Methanocatella millerae SM9 - Revision history

Rodriguezcrj: /* Methylome */ Updating methylome

2026-10-30T15:40:19Z

Methylome: Updating methylome

@@ Line 33: / Line 33: @@
 === Methylation pattern ===
-Pending Roy's input.
+{| class="wikitable"
 === DefenseFinder Results ===
 add here

Nanashao at 18:46, 28 October 2026

2026-10-28T18:46:23Z

← Older revision		Revision as of 18:46, 28 October 2026
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	[[File:Puromycin MIC determination in M. millerae SM9. Source- Dr. Nana Shao..jpg\|thumb\|246x246px\|Puromycin MIC determination in ''M. millerae'' SM9. Source: Dr. Nana Shao\|left]]'''Solid Medium'''		[[File:Puromycin MIC determination in M. millerae SM9. Source- Dr. Nana Shao..jpg\|thumb\|246x246px\|Puromycin MIC determination in ''M. millerae'' SM9. Source: Dr. Nana Shao\|left]]'''Solid Medium'''

	Puromycin susceptibility of ''M. millerae'' SM9 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 20 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. millerae'' SM9 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 20 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 17:14, 28 October 2026

2026-10-28T17:14:57Z

← Older revision		Revision as of 17:14, 28 October 2026
Line 64:		Line 64:
	[[File:Puromycin MIC determination in M. millerae SM9. Source- Dr. Nana Shao..jpg\|thumb\|246x246px\|Puromycin MIC determination in ''M. millerae'' SM9. Source: Dr. Nana Shao\|left]]'''Solid Medium'''		[[File:Puromycin MIC determination in M. millerae SM9. Source- Dr. Nana Shao..jpg\|thumb\|246x246px\|Puromycin MIC determination in ''M. millerae'' SM9. Source: Dr. Nana Shao\|left]]'''Solid Medium'''

	Puromycin susceptibility of ''M. millerae'' SM9 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 20 µg/mL at 10<sup>7</sup> cells/plate.		Puromycin susceptibility of ''M. millerae'' SM9 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 20 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 */

2026-10-28T00:22:00Z

Antimicrobial MIC Tests

← Older revision		Revision as of 00:22, 28 October 2026
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	\|[[File:Nourseothricin MIC determination in M. millerae SM9 in liquid MMSM.jpg\|center\|thumb\|411x411px\|Nourseothricin MIC determination in ''M. millerae'' SM9 in liquid MMSM. Source: Dr. Nana Shao]]		\|[[File:Nourseothricin MIC determination in M. millerae SM9 in liquid MMSM.jpg\|center\|thumb\|411x411px\|Nourseothricin MIC determination in ''M. millerae'' SM9 in liquid MMSM. Source: Dr. Nana Shao]]
	\|}		\|}
	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. 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 ~~107~~ cells, the MIC represents the lowest concentration that completely inhibits growth of spontaneous resistance mutants.		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. 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: /* Antimicrobial MIC Tests */

2026-10-28T00:21:14Z

Antimicrobial MIC Tests

← Older revision		Revision as of 00:21, 28 October 2026
Line 93:		Line 93:
	\|[[File:Nourseothricin MIC determination in M. millerae SM9 in liquid MMSM.jpg\|center\|thumb\|411x411px\|Nourseothricin MIC determination in ''M. millerae'' SM9 in liquid MMSM. Source: Dr. Nana Shao]]		\|[[File:Nourseothricin MIC determination in M. millerae SM9 in liquid MMSM.jpg\|center\|thumb\|411x411px\|Nourseothricin MIC determination in ''M. millerae'' SM9 in liquid MMSM. Source: Dr. Nana Shao]]
	\|}		\|}
	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. 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>8</sup>~~ cells, the MIC represents the lowest concentration that completely inhibits growth of spontaneous resistance mutants.		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. 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 107 cells, the MIC represents the lowest concentration that completely inhibits growth of spontaneous resistance mutants.

	== Protocols ==		== Protocols ==

Nanashao at 00:18, 28 October 2026

2026-10-28T00:18:07Z

← Older revision		Revision as of 00:18, 28 October 2026
Line 93:		Line 93:
	\|[[File:Nourseothricin MIC determination in M. millerae SM9 in liquid MMSM.jpg\|center\|thumb\|411x411px\|Nourseothricin MIC determination in ''M. millerae'' SM9 in liquid MMSM. Source: Dr. Nana Shao]]		\|[[File:Nourseothricin MIC determination in M. millerae SM9 in liquid MMSM.jpg\|center\|thumb\|411x411px\|Nourseothricin MIC determination in ''M. millerae'' SM9 in liquid MMSM. Source: Dr. Nana Shao]]
	\|}		\|}
	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. 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>8</sup> cells, the MIC represents the lowest concentration that completely inhibits growth of spontaneous resistance mutants.

	== Protocols ==		== Protocols ==

Nanashao: /* Methylation pattern */

2026-10-26T15:36:24Z

Methylation pattern

← Older revision		Revision as of 15:36, 26 October 2026
Line 47:		Line 47:

	=== 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.~~		add here

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

Nanashao at 15:34, 26 October 2026

2026-10-26T15:34:18Z

← Older revision		Revision as of 15:34, 26 October 2026
Line 30:		Line 30:
	add here		add here

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

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

Line 44:		Line 43:
	* 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~~		''E. coli'' strain AG21365 developed by ORNL was used as a host to generate plasmids with ''M. gottschalkii'' HO methylation motifs shown above.

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

Nanashao: /* Growth requirements */

2026-10-24T01:15:14Z

Growth requirements

← Older revision		Revision as of 01:15, 24 October 2026
Line 52:		Line 52:

	== Growth requirements ==		== Growth requirements ==
	''M. millerae'' SM9 requires rumen fluid, yeast extract, and tryptone for optimal growth in MMSM. Omission of rumen fluid markedly reduces growth, whereas omission of either yeast extract or tryptone results in a moderate reduction in growth yield. Either cysteine (3 mM; autoclaved or filter-sterilized) or sodium sulfide (Na₂S; 0.4-1 mM) supports robust growth as a sulfur source, with no clear preference between the two. Under these conditions, cultures reach a maximum ~~OD₆₀₀~~ of approximately ~1.3. No growth was observed with formate as the sole energy substrate under the conditions tested.		''M. millerae'' SM9 requires rumen fluid, yeast extract, and tryptone for optimal growth in MMSM. Omission of rumen fluid markedly reduces growth, whereas omission of either yeast extract or tryptone results in a moderate reduction in growth yield. Either cysteine (3 mM; autoclaved or filter-sterilized) or sodium sulfide (Na₂S; 0.4-1 mM) supports robust growth as a sulfur source, with no clear preference between the two. Under these conditions, cultures reach a maximum OD<sub>600</sub> of approximately ~1.3. No growth was observed with formate as the sole energy substrate under the conditions tested.
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+

Nanashao: /* Growth requirements */

2026-10-24T01:13:09Z

Growth requirements

← Older revision		Revision as of 01:13, 24 October 2026
Line 53:		Line 53:
	== Growth requirements ==		== Growth requirements ==
	''M. millerae'' SM9 requires rumen fluid, yeast extract, and tryptone for optimal growth in MMSM. Omission of rumen fluid markedly reduces growth, whereas omission of either yeast extract or tryptone results in a moderate reduction in growth yield. Either cysteine (3 mM; autoclaved or filter-sterilized) or sodium sulfide (Na₂S; 0.4-1 mM) supports robust growth as a sulfur source, with no clear preference between the two. Under these conditions, cultures reach a maximum OD₆₀₀ of approximately ~1.3. No growth was observed with formate as the sole energy substrate under the conditions tested.		''M. millerae'' SM9 requires rumen fluid, yeast extract, and tryptone for optimal growth in MMSM. Omission of rumen fluid markedly reduces growth, whereas omission of either yeast extract or tryptone results in a moderate reduction in growth yield. Either cysteine (3 mM; autoclaved or filter-sterilized) or sodium sulfide (Na₂S; 0.4-1 mM) supports robust growth as a sulfur source, with no clear preference between the two. Under these conditions, cultures reach a maximum OD₆₀₀ of approximately ~1.3. No growth was observed with formate as the sole energy substrate under the conditions tested.
			{\| class="wikitable"
			\|+
			\|[[File:Rumen fluid, yeast extract and tryptone are all required for optimal growth of M. millerae SM9 .jpg\|thumb\|Rumen fluid, yeast extract and tryptone are all required for optimal growth of ''M. millerae'' SM9. Source: Dr. Nana Shao]]
			\|[[File:Sulfur source of M. millerae SM9.jpg\|thumb\|Sulfur source of ''M. millerae'' SM9. Source: Dr. Nana Shao]]
			\|[[File:Influence of Na2S concentration on M. millerae SM9 growth.jpg\|thumb\|Influence of Na<sub>2</sub>S concentration on ''M. millerae'' SM9 growth. Source: Dr. Nana Shao]]
			\|}

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