Archive BacDiveID:10.13145/bacdive6963.20230509.8.1

Strain identifier

BacDive ID: 6963

Type strain:

Species: Methanobrevibacter smithii

Strain Designation: PS

Strain history: DSM 861 <-- M. P. Bryant <-- P. H. Smith strain PS.

NCBI tax ID(s): 420247 (strain), 2173 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 464

BacDive-ID: 6963

DSM-Number: 861

keywords: genome sequence, 16S sequence, Archaea, anaerobe, mesophilic, Gram-negative

description: Methanobrevibacter smithii PS is an anaerobe, mesophilic, Gram-negative archaeon that was isolated from primary sewage digester.

NCBI tax id

NCBI tax id	Matching level
2173	species
420247	strain

strain history

@ref	history
464	<- M. P. Bryant, University of Illinois, Departments of Dairy Science and Microbiology, Urbana, USA; PS <- P. H. Smith, University of California, Davis (Methanobacterium ruminantium) {1964}
67770	DSM 861 <-- M. P. Bryant <-- P. H. Smith strain PS.

doi: 10.13145/bacdive6963.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/archaea
keyword: phylum/methanobacteriota
domain: Archaea
phylum: Methanobacteriota
class: Methanobacteria
order: Methanobacteriales
family: Methanobacteriaceae
genus: Methanobrevibacter
species: Methanobrevibacter smithii
full scientific name: Methanobrevibacter smithii Balch and Wolfe 1981

@ref: 464

domain: Archaea

phylum: Euryarchaeota

class: Methanobacteria

order: Methanobacteriales

family: Methanobacteriaceae

genus: Methanobrevibacter

species: Methanobrevibacter smithii

full scientific name: Methanobrevibacter smithii Balch and Wolfe 1981

strain designation: PS

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.89

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
464	MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523)	yes	https://mediadive.dsmz.de/medium/1523	Name: MODIFIED METHANOBACTERIUM MEDIUM (DSMZ Medium 1523) Composition: Brain heart infusion 5.98802 g/l Proteose peptone 5.98802 g/l NaHCO3 3.99202 g/l Yeast extract 1.99601 g/l Na-formate 1.99601 g/l Na-acetate 0.998004 g/l Na2S x 9 H2O 0.499002 g/l KH2PO4 0.499002 g/l L-Cysteine HCl x H2O 0.499002 g/l MgSO4 x 7 H2O 0.399202 g/l NH4Cl 0.399202 g/l NaCl 0.399202 g/l CaCl2 x 2 H2O 0.0499002 g/l HCl 0.00249501 g/l FeCl2 x 4 H2O 0.00149701 g/l Sodium resazurin 0.000499002 g/l Pyridoxine hydrochloride 0.000299401 g/l Thiamine-HCl x 2 H2O 0.000199601 g/l Nicotinic acid 0.000199601 g/l CoCl2 x 6 H2O 0.000189621 g/l Calcium pantothenate 9.98004e-05 g/l Vitamin B12 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l p-Aminobenzoic acid 7.98403e-05 g/l ZnCl2 6.98603e-05 g/l Na2MoO4 x 2 H2O 3.59281e-05 g/l NiCl2 x 6 H2O 2.39521e-05 g/l D-(+)-biotin 1.99601e-05 g/l H3BO3 5.98802e-06 g/l CuCl2 x 2 H2O 1.99601e-06 g/l Distilled water
464	METHANOBACTERIUM MEDIUM (DSMZ Medium 119)	yes	https://mediadive.dsmz.de/medium/119	Name: METHANOBACTERIUM MEDIUM (DSMZ Medium 119) Composition: NaHCO3 3.98804 g/l Na-formate 1.99402 g/l Na-acetate 0.997009 g/l Na2S x 9 H2O 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l KH2PO4 0.498504 g/l NH4Cl 0.398804 g/l NaCl 0.398804 g/l MgSO4 x 7 H2O 0.398804 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.0498504 g/l HCl 0.00249252 g/l FeSO4 x 7 H2O 0.00199402 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Isobutyric acid DL-2-Methylbutyric acid Valeric acid Isovaleric acid H2SO4 Sludge Distilled water

culture temp

@ref	growth	type	temperature	range
464	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
464	anaerobe
69480	anaerobe	99.047

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.891

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
464	primary sewage digester	Florida, Gainesville	USA	USA	North America
67770	Primary sewage digester	Gainesville, FL	USA	USA	North America

isolation source categories

Cat1: #Engineered
Cat2: #Waste
Cat3: #Wastewater

Safety information

risk assessment

@ref: 464
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20218
description: Methanobrevibacter smithii ATCC 35061 strain PS 16S ribosomal RNA gene, partial sequence
accession: JQ346750
length: 1268
database: ena
NCBI tax ID: 420247

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methanobrevibacter smithii ATCC 35061 ATCC 35061; PS; DSMZ 861	GCA_000016525	complete	ncbi	420247
66792	Methanobrevibacter smithii PS, ATCC 35061	640427121	complete	img	420247
66792	Methanobrevibacter smithii ATCC 35061	420247.28	complete	patric	420247
66792	Methanobrevibacter smithii ATCC 35061 DSM 861	GCA_028743435	complete	ncbi	420247

GC content

@ref: 464
GC-content: 31.0

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	91.61	no
flagellated	no	96.13	no
gram-positive	no	94.364	no
anaerobic	yes	98.975	no
halophile	no	76.251	no
spore-forming	no	95.973	no
thermophile	no	94.216	yes
glucose-util	yes	65.152	no
aerobic	no	95.902	yes
glucose-ferment	no	58.11	no

External links

@ref: 464

culture collection no.: DSM 861, ATCC 35061, JCM 30028, OCM 144

straininfo link

@ref: 76425
straininfo: 40847

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Pathogenicity	11306786	Isolation and antimicrobial susceptibility testing of fecal strains of the archaeon Methanobrevibacter smithii.	Dermoumi HL, Ansorg RA	Chemotherapy	10.1159/000063219	2001	Anti-Bacterial Agents/pharmacology, Drug Resistance, Microbial, Feces/microbiology, Humans, Methanobacteriaceae/drug effects/isolation & purification/physiology, Metronidazole/pharmacology, Microbial Sensitivity Tests, Reference Values	Phylogeny
Metabolism	19759898	High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol.	Dridi B, Henry M, El Khechine A, Raoult D, Drancourt M	PLoS One	10.1371/journal.pone.0007063	2009	Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, DNA, Archaeal/analysis, Feces, Female, Gene Expression Regulation, Bacterial, Humans, Infant, Infant, Newborn, Infections/epidemiology/microbiology, Intestines/microbiology, Male, Methanobacteriaceae/metabolism, Methanobrevibacter/metabolism, Microbiological Techniques, Middle Aged, RNA, Ribosomal, 16S/metabolism, Reverse Transcriptase Polymerase Chain Reaction/*methods	Pathogenicity
Enzymology	21848695	Relationship between rumen methanogens and methane production in dairy cows fed diets supplemented with a feed enzyme additive.	Zhou M, Chung YH, Beauchemin KA, Holtshausen L, Oba M, McAllister TA, Guan LL	J Appl Microbiol	10.1111/j.1365-2672.2011.05126.x	2011	Animals, Cattle/microbiology, DNA, Bacterial/genetics, Denaturing Gradient Gel Electrophoresis, Diet/veterinary, Dietary Supplements, Enzymes/administration & dosage, Female, Gene Dosage, Lactation, Methane/biosynthesis, Methanobrevibacter/genetics/growth & development/isolation & purification, RNA, Ribosomal, 16S/genetics, Rumen/microbiology, Sequence Analysis, DNA	Phylogeny
Genetics	29449383	Complete Genome Sequence of Methanobrevibacter smithii Strain KB11, Isolated from a Korean Fecal Sample.	Kim BC, Jeong H	Genome Announc	10.1128/genomeA.00038-18	2018		Phylogeny
Cultivation	35699469	Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative.	Low A, Lee JKY, Gounot JS, Ravikrishnan A, Ding Y, Saw WY, Tan LWL, Moong DKN, Teo YY, Nagarajan N, Seedorf H	Microbiol Spectr	10.1128/spectrum.00849-22	2022

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
464	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 861)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-861
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
76425	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID40847.1	StrainInfo: A central database for resolving microbial strain identifiers