Selenomonas ruminantium HD4

Scanning electron microscopic image of Selenomonas ruminantium HD4. This photo belongs to the GMH Project and was taken by Kingsley Boateng.

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, Macike 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

Circos plot of Selenomonas ruminantium HD4. Source: Makoto Adachi

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

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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

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Transformation Results

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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.