Salinimicrobium terrae (DSM 17865, CGMCC 1.6308, YIM-C338)

Name: Salinimicrobium terrae (DSM 17865, CGMCC 1.6308, YIM-C338)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5735

Type strain

Strain Designation YIM-C338

Culture col. no. DSM 17865 CGMCC 1.6308 YIM-C338

NCBI tax ID(s) 1123234 470866

Special Collections DSMZ Literature strains

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Salinimicrobium terrae YIM-C338 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from saline soil from the bank of Chaka salt lake.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404047

DSM 17865

@ref 20215

Last LPSN update 2025-12-16 09:48:08

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Salinimicrobium

Species Salinimicrobium terrae

Full scientific name Salinimicrobium terrae Chen et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32658	negative	02-04 µm	0.6-1 µm	rod-shaped
125439	negative				98.7
125438					92.979
125438	negative				99

Pigmentation

32658

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7147	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7147	positive	growth	28	mesophilic
32658	positive	growth	04-37
32658	positive	optimum	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
32658	positive	optimum	7
32658	positive	growth	06-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32658	aerobe
125439	obligate aerobe	90.1

Spore formation

@ref	Spore formation	Confidence
32658
125439		94.9
125438		91.833

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32658	NaCl	positive	growth	0.5-8 %
32658	NaCl	positive	optimum	01-03 %

Observation

32658

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32658	30089 ChEBI	acetate	+	carbon source
32658	40585 ChEBI	alpha-cyclodextrin	+	carbon source
32658	22599 ChEBI	arabinose	+	carbon source
32658	17057 ChEBI	cellobiose	+	carbon source
32658	16947 ChEBI	citrate	+	carbon source
32658	23652 ChEBI	dextrin	+	carbon source
32658	4853 ChEBI	esculin	+	hydrolysis
32658	15740 ChEBI	formate	+	carbon source
32658	28757 ChEBI	fructose	+	carbon source
32658	28260 ChEBI	galactose	+	carbon source
32658	24265 ChEBI	gluconate	+	carbon source
32658	17234 ChEBI	glucose	+	carbon source
32658	29987 ChEBI	glutamate	+	carbon source
32658	17754 ChEBI	glycerol	+	carbon source
32658	28087 ChEBI	glycogen	+	carbon source
32658	18403 ChEBI	L-arabitol	+	carbon source
32658	24996 ChEBI	lactate	+	carbon source
32658	25017 ChEBI	leucine	+	carbon source
32658	15792 ChEBI	malonate	+	carbon source
32658	17306 ChEBI	maltose	+	carbon source
32658	29864 ChEBI	mannitol	+	carbon source
32658	37684 ChEBI	mannose	+	carbon source
32658	51850 ChEBI	methyl pyruvate	+	carbon source
32658	17632 ChEBI	nitrate	+	reduction
32658	26271 ChEBI	proline	+	carbon source
32658	30031 ChEBI	succinate	+	carbon source
32658	17992 ChEBI	sucrose	+	carbon source
32658	26986 ChEBI	threonine	+	carbon source
32658	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32658	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7147	saline soil from the bank of Chaka salt lake	north-west China, Qinghai Province, Qaidam Basin	China	CHN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7147	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM42466v1 assembly for Salinimicrobium terrae DSM 17865	scaffold	GCA_000424665	1123234.4	2522125157	1123234	74.13

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7147	Salinimicrobium terrae strain YIM-C338 16S ribosomal RNA gene, partial sequence	EU135614	1467		470866

GC content

@ref	GC-content (mol%)	Method
7147	42.8	thermal denaturation, midpoint method (Tm)
32658	42.8
7147	40.4	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Salinimicrobium terrae DSM 17865
NCBI: GCA_000424665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.10	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	motility	BacteriaNetⓘ	no	76.00	no
125439	spore_formation	BacteriaNetⓘ	no	94.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Salinimicrobium terrae DSM 17865 DSM 17865
NCBI: GCA_000424665.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	94.99	yes
125438	aerobic	aerobicⓘ	yes	77.97	yes
125438	spore-forming	spore-formingⓘ	no	91.83	no
125438	thermophilic	thermophileⓘ	no	96.35	yes
125438	flagellated	motile2+ⓘ	no	92.98	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Computational host range prediction-The good, the bad, and the ugly.	Howell AA, Versoza CJ, Pfeifer SP.	Virus Evol	10.1093/ve/vead083	2024
	Two new 2-alkylquinolones, inhibitory to the fish skin ulcer pathogen Tenacibaculum maritimum, produced by a rhizobacterium of the genus Burkholderia sp.	Li D, Oku N, Hasada A, Shimizu M, Igarashi Y.	Beilstein J Org Chem	10.3762/bjoc.14.122	2018
	The Small RNA NcS25 Regulates Biological Amine-Transporting Outer Membrane Porin BCAL3473 in Burkholderia cenocepacia.	Sass AM, Coenye T.	mSphere	10.1128/msphere.00083-23	2023
	Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005.	Panschin I, Huang S, Meier-Kolthoff JP, Tindall BJ, Rohde M, Verbarg S, Lapidus A, Han J, Trong S, Haynes M, Reddy TB, Huntemann M, Pati A, Ivanova NN, Mavromatis K, Markowitz V, Woyke T, Goker M, Klenk HP, Kyrpides NC, Hahnke RL.	Stand Genomic Sci	10.1186/s40793-016-0163-9	2016
Genetics	Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features-Proposal for the Definition of a P. hospita Species Cluster.	Pratama AA, Jimenez DJ, Chen Q, Bunk B, Sproer C, Overmann J, van Elsas JD.	Genome Biol Evol	10.1093/gbe/evaa031	2020
Phylogeny	Ilyomonas limi gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from mud.	Chhetri G, Kim J, Kim H, Kim I, Kim MK, Seo T.	Antonie Van Leeuwenhoek	10.1007/s10482-019-01300-9	2019
Enzymology	Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp.	de Menezes CB, Afonso RS, de Souza WR, Parma M, de Melo IS, Zucchi TD, Fantinatti-Garboggini F.	Antonie Van Leeuwenhoek	10.1007/s10482-015-0632-y	2016
Phylogeny	Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam.	Soddell JA, Stainsby FM, Eales KL, Seviour RJ, Goodfellow M.	Int J Syst Evol Microbiol	10.1099/ijs.0.64034-0	2006
Phylogeny	Salinimicrobium sediminis sp. nov., isolated from a deep-sea sediment.	Subhash Y, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.058149-0	2013
Phylogeny	Salinimicrobium terrae sp. nov., isolated from saline soil, and emended description of the genus Salinimicrobium.	Chen YG, Cui XL, Zhang YQ, Li WJ, Wang YX, Kim CJ, Lim JM, Xu LH, Jiang CL	Int J Syst Evol Microbiol	10.1099/ijs.0.65860-0	2008
Phylogeny	Salinimicrobium sediminilitoris sp. nov., Isolated from a Tidal Flat.	Xia CQ, Niu HJ, Dong KS, Guan L, Sun LP, Wang Q, Zhang YJ, Li Y, Pei CX	Curr Microbiol	10.1007/s00284-022-03037-7	2022

References

#7147	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17865
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#32658	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28869 (see below)
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Salinimicrobium terrae (DSM 17865, CGMCC 1.6308, YIM-C338)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000424665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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