Methanocatella gottschalkii HO - Revision history

Heryakusuma: /* DefenseFinder Results */

2026-11-03T20:35:50Z

DefenseFinder Results

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			'''''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.

Heryakusuma: /* DefenseFinder Results */

2026-11-03T20:23:00Z

DefenseFinder Results

← Older revision		Revision as of 20:23, 3 November 2026
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	!Components		!Components
	\|-		\|-
	\|Cas		\|CRISPR-Cas
	\|CAS Cluster		\|CAS Cluster
	\|~~Cas1~~, ~~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)
	\|-		\|-

Heryakusuma: /* DefenseFinder Results */

2026-11-03T19:59:06Z

DefenseFinder Results

← Older revision		Revision as of 19:59, 3 November 2026
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	\|Cas		\|Cas
	\|CAS Cluster		\|CAS Cluster
	\|Cas1, ~~<br>~~Cas2		\|Cas1, Cas2
	\|-		\|-
	\|RM Type I		\|RM Type I

Heryakusuma: /* Introduction */

2026-11-03T19:48:54Z

Introduction

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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.

Heryakusuma: /* DefenseFinder Results */

2026-11-03T19:46:01Z

DefenseFinder Results

← Older revision		Revision as of 19:46, 3 November 2026
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	\|Cas		\|Cas
	\|CAS Cluster		\|CAS Cluster
	\|Cas1, Cas2		\|Cas1, <br>Cas2
	\|-		\|-
	\|RM Type I		\|RM Type I
	\|N6-adenine methylation (m6A)		\|N6-adenine methylation (m6A)
	\|Type I RM methyltransferase (HsdM), Type I RM restriction endonuclease (HsdR), 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)
	\|-		\|-
	\|Prometheus		\|Prometheus
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	\|RM Type II		\|RM Type II
	\|DNA methylase and Type II REase of the PD-(D/E)xK superfamily		\|DNA methylase and Type II REase of the PD-(D/E)xK superfamily
	\|Type II DNA methyltransferase, Type II restriction endonuclease (profile 12)		\|Type II DNA methyltransferase, <br>Type II restriction endonuclease (profile 12)
	\|}		\|}

Heryakusuma: /* DefenseFinder Results */

2026-11-03T19:44:26Z

DefenseFinder Results

← Older revision		Revision as of 19:44, 3 November 2026
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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, 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), Type I RM restriction endonuclease (HsdR), 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, Type II restriction endonuclease (profile 12)
	~~RM_Type_II__Type_II_REase12~~
	\|}		\|}

Heryakusuma: /* Introduction */

2026-11-03T19:38:57Z

Introduction

← Older revision		Revision as of 19:38, 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.]]
	''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.

Heryakusuma: /* DefenseFinder Results */

2026-11-03T19:33:57Z

DefenseFinder Results

← Older revision		Revision as of 19:33, 3 November 2026
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	\|RM_Type_I		\|RM_Type_I
	\|N6_RM_Type_I		\|N6_RM_Type_I
	\|RM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_06,RM__Type_I_S_51		\|RM__Type_I_MTases_FAM_0,
			RM__Type_I_REases_FAM_0.einsi_trimmed,
			RM__Type_I_S_06,
			RM__Type_I_S_51
	\|-		\|-
	\|Prometheus		\|Prometheus
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	\|RM_Type_II		\|RM_Type_II
	\|DNA_met_RM_Type_II_PDDEXK		\|DNA_met_RM_Type_II_PDDEXK
	\|RM_Type_II__Type_II_MTases_FAM_0,RM_Type_II__Type_II_REase12		\|RM_Type_II__Type_II_MTases_FAM_0,
			RM_Type_II__Type_II_REase12
	\|}		\|}


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

Heryakusuma at 19:33, 3 November 2026

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 === DefenseFinder Results ===
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 === Methylating ''E. coli'' ===

Heryakusuma: /* Genome */

2026-11-03T00:21:49Z

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.