Methanobrevibacter olleyae YLM1 - Revision history

Rodriguezcrj: /* Methylation pattern */ Updating methylome

2026-10-30T15:55:04Z

Methylation pattern: Updating methylome

← Older revision		Revision as of 15:55, 30 October 2026
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	=== Methylation pattern ===		=== Methylation pattern ===
	~~Pending Roy's input.~~		{\| class="wikitable"
	* Searching dataset for following motifs: GSNGA, GNSNGA		\|+
	* Motifs explain the following about the (6mA) modified dataset:		!Methylated motif
	* Low-quality methylated ~~sites: 7170/6856 explained (104.57992998833139%)~~		!Percent methylated
	* Mid-~~quality methylated sites: 7158/6524 explained~~ (~~109.71796443899449%~~)		\|-
	* High-quality methylated sites: 300/~~244 explained~~ (~~122.95081967213115%~~)		\|GSNG(6mA)/GNSNG(6mA)
	* No 5mC motifs present in output file, skipping...		\|98.35/95.91
	* No 4mC motifs present in output file, skipping...		\|}
	* Only one replicon present, skipping differential genomic coverage
	=== DefenseFinder Results ===		=== DefenseFinder Results ===
	add here		add here

Nanashao at 18:47, 28 October 2026

2026-10-28T18:47:22Z

← Older revision		Revision as of 18:47, 28 October 2026
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	[[File:Puromycin MIC determination in M. olleyae YLM1. Source- Dr. Nana Shao.jpg\|thumb\|Puromycin MIC determination in ''M. olleyae'' YLM1. Source: Dr. Nana Shao\|left\|290x290px]]'''Solid Medium'''		[[File:Puromycin MIC determination in M. olleyae YLM1. Source- Dr. Nana Shao.jpg\|thumb\|Puromycin MIC determination in ''M. olleyae'' YLM1. Source: Dr. Nana Shao\|left\|290x290px]]'''Solid Medium'''

	Puromycin susceptibility of ''M.'' ''olleyae'' YLM1 was assessed on solid medium under anaerobic conditions, ~~using~~ the absence of visible colonies as the endpoint. The apparent MIC was 10 µg/mL at an inoculum of 10<sup>5</sup> cells/plate and 15 µg/mL at 10<sup>7</sup> cells/plate. Below the MIC, confluent growth or numerous small colonies are observed on the agar surface. Large colonies are observed when fewer than 100 cells survive. When growth is inhibited but not completely suppressed, small colonies are observed.		Puromycin susceptibility of ''M.'' ''olleyae'' YLM1 was assessed on MMSM solid medium under anaerobic conditions, with the bottle preparation and incubation performed as described in the [[Modified Methanobrevibacter smithii and Methanosphaera stadtmanae medium (MMSM)\|MMSM protocol]]. The absence of visible colonies was used as the endpoint. The apparent MIC was 10 µg/mL at an inoculum of 10<sup>5</sup> cells/plate and 15 µg/mL at 10<sup>7</sup> cells/plate. Below the MIC, confluent growth or numerous small colonies are observed on the agar surface. Large colonies are observed when fewer than 100 cells survive. When growth is inhibited but not completely suppressed, small colonies are observed.

	'''Liquid Medium'''		'''Liquid Medium'''

Nanashao at 17:15, 28 October 2026

2026-10-28T17:15:20Z

← Older revision		Revision as of 17:15, 28 October 2026
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	[[File:Puromycin MIC determination in M. olleyae YLM1. Source- Dr. Nana Shao.jpg\|thumb\|Puromycin MIC determination in ''M. olleyae'' YLM1. Source: Dr. Nana Shao\|left\|290x290px]]'''Solid Medium'''		[[File:Puromycin MIC determination in M. olleyae YLM1. Source- Dr. Nana Shao.jpg\|thumb\|Puromycin MIC determination in ''M. olleyae'' YLM1. Source: Dr. Nana Shao\|left\|290x290px]]'''Solid Medium'''

	Puromycin susceptibility of ''M.'' ''olleyae'' YLM1 was assessed on solid medium under anaerobic conditions, using the absence of visible colonies as the endpoint. The apparent MIC was 10 µg/mL at an inoculum of 10<sup>5</sup> cells/plate and 15 µg/mL at 10<sup>7</sup> cells/plate.		Puromycin susceptibility of ''M.'' ''olleyae'' YLM1 was assessed on solid medium under anaerobic conditions, using the absence of visible colonies as the endpoint. The apparent MIC was 10 µg/mL at an inoculum of 10<sup>5</sup> cells/plate and 15 µg/mL at 10<sup>7</sup> cells/plate. Below the MIC, confluent growth or numerous small colonies are observed on the agar surface. Large colonies are observed when fewer than 100 cells survive. When growth is inhibited but not completely suppressed, small colonies are observed.

	'''Liquid Medium'''		'''Liquid Medium'''

Nanashao: /* Antimicrobial MIC Tests */

2026-10-28T00:46:34Z

Antimicrobial MIC Tests

← Older revision		Revision as of 00:46, 28 October 2026
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	Overall, the results demonstrated inoculum-dependent inhibition under the tested conditions, with higher apparent MICs at higher inoculum densities in both solid and liquid media.		Overall, the results demonstrated inoculum-dependent inhibition under the tested conditions, with higher apparent MICs at higher inoculum densities in both solid and liquid media.

	Overall, puromycin showed inoculum-dependent inhibition on solid medium and prevented detectable growth in liquid medium, whereas nourseothricin delayed but did not prevent growth at the tested concentrations.		Overall, puromycin showed inoculum-dependent inhibition on solid medium and prevented detectable growth in liquid medium, whereas nourseothricin delayed but did not prevent growth at the tested concentrations. For the lower inoculum of about 10<sup>5</sup> cells, the MIC represents the lowest concentration that completely inhibits growth of wild-type cells. For the higher inoculum of about 10<sup>7</sup> cells, the MIC represents the lowest concentration that completely inhibits growth of spontaneous resistance mutants.

	== Protocols ==		== Protocols ==

Nanashao at 00:40, 28 October 2026

2026-10-28T00:40:46Z

← Older revision		Revision as of 00:40, 28 October 2026
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	== Introduction ==		== Introduction ==
	''Methanobrevibacter olleyae'' YLM1 ~~was~~ a hydrogenotrophic methanogen isolated from the rumen of a lamb<ref>Skillman LC, Evans PN, Naylor GE, Morvan B, Jarvis GN, Joblin KN. 16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs. Anaerobe. 2004 Oct;10(5):277-85. doi: [https://www.sciencedirect.com/science/article/pii/S1075996404000496?via%3Dihub 10.1016/j.anaerobe.2004.05.003]. </ref>. Unlike ''Methanobrevibacter ruminantium'' M1<ref>Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT. The genome sequence of the rumen methanogen ''Methanobrevibacter ruminantium'' reveals new possibilities for controlling ruminant methane emissions. PLoS One. 2010 Jan 28;5(1):e8926. doi: [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008926 10.1371/journal.pone.0008926].</ref>, YLM1 ~~carries~~ ''com''ADE genes supporting ~~its predicted ability to synthesize~~ coenzyme M. It also possesses the ''mrt''BDGA operon encoding methyl-coenzyme M reductase II, which is absent from M1 and may contribute to differences in growth under varying hydrogen concentrations<ref name=":0">Kelly WJ, Li D, Lambie SC, Cox F, Attwood GT, Altermann E, Leahy SC. Draft Genome Sequence of the Rumen Methanogen ''Methanobrevibacter olleyae'' YLM1. Genome Announc. 2016 Apr 7;4(2):e00232-16. doi: [https://journals.asm.org/doi/10.1128/genomea.00232-16 10.1128/genomeA.00232-16].</ref>. These genomic features make YLM1 a useful strain for comparative studies of rumen methanogen physiology and the development of methane mitigation strategies. Its robust growth and high plating efficiency, observed in the Whitman Lab, make it particularly valuable for research supported by the Global Methane Hub.		''Methanobrevibacter olleyae'' YLM1 is a hydrogenotrophic methanogen isolated from the rumen of a lamb<ref>Skillman LC, Evans PN, Naylor GE, Morvan B, Jarvis GN, Joblin KN. 16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs. Anaerobe. 2004 Oct;10(5):277-85. doi: [https://www.sciencedirect.com/science/article/pii/S1075996404000496?via%3Dihub 10.1016/j.anaerobe.2004.05.003]. </ref>. Unlike the type species of the genus ''Methanobrevibacter ruminantium'' M1<ref>Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT. The genome sequence of the rumen methanogen ''Methanobrevibacter ruminantium'' reveals new possibilities for controlling ruminant methane emissions. PLoS One. 2010 Jan 28;5(1):e8926. doi: [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008926 10.1371/journal.pone.0008926].</ref>, YLM1 possesses the ''com''ADE genes, supporting the prediction that it can biosynthesize coenzyme M. It also possesses the ''mrt''BDGA operon encoding methyl-coenzyme M reductase II, which is absent from M1 and may contribute to differences in growth under varying hydrogen gas concentrations<ref name=":0">Kelly WJ, Li D, Lambie SC, Cox F, Attwood GT, Altermann E, Leahy SC. Draft Genome Sequence of the Rumen Methanogen ''Methanobrevibacter olleyae'' YLM1. Genome Announc. 2016 Apr 7;4(2):e00232-16. doi: [https://journals.asm.org/doi/10.1128/genomea.00232-16 10.1128/genomeA.00232-16].</ref>. These genomic features make YLM1 a useful strain for comparative studies of rumen methanogen physiology and the development of methane mitigation strategies. Its robust growth and high plating efficiency, observed in the Whitman Lab, make it particularly valuable for research supported by the Global Methane Hub.

	== Global Methane Hub Metadata ==		== Global Methane Hub Metadata ==
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	== Genome ==		== Genome ==
	The draft genome of ''Methanobrevibacter olleyae'' YLM1 is 2,201,192 bp, with a GC content of 26.9% and 1,834 predicted protein-coding genes<ref name=":0" />. It contains one approximately 40-kb prophage, two CRISPR regions, and no identified plasmids. Notable features include the ''hdr''ABC ~~gene~~ encoding CoB-CoM heterodisulfide reductase subunits, the ''com''ADE genes involved in coenzyme M biosynthesis, the ''mrt''BDGA operon encoding methyl-coenzyme M reductase II, and 64 large adhesin-like protein genes. The GenBank accession number is [https://www.ncbi.nlm.nih.gov/nuccore/CP014265.1/ CP014265].		The draft genome of ''Methanobrevibacter olleyae'' YLM1 is 2,201,192 bp, with a GC content of 26.9% and 1,834 predicted protein-coding genes<ref name=":0" />. It contains one approximately 40-kb prophage, two CRISPR regions, and no identified plasmids. Notable features include the ''hdr''ABC genes encoding CoB-CoM heterodisulfide reductase subunits, the ''com''ADE genes involved in coenzyme M biosynthesis, the ''mrt''BDGA operon encoding methyl-coenzyme M reductase II, and 64 large adhesin-like protein genes. The GenBank accession number is [https://www.ncbi.nlm.nih.gov/nuccore/CP014265.1/ CP014265].

	== Methylome ==		== Methylome ==
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	== Growth requirements ==		== Growth requirements ==
	''M. olleyae'' YLM1 requires rumen fluid for robust growth in MMSM, whereas yeast extract and tryptone are individually dispensable under the conditions tested. Omission of rumen fluid markedly reduces growth, while omission of either yeast extract or tryptone ~~supports~~ growth to ~~higher maximum~~ OD<sub>600</sub> values at ~1.4. ~~Sulfide~~ serves as a sulfur source this ~~this strains~~.		''M. olleyae'' YLM1 requires rumen fluid for robust growth in MMSM, whereas yeast extract and tryptone are individually dispensable under the conditions tested. Omission of rumen fluid markedly reduces growth, while omission of either yeast extract or tryptone still allows growth to OD<sub>600</sub> values of ~1.4. The inability of filter-sterilized cysteine to support good growth indicates that is not used as a sulfur source and that sulfide from the breakdown of cysteine serves as a sulfur source for this strain.
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+

Nanashao at 15:36, 26 October 2026

2026-10-26T15:36:07Z

← Older revision		Revision as of 15:36, 26 October 2026
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	The draft genome of ''Methanobrevibacter olleyae'' YLM1 is 2,201,192 bp, with a GC content of 26.9% and 1,834 predicted protein-coding genes<ref name=":0" />. It contains one approximately 40-kb prophage, two CRISPR regions, and no identified plasmids. Notable features include the ''hdr''ABC gene encoding CoB-CoM heterodisulfide reductase subunits, the ''com''ADE genes involved in coenzyme M biosynthesis, the ''mrt''BDGA operon encoding methyl-coenzyme M reductase II, and 64 large adhesin-like protein genes. The GenBank accession number is [https://www.ncbi.nlm.nih.gov/nuccore/CP014265.1/ CP014265].		The draft genome of ''Methanobrevibacter olleyae'' YLM1 is 2,201,192 bp, with a GC content of 26.9% and 1,834 predicted protein-coding genes<ref name=":0" />. It contains one approximately 40-kb prophage, two CRISPR regions, and no identified plasmids. Notable features include the ''hdr''ABC gene encoding CoB-CoM heterodisulfide reductase subunits, the ''com''ADE genes involved in coenzyme M biosynthesis, the ''mrt''BDGA operon encoding methyl-coenzyme M reductase II, and 64 large adhesin-like protein genes. The GenBank accession number is [https://www.ncbi.nlm.nih.gov/nuccore/CP014265.1/ CP014265].

	== ~~DefenseFinder Results~~ ==		== Methylome ==
	~~add here~~

	== ~~Methylome~~ ==		=== Methylation pattern ===
	Pending Roy's input.		Pending Roy's input.

	* Searching dataset for following motifs: GSNGA, GNSNGA		* Searching dataset for following motifs: GSNGA, GNSNGA
	* Motifs explain the following about the (6mA) modified dataset:		* Motifs explain the following about the (6mA) modified dataset:
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	* No 4mC motifs present in output file, skipping...		* No 4mC motifs present in output file, skipping...
	* Only one replicon present, skipping differential genomic coverage		* Only one replicon present, skipping differential genomic coverage
			=== DefenseFinder Results ===
			add here

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

Nanashao: /* Growth requirements */

2026-10-24T01:40:06Z

Growth requirements

← Older revision		Revision as of 01:40, 24 October 2026
Line 52:		Line 52:

	== Growth requirements ==		== Growth requirements ==
	''M. olleyae'' YLM1 requires rumen fluid for robust growth in MMSM, whereas yeast extract and tryptone are individually dispensable under the conditions tested. Omission of rumen fluid markedly reduces growth, while omission of either yeast extract or tryptone supports growth to higher maximum OD<sub>600</sub> values at ~1.4. Sulfide serves as a sulfur source this this strains.		''M. olleyae'' YLM1 requires rumen fluid for robust growth in MMSM, whereas yeast extract and tryptone are individually dispensable under the conditions tested. Omission of rumen fluid markedly reduces growth, while omission of either yeast extract or tryptone supports growth to higher maximum OD<sub>600</sub> values at ~1.4. Sulfide serves as a sulfur source this this strains.
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+

Nanashao: /* Growth requirements */

2026-10-24T01:39:48Z

Growth requirements

← Older revision		Revision as of 01:39, 24 October 2026
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	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+
	\|[[File:Rumen fluid is required for M. olleyae YLM1 growth.jpg\|thumb\|Rumen fluid is required for ''M. olleyae'' YLM1 growth. Source: Dr. Nana Shao\|center\|~~252x252px~~]]		\|[[File:Rumen fluid is required for M. olleyae YLM1 growth.jpg\|thumb\|Rumen fluid is required for ''M. olleyae'' YLM1 growth. Source: Dr. Nana Shao\|center\|333x333px]]
	\|[[File:Sulfide serves as a sulfur source for M. olleyae YLM1 .jpg\|thumb\|524x524px\|Sulfide serves as a sulfur source for ''M. olleyae'' YLM1. Source: Nana Shao\|center]]		\|[[File:Sulfide serves as a sulfur source for M. olleyae YLM1 .jpg\|thumb\|524x524px\|Sulfide serves as a sulfur source for ''M. olleyae'' YLM1. Source: Nana Shao\|center]]
	\|}		\|}

Nanashao: /* Growth requirements */

2026-10-24T01:39:34Z

Growth requirements

← Older revision		Revision as of 01:39, 24 October 2026
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	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+
	\|[[File:Rumen fluid is required for M. olleyae YLM1 growth.jpg\|thumb\|Rumen fluid is required for ''M. olleyae'' YLM1 growth. Source: Dr. Nana Shao]]		\|[[File:Rumen fluid is required for M. olleyae YLM1 growth.jpg\|thumb\|Rumen fluid is required for ''M. olleyae'' YLM1 growth. Source: Dr. Nana Shao\|center\|252x252px]]
	\|[[File:Sulfide serves as a sulfur source for M. olleyae YLM1 .jpg\|thumb\|~~318x318px~~\|Sulfide serves as a sulfur source for ''M. olleyae'' YLM1. Source: Nana Shao]]		\|[[File:Sulfide serves as a sulfur source for M. olleyae YLM1 .jpg\|thumb\|524x524px\|Sulfide serves as a sulfur source for ''M. olleyae'' YLM1. Source: Nana Shao\|center]]
	\|}		\|}

Nanashao at 01:38, 24 October 2026

2026-10-24T01:38:56Z

← Older revision		Revision as of 01:38, 24 October 2026
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	== Growth requirements ==		== Growth requirements ==
	~~add here~~		''M. olleyae'' YLM1 requires rumen fluid for robust growth in MMSM, whereas yeast extract and tryptone are individually dispensable under the conditions tested. Omission of rumen fluid markedly reduces growth, while omission of either yeast extract or tryptone supports growth to higher maximum OD<sub>600</sub> values at ~1.4. Sulfide serves as a sulfur source this this strains.
			{\| class="wikitable"
			\|+
			\|[[File:Rumen fluid is required for M. olleyae YLM1 growth.jpg\|thumb\|Rumen fluid is required for ''M. olleyae'' YLM1 growth. Source: Dr. Nana Shao]]
			\|[[File:Sulfide serves as a sulfur source for M. olleyae YLM1 .jpg\|thumb\|318x318px\|Sulfide serves as a sulfur source for ''M. olleyae'' YLM1. Source: Nana Shao]]
			\|}

	== Antimicrobial MIC Tests ==		== Antimicrobial MIC Tests ==