)ATG
| align="right" |70.48
|-
|TC(4mC)AT
| align="right" |58.71
|}

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

== Culturing Conditions ==
''S. ruminantium'' HD4 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''S. ruminantium'' HD4 on M10 agar is close to 96%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|10.39
|-
|Chlorhamphenicol
|0.98
|-
|Erythromycin
|40
|-
|Gentamycin
|40.4
|-
|Kanamycin
|72.13
|-
|Streptomycin
|Resistance > 200
|-
|Tetracycline
|1.78
|}

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

Selenomonas ruminantium HD4

2026-10-29T17:16:51Z

Madachi: /* Global Methane Hub Metadata */

[[File:Image1-9.png|thumb|350x350px|Scanning electron microscopic image of ''Selenomonas ruminantium'' HD4.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

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

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

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

NCBI: ''Pseudoselenomonas ruminantium''.

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

Risk group: 1.

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

== Genome ==
[[File:8YPGLC 1 S.rum HD4 1 circos.png|center|thumb|300x300px|Circos plot of ''Selenomonas ruminantium'' HD4. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|Motif
|Percent methylated
|-
|GTC(6mA)NNNNNNNTGG
| align="right" |87.64
|-
|CC(6mA)NNNNNNNTGAC
| align="right" |96.03
|-
|AC(6mA)YNNNNNNTGAY
| align="right" |97.49
|-
|RA(6mA)CNNNNNNNTAYG
| align="right" |95.97
|-
|CRT(6mA)NNNNNNNGTTY
| align="right" |89.93
|-
|RTC(6mA)NNNNNNRTGT
| align="right" |87.72
|-
|TC(4mC)ATG
| align="right" |70.48
|-
|TC(4mC)AT
| align="right" |58.71
|}

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

== Culturing Conditions ==
''S. ruminantium'' HD4 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''S. ruminantium'' HD4 on M10 agar is close to 96%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|10.39
|-
|Chlorhamphenicol
|0.98
|-
|Erythromycin
|40
|-
|Gentamycin
|40.4
|-
|Kanamycin
|72.13
|-
|Streptomycin
|Resistance > 200
|-
|Tetracycline
|1.78
|}

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

File:Image1-9.png

2026-10-29T17:15:04Z

Madachi:

File:8YPGLC 1 S.rum HD4 1 circos.png

2026-10-29T01:11:24Z

Madachi:

Circos plot of Selenomonas ruminantium HD4. Source: Makoto Adachi

Selenomonas ruminantium HD4

2026-10-29T01:02:00Z

Madachi: /* Global Methane Hub Metadata */

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

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

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

NCBI: ''Pseudoselenomonas ruminantium''.

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

Risk group: 1.

== Global Methane Hub Metadata ==
{| class="wikitable"
|Origin:
|United States of America, Macike lab
|-
|Sequenced by:
|Who did that...?
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|Jill Walton
|-
|MIC and Culturing Conditions by:
|Makoto Adachi
|-
|Transformation by:
|
|}

== Genome ==
add here

== DefenseFinder Results ==
add here

== Methylome ==
add here

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

== Culturing Conditions ==
add here

== Antimicrobial MIC Tests ==
add here

== Protocols ==
add here

== Transformation Results ==
add here

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

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

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

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

Ruminococcus flavefaciens AE3010

2026-10-29T00:58:40Z

Madachi: Created page with "Scanning electron microscopic image of ''Ruminococcus flavefaciens'' AE3010. This photo belongs to the GMH Project and was taken by Kingsley Boateng. == Introduction == '''''Ruminococcus flavefaciens''''' '''AE3010''' ''Ruminococcus flavefaciens'' AE3010 is an obligately anaerobic, fibrolytic bacterium isolated from the rumen of a cow in New Zealand and selected as a key reference genome for the global Hungate1000 pro..."

List of GMH Strains

2026-10-29T00:49:04Z

Madachi:

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

File:Image4.png

2026-10-29T00:34:23Z

Madachi:

File:55RBRH 1 Rum E3010 1 circos.png

2026-10-29T00:28:55Z

Madachi:

Ruminococcus flavefaciens FD-1

2026-10-29T00:21:11Z

Madachi: Created page with "Scanning electron microscopic image of ''Ruminococcus flavefaciens'' FD-1. This photo belongs to the GMH Project and was taken by Kingsley Boateng. == Introduction == '''''Ruminococcus flavefaciens''''' '''FD-1''' ''Ruminococcus flavefaciens'' FD-1 is a strictly anaerobic bacterium isolated from the bovine rumen by Marvin P. Bryant in 1953. This bacterium is known to deconstruct lignocellulose efficiently using cellul..."

[[File:Image3.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus flavefaciens'' FD-1.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus flavefaciens''''' '''FD-1'''

''Ruminococcus flavefaciens'' FD-1 is a strictly anaerobic bacterium isolated from the bovine rumen by Marvin P. Bryant in 1953. This bacterium is known to deconstruct lignocellulose efficiently using cellulosomes, which are highly modular enzymatic complexes [1]. The efficient degradation of lignocellulose by strain FD-1 results in the production of volatile fatty acids that are absorbed across the rumen epithelium, directly supporting the metabolic and energetic requirements of the ruminant host. Furthermore, the hydrogen evolved during its fermentation process is utilized by syntrophic methanogens, linking the robust fibrolytic activity of FD-1 to ruminal methanogenesis. The extensive genetic and structural mapping of ''R. flavefaciens'' FD-1 has established it as a critical benchmark strain for understanding the molecular assembly of bacterial cellulosomes and exploring biotechnological applications in lignocellulose bioconversion.

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

== Genome ==
[[File:MRGXBF 2 FD1 2 1 circos.png|center|thumb|300x300px|Circos plot of ''R. flavefaciens'' FD-1. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|Motif
|Percent methylated
|-
|GA(6mA)GG
| align="right" |99.08
|-
|TGAA(6mA)T
| align="right" |80.83
|-
|GC(6mA)YNNNNNTCG
| align="right" |95.53
|-
|(6mA)CGNNNNNNTCAA
| align="right" |96.06
|-
|CGCC(6mA)G
| align="right" |89.77
|-
|CCN(6mA)CC
| align="right" |93.94
|-
|TTG(6mA)NNNNNNCGT
| align="right" |98.13
|-
|GTA(6mA)NNNNNGRTA
| align="right" |97.72
|-
|CG(6mA)NNNNNRTGC
| align="right" |98.68
|-
|T(6mA)YCNNNNNTTAC
| align="right" |92.71
|-
|CACA(6mA)TW
| align="right" |77.18
|-
|SAG(5mC)TS
| align="right" |81.6
|-
|GGN(5mC)C
| align="right" |47.52
|}

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

== Culturing Conditions ==
''R. flavefaciens'' FD-1 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. falvefaciens'' FD-1 on M10 agar is close to 72%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.13
|-
|Chlorhamphenicol
|1.8
|-
|Erythromycin
|1.7
|-
|Gentamycin
|0.5
|-
|Kanamycin
|Resistance (>200)
|-
|Streptomycin
|0.1
|-
|Tetracycline
|0.1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Israeli-Ruimy V, Bule P, Jindou S, Dassa B, Moraïs S, Borovok I, Barak Y, Slutzki M, Hamberg Y, Cardoso V, Alves VD, Najmudin S, White BA, Flint HJ, Gilbert HJ, Lamed R, Fontes CMGA, Bayer EA. 2017. Complexity of the Ruminococcus flavefaciens FD-1 cellulosome reflects an expansion of family-related protein-protein interactions. Sci Rep 7:42355.

File:Image3.png

2026-10-28T23:58:53Z

Madachi:

File:MRGXBF 2 FD1 2 1 circos.png

2026-10-28T23:55:39Z

Madachi:

Ruminococcus albus 8

2026-10-28T23:52:57Z

Madachi: /* Methylome */

[[File:Image2.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 8.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''8'''

''Ruminococcus albus'' 8 is an obligately anaerobic, fibrolytic bacterium originally isolated from the rumen of an alfalfa-fed cow by Marvin P. Bryant.

While ''R. albus'' 8 shares core phenotypic characteristics with other strains, genomic and transcriptomic analyses indicate that it exhibits a specialized ecological preference for hemicellulose and xylan degradation over highly crystalline cellulose, distinguishing it from the highly cellulolytic ''R. albus'' 7 [1]. The strain secretes multiple endoxylanases and utilizes a unique phosphoketolase pathway for the rapid catabolism of pentose sugars, producing acetate, ethanol, formate, and hydrogen [2]. In the rumen, ''R. albus'' 8 contributes to the energy acquisition of the host animal through the production of volatile fatty acids, while acting in syntrophy with methanogenic archaea by providing the hydrogen necessary for enteric methane production.

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

== Genome ==
[[File:2N52CS 1 R8 1 circos.png|center|thumb|300x300px|Circos plot of ''R. albus'' 8. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
!Motif
!Percent methylated
|-
|G(6mA)TCC
|99.53
|-
|GG(6mA)TC
|99.93
|-
|GG(6mA)GG
|98.88
|-
|GNC(6mA)YNNNNNNCCT
|97.47
|-
|(6mA)GGNNNNNNRTGNC
|99.28
|-
|G(6mA)TNNNNCTCA
|98.36
|-
|TG(6mA)GNNNNATC
|97.64
|-
|A(5mC)GGG
|97.16
|-
|C(5mC)CGT
|87.25
|-
|G(5mC)CTCC
|85.17
|}

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

== Culturing Conditions ==
''R. albus'' 8 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 8 on M10 agar is close to 89%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.1
|-
|Chlorhamphenicol
|Resistance (>200)
|-
|Erythromycin
|0.1
|-
|Gentamycin
|0.1
|-
|Kanamycin
|0.6
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Kwon I. 2016. Comparative whole genome transcriptional responses of ''Ruminococcus albus'' strain 7 and 8: a case for specialization and niche differentiation. Ph.D. dissertation. University of Illinois at Urbana-Champaign, Urbana, IL.

[2] Moon YH, Iakiviak M, Bauer S, Mackie RI, Cann IKO. 2011. Biochemical analyses of multiple endoxylanases from the rumen bacterium Ruminococcus albus 8 and their synergistic activities with accessory hemicellulose-degrading enzymes. Appl Environ Microbiol 77:5157–5169.

Ruminococcus albus 7

2026-10-28T23:49:26Z

Madachi: /* Antimicrobial MIC Tests */

[[File:Image1.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 7.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''7'''

''Ruminococcus albus'' (strain 7) is an obligately anaerobic, Gram-positive bacterium first isolated from the bovine rumen by Robert Edward Hungate in 1951 [1]. This strain primarily utilizes plant-derived carbohydrates, such as cellulose, xylan, and cellobiose, as fermentation substrates, and produces ethanol and CO2 as it primary fermentation end products, along with relatively law amount of acetate [2].

This bacterium have high cellolytic ability and play a key roll for initial fiber degradation in rumen. Additioally, the production of H2 during fermentation by ''R. albus'', providing electrons for CO₂ reduction and methane production by methanogenic archaea [3]. Consequently, understanding the metabolic pathways and symbiotic relationships of ''R. albus'' 7 is essential for ongoing research aimed at mitigating enteric methane emissions from livestock.

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

== Genome ==
[[File:Image.png|thumb|center|Circos plot of ''R. albus'' 7. Source: Makoto Adachi|300x300px]]
== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|
|-
|GCGC(6mA)G
|
|-
|CAG(6mA)KC
|
|-
|CTYR(6mA)G
|
|-
|C(6mA)GNNNNNNNTTYG/

CRA(6mA)NNNNNNNCTG
|
|-
|G(6mA)STC
|
|-
|GAGG(6mA)G
|
|-
|G(5mC)WGC
|
|-
|GGN(5mC)C
|
|-
|CTC(4mC)TC
|
|}

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

== Culturing Conditions ==
''R. albus'' 7 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 7 on M10 agar is close to 100%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|2.92
|-
|Chlorhamphenicol
|0.08
|-
|Erythromycin
|1.79
|-
|Gentamycin
|4.67
|-
|Kanamycin
|5.77
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1.0
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Hungate RE. 1957. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 3:289–311.

[2] Pavlostathis SG, Miller TL, Wolin MJ. 1988. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus. Appl Environ Microbiol 54:2655–2659.

[3] Kim NK, Koike S, Kelly W, Attwood GT, Cook GM, Cann I, Mackie RI. 2026. Transcriptomic and metabolic analyses of interspecies hydrogen and electron transfer during syntrophic growth of Ruminococcus albus 7 with four different hydrogen-utilizing Methanobrevibacter strains. Anim Microbiome <nowiki>https://doi.org/10.1186/s42523-026-00644-8</nowiki>.

Ruminococcus albus 8

2026-10-28T23:48:53Z

Madachi: /* Antimicrobial MIC Tests */

[[File:Image2.png|thumb|350x350px|Scanning electron microscopic image of ''Ruminococcus albus'' 8.
This photo belongs to the GMH Project and was taken by Kingsley Boateng.]]

== Introduction ==
'''''Ruminococcus albus''''' '''8'''

''Ruminococcus albus'' 8 is an obligately anaerobic, fibrolytic bacterium originally isolated from the rumen of an alfalfa-fed cow by Marvin P. Bryant.

While ''R. albus'' 8 shares core phenotypic characteristics with other strains, genomic and transcriptomic analyses indicate that it exhibits a specialized ecological preference for hemicellulose and xylan degradation over highly crystalline cellulose, distinguishing it from the highly cellulolytic ''R. albus'' 7 [1]. The strain secretes multiple endoxylanases and utilizes a unique phosphoketolase pathway for the rapid catabolism of pentose sugars, producing acetate, ethanol, formate, and hydrogen [2]. In the rumen, ''R. albus'' 8 contributes to the energy acquisition of the host animal through the production of volatile fatty acids, while acting in syntrophy with methanogenic archaea by providing the hydrogen necessary for enteric methane production.

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

== Genome ==
[[File:2N52CS 1 R8 1 circos.png|center|thumb|300x300px|Circos plot of ''R. albus'' 8. Source: Makoto Adachi]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|
|
|-
|
|
|-
|
|
|-
|
|
|-
|
|
|-
|
|
|-
|
|
|-
|
|
|-
|
|
|-
|
|
|}

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

== Culturing Conditions ==
''R. albus'' 8 grown well in [[M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''R. albus'' 8 on M10 agar is close to 89%.

== Antimicrobial MIC Tests ==
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
{| class="wikitable"
|+
!'''Antibiotic'''
!'''Concentration (µg/ml)'''
|-
|Ampicilin
|0.1
|-
|Chlorhamphenicol
|Resistance (>200)
|-
|Erythromycin
|0.1
|-
|Gentamycin
|0.1
|-
|Kanamycin
|0.6
|-
|Streptomycin
|Resistance (>200)
|-
|Tetracycline
|1
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Kwon I. 2016. Comparative whole genome transcriptional responses of ''Ruminococcus albus'' strain 7 and 8: a case for specialization and niche differentiation. Ph.D. dissertation. University of Illinois at Urbana-Champaign, Urbana, IL.

[2] Moon YH, Iakiviak M, Bauer S, Mackie RI, Cann IKO. 2011. Biochemical analyses of multiple endoxylanases from the rumen bacterium Ruminococcus albus 8 and their synergistic activities with accessory hemicellulose-degrading enzymes. Appl Environ Microbiol 77:5157–5169.