Name: Lacticigenium naphthae MIC1-18
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2287

Type strain:

Species: Lacticigenium naphthae

Strain Designation: MIC1-18

Culture col. no.: DSM 19658, NBRC 101988

Strain history: <- T. Iino, NBRC; MIC1-18

NCBI tax ID(s): 1122143 (strain), 515351 (species)

SI-ID 397742

DSM 19658

Section

Lacticigenium naphthae MIC1-18 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from spilled crude oil, oil-water well.

Gram-negative
motile
rod-shaped
anaerobe
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	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Carnobacteriaceae*
	Genus	*Lacticigenium*
	Species	**Lacticigenium naphthae**
	Full Scientific Name (LPSN)	Lacticigenium naphthae corrig. Iino et al. 2009

Synonym

Lacticigenium naphtae

Information on morphological and physiological properties Morphology

[Ref.: #28990]	Gram stain	negative
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #28990]	Cell length	2.15 µm

[Ref.: #28990]	Cell width	0.65 µm

[Ref.: #28990]	Cell shape	rod-shaped

[Ref.: #28990]	Motility	yes

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8236]

Culture medium

METHANOGENIUM MEDIUM (H2/CO2) (DSMZ Medium 141)

[Ref.: #8236]

Culture medium growth

[Ref.: #8236]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8236]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8236]	growth	30 °C
[Ref.: #28990]	growth	04-30 °C
[Ref.: #28990]	optimum	30 °C

[Ref.: #8236]	Temperature range	mesophilic
[Ref.: #28990]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28990]			optimum	7
[Ref.: #28990]			growth	6.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8236]	Oxygen tolerance	anaerobe
[Ref.: #28990]	Oxygen tolerance	facultative anaerobe

[Ref.: #28990]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.983

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28990]		NaCl		growth	<17	%
[Ref.: #28990]		NaCl		optimum	3	%

[Ref.: #8236]	Murein short key	A11.33
[Ref.: #8236]	Murein types	A4alpha L-Lys-D-Glu

[Ref.: #28990]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28990]	alanine ChEBI	+	carbon source
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	cellobiose ChEBI	+	carbon source
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #28990]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	glucose ChEBI	+	carbon source
[Ref.: #28990]	glutamate ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	ribose ChEBI	+	carbon source
[Ref.: #28990]	salicin ChEBI	+	carbon source
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #28990]	trehalose ChEBI	+	carbon source
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #8236]	14399	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #8236]	Sample type/isolated from	spilled crude oil, oil-water well
[Ref.: #8236]	Geographic location (country and/or sea, region)	Akita
[Ref.: #8236]	Country	Japan
[Ref.: #8236]	Country ISO 3 Code	JPN
[Ref.: #8236]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Oil reservoir
#Environmental	#Aquatic	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB430339 (>99% sequence identity) for Lacticigenium naphthae subclade from Microbeatlas

Aquatic Samples	949
Soil Samples	292
Animal Samples	3390
Plant Samples	207
Total Samples	4838

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

[Ref.: #8236]

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.: #8236]	Lacticigenium naphtae gene for 16S rRNA, partial sequence	AB430339	1446	ENA	515351 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lacticigenium naphthae DSM 19658	GCA_000425865	scaffold	GenBank	1122143 tax ID	*
[Ref.: #66792]	Lacticigenium naphtae DSM 19658	1122143.3	wgs	PATRIC	1122143 tax ID	*
[Ref.: #66792]	Lacticigenium naphtae DSM 19658	2524023191	draft	JGI IMG/M	1122143 tax ID	*

[Ref.: #8236]

GC-content

37.8 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: Lacticigenium napthae DSM 19658 DSM 19658 NCBI: GCA_000425865.1
[Ref.: #69481]	spore-forming	no	84	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lacticigenium napthae DSM 19658 DSM 19658 NCBI: GCA_000425865.1
[Ref.: #69480]	motile	yes	63.67	yes
[Ref.: #69480]	flagellated	no	88.791	no
[Ref.: #69480]	gram-positive	yes	89.386	no
[Ref.: #69480]	anaerobic	no	91.778	no
[Ref.: #69480]	aerobic	no	93.933	yes
[Ref.: #69480]	halophile	yes	93.191	yes
[Ref.: #69480]	spore-forming	no	91.933	yes
[Ref.: #69480]	thermophile	no	97.037	yes
[Ref.: #69480]	glucose-util	yes	88.753	yes
[Ref.: #69480]	glucose-ferment	yes	80.162	no

Availability in culture collections External links

[Ref.: #8236]

Culture collection no.

DSM 19658, NBRC 101988

[Ref.: #71845]

SI-ID 397742

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lacticigenium naphtae gen. nov., sp. nov., a halotolerant and motile lactic acid bacterium isolated from crude oil.	Iino T, Suzuki K, Harayama S	Int J Syst Evol Microbiol	10.1099/ijs.0.003293-0	2009	*

References

#8236

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19658

#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 )

#28990

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 #25423 (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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#68371

Automatically annotated from API 50CH acid .

#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 )

#71845

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-ID397742.1 )

#25423

IJSEM 775 2009 ( DOI 10.1099/ijs.0.003293-0 , PubMed 19329605 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Lacticigenium naphthae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Lacticigenium napthae DSM 19658 DSM 19658

Lacticigenium napthae DSM 19658 DSM 19658

Change proposal

Change proposal