Strain template - Revision history

Alexanderwg: Removed errant edits to the template page.

2026-10-28T19:34:45Z

Removed errant edits to the template page.

@@ Line 29: / Line 29: @@
 == DefenseFinder Results ==
 == Methylome ==
 == Methylating E. coli Strains ==
 == Culturing Conditions ==
 == Antibiotic MIC Tests ==
 == Protocols ==
 == Transformation Results ==
 == External Links ==

Ahetta at 22:17, 27 October 2026

2026-10-27T22:17:51Z

← Older revision		Revision as of 22:17, 27 October 2026
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	~~[[File:SEM electron micrograph of Streptococcus bovis JB1.jpg\|thumb\|150x150px\|''S. azabuensis'' KH1P5 in liquid culture exhibiting its dense layer of EPS. Source: Dr. Roy Rodriguez Carrero]]~~

	== Introduction ==		== Introduction ==
	''Streptococcus bovis'' JB1 was isolated from the rumen of alfalfa-fed cow. It is a major amylolytic bacterium that depolymerize starch to glucose, fermenting it to large amounts of lactic acid that can lead to lactic acidosis in ruminants.

	== Global Methane Hub Metadata ==		== Global Methane Hub Metadata ==
Line 8:		Line 5:
	\|+		\|+
	\|Origin:		\|Origin:
	\|~~Illinois, Mackie Lab~~		\|
	\|-		\|-
	\|Sequenced by:		\|Sequenced by:
	\|~~Ahmed Hetta and Yuqi Li~~		\|
	\|-		\|-
	\|Assembled by:		\|Assembled by:
	\|~~William G. Alexander~~		\|
	\|-		\|-
	\|Methylome called by:		\|Methylome called by:
	\|~~William G. Alexander~~		\|
	\|-		\|-
	\|Methyltransferases cloned by:		\|Methyltransferases cloned by:
	\|~~No methylation motifs have been detected~~		\|
	\|-		\|-
	\|MIC and Culturing Conditions by:		\|MIC and Culturing Conditions by:
	\|~~Ahmed Hetta and Yuqi Li~~		\|
	\|-		\|-
	\|Transformation by:		\|Transformation by:
	\|~~Ahmed Hetta~~		\|
	\|}		\|}

	== Genome ==		== Genome ==
	~~[[File:Streptococcus bovis JB1 1 1 circos.png\|center\|thumb\|Circos plot of ''S. azabuensis'' KH1P5. Source: Dr. William G. Alexander]]~~

	== DefenseFinder Results ==		== DefenseFinder Results ==
	== Methylome ==		== Methylome ==
Line 40:		Line 35:

	== Culturing Conditions ==		== Culturing Conditions ==
	''Streptococcus bovis'' JB1 grows on both M2GSC and SDM (Semi Defined medium). Cells grow overnight at 37 °C in SDM or M2GSC culture medium with head space composed of 95% CO<sub>2</sub> and 5% H<sub>2</sub>. Similarly, ''Streptococcus bovis'' JB1 grows overnight on SDM agar plates. Agar plates were placed in anaerobic Jar and incubated in anaerobic chamber under gas mixture that is composed of 95% CO<sub>2</sub> and 5% H<sub>2</sub>.
	== Antibiotic MIC Tests ==		== Antibiotic MIC Tests ==
	~~[[File:Streptococcus bovis JB1 MIC.png\|left\|thumb\|MIC tests of ''S. azabuensis''. Source: Dr. Roy Rodriguez Carrero]]~~
	{\| class="wikitable"		{\| class="wikitable"
	!antibiotic		!antibiotic
Line 76:		Line 69:
	== Transformation Results ==		== Transformation Results ==
	== External Links ==		== External Links ==
	[1] Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC, Cookson AL, Eloe-Fadrosh EA, Pavlopoulos GA, Hadjithomas M, Varghese NJ, Paez-Espino D; 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.

	[2] Kumar S, Treloar BP, Teh KH, McKenzie CM, Henderson G, Attwood GT, Waters SM, Patchett ML, Janssen PH. 2018. Sharpea and Kandleria are lactic acid producing rumen bacteria that do not change their fermentation products when co-cultured with a methanogen. Anaerobe 54: 31-38. doi: 10.1016/j.anaerobe.2018.07.008.

	[3] Kittelmann S, Pinares-Patiño CS, Seedorf H, Kirk MR, Ganesh S, McEwan JC, Janssen PH. 2014. Two different bacterial community types are linked with the low-methane emission trait in sheep. PLoS One 9: e103171. doi: 10.1371/journal.pone.0103171.

	[4] Kamke J, Kittelmann S, Soni P, Li Y, Tavendale M, Ganesh S, Janssen PH, Shi W, Froula J, Rubin EM, Attwood GT. 2016. Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation. Microbiome 4: 56. doi: 10.1186/s40168-016-0201-2.

	[5] Morita H, Shiratori C, Murakami M, Takami H, Toh H, Kato Y, Nakajima F, Takagi M, Akita H, Masaoka T, Hattori M. 2008. Sharpea azabuensis gen. nov., sp. nov., a Gram-positive, strictly anaerobic bacterium isolated from the faeces of thoroughbred horses. Int J Syst Evol Microbiol 58: 2682-2686 doi: 10.1099/ijs.0.65543-0.

Ahetta at 20:49, 27 October 2026

2026-10-27T20:49:51Z

← Older revision		Revision as of 20:49, 27 October 2026
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	== Culturing Conditions ==		== Culturing Conditions ==
	''Streptococcus bovis'' JB1 grows on both M2GSC and SDM (Semi Defined medium). Cells grow overnight at 37 °C in SDM or M2GSC culture medium with head space composed of 95% CO<sub>2</sub> and 5% H<sub>2</sub>. Similarly, ''Streptococcus bovis'' JB1 grows overnight on SDM agar plates. Agar plates were placed in anaerobic Jar and incubated in anaerobic chamber under gas mixture that is composed of 95% CO<sub>2</sub> and 5% H<sub>2</sub>. ~~[[File:KH1P5_micrograph.jpg\|thumb\|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]~~		''Streptococcus bovis'' JB1 grows on both M2GSC and SDM (Semi Defined medium). Cells grow overnight at 37 °C in SDM or M2GSC culture medium with head space composed of 95% CO<sub>2</sub> and 5% H<sub>2</sub>. Similarly, ''Streptococcus bovis'' JB1 grows overnight on SDM agar plates. Agar plates were placed in anaerobic Jar and incubated in anaerobic chamber under gas mixture that is composed of 95% CO<sub>2</sub> and 5% H<sub>2</sub>.

	== Antibiotic MIC Tests ==		== Antibiotic MIC Tests ==
	[[File:~~Sabu_MIC~~.png\|left\|thumb\|MIC tests of ''S. azabuensis''. Source: Dr. Roy Rodriguez Carrero]]		[[File:Streptococcus bovis JB1 MIC.png\|left\|thumb\|MIC tests of ''S. azabuensis''. Source: Dr. Roy Rodriguez Carrero]]
	{\| class="wikitable"		{\| class="wikitable"
	!antibiotic		!antibiotic

Ahetta: /* Antibiotic MIC Tests */

2026-10-27T20:10:40Z

Antibiotic MIC Tests

← Older revision		Revision as of 20:10, 27 October 2026
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	!concentration (ug/mL)		!concentration (ug/mL)
	\|-		\|-
	\|~~carbenicillin~~		\|Ampicillin
	\|5		\|5
	\|-		\|-
	\|~~chloramphenicol~~		\|Kanamycin
	\|0.38		\|0.38
	\|-		\|-
	\|~~clarithromycin~~		\|Chloramphenicol
	\|25		\|25
	\|-		\|-
	\|~~erythromycin~~		\|Tetracycline
	\|1		\|1
	\|-		\|-
	\|~~kanamycin~~		\|Gentamicin
	\|insensitive		\|insensitive
	\|-		\|-
	\|~~spectinomycin~~		\|Streptomycin
	\|96		\|96
	\|-		\|-
	\|~~tetracycline~~		\|Erythromycin
	\|0.23		\|0.23
	\|-
	~~\|thiamphenicol~~
	\|5
	\|}		\|}

Ahetta: /* Culturing Conditions */

2026-10-27T20:05:46Z

Culturing Conditions

← Older revision		Revision as of 20:05, 27 October 2026
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	== Culturing Conditions ==		== Culturing Conditions ==
	''Streptococcus bovis'' JB1 grows on both M2GSC and SDM (Semi Defined medium). Cells grow overnight at 37 °C with head space composed of 95% ~~CO2~~ and 5% H2. [[File:KH1P5_micrograph.jpg\|thumb\|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]		''Streptococcus bovis'' JB1 grows on both M2GSC and SDM (Semi Defined medium). Cells grow overnight at 37 °C in SDM or M2GSC culture medium with head space composed of 95% CO<sub>2</sub> and 5% H<sub>2</sub>. Similarly, ''Streptococcus bovis'' JB1 grows overnight on SDM agar plates. Agar plates were placed in anaerobic Jar and incubated in anaerobic chamber under gas mixture that is composed of 95% CO<sub>2</sub> and 5% H<sub>2</sub>. [[File:KH1P5_micrograph.jpg\|thumb\|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

	== Antibiotic MIC Tests ==		== Antibiotic MIC Tests ==

Ahetta at 19:54, 27 October 2026

2026-10-27T19:54:36Z

← Older revision		Revision as of 19:54, 27 October 2026
Line 40:		Line 40:

	== Culturing Conditions ==		== Culturing Conditions ==
	''~~S. azabuensis~~'' ~~KH1P5~~ grows well in stock [[RCM]] at 37 °C. However, the inclusion of agar in commercially made RCM causes the strain to produce a thick, mucoidal layer of [[wikipedia:Extracellular_polymeric_substance\|extracellular polymeric substance (~~EPS~~)~~]] that requires [[Sharpea azabuensis KH1P5#Protocols\|removal via washing]] with chelating agents and detergent before work with the culture~~. ~~Growing the organism in lab made RCM without agar eliminates the dense EPS layer.~~		''Streptococcus bovis'' JB1 grows on both M2GSC and SDM (Semi Defined medium). Cells grow overnight at 37 °C with head space composed of 95% CO2 and 5% H2. [[File:KH1P5_micrograph.jpg\|thumb\|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

	~~KH1P5 also grows well on M2G medium~~ at 39 °C, with ~~10 ml cultures reaching stationary phase after 6-7 h at optical densities~~ of ~~~4-~~5. ~~Cells of KH1P5 form long chains.~~
	[[File:KH1P5_micrograph.jpg\|thumb\|Phase-contrast micrograph of ''S. azabuensis'' KH1P5 grown in M2G medium. Source: Dr. Sam Mahoney-Kurpe.]]

	== Antibiotic MIC Tests ==		== Antibiotic MIC Tests ==

Ahetta: /* Genome */

2026-10-27T19:47:32Z

Genome

← Older revision		Revision as of 19:47, 27 October 2026
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	== Genome ==		== Genome ==
	[[File:~~S_azabuensis_circos~~.png\|center\|thumb\|Circos plot of ''S. azabuensis'' KH1P5. Source: Dr. William G. Alexander]]		[[File:Streptococcus bovis JB1 1 1 circos.png\|center\|thumb\|Circos plot of ''S. azabuensis'' KH1P5. Source: Dr. William G. Alexander]]

	== DefenseFinder Results ==		== DefenseFinder Results ==
	== Methylome ==		== Methylome ==
	~~While ''S. azabuensis'' KH1P5 possesses two putative Type II restriction endonucleases, no~~ methylation ~~is detectable~~ in ~~the isolate. Also, these two genes do not methylate in '~~'~~E. coli~~'' ~~strains, suggesting that they~~'~~re vestigial defense systems~~.		No methylation motifs were detected in ''Streptococcus bovis'' JB1.

	== Methylating E. coli Strains ==		== Methylating E. coli Strains ==
	~~Use a strain of~~ ''E. coli'' ~~that lacks dam, dcm, and hsdRMS, such as AG5589~~.		No ''E. coli'' methylation strain has been constructed for ''S. bovis'' JB1 strain

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

Ahetta at 19:36, 27 October 2026

2026-10-27T19:36:38Z

← Older revision		Revision as of 19:36, 27 October 2026
Line 1:		Line 1:
	[[File:~~Sabu_tube~~.~~png~~\|thumb\|~~346x346px~~\|''S. azabuensis'' KH1P5 in liquid culture exhibiting its dense layer of EPS. Source: Dr. Roy Rodriguez Carrero]]		[[File:SEM electron micrograph of Streptococcus bovis JB1.jpg\|thumb\|150x150px\|''S. azabuensis'' KH1P5 in liquid culture exhibiting its dense layer of EPS. Source: Dr. Roy Rodriguez Carrero]]

	== Introduction ==		== Introduction ==
	'''~~Sharpea azabuensis KH1P5~~'''		''Streptococcus bovis'' JB1 was isolated from the rumen of alfalfa-fed cow. It is a major amylolytic bacterium that depolymerize starch to glucose, fermenting it to large amounts of lactic acid that can lead to lactic acidosis in ruminants.

	~~Sharpea azabuensis KH1P5~~ was isolated from ~~bovine~~ rumen ~~contents in NZ using KH medium which was supplemented with haemin and vitamin K [1]. KH1P5 ferments glucose, fructose, galactose, cellobiose, sucrose, lactose and raffinose with D~~-~~lactate as the main fermentation product together with small amounts of acetate, formate and ethanol [2]~~. It is a ~~member of the family Coprobacillaceae.~~

	~~Sharpea and Kandleria were identified as key bacteria associated with the S-type (Sharpea-enriched) bacterial community~~, one of the two low-CH<sub>4</sub> community types in rumen samples from sheep that differed in the amount of CH<sub>4</sub> formed per unit of feed consumed when these sheep were fed pelletized lucerne [3]. A metagenomic and metatranscriptomic study conducted by Kamke et al. [4] confirmed that the relative abundance of ~~Sharpea spp. was greater in a group of low-CH<sub>4</sub>emitting sheep than in their high-CH<sub>4</sub> emitting flock mates. It was hypothesized~~ that ~~lactate produced by these bacteria is further converted~~ to ~~butyrate by Megasphaera spp., resulting~~ in ~~lower CH<sub>4</sub> emissions~~.

	~~The draft genome for KH1P5 (2,329,465 bp) was generated through the Hungate1000 project with JGI [1]. Resequencing gave a single chromosome of 2,465,508 bp.~~

	~~LPSN: ''Sharpea azabuensis'' Morita ''et al.'' 2008~~

	~~NCBI: Sharpea azabuensis.~~

	~~GTDB: Sharpea azabuensis. KH1P5 groups with the type strain (ST18, DSM 18934) [5]~~

	~~Risk group: 1~~

	== Global Methane Hub Metadata ==		== Global Methane Hub Metadata ==
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	\|+		\|+
	\|Origin:		\|Origin:
	\|~~New Zealand~~, ~~Kelly~~ Lab		\|Illinois, Mackie Lab
	\|-		\|-
	\|Sequenced by:		\|Sequenced by:
	\|~~Sam Mahoney Kurpe~~		\|Ahmed Hetta and Yuqi Li
	\|-		\|-
	\|Assembled by:		\|Assembled by:
Line 34:		Line 20:
	\|-		\|-
	\|Methyltransferases cloned by:		\|Methyltransferases cloned by:
	\|~~Roy Rodriguez Carrero~~		\|No methylation motifs have been detected
	\|-		\|-
	\|MIC and Culturing Conditions by:		\|MIC and Culturing Conditions by:
	\|~~Roy Rodriguez Carrero~~		\|Ahmed Hetta and Yuqi Li
	\|-		\|-
	\|Transformation by:		\|Transformation by:
	\|~~Roy Rodriguez Carrero~~		\|Ahmed Hetta
	\|}		\|}

Ahetta at 17:44, 27 October 2026

2026-10-27T17:44:28Z

@@ Line 1: / Line 1: @@
 == Introduction ==
-add here
+'''Sharpea azabuensis KH1P5'''
 == Global Methane Hub Metadata ==
-add here
+{| class="wikitable"
 == Genome ==
-add here
+[[File:S_azabuensis_circos.png|center|thumb|Circos plot of ''S. azabuensis'' KH1P5. Source: Dr. William G. Alexander]]
 == DefenseFinder Results ==
 == Methylome ==
-add here
+While ''S. azabuensis'' KH1P5 possesses two putative Type II restriction endonucleases, no methylation is detectable in the isolate. Also, these two genes do not methylate in ''E. coli'' strains, suggesting that they're vestigial defense systems.
-== Methylating ''E. coli'' ==
+== Methylating E. coli Strains ==
-add here
+Use a strain of ''E. coli'' that lacks dam, dcm, and hsdRMS, such as AG5589.
 == Culturing Conditions ==
-add here
+''S. azabuensis'' KH1P5 grows well in stock [[RCM]] at 37 °C. However, the inclusion of agar in commercially made RCM causes the strain to produce a thick, mucoidal layer of [[wikipedia:Extracellular_polymeric_substance|extracellular polymeric substance (EPS)]] that requires [[Sharpea azabuensis KH1P5#Protocols|removal via washing]] with chelating agents and detergent before work with the culture. Growing the organism in lab made RCM without agar eliminates the dense EPS layer.
 == Protocols ==
-add here
 == Transformation Results ==
-add here
+== External Links ==
-== External Links ==
+[5] Morita H, Shiratori C, Murakami M, Takami H, Toh H, Kato Y, Nakajima F, Takagi M, Akita H, Masaoka T, Hattori M. 2008. Sharpea azabuensis gen. nov., sp. nov., a Gram-positive, strictly anaerobic bacterium isolated from the faeces of thoroughbred horses. Int J Syst Evol Microbiol 58: 2682-2686 doi: 10.1099/ijs.0.65543-0.

Alexanderwg: Alexanderwg moved page Species template to Strain template: Misspelled title

2026-10-14T19:47:27Z

Alexanderwg moved page Species template to Strain template: Misspelled title

← Older revision		Revision as of 19:47, 14 October 2026
(No difference)