Name: Labilibacter sediminis JCM 33138
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 164461

Type strain:

Species: Labilibacter sediminis

Culture col. no.: JCM 33138, MCCC 1K03739, CG 51

Strain history: Z.-J. Du; Shandong Univ. at Weihai, China; CG51.

NCBI tax ID(s): 2570926 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Labilibacter sediminis JCM 33138 is a facultative anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Marine sediment collected from a coastal area in Weihai.

colony-forming
Gram-negative
facultative anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Marinilabiliaceae*
	Genus	Labilibacter
	Species	Labilibacter sediminis
	Full Scientific Name (LPSN)	Labilibacter sediminis Wang et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #69672]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %97.4
[Ref.: #125438]	Gram stain	negative Confidence in %94.785

[Ref.: #69672]	Cell length	1.2-2 µm

[Ref.: #69672]	Cell width	0.3-0.6 µm

[Ref.: #69672]	Cell shape	rod-shaped

[Ref.: #69672]	Motility	yes

[Ref.: #69672]	Flagellum arrangement	gliding

[Ref.: #69672]	Colony size	0.5 mm
[Ref.: #69672]	Colony color	beige
[Ref.: #69672]	Colony shape	circular
[Ref.: #69672]	Incubation period	5 days
[Ref.: #69672]	Cultivation medium used	marine agar 2216

Information on culture and growth conditions Culture and growth conditions

[Ref.: #69672]

Culture medium

marine agar 2216

[Ref.: #69672]

Culture medium growth

		Temperature
[Ref.: #67770]	growth	30 °C
[Ref.: #69672]	growth	4-37 °C
[Ref.: #69672]	optimum	28-30 °C

	pH	Kind of pH		pH
[Ref.: #69672]			optimum	7-7.5
[Ref.: #69672]			growth	6-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69672]

Oxygen tolerance

facultative anaerobe

[Ref.: #125439]

Ability of spore formation

no Confidence in %95.3

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #69672]		NaCl		growth	1-6	%(w/v)
[Ref.: #69672]		NaCl		optimum	2-3	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #69672]	(-)-quinic acid ChEBI	+	carbon source
[Ref.: #69672]	(-)-quinic acid ChEBI	+	energy source
[Ref.: #69672]	2-oxobutanoate ChEBI	+	carbon source
[Ref.: #69672]	2-oxobutanoate ChEBI	+	energy source
[Ref.: #69672]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #69672]	2-oxoglutarate ChEBI	+	energy source
[Ref.: #69672]	4-hydroxyphenylacetic acid ChEBI	+	carbon source
[Ref.: #69672]	4-hydroxyphenylacetic acid ChEBI	+	energy source
[Ref.: #69672]	agar ChEBI	+	hydrolysis
[Ref.: #69672]	alginate ChEBI	+	hydrolysis
[Ref.: #69672]	amygdalin ChEBI	+	builds acid from
[Ref.: #69672]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #69672]	casein	-	hydrolysis
[Ref.: #69672]	cellobiose ChEBI	+	builds acid from
[Ref.: #69672]	cellobiose ChEBI	+	carbon source
[Ref.: #69672]	cellobiose ChEBI	+	energy source
[Ref.: #69672]	citrate ChEBI	-	assimilation
[Ref.: #69672]	D-aspartate ChEBI	+	carbon source
[Ref.: #69672]	D-aspartate ChEBI	+	energy source
[Ref.: #69672]	D-galactose ChEBI	+	builds acid from
[Ref.: #69672]	D-gluconate ChEBI	+	carbon source
[Ref.: #69672]	D-gluconate ChEBI	+	energy source
[Ref.: #69672]	D-glucose ChEBI	+	builds acid from
[Ref.: #69672]	D-mannose ChEBI	+	builds acid from
[Ref.: #69672]	D-serine ChEBI	+	carbon source
[Ref.: #69672]	D-serine ChEBI	+	energy source
[Ref.: #69672]	D-sorbitol ChEBI	+	carbon source
[Ref.: #69672]	D-sorbitol ChEBI	+	energy source
[Ref.: #69672]	esculin ChEBI	+	builds acid from
[Ref.: #69672]	gelatin ChEBI	+	carbon source
[Ref.: #69672]	gelatin ChEBI	+	energy source
[Ref.: #69672]	gelatin ChEBI	+	hydrolysis
[Ref.: #69672]	gentiobiose ChEBI	+	builds acid from
[Ref.: #69672]	gentiobiose ChEBI	+	carbon source
[Ref.: #69672]	gentiobiose ChEBI	+	energy source
[Ref.: #69672]	glucuronamide ChEBI	+	carbon source
[Ref.: #69672]	glucuronamide ChEBI	+	energy source
[Ref.: #69672]	glycogen ChEBI	+	builds acid from
[Ref.: #69672]	L-alanine ChEBI	+	carbon source
[Ref.: #69672]	L-alanine ChEBI	+	energy source
[Ref.: #69672]	L-rhamnose ChEBI	+	carbon source
[Ref.: #69672]	L-rhamnose ChEBI	+	energy source
[Ref.: #69672]	L-serine ChEBI	+	carbon source
[Ref.: #69672]	L-serine ChEBI	+	energy source
[Ref.: #69672]	lactose ChEBI	+	builds acid from
[Ref.: #69672]	maltose ChEBI	+	builds acid from
[Ref.: #69672]	myo-inositol ChEBI	+	carbon source
[Ref.: #69672]	myo-inositol ChEBI	+	energy source
[Ref.: #69672]	nitrate ChEBI	+	reduction
[Ref.: #69672]	raffinose ChEBI	+	carbon source
[Ref.: #69672]	raffinose ChEBI	+	energy source
[Ref.: #69672]	stachyose ChEBI	+	carbon source
[Ref.: #69672]	stachyose ChEBI	+	energy source
[Ref.: #69672]	starch ChEBI	+	builds acid from
[Ref.: #69672]	starch ChEBI	+	hydrolysis
[Ref.: #69672]	sucrose ChEBI	+	builds acid from
[Ref.: #69672]	sucrose ChEBI	+	carbon source
[Ref.: #69672]	sucrose ChEBI	+	energy source
[Ref.: #69672]	turanose ChEBI	+	carbon source
[Ref.: #69672]	turanose ChEBI	+	energy source
[Ref.: #69672]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #69672]	amoxicillin ChEBI	yes	25	µg (disc)
[Ref.: #69672]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #69672]	ceftriaxone ChEBI				yes	30	µg (disc)
[Ref.: #69672]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #69672]	ciprofloxacin ChEBI	yes	10	µg (disc)
[Ref.: #69672]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #69672]	florfenicol ChEBI	yes	30	µg (disc)
[Ref.: #69672]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #69672]	norfloxacin ChEBI	yes	10	µg (disc)
[Ref.: #69672]	oxytetracycline ChEBI				yes	10	µg (disc)
[Ref.: #69672]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #69672]	sulfamethoxypyrazine ChEBI				yes	25	µg (disc)
[Ref.: #69672]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #69672]	vancomycin ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #69672]	acetoin ChEBI	no
[Ref.: #69672]	hydrogen sulfide ChEBI	no
[Ref.: #69672]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #69672]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #69672]	acid phosphatase	+	3.1.3.2
[Ref.: #69672]	alkaline phosphatase	+	3.1.3.1
[Ref.: #69672]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #69672]	alpha-galactosidase	+	3.2.1.22
[Ref.: #69672]	alpha-glucosidase	-	3.2.1.20
[Ref.: #69672]	alpha-mannosidase	-	3.2.1.24
[Ref.: #69672]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #69672]	beta-galactosidase	-	3.2.1.23
[Ref.: #69672]	beta-glucosidase	-	3.2.1.21
[Ref.: #69672]	beta-glucuronidase	-	3.2.1.31
[Ref.: #69672]	catalase	-	1.11.1.6
[Ref.: #69672]	cystine arylamidase	-	3.4.11.3
[Ref.: #69672]	cytochrome oxidase	+	1.9.3.1
[Ref.: #69672]	esterase (C 4)	+
[Ref.: #69672]	esterase Lipase (C 8)	+
[Ref.: #69672]	leucine arylamidase	-	3.4.11.1
[Ref.: #69672]	lipase (C 14)	+
[Ref.: #69672]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #69672]	naphthol-AS-BI-phosphohydrolase	-
[Ref.: #69672]	trypsin	-	3.4.21.4
[Ref.: #69672]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #69672]

Fatty acid	Percentage
iso-C15:0	25.6
anteiso-C15:0	16.9
iso-C14:0	10.6
iso-C16:0 3OH	9.4
iso-C15:0 3OH	5.6
iso-C16:0	4.6
C15:1 w6c	4.1
iso-C17:0 3OH	3.5
C15:0 3OH	3.3
C16:0	1.4
C17:0 2OH	1.3
C14:0	1.2
C16:0 3OH	1
C17:0	0.9
C15:0 2OH	0.9
C11:0 2OH	0.8
iso-C16:1 h	0.8
iso-C17:0	0.7
iso-C15:1 H / C13:0 3OH	0.7
C17:0 3OH	0.7
C18:0	0.6
C17:1 w6c	0.6
C16:1 w5c	0.6

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

[Ref.: #67770]	Sample type/isolated from	Marine sediment collected from a coastal area in Weihai
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia

[Ref.: #69672]	Sample type/isolated from	marine sediment
[Ref.: #69672]	Sampling date	2018-08-01
[Ref.: #69672]	Geographic location (country and/or sea, region)	Weihai
[Ref.: #69672]	Country	China
[Ref.: #69672]	Country ISO 3 Code	CHN
[Ref.: #69672]	Continent	Asia
[Ref.: #69672]	Geographic location	36.6000°/121.7000°
[Ref.: #69672]	Enrichment culture	marine agar 2216
* marker position based on {}

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.: #67770]	Labilibacter sediminis 16S ribosomal RNA gene, partial sequence	MK975475	1510	GenBank ENA	2570926 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Labilibacter sediminis CG51	GCA_005877885	scaffold	GenBank ENA	2570926 tax ID
[Ref.: #69672]	Whole genome shotgun	VCHY00000000		GenBank ENA	2570926 tax ID

[Ref.: #67770]

GC-content

35.9 mol%

genome sequence analysis

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Labilibacter sediminis CG51 NCBI: GCA_005877885.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	94.785	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	75.137	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	66.141	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	86.518	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	91.643	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	81.455	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Labilibacter sediminis CG51 NCBI: GCA_005877885
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	95.3
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	70.9
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	76.8

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 33138, MCCC 1K03739, CG 51

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Labilibacter sediminis sp. nov., isolated from marine sediment.	Wang FQ, Chen ZJ, Yang JM, Wang WJ, Feng YW, Li Z, Sun GH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003758	2020	*

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69672

Feng-Qing Wang, Zhu-Jie Chen, Jian-Min Yang, Wei-Jun Wang, Yan-Wei Feng, Zan Li, Guo-Hua Sun: Labilibacter sediminis sp. nov., isolated from marine sediment. IJSEM 70: 321 - 326 2020 ( DOI 10.1099/ijsem.0.003758 )

#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 .

* These data were automatically processed and therefore are not curated

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Labilibacter sediminis CG51

Labilibacter sediminis CG51

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