Selenomonas ruminantium HD4: Difference between revisions
Introduction and external links |
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[[File:Image1-9.png|thumb|350x350px|Scanning electron microscopic image of ''Selenomonas ruminantium'' HD4. | |||
<small>This photo belongs to the GMH Project and was taken by Kingsley Boateng.</small>]] | |||
== Introduction == | == Introduction == | ||
| Line 14: | Line 16: | ||
== Global Methane Hub Metadata == | == Global Methane Hub Metadata == | ||
{| class="wikitable" | |||
|Origin: | |||
|United States of America, Mackie lab | |||
|- | |||
|Sequenced by: | |||
|Add here | |||
|- | |||
|Assembled by: | |||
|William G. Alexander | |||
|- | |||
|Methylome called by: | |||
|William G. Alexander | |||
|- | |||
|Methyltransferases cloned by: | |||
|Jill Walton | |||
|- | |||
|MIC and Culturing Conditions by: | |||
|Makoto Adachi | |||
|- | |||
|Transformation by: | |||
| | |||
|} | |||
== Genome == | == Genome == | ||
[[File:8YPGLC 1 S.rum HD4 1 circos.png|center|thumb|300x300px|Circos plot of ''Selenomonas ruminantium'' HD4. Source: Makoto Adachi]] | |||
== DefenseFinder Results == | == DefenseFinder Results == | ||
== Methylome == | == Methylome == | ||
{| class="wikitable" | |||
|'''Motif''' | |||
|'''Percent methylated''' | |||
|- | |||
|GTC(6mA)NNNNNNNTGG | |||
| align="right" |87.64 | |||
|- | |||
|CC(6mA)NNNNNNNTGAC | |||
| align="right" |96.03 | |||
|- | |||
|AC(6mA)YNNNNNNTGAY | |||
| align="right" |97.49 | |||
|- | |||
|RA(6mA)CNNNNNNNTAYG | |||
| align="right" |95.97 | |||
|- | |||
|CRT(6mA)NNNNNNNGTTY | |||
| align="right" |89.93 | |||
|- | |||
|RTC(6mA)NNNNNNRTGT | |||
| align="right" |87.72 | |||
|- | |||
|TC(4mC)ATG | |||
| align="right" |70.48 | |||
|- | |||
|TC(4mC)AT | |||
| align="right" |58.71 | |||
|} | |||
== Methylating ''E. coli'' == | == Methylating ''E. coli'' == | ||
| Line 29: | Line 78: | ||
== Culturing Conditions == | == Culturing Conditions == | ||
''S. ruminantium'' HD4 grown well in [[M2GSC Medium|M2GSC]] and [[M10 Medium|M10]] medium at 37°C. Plating efficiency of ''S. ruminantium'' HD4 on M10 agar is close to 96%. | |||
== Antimicrobial MIC Tests == | == Antimicrobial MIC Tests == | ||
Note: Antimicrobial MIC was assessed using [[M2GSC Medium|M2GSC]] liquid medium. | |||
{| class="wikitable" | |||
|+ | |||
!'''Antibiotic''' | |||
!'''Concentration (µg/ml)''' | |||
|- | |||
|Ampicilin | |||
|10.39 | |||
|- | |||
|Chlorhamphenicol | |||
|0.98 | |||
|- | |||
|Erythromycin | |||
|40 | |||
|- | |||
|Gentamycin | |||
|40.4 | |||
|- | |||
|Kanamycin | |||
|72.13 | |||
|- | |||
|Streptomycin | |||
|Resistance > 200 | |||
|- | |||
|Tetracycline | |||
|1.78 | |||
|} | |||
== Protocols == | == Protocols == | ||
Latest revision as of 18:23, 30 October 2026
Introduction
Pseudoselenomonas ruminantium HD4
Pseudoselenomonas ruminantium HD4 was isolated from bovine rumen contents in the USA [1] and characterised along with other Selenomonas strains [2]. HD4 is an anaerobic bacterium that ferments a broad range of carbohydrates and produces primarily propionate, and acetate. Lactate is fermented [2] and HD4 can reduce nitrate, sulfate and fumarate.
The draft genome for HD4 (3,116,786 bp) was generated through the Hungate1000 project with JGI [3]. A 4.8 kb plasmid has been reported from HD4 [4] and a 4,899 bp plasmid was predicted from the draft genome sequence. Resequencing gave a genome of 3,180,636 bp consisting of a 2,987,729 bp chromosome and a 192,907 bp plasmid.
NCBI: Pseudoselenomonas ruminantium.
GTDB: Selenomonas_A ruminantium_D. HD4 belongs in a different species group than the type strain of P. ruminantium (GA192, DSM 2150).
Risk group: 1.
Global Methane Hub Metadata
| Origin: | United States of America, Mackie lab |
| Sequenced by: | Add here |
| Assembled by: | William G. Alexander |
| Methylome called by: | William G. Alexander |
| Methyltransferases cloned by: | Jill Walton |
| MIC and Culturing Conditions by: | Makoto Adachi |
| Transformation by: |
Genome
DefenseFinder Results
Methylome
| Motif | Percent methylated |
| GTC(6mA)NNNNNNNTGG | 87.64 |
| CC(6mA)NNNNNNNTGAC | 96.03 |
| AC(6mA)YNNNNNNTGAY | 97.49 |
| RA(6mA)CNNNNNNNTAYG | 95.97 |
| CRT(6mA)NNNNNNNGTTY | 89.93 |
| RTC(6mA)NNNNNNRTGT | 87.72 |
| TC(4mC)ATG | 70.48 |
| TC(4mC)AT | 58.71 |
Methylating E. coli
add here
Culturing Conditions
S. ruminantium HD4 grown well in M2GSC and M10 medium at 37°C. Plating efficiency of S. ruminantium HD4 on M10 agar is close to 96%.
Antimicrobial MIC Tests
Note: Antimicrobial MIC was assessed using M2GSC liquid medium.
| Antibiotic | Concentration (µg/ml) |
|---|---|
| Ampicilin | 10.39 |
| Chlorhamphenicol | 0.98 |
| Erythromycin | 40 |
| Gentamycin | 40.4 |
| Kanamycin | 72.13 |
| Streptomycin | Resistance > 200 |
| Tetracycline | 1.78 |
Protocols
add here
Transformation Results
add here
External Links
[1] Huhtanen C N, Gall LS. 1953. Rumen organisms I. Curved rods and a related rod type. J Bacteriol 65, 548-553. doi: 10.1128/jb.65.5.548-553.1953.
[2] Bryant MP. 1956. The characteristics of strains of Selenomonas isolated from bovine rumen contents. J Bacteriol 72: 162-7. doi: 10.1128/jb.72.2.162-167.1956.
[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.
[4] Martin SA, Dean RG. 1989. Characterization of a plasmid from the ruminal bacterium Selenomonas ruminantium. Appl Environ Microbiol 55: 3035–3038. doi: 10.1128/aem.55.12.3035-3038.1989.
