Global Methane Hub Wikipedia - Recent changes [en]

Lachnospiraceae bacterium NK3A20

Mahoneykurpe — Sun, 08 Nov 2026 20:59:23 GMT

Genome

← Older revision		Revision as of 20:59, 8 November 2026
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	\|+		\|+
	\|Origin:		\|Origin:
	\|		\|New Zealand, isolated by Nikki Kenters [1]
	\|-		\|-
	\|Sequenced by:		\|Sequenced by:
	\|		\|Sam Mahoney-Kurpe
	\|-		\|-
	\|Assembled by:		\|Assembled by:
	\|		\|William G. Alexander
	\|-		\|-
	\|Methylome called by:		\|Methylome called by:
	\|		\|William G. Alexander
	\|-		\|-
	\|Methyltransferases cloned by:		\|Methyltransferases cloned by:
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	== Genome ==		== Genome ==
			{\| class="wikitable"
			\|+
			! colspan="2" \|Genome characteristics
			\|-
			\|Contigs
			\|1
			\|-
			\|size (bp)
			\|3,001,182
			\|-
			\|GC %
			\|54.2
			\|-
			\|CDS
			\|2513
			\|-
			\|rRNA
			\|9
			\|-
			\|tRNA
			\|46
			\|-
			\|CRISPR
			\|1
			\|}

	== DefenseFinder Results ==		== DefenseFinder Results ==

Aristaeella lactis WTE2008T

Mahoneykurpe — Sun, 08 Nov 2026 20:49:26 GMT

Genome

← Older revision		Revision as of 20:49, 8 November 2026
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	\|+		\|+
	\|Origin:		\|Origin:
	\|		\|New Zealand, isolated by Samantha J. Noel [1]
	\|-		\|-
	\|Sequenced by:		\|Sequenced by:
	\|		\|Sam Mahoney-Kurpe
	\|-		\|-
	\|Assembled by:		\|Assembled by:
	\|		\|William G. Alexander
	\|-		\|-
	\|Methylome called by:		\|Methylome called by:
	\|		\|William G. Alexander
	\|-		\|-
	\|Methyltransferases cloned by:		\|Methyltransferases cloned by:
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	== Genome ==		== Genome ==
			{\| class="wikitable"
			\|+
			! colspan="2" \|Genome characteristics
			\|-
			\|Contigs
			\|1
			\|-
			\|size (bp)
			\|3,442,562
			\|-
			\|GC %
			\|53.5
			\|-
			\|CDS
			\|3022
			\|-
			\|rRNA
			\|10
			\|-
			\|tRNA
			\|48
			\|-
			\|CRISPR
			\|0
			\|}

	== DefenseFinder Results ==		== DefenseFinder Results ==

Aristaeella hokkaidonensis R-7T

Mahoneykurpe — Sun, 08 Nov 2026 20:30:33 GMT

Genome

@@ Line 1: / Line 1: @@
 == Introduction ==
 == Global Methane Hub Metadata ==
@@ Line 28: / Line 29: @@
 == Genome ==
 == DefenseFinder Results ==
@@ Line 64: / Line 90: @@
 == External Links ==

Sharpea azabuensis KH1P5

Mahoneykurpe — Sun, 08 Nov 2026 20:00:31 GMT

Genome

← Older revision		Revision as of 20:00, 8 November 2026
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	== Genome ==		== Genome ==
			{\| class="wikitable"
			\|+
			! colspan="2" \|Genome characteristics
			\|-
			\|Contigs
			\|1
			\|-
			\|size (bp)
			\|2,465,508
			\|-
			\|GC %
			\|37.5
			\|-
			\|CDS
			\|2364
			\|-
			\|rRNA
			\|16
			\|-
			\|tRNA
			\|66
			\|-
			\|CRISPR
			\|2
			\|}
	[[File:S azabuensis circos.png\|Circos plot of ''S. azabuensis'' KH1P5. Source: Dr. William G. Alexander\|center\|thumb]]		[[File:S azabuensis circos.png\|Circos plot of ''S. azabuensis'' KH1P5. Source: Dr. William G. Alexander\|center\|thumb]]

List of GMH Strains

Heryakusuma — Wed, 04 Nov 2026 00:15:44 GMT

← Older revision		Revision as of 00:15, 4 November 2026
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	* [[Methanobrevibacter olleyae YLM1\|''Methanobrevibacter olleyae'' YLM1]]		* [[Methanobrevibacter olleyae YLM1\|''Methanobrevibacter olleyae'' YLM1]]
	* [[Methanobrevibacter ruminantium M1T\|''Methanobrevibacter ruminantium'' M1<sup>T</sup>]]		* [[Methanobrevibacter ruminantium M1T\|''Methanobrevibacter ruminantium'' M1<sup>T</sup>]]
	* [[Methanobrevibacter sp. D5]] ~~- group 1 to check nomenclature~~		* [[Methanobrevibacter sp. D5\|''Methanobrevibacter sp.'' D5]]
	* [[Methanobrevibacter thaueri ISO4-G16\|''Methanocatella thaueri'' G16]]		* [[Methanobrevibacter thaueri ISO4-G16\|''Methanocatella thaueri'' G16]]
	* [[Methanobrevibacter thaueri CWT\|''Methanocatella thaueri'' CW<sup>T</sup>]]		* [[Methanobrevibacter thaueri CWT\|''Methanocatella thaueri'' CW<sup>T</sup>]]
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	* [[Methanosarcina barkeri CM1\|''Methanosarcina barkeri'' CM1]]		* [[Methanosarcina barkeri CM1\|''Methanosarcina barkeri'' CM1]]
	* [[Methanosarcina thermophila Ms97\|''Methanosarcina thermophila'' Ms97]]		* [[Methanosarcina thermophila Ms97\|''Methanosarcina thermophila'' Ms97]]
	* [[Methanosphaera sp. A4]] ~~- group 1 to check nomenclature~~		* [[Methanosphaera sp. A4\|''Methanosphaera sp.'' A4]]
	* [[Methanosphaera sp. ISO3-F5\|''Methanosphaera sp.'' ISO3-F5]]		* [[Methanosphaera sp. ISO3-F5\|''Methanosphaera sp.'' ISO3-F5]]
	* [[Olsenella sp. KH2P3]]		* [[Olsenella sp. KH2P3]]

Talk:Methanocatella gottschalkii HO

Heryakusuma — Tue, 03 Nov 2026 23:18:37 GMT

← Older revision		Revision as of 23:18, 3 November 2026
Line 1:		Line 1:
	Question: how was the circos plot generated here?		'''Question:''' how was the circos plot generated here?
			<br>'''Answer:''' I used the ''M. gottschalkii'' HO gDNA sequence and then plugged them to the Python package pycirclize (with the help of AI) to make the Circos plot.

Methanobacterium formicicum BRM9

Heryakusuma — Tue, 03 Nov 2026 20:45:06 GMT

DefenseFinder Results

← Older revision		Revision as of 20:45, 3 November 2026
(One intermediate revision by the same user not shown)
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	\|DnaQ/DEDDh exonuclease, <br>cas1_I_II_III_IV_V_VI_7, <br>cas2_I_II_III_IV_V_VI_5, <br>cas3_I_2, <br>cas4_I_II_III_IV_V_VI_6, <br>cas5_I-B_6, <br>cas6_I_II_III_IV_V_VI_10, <br>cas7_I-B_6, <br>cas8b1_I-B_13		\|DnaQ/DEDDh exonuclease, <br>cas1_I_II_III_IV_V_VI_7, <br>cas2_I_II_III_IV_V_VI_5, <br>cas3_I_2, <br>cas4_I_II_III_IV_V_VI_6, <br>cas5_I-B_6, <br>cas6_I_II_III_IV_V_VI_10, <br>cas7_I-B_6, <br>cas8b1_I-B_13
	\|}		\|}
			'''''Abbreviation:''''' CBASS, cyclic-oligonucleotide-based antiphage signalling system<ref>Cohen, D., Melamed, S., Millman, A. ''et al.'' Cyclic GMP–AMP signalling protects bacteria against viral infection. ''Nature'' '''574''', 691–695 (2019). https://doi.org/10.1038/s41586-019-1605-5. </ref>; CRISPR-Cas, Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated enzymes; Prometheus, DNA replication helicase/nuclease 2 (DNA2)-containing anti-phage defense protein<ref>van den Berg DF, Costa AR, Esser JQ, Stanciu I, Geissler JQ, Zoumaro-Djayoon AD, Haas PJ, Brouns SJJ. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses. Cell Host Microbe. 2024 Aug 14;32(8):1427-1443.e8. https://doi.org/10.1016/j.chom.2024.07.007.</ref>; RM, restriction-modification; Avs, antiviral STAND (Signal Transduction ATPases with Numerous Domains)<ref>Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F. Prokaryotic innate immunity through pattern recognition of conserved viral proteins. Science. 2022 Aug 12;377(6607):eabm4096. https://doi.org/10.1126/science.abm4096. </ref>.

	=== Methylating ''E. coli'' ===		=== Methylating ''E. coli'' ===

Methanocatella gottschalkii HO

Heryakusuma — Tue, 03 Nov 2026 20:35:50 GMT

DefenseFinder Results

← Older revision		Revision as of 20:35, 3 November 2026
Line 152:		Line 152:
	\|}		\|}

			'''''Abbreviation:''''' CRISPR-Cas, Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated enzymes; RM, restriction-modification; Prometheus, DNA replication helicase/nuclease 2 (DNA2)-containing anti-phage defense protein<ref>van den Berg DF, Costa AR, Esser JQ, Stanciu I, Geissler JQ, Zoumaro-Djayoon AD, Haas PJ, Brouns SJJ. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses. Cell Host Microbe. 2024 Aug 14;32(8):1427-1443.e8. https://doi.org/10.1016/j.chom.2024.07.007.</ref>; RAZR, ring-activated zinc-finger RNase<ref>Zhang, T., Lyu, Y., Beck, C.R. ''et al.'' Bacterial immune activation via supramolecular assembly with phage triggers. ''Nature'' '''651''', 1051–1059 (2026). https://doi.org/10.1038/s41586-025-10060-8. </ref>; PD-T7-4, phage defense selecting against T7 bacteriophage system 4<ref>Vassallo CN, Doering CR, Littlehale ML, Teodoro GIC, Laub MT. A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome. Nat Microbiol. 2022 Oct;7(10):1568-1579. doi: 10.1038/s41564-022-01219-4. Epub 2022 Sep 19. Erratum in: Nat Microbiol. 2024 Oct;9(10):2760-2761. https://doi.org/10.1038/s41564-024-01724-8. </ref>; REase, restriction endonuclease.
	=== Methylating ''E. coli'' ===		=== Methylating ''E. coli'' ===
	''E. coli'' strain AG21365 developed by ORNL was used as a host to generate plasmids with ''M. gottschalkii'' HO methylation motifs shown above.		''E. coli'' strain AG21365 developed by ORNL was used as a host to generate plasmids with ''M. gottschalkii'' HO methylation motifs shown above.

Methanobacterium formicicum BRM9

Heryakusuma — Tue, 03 Nov 2026 20:26:36 GMT

DefenseFinder Results

← Older revision		Revision as of 20:26, 3 November 2026
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	\|CBASS		\|CBASS
	\|CBASS Type II with a Cap4 effector		\|CBASS Type II with a Cap4 effector
	\|Cap2 - E1 (ThiF/adenylyltransferase) module, <br>CD-NTase / cyclase (Type II allele), <br>Cap3 - JAB/JAMM isopeptidase, <br>Cap4 - SAVED + HNH effector		\|Cap2 - E1 (ThiF/adenylyltransferase) module, <br>CD-NTase / cyclase (Type II allele), <br>Cap3 - JAB/JAMM isopeptidase, <br>Cap4 - SAVED and HNH effector
	\|-		\|-
	\|Cas		\|CRISPR-Cas
	\|CAS Class1 Subtype IB		\|CAS Class1 Subtype IB
	\|~~Cas1~~, ~~Cas2~~, ~~Cas3~~, ~~Cas4~~, ~~Cas5~~, ~~Cas6~~, ~~Cas7b~~, ~~Cas8b1~~		\|cas1_I_II_III_IV_V_VI_7, <br>cas2_I_II_III_IV_V_VI_5, <br>cas3_I_5, <br>cas4_I_II_III_IV_V_VI_6, <br>cas5_I-B_17, <br>cas6_I_II_III_IV_V_VI_10, <br>cas7b_I-B_I-C_2, <br>cas8b1_I-B_5

	\|-		\|-
	\|Prometheus		\|Prometheus
Line 155:		Line 156:
	\|Avs2		\|Avs2
	\|-		\|-
	\|Cas		\|CRISPR-Cas
	\|~~CAS_Class1-~~Subtype~~-I-B~~		\|CAS Class1 Subtype IB
	\|DnaQ/DEDDh exonuclease, ~~Cas1~~, ~~Cas2~~, ~~Cas3~~, ~~Cas4~~, ~~Cas5_I~~-B_6,cas6_I_II_III_IV_V_VI_10,cas7_I-B_6,cas8b1_I-B_13		\|DnaQ/DEDDh exonuclease, <br>cas1_I_II_III_IV_V_VI_7, <br>cas2_I_II_III_IV_V_VI_5, <br>cas3_I_2, <br>cas4_I_II_III_IV_V_VI_6, <br>cas5_I-B_6, <br>cas6_I_II_III_IV_V_VI_10, <br>cas7_I-B_6, <br>cas8b1_I-B_13
	\|}		\|}

Methanocatella gottschalkii HO

Heryakusuma — Tue, 03 Nov 2026 20:23:00 GMT

DefenseFinder Results

← Older revision		Revision as of 20:23, 3 November 2026
(One intermediate revision by the same user not shown)
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	!Components		!Components
	\|-		\|-
	\|Cas		\|CRISPR-Cas
	\|CAS Cluster		\|CAS Cluster
	\|~~Cas1~~, <br>~~Cas2~~		\|cas1_I_II_III_IV_V_VI_10, <br>cas2_I_II_III_IV_V_VI_3
	\|-		\|-
	\|RM Type I		\|RM Type I
	\|N6-adenine ~~methylation~~ (m6A)		\|N6-adenine methylating (m6A) Type I RM
	\|Type I RM methyltransferase (HsdM), <br>Type I RM restriction endonuclease (HsdR), <br>Type I RM specificity subunit (HsdS)		\|Type I RM methyltransferase (HsdM), <br>Type I RM restriction endonuclease (HsdR), <br>Type I RM specificity subunit (HsdS)
	\|-		\|-

Methanobacterium formicicum BRM9

Heryakusuma — Tue, 03 Nov 2026 19:58:24 GMT

DefenseFinder Results

← Older revision		Revision as of 19:58, 3 November 2026
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	\|-		\|-
	\|CBASS		\|CBASS
	\|~~CBASS_II_Cap4~~		\|CBASS Type II with a Cap4 effector
	\|~~CBASS__AG_E1_ThiF~~,~~CBASS__Cyclase_II~~,~~CBASS__Jab~~,~~CBASS__SAVED_Cap4~~		\|Cap2 - E1 (ThiF/adenylyltransferase) module, <br>CD-NTase / cyclase (Type II allele), <br>Cap3 - JAB/JAMM isopeptidase, <br>Cap4 - SAVED + HNH effector
	\|-		\|-
	\|Cas		\|Cas
	\|~~CAS_Class1-~~Subtype~~-I-B~~		\|CAS Class1 Subtype IB
	\|~~cas1_I_II_III_IV_V_VI_7~~,~~cas2_I_II_III_IV_V_VI_5~~,~~cas3_I_5~~,~~cas4_I_II_III_IV_V_VI_6~~,~~cas5_I-B_17~~,~~cas6_I_II_III_IV_V_VI_10~~,~~cas7b_I-B_I-C_2~~,~~cas8b1_I-B_5~~		\|Cas1, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7b, Cas8b1
	\|-		\|-
	\|Prometheus		\|Prometheus
	\|Prometheus		\|Prometheus
	\|~~Prometheus__ProA~~		\|ProA
	\|-		\|-
	\|~~RM_Type_I~~		\|RM Type I
	\|~~N6_RM_Type_I~~		\|N6-adenine methylation (m6A)
	\|~~RM__Type_I_MTases_FAM_0~~,~~RM__Type_I_REases_FAM_0.einsi_trimmed~~,~~RM__Type_I_S_51,RM__Type_I_S_51~~		\|Type I RM methyltransferase (HsdM), <br>Type I RM restriction endonuclease (HsdR), <br>Type I RM specificity subunit (HsdS)
	\|-		\|-
	\|Avs		\|Avs
			\|Avs family 2
	\|Avs2		\|Avs2
	~~\|Avs2__Avs2~~
	\|-		\|-
	\|Cas		\|Cas
	\|CAS_Class1-Subtype-I-B		\|CAS_Class1-Subtype-I-B
	\|~~DEDDh_I_II_III_IV_V_VI_1~~,~~cas1_I_II_III_IV_V_VI_7~~,~~cas2_I_II_III_IV_V_VI_5~~,~~cas3_I_2~~,~~cas4_I_II_III_IV_V_VI_6~~,~~cas5_I~~-B_6,cas6_I_II_III_IV_V_VI_10,cas7_I-B_6,cas8b1_I-B_13		\|DnaQ/DEDDh exonuclease, Cas1, Cas2, Cas3, Cas4, Cas5_I-B_6,cas6_I_II_III_IV_V_VI_10,cas7_I-B_6,cas8b1_I-B_13
	\|}		\|}


	=== Methylating ''E. coli'' ===		=== Methylating ''E. coli'' ===

Methanocatella gottschalkii HO

Heryakusuma — Tue, 03 Nov 2026 19:48:54 GMT

Introduction

← Older revision		Revision as of 19:48, 3 November 2026
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	== Introduction ==		== Introduction ==
	[[File:Mgot HO.gif\|thumb\|Phase-contrast (top) and epifluorescence (bottom) microscopy of ''Methanocatella gottschalkii'' HO.]]		[[File:Mgot HO.gif\|thumb\|Phase-contrast (top) and epifluorescence (bottom) microscopy of ''Methanocatella gottschalkii'' HO. '''Source:''' Christian Heryakusuma.]]
	''Methanocatella gottschalkii'' HO<sup>T</sup> (formerly ''Methanobrevibacter gottschalkii'') is a type strain isolated from the enrichment of horse faeces<ref>Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.</ref>. ''M. gottschalkii'', along with ''Methanobrevibacter ruminantium'', comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets<ref>Henderson, G., Cox, F., Ganesh, S. ''et al.'' Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. ''Sci Rep'' '''5''', 14567 (2015). https://doi.org/10.1038/srep14567. </ref>. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens.		''Methanocatella gottschalkii'' HO<sup>T</sup> (formerly ''Methanobrevibacter gottschalkii'') is a type strain isolated from the enrichment of horse faeces<ref>Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.</ref>. ''M. gottschalkii'', along with ''Methanobrevibacter ruminantium'', comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets<ref>Henderson, G., Cox, F., Ganesh, S. ''et al.'' Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. ''Sci Rep'' '''5''', 14567 (2015). https://doi.org/10.1038/srep14567. </ref>. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens.

Methanobacterium formicicum BRM9

Heryakusuma — Tue, 03 Nov 2026 19:48:26 GMT

Introduction

← Older revision		Revision as of 19:48, 3 November 2026
Line 1:		Line 1:
	== Introduction ==		== Introduction ==
			[[File:Mfor BRM9.gif\|thumb\|Phase-contrast (top) and epifluorescence (bottom) microscopy of ''Methanobacterium formicicum'' BRM9. '''Source:''' Christian Heryakusuma.]]
	''Methanobacterium formicicum'' BRM9 is isolated from the rumen enrichment of non-lactating, rumen-fistulated, 6-year-old New Zealand Friesian cows grazing ryegrass/clover pastures<ref>Jarvis, G., Strömpl, C., Burgess, D. ''et al.'' Isolation and Identification of Ruminal Methanogens from Grazing Cattle. ''Curr Microbiol'' '''40''', 327–332 (2000). https://doi.org/10.1007/s002849910065. </ref>. Although ''Methanobacterium'' species are relatively low in abundance in the rumen environment<ref>Janssen PH, Kirs M. Structure of the archaeal community of the rumen. Appl Environ Microbiol. 2008 Jun;74(12):3619-25. https://doi.org/10.1128/AEM.02812-07. Epub 2008 Apr 18. PMID: 18424540; PMCID: PMC2446570.</ref>, they have been found as endosymbionts of anaerobic amoebae and ciliate protozoa<ref>Kelly WJ, Leahy SC, Li D, Perry R, Lambie SC, Attwood GT, Altermann E. The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. Stand Genomic Sci. 2014 Dec 8;9:15. https://doi.org/10.1186/1944-3277-9-15. PMID: 25780506; PMCID: PMC4335013.</ref>. This uniqueness makes ''M. formicicu''m BRM9 a methanogen of interest for GMH, as understanding these methanogenic endosymbiont interactions might open a venue for novel strategies in livestock methane mitigation.		''Methanobacterium formicicum'' BRM9 is isolated from the rumen enrichment of non-lactating, rumen-fistulated, 6-year-old New Zealand Friesian cows grazing ryegrass/clover pastures<ref>Jarvis, G., Strömpl, C., Burgess, D. ''et al.'' Isolation and Identification of Ruminal Methanogens from Grazing Cattle. ''Curr Microbiol'' '''40''', 327–332 (2000). https://doi.org/10.1007/s002849910065. </ref>. Although ''Methanobacterium'' species are relatively low in abundance in the rumen environment<ref>Janssen PH, Kirs M. Structure of the archaeal community of the rumen. Appl Environ Microbiol. 2008 Jun;74(12):3619-25. https://doi.org/10.1128/AEM.02812-07. Epub 2008 Apr 18. PMID: 18424540; PMCID: PMC2446570.</ref>, they have been found as endosymbionts of anaerobic amoebae and ciliate protozoa<ref>Kelly WJ, Leahy SC, Li D, Perry R, Lambie SC, Attwood GT, Altermann E. The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. Stand Genomic Sci. 2014 Dec 8;9:15. https://doi.org/10.1186/1944-3277-9-15. PMID: 25780506; PMCID: PMC4335013.</ref>. This uniqueness makes ''M. formicicu''m BRM9 a methanogen of interest for GMH, as understanding these methanogenic endosymbiont interactions might open a venue for novel strategies in livestock methane mitigation.

File:Mfor BRM9.gif

Heryakusuma — Tue, 03 Nov 2026 19:47:09 GMT

Heryakusuma uploaded File:Mfor BRM9.gif

New page

Microscopy of Mfor BRM9

Methanocatella gottschalkii HO

Heryakusuma — Tue, 03 Nov 2026 19:46:01 GMT

DefenseFinder Results

← Older revision		Revision as of 19:46, 3 November 2026
(2 intermediate revisions by the same user not shown)
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	== Introduction ==		== Introduction ==
			[[File:Mgot HO.gif\|thumb\|Phase-contrast (top) and epifluorescence (bottom) microscopy of ''Methanocatella gottschalkii'' HO.]]
	''Methanocatella gottschalkii'' HO<sup>T</sup> (formerly ''Methanobrevibacter gottschalkii'') is a type strain isolated from the enrichment of horse faeces<ref>Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.</ref>. ''M. gottschalkii'', along with ''Methanobrevibacter ruminantium'', comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets<ref>Henderson, G., Cox, F., Ganesh, S. ''et al.'' Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. ''Sci Rep'' '''5''', 14567 (2015). https://doi.org/10.1038/srep14567. </ref>. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens.		''Methanocatella gottschalkii'' HO<sup>T</sup> (formerly ''Methanobrevibacter gottschalkii'') is a type strain isolated from the enrichment of horse faeces<ref>Miller, T. L. (2002). "Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov". International Journal of Systematic and Evolutionary Microbiology. 52 (3): 819–822. https://doi.org/10.1099/00207713-52-3-819.</ref>. ''M. gottschalkii'', along with ''Methanobrevibacter ruminantium'', comprises about 74% of total archaeal OTUs from rumen samples collected across a wide range of geographical regions, hosts, and diets<ref>Henderson, G., Cox, F., Ganesh, S. ''et al.'' Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. ''Sci Rep'' '''5''', 14567 (2015). https://doi.org/10.1038/srep14567. </ref>. This universality makes them methanogens of particular interest to the Global Methane Hub, as it enables strategies to mitigate methane emissions by targeting these dominant methanogens.

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	\|-		\|-
	\|Cas		\|Cas
	\|~~CAS_Cluster~~		\|CAS Cluster
	\|~~cas1_I_II_III_IV_V_VI_10~~,~~cas2_I_II_III_IV_V_VI_3~~		\|Cas1, <br>Cas2
	\|-		\|-
	\|~~RM_Type_I~~		\|RM Type I
	\|~~N6_RM_Type_I~~		\|N6-adenine methylation (m6A)
	\|~~RM__Type_I_MTases_FAM_0~~,		\|Type I RM methyltransferase (HsdM), <br>Type I RM restriction endonuclease (HsdR), <br>Type I RM specificity subunit (HsdS)
	~~RM__Type_I_REases_FAM_0.einsi_trimmed,~~
	~~RM__Type_I_S_06~~,
	~~RM__Type_I_S_51~~
	\|-		\|-
	\|Prometheus		\|Prometheus
	\|Prometheus		\|Prometheus
	\|~~Prometheus__ProA~~		\|ProA
	\|-		\|-
	\|RAZR		\|RAZR
	\|RAZR		\|RAZR
	\|PD~~-T7-4__PD~~-T7-4		\|PD-T7-4
	\|-		\|-
	\|~~RM_Type_II~~		\|RM Type II
	\|~~DNA_met_RM_Type_II_PDDEXK~~		\|DNA methylase and Type II REase of the PD-(D/E)xK superfamily
	\|~~RM_Type_II__Type_II_MTases_FAM_0~~,		\|Type II DNA methyltransferase, <br>Type II restriction endonuclease (profile 12)
	~~RM_Type_II__Type_II_REase12~~
	\|}		\|}

File:Mgot HO.gif

Heryakusuma — Tue, 03 Nov 2026 19:37:34 GMT

Heryakusuma uploaded File:Mgot HO.gif

New page

Microscopy of Mgot HO

Methanobacterium formicicum BRM9

Heryakusuma — Tue, 03 Nov 2026 19:35:20 GMT

DefenseFinder Results

@@ Line 128: / Line 128: @@
 === DefenseFinder Results ===
-add here
+{| class="wikitable"
 === Methylating ''E. coli'' ===

Methanocatella gottschalkii HO

Heryakusuma — Tue, 03 Nov 2026 19:33:57 GMT

DefenseFinder Results

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 === DefenseFinder Results ===
-add here
+{| class="wikitable"
 === Methylating ''E. coli'' ===

Methanobacterium formicicum BRM9

Heryakusuma — Tue, 03 Nov 2026 00:43:49 GMT

Introduction

← Older revision		Revision as of 00:43, 3 November 2026
(One intermediate revision by the same user not shown)
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	== Introduction ==		== Introduction ==
	''Methanobacterium formicicum'' BRM9 is isolated from the rumen enrichment of non-lactating, rumen-fistulated, 6-year-old New Zealand Friesian cows grazing ryegrass/clover pastures<ref>Jarvis, G., Strömpl, C., Burgess, D. ''et al.'' Isolation and Identification of Ruminal Methanogens from Grazing Cattle. ''Curr Microbiol'' '''40''', 327–332 (2000). https://doi.org/10.1007/s002849910065. </ref>.		''Methanobacterium formicicum'' BRM9 is isolated from the rumen enrichment of non-lactating, rumen-fistulated, 6-year-old New Zealand Friesian cows grazing ryegrass/clover pastures<ref>Jarvis, G., Strömpl, C., Burgess, D. ''et al.'' Isolation and Identification of Ruminal Methanogens from Grazing Cattle. ''Curr Microbiol'' '''40''', 327–332 (2000). https://doi.org/10.1007/s002849910065. </ref>. Although ''Methanobacterium'' species are relatively low in abundance in the rumen environment<ref>Janssen PH, Kirs M. Structure of the archaeal community of the rumen. Appl Environ Microbiol. 2008 Jun;74(12):3619-25. https://doi.org/10.1128/AEM.02812-07. Epub 2008 Apr 18. PMID: 18424540; PMCID: PMC2446570.</ref>, they have been found as endosymbionts of anaerobic amoebae and ciliate protozoa<ref>Kelly WJ, Leahy SC, Li D, Perry R, Lambie SC, Attwood GT, Altermann E. The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. Stand Genomic Sci. 2014 Dec 8;9:15. https://doi.org/10.1186/1944-3277-9-15. PMID: 25780506; PMCID: PMC4335013.</ref>. This uniqueness makes ''M. formicicu''m BRM9 a methanogen of interest for GMH, as understanding these methanogenic endosymbiont interactions might open a venue for novel strategies in livestock methane mitigation.

	== Global Methane Hub Metadata ==		== Global Methane Hub Metadata ==

Methanocatella gottschalkii HO

Heryakusuma — Tue, 03 Nov 2026 00:21:49 GMT

Genome

← Older revision		Revision as of 00:21, 3 November 2026
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	<div style="clear: both;"></div>		<div style="clear: both;"></div>

	Genomic DNA (gDNA) of ''M. gottschalkii'' HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch<sup>®</sup> Spin gDNA Extraction Kit following manufacturer protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with phage ΨM2 pseudomurein endoisopeptidase of ''Methanothermobacter marburgensis'' (PeiP)<ref>Luo Y, Pfister P, Leisinger T, Wasserfallen A. Pseudomurein endoisopeptidases PeiW and PeiP, two moderately related members of a novel family of proteases produced in Methanothermobacter strains. FEMS Microbiol Lett. 2002 Feb 19;208(1):47-51. https://doi.org/10.1111/j.1574-6968.2002.tb11059.x. </ref>.		Genomic DNA (gDNA) of ''M. gottschalkii'' HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch<sup>®</sup> Spin gDNA Extraction Kit following the manufacturer's protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with the phage ΨM2 pseudomurein endoisopeptidase of ''Methanothermobacter marburgensis'' (PeiP)<ref>Luo Y, Pfister P, Leisinger T, Wasserfallen A. Pseudomurein endoisopeptidases PeiW and PeiP, two moderately related members of a novel family of proteases produced in Methanothermobacter strains. FEMS Microbiol Lett. 2002 Feb 19;208(1):47-51. https://doi.org/10.1111/j.1574-6968.2002.tb11059.x. </ref>.

	The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.		The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.

Methanobacterium formicicum BRM9

Heryakusuma — Tue, 03 Nov 2026 00:21:15 GMT

Genome

← Older revision		Revision as of 00:21, 3 November 2026
Line 95:		Line 95:
	<div style="clear: both;"></div>		<div style="clear: both;"></div>

	Genomic DNA (gDNA) of ''M. formicicum'' BRM9 was extracted using NEB Monarch<sup>®</sup> Spin gDNA Extraction Kit following manufacturer protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with phage pseudomurein endoisopeptidase of ''~~Methanocatella smithii~~'' PS (~~PeiS~~); ~~an ''Escherichia coli'' strain encoding the PeiS gene was kindly provided by Prof~~. ~~Metcalf (University of Illinois Urbana~~-~~Champaign)~~.		Genomic DNA (gDNA) of ''M. formicicum'' BRM9 was extracted using NEB Monarch<sup>®</sup> Spin gDNA Extraction Kit following the manufacturer's protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with the phage ΨM2 pseudomurein endoisopeptidase of ''Methanothermobacter marburgensis'' (PeiP)<ref>Luo Y, Pfister P, Leisinger T, Wasserfallen A. Pseudomurein endoisopeptidases PeiW and PeiP, two moderately related members of a novel family of proteases produced in Methanothermobacter strains. FEMS Microbiol Lett. 2002 Feb 19;208(1):47-51. https://doi.org/10.1111/j.1574-6968.2002.tb11059.x. </ref>.

	The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.		The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.

Methanocatella gottschalkii HO

Heryakusuma — Tue, 03 Nov 2026 00:12:51 GMT

Genome

← Older revision		Revision as of 00:12, 3 November 2026
(One intermediate revision by the same user not shown)
Line 96:		Line 96:
	<div style="clear: both;"></div>		<div style="clear: both;"></div>

	Genomic DNA (gDNA) of ''M. gottschalkii'' HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch<sup>®</sup> Spin gDNA Extraction Kit following manufacturer protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with phage pseudomurein endoisopeptidase of ''~~Methanocatella smithii~~'' PS (~~PeiS~~); ~~an ''Escherichia coli'' strain encoding the PeiS gene was kindly provided by Prof~~. ~~Metcalf (University of Illinois Urbana~~-~~Champaign)~~.		Genomic DNA (gDNA) of ''M. gottschalkii'' HO (collection number: DSM 11977, OCM 817) was extracted using NEB Monarch<sup>®</sup> Spin gDNA Extraction Kit following manufacturer protocols for gram-positive bacteria and archaea, except that lysozyme was replaced with phage ΨM2 pseudomurein endoisopeptidase of ''Methanothermobacter marburgensis'' (PeiP)<ref>Luo Y, Pfister P, Leisinger T, Wasserfallen A. Pseudomurein endoisopeptidases PeiW and PeiP, two moderately related members of a novel family of proteases produced in Methanothermobacter strains. FEMS Microbiol Lett. 2002 Feb 19;208(1):47-51. https://doi.org/10.1111/j.1574-6968.2002.tb11059.x. </ref>.

	The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.		The extracted gDNA was sequenced with Oxford Nanopore, then assembled with Flye<ref>Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019 May;37(5):540-546. https://doi.org/10.1038/s41587-019-0072-8. Epub 2019 Apr 1. PMID: 30936562.</ref> and polished with medaka (https://github.com/nanoporetech/medaka). The assembled genome was evaluated for completeness and contamination using QUAST<ref>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. https://doi.org/10.1093/bioinformatics/btt086. Epub 2013 Feb 19. PMID: 23422339; PMCID: PMC3624806.</ref> and CheckM2<ref>Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. https://doi.org/10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.</ref>. Bakta v1.12.0<ref>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. https://doi.org/10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.</ref> with database v6.0 full (https://github.com/oschwengers/bakta) was used for genome annotation. All these bioinformatics analyses were performed at the Virginia Tech Advanced Research Computing (VT-ARC) facility.

Talk:Methanocatella gottschalkii HO

Alexanderwg — Mon, 02 Nov 2026 16:51:30 GMT

Created page with "Question: how was the circos plot generated here?"

New page

Question: how was the circos plot generated here?

Talk:Ruminococcus albus

Alexanderwg — Mon, 02 Nov 2026 16:47:29 GMT

← Older revision		Revision as of 16:47, 2 November 2026
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	TBD: ~~clone this~~ species ~~and genus~~ page ~~from~~ English Wiki ~~and insert GMH~~		TBD: create ''de novo'' species page for English Wikipedia as well as GMH Wiki?

Main Page

Alexanderwg — Mon, 02 Nov 2026 16:42:31 GMT

← Older revision		Revision as of 16:42, 2 November 2026
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	= <strong>Welcome to the Global Methane Hub Wiki!</strong> =		= <strong>Welcome to the Global Methane Hub Wiki!</strong> =

	~~== ATTENTION: ACTION ITEM FROM EDITOR-IN-CHIEF ==~~
	~~2045z 15 Oct 2026~~

	Hi everyone! I have added what I believe to be a comprehensive list of our relevant strains on this page. However, as was mentioned in our meeting today, there are some strains that have new genera that need to be updated. I'm asking '''those in the relevant working groups containing these organisms to edit their name in the master list'''. If a page has already been made with the older, wrong name, that's great! When I move the page to the right name, it'll leave behind a link. So, please do '''tell me if any pages need to be renamed''' and I'll do it ASAP.

	~~Thanks!~~

	~~-Bill Alexander~~

	== Getting started ==		== Getting started ==

Aristaeella lactis WTE2008T

Mahoneykurpe — Mon, 02 Nov 2026 07:38:43 GMT

Introduction

← Older revision		Revision as of 07:38, 2 November 2026
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	== Introduction ==		== Introduction ==
			''Aristaeella lactis'' WTE2008<sup>T</sup> (DSM 112788, JCM 34734) was isolated from rumen contents of a dairy cow grazing a ryegrass pasture in New Zealand [1]. WTE2008 ferments a variety of substrates including the plant cell wall polysaccharides xylan and pectin, forming acetate, lactate, ethanol and hydrogen as end products [2].

			NCBI: Aristaeella lactis

			Risk Group: 1

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

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

Selenomonas ruminantium PC18

Mahoneykurpe — Mon, 02 Nov 2026 04:22:22 GMT

Methylating E. coli Strains

@@ Line 46: / Line 46: @@
 == Methylating E. coli Strains ==
 == Culturing Conditions ==
 == Antibiotic MIC Tests ==
 == Protocols ==

Aristaeella lactis WTE2008T

Mahoneykurpe — Mon, 02 Nov 2026 04:07:30 GMT

Methylome

← Older revision		Revision as of 04:07, 2 November 2026
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	== Methylating E. coli Strains ==		== Methylating E. coli Strains ==
			{\| class="wikitable"
			\|+
			!Methylated motif
			!Percent methylated
			\|-
			\|CCAAA(6mA)
			\|95.7
			\|-
			\|A(5mC)GGG
			\|96.1
			\|-
			\|C(5mC)CGT
			\|76.8
			\|}

	== Culturing Conditions ==		== Culturing Conditions ==

Aristaeella hokkaidonensis R-7T

Mahoneykurpe — Mon, 02 Nov 2026 03:58:35 GMT

Methylome

← Older revision		Revision as of 03:58, 2 November 2026
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	== Methylome ==		== Methylome ==
			{\| class="wikitable"
			\|+
			!Methylated motif
			!Percent methylated
			\|-
			\|(6mA)CGNNNNNTGC
			\|98.0
			\|-
			\|GC(6mA)NNNNNCGT
			\|92.7
			\|-
			\|TGG(6mA)NNNNNNTRC
			\|99.8
			\|-
			\|GY(6mA)NNNNNNTCCA
			\|93.3
			\|-
			\|CCAAA(6mA)
			\|97.1
			\|}

	== Methylating E. coli Strains ==		== Methylating E. coli Strains ==

Lachnospiraceae bacterium NK3A20

Mahoneykurpe — Mon, 02 Nov 2026 03:42:57 GMT

Methylome

← Older revision		Revision as of 03:42, 2 November 2026
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	== Methylome ==		== Methylome ==
			{\| class="wikitable"
			\|+
			!Methylated motif
			!Percent methylated
			\|-
			\|C(6mA)YCNNNNNTGG
			\|99.1
			\|-
			\|CC(6mA)NNNNNGRTG
			\|99.2
			\|-
			\|C(5mC)GG
			\|76.5
			\|}

	== Methylating E. coli Strains ==		== Methylating E. coli Strains ==

Methanobrevibacter wolinii SHT

Billkelleydonvis — Sun, 01 Nov 2026 22:46:27 GMT

Introduction and external links

New page

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

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

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

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

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

NCBI: ''Methanobrevibacter wolinii''.

GTDB: ''Methanarmilla wolinii''.

Risk group: 1.

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

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

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

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

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

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

Lachnospiraceae bacterium NK3A20

Billkelleydonvis — Sun, 01 Nov 2026 20:44:56 GMT

Introduction: and external links

@@ Line 1: / Line 1: @@
 == Introduction ==
 == Global Methane Hub Metadata ==
@@ Line 44: / Line 55: @@
 == External Links ==

Lachnospiraceae bacterium YSB2008

Billkelleydonvis — Sun, 01 Nov 2026 20:43:05 GMT

Introduction and external links

New page

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

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

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

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

NCBI: ''Lachnospiraceae'' bacterium.

GTDB: ''Eubacterium_Q'' sp000687655.

Risk group: 1.

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

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

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

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

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

Lachnospiraceae bacterium NK4A136

Billkelleydonvis — Sun, 01 Nov 2026 20:41:36 GMT

Introduction and external links

New page

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

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

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

NCBI: ''Lachnospiraceae'' bacterium.

GTDB: NK4A136 sp000687675.

Risk group: 1.

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

== Genome ==

== DefenseFinder Results ==

== Methylome ==

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

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

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

Eubacterium maltosivorans SA11

Mahoneykurpe — Sun, 01 Nov 2026 00:39:12 GMT

Protocols

← Older revision		Revision as of 00:39, 1 November 2026
Line 54:		Line 54:

	== Protocols ==		== Protocols ==
	~~add here~~
			* [[Eubacterium maltosivorans SA11 transformation protocol (BSI)]]

	== Transformation Results ==		== Transformation Results ==

Ruminococcus productus B43

Yuqili — Fri, 30 Oct 2026 22:05:35 GMT

← Older revision		Revision as of 22:05, 30 October 2026
(2 intermediate revisions by the same user not shown)
Line 1:		Line 1:

			[[File:B43SEM.jpg\|thumb\|Scanning electron microscopy image of ''Blautia producta'' B43. Source: Yuqi Li]]

	== Introduction ==		== Introduction ==

File:B43SEM.jpg

Yuqili — Fri, 30 Oct 2026 22:04:36 GMT

Yuqili uploaded File:B43SEM.jpg

New page

B43SEM

Ruminococcus productus B43

Yuqili — Fri, 30 Oct 2026 21:35:29 GMT

@@ Line 11: / Line 11: @@
 GTDB: Taxonomic assignment of B43 requires genome-based confirmation.
-Type strain: JCM 1471ᵀ (= DSM 2950 = ATCC 27340).
+Type strain: JCM 1471<sup>T</sup> (= DSM 2950 = ATCC 27340).
-Risk group: 2 (species-level classification reported by LPSN; strain-specific assessment should be confirmed).
+Risk group: 2
 == Global Methane Hub Metadata ==
@@ Line 57: / Line 57: @@
 == Culturing Conditions ==
 == Antibiotic MIC Tests ==
 == Protocols ==

File:B43MIC.jpg

Yuqili — Fri, 30 Oct 2026 21:32:01 GMT

Yuqili uploaded File:B43MIC.jpg

New page

B43MIC

← Older revision		Revision as of 00:15, 4 November 2026
Line 46:		Line 46:
	* [[Methanobrevibacter olleyae YLM1\|''Methanobrevibacter olleyae'' YLM1]]		* [[Methanobrevibacter olleyae YLM1\|''Methanobrevibacter olleyae'' YLM1]]
	* [[Methanobrevibacter ruminantium M1T\|''Methanobrevibacter ruminantium'' M1<sup>T</sup>]]		* [[Methanobrevibacter ruminantium M1T\|''Methanobrevibacter ruminantium'' M1<sup>T</sup>]]
	* [[Methanobrevibacter sp. D5]] ~~- group 1 to check nomenclature~~		* [[Methanobrevibacter sp. D5\|''Methanobrevibacter sp.'' D5]]
	* [[Methanobrevibacter thaueri ISO4-G16\|''Methanocatella thaueri'' G16]]		* [[Methanobrevibacter thaueri ISO4-G16\|''Methanocatella thaueri'' G16]]
	* [[Methanobrevibacter thaueri CWT\|''Methanocatella thaueri'' CW<sup>T</sup>]]		* [[Methanobrevibacter thaueri CWT\|''Methanocatella thaueri'' CW<sup>T</sup>]]
Line 56:		Line 56:
	* [[Methanosarcina barkeri CM1\|''Methanosarcina barkeri'' CM1]]		* [[Methanosarcina barkeri CM1\|''Methanosarcina barkeri'' CM1]]
	* [[Methanosarcina thermophila Ms97\|''Methanosarcina thermophila'' Ms97]]		* [[Methanosarcina thermophila Ms97\|''Methanosarcina thermophila'' Ms97]]
	* [[Methanosphaera sp. A4]] ~~- group 1 to check nomenclature~~		* [[Methanosphaera sp. A4\|''Methanosphaera sp.'' A4]]
	* [[Methanosphaera sp. ISO3-F5\|''Methanosphaera sp.'' ISO3-F5]]		* [[Methanosphaera sp. ISO3-F5\|''Methanosphaera sp.'' ISO3-F5]]
	* [[Olsenella sp. KH2P3]]		* [[Olsenella sp. KH2P3]]