Name: Fodinibius sediminis DSM 21194
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24788

Type strain:

Species: Fodinibius sediminis

Culture col. no.: DSM 21194, ACCC 10714, YIM J21

Strain history: <- X.-L. Cui, YIM <- J.-H. Liu; YIM J21

NCBI tax ID(s): 1214077 (species)

SI-ID 406851

DSM 21194

Section

Fodinibius sediminis DSM 21194 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment from a salt mine.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Balneolota*
	Class	*Balneolia*
	Order	*Balneolales*
	Family	*Balneolaceae*
	Genus	*Fodinibius*
	Species	**Fodinibius sediminis**
	Full Scientific Name (LPSN)	Fodinibius sediminis (Wang et al. 2013) Galisteo et al. 2023

Synonym

Aliifodinibius sediminis

Information on morphological and physiological properties Morphology

[Ref.: #30765]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.996

[Ref.: #30765]	Cell length	0.55 µm

[Ref.: #30765]	Cell width	0.3 µm

[Ref.: #30765]	Cell shape	rod-shaped

[Ref.: #30765]	Motility	no

[Ref.: #30765]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21260]

Culture medium

MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)

[Ref.: #21260]

Culture medium growth

[Ref.: #21260]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21260]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21260]	growth	28 °C
[Ref.: #30765]	growth	25-45 °C
[Ref.: #30765]	optimum	28 °C

[Ref.: #21260]	Temperature range	mesophilic
[Ref.: #30765]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30765]			optimum	7
[Ref.: #30765]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30765]

Oxygen tolerance

aerobe

[Ref.: #30765]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30765]		NaCl		growth	04-16	%
[Ref.: #30765]		NaCl		optimum	8	%

[Ref.: #30765]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30765]	acetate ChEBI	+	carbon source
[Ref.: #30765]	aspartate ChEBI	+	carbon source
[Ref.: #30765]	esculin ChEBI	+	hydrolysis
[Ref.: #30765]	galactose ChEBI	+	carbon source
[Ref.: #30765]	glucose ChEBI	+	carbon source
[Ref.: #30765]	glycerol ChEBI	+	carbon source
[Ref.: #30765]	maltose ChEBI	+	carbon source
[Ref.: #30765]	mannose ChEBI	+	carbon source
[Ref.: #30765]	sorbitol ChEBI	+	carbon source
[Ref.: #30765]	sucrose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #30765]	acid phosphatase	+	3.1.3.2
[Ref.: #30765]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30765]	alpha-galactosidase	+	3.2.1.22
[Ref.: #30765]	catalase	+	1.11.1.6
[Ref.: #30765]	cytochrome oxidase	+	1.9.3.1
[Ref.: #30765]	gelatinase	+
[Ref.: #30765]	urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #21260]	Sample type/isolated from	sediment from a salt mine
[Ref.: #21260]	Geographic location (country and/or sea, region)	Yunnan, Mengye salt mine (22° 71' N 101° 63' E)
[Ref.: #21260]	Country	China
[Ref.: #21260]	Country ISO 3 Code	CHN
[Ref.: #21260]	Continent	Asia
[Ref.: #21260]	Geographic location	23.1833°/102.0500°
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Condition	#Saline	-
#Environmental	#Terrestrial	#Sediment
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ923476 (>99% sequence identity) for Aliifodinibius sediminis from Microbeatlas

Aquatic Samples	3
Soil Samples	10
Animal Samples
Plant Samples
Total Samples	13

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #21260]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #21260]	Aliifodinibius sediminis strain YIM J21 16S ribosomal RNA gene, partial sequence	JQ923476	1421	ENA	1214077 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Fodinibius sediminis DSM 21194	GCA_900182555	scaffold	GenBank	1214077 tax ID	*
[Ref.: #66792]	Aliifodinibius sediminis strain DSM 21194	1214077.3	wgs	PATRIC	1214077 tax ID	*
[Ref.: #66792]	Aliifodinibius sediminis DSM 21194	2724679783	draft	JGI IMG/M	1214077 tax ID	*

[Ref.: #21260]	GC-content	48.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30765]	GC-content	48.4 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Aliifodinibius sediminis DSM 21194 NCBI: GCA_900182555.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Aliifodinibius sediminis DSM 21194 NCBI: GCA_900182555.1
[Ref.: #69480]	motile	no	63.611	no
[Ref.: #69480]	flagellated	no	93.868	yes
[Ref.: #69480]	gram-positive	no	97.451	yes
[Ref.: #69480]	anaerobic	no	98.687	no
[Ref.: #69480]	aerobic	yes	87.942	yes
[Ref.: #69480]	halophile	yes	68.237	no
[Ref.: #69480]	spore-forming	no	92.734	yes
[Ref.: #69480]	thermophile	no	87.706	yes
[Ref.: #69480]	glucose-util	yes	88.759	no
[Ref.: #69480]	glucose-ferment	no	74.92	no

Availability in culture collections External links

[Ref.: #21260]

Culture collection no.

DSM 21194, ACCC 10714, YIM J21

[Ref.: #88612]

SI-ID 406851

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Aliifodinibius salipaludis sp. nov., Isolated from Saline-Alkaline Soil.	Zhao X, Miao S, Sun Y, Gong Q, Zhao J, Wang J, Zhang G	Curr Microbiol	10.1007/s00284-019-01863-w	2020	*
Phylogeny	Aliifodinibius halophilus sp. nov., a moderately halophilic member of the genus Aliifodinibius, and proposal of Balneolaceae fam. nov.	Xia J, Ling SK, Wang XQ, Chen GJ, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001012	2016	*
Phylogeny	Aliifodinibius roseus gen. nov., sp. nov., and Aliifodinibius sediminis sp. nov., two moderately halophilic bacteria isolated from salt mine samples.	Wang YX, Liu JH, Xiao W, Ma XL, Lai YH, Li ZY, Ji KY, Wen ML, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.043869-0	2013	*

References

#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 )

#21260

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21194

#30765

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 #27096 (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) .

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#88612

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID406851.1 )

#27096

IJSEM 2907 2013 ( DOI 10.1099/ijs.0.043869-0 , PubMed 23334882 )

* These data were automatically processed and therefore are not curated

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Aliifodinibius sediminis DSM 21194

Aliifodinibius sediminis DSM 21194

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