Name: Serpentinicella alkaliphila 3b
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132680

Type strain:

Species: Serpentinicella alkaliphila

Strain Designation: 3b

Culture col. no.: DSM 100013, JCM 30645

Strain history: M. Quemeneur; Mediterr. Inst. of Oceanogr., France; 3b.

NCBI tax ID(s): 1734049 (species)

SI-ID 406320

DSM 100013

Special Collections

Section

Serpentinicella alkaliphila 3b is an obligate anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from hyperalkaline spring in a serpentinite-hosted hydrothermal field, carbonate chimney.

colony-forming
Gram-positive
motile
rod-shaped
spore-forming
obligate anaerobe
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	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Serpentinicella*
	Species	**Serpentinicella alkaliphila**
	Full Scientific Name (LPSN)	Serpentinicella alkaliphila Mei et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25025]	Gram stain	positive

[Ref.: #25025]	Cell length	1.0-10.0 µm

[Ref.: #25025]	Cell width	0.4-0.6 µm

[Ref.: #25025]	Cell shape	rod-shaped

[Ref.: #25025]	Motility	yes

[Ref.: #25025]	Colony size	1.0-2.0 mm
[Ref.: #25025]	Colony color	yellow
[Ref.: #25025]	Colony shape	circular
[Ref.: #25025]	Incubation period	7 days
[Ref.: #25025]	Cultivation medium used	BYG medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25025]

Culture medium

BYG medium

[Ref.: #25025]

Culture medium growth

[Ref.: #24469]

Culture medium

SERPENTINICELLA MEDIUM (DSMZ Medium 898b)

[Ref.: #24469]

Culture medium growth

[Ref.: #24469]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24469]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24469]	growth	37 °C
[Ref.: #25025]	growth	30-43 °C
[Ref.: #25025]	optimum	37 °C
[Ref.: #67770]	growth	35 °C

	pH	Kind of pH		pH
[Ref.: #25025]			optimum	9.5
[Ref.: #25025]			growth	7.8-10.1

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25025]

Oxygen tolerance

obligate anaerobe

[Ref.: #25025]	Spore description	terminal without swollen sporangia, 0.5–0.7 µm in diameter
[Ref.: #25025]	Type of spore	spore
[Ref.: #25025]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25025]		NaCl		growth	0-4.0	%(w/v)
[Ref.: #25025]		NaCl		optimum	0-0.2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25025]	acetoacetate ChEBI	-	electron donor
[Ref.: #25025]	arabinose ChEBI	-	electron donor
[Ref.: #25025]	arsenate ChEBI	-	electron acceptor
[Ref.: #25025]	casamino acids	-	electron donor
[Ref.: #25025]	cellobiose ChEBI	-	electron donor
[Ref.: #25025]	chromate ChEBI	-	electron acceptor
[Ref.: #25025]	crotonate ChEBI	+	electron donor
[Ref.: #25025]	dimethyl sulfoxide ChEBI	-	electron acceptor
[Ref.: #25025]	elemental sulfur ChEBI	-	electron acceptor
[Ref.: #25025]	ethanol ChEBI	-	electron donor
[Ref.: #25025]	ethylenediaminetetraacetatoferrate ChEBI	-	electron acceptor
[Ref.: #25025]	ferric citrate ChEBI	-	electron acceptor
[Ref.: #25025]	ferric iron ChEBI	-	electron acceptor
[Ref.: #25025]	formate ChEBI	-	electron donor
[Ref.: #25025]	fructose ChEBI	-	electron donor
[Ref.: #25025]	fumarate ChEBI	-	electron donor
[Ref.: #25025]	fumarate ChEBI	+	electron acceptor
[Ref.: #25025]	galactose ChEBI	-	electron donor
[Ref.: #25025]	glucose ChEBI	-	electron donor
[Ref.: #25025]	glycerol ChEBI	-	electron donor
[Ref.: #25025]	iron trichloride ChEBI	-	electron acceptor
[Ref.: #25025]	lactate ChEBI	+	electron donor
[Ref.: #25025]	lactose ChEBI	-	electron donor
[Ref.: #25025]	maltose ChEBI	-	electron donor
[Ref.: #25025]	mannose ChEBI	-	electron donor
[Ref.: #25025]	nitrate ChEBI	-	electron acceptor
[Ref.: #25025]	nitrite ChEBI	-	electron acceptor
[Ref.: #25025]	peptone	-	electron donor
[Ref.: #25025]	pyruvate ChEBI	+	electron donor
[Ref.: #25025]	raffinose ChEBI	-	electron donor
[Ref.: #25025]	rhamnose ChEBI	-	electron donor
[Ref.: #25025]	ribose ChEBI	-	electron donor
[Ref.: #25025]	selenite ChEBI	-	electron acceptor
[Ref.: #25025]	sodium chloride ChEBI	-	required for growth
[Ref.: #25025]	sucrose ChEBI	-	electron donor
[Ref.: #25025]	sulfate ChEBI	-	electron acceptor
[Ref.: #25025]	sulfite ChEBI	-	electron acceptor
[Ref.: #25025]	thiosulfate ChEBI	-	electron acceptor
[Ref.: #25025]	xylose ChEBI	-	electron donor
[Ref.: #25025]	yeast extract	+	required for growth
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	phenylalanine metabolism	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	non-pathway related	47.37	18 of 38
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	flavin biosynthesis	40	6 of 15
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #24469]	Sample type/isolated from	hyperalkaline spring in a serpentinite-hosted hydrothermal field, carbonate chimney
[Ref.: #24469]	Geographic location (country and/or sea, region)	New Caledonia, Prony Bay, Rivière des Kaoris
[Ref.: #24469]	Country	France
[Ref.: #24469]	Country ISO 3 Code	FRA
[Ref.: #24469]	Continent	Europe
[Ref.: #24469]	Geographic location	-22.2995°/166.8620°

[Ref.: #67770]	Sample type/isolated from	Carbonaceous hydrothermal chimney in Prony Bay
[Ref.: #67770]	Geographic location (country and/or sea, region)	New Caledonia
[Ref.: #67770]	Country	French Overseas
[Ref.: #67770]	Country ISO 3 Code	FRA
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Thermal spring
#Condition	#Alkaline	-
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KR349722 (>99% sequence identity) for Serpentinicella alkaliphila subclade from Microbeatlas

Aquatic Samples	55
Soil Samples	9
Animal Samples	2
Plant Samples	4
Total Samples	70

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

[Ref.: #24469]

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.: #24469]	Serpentinicella alkaliphila strain 3b 16S ribosomal RNA gene, partial sequence	KR349722	1417	GenBank ENA	1734049 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Serpentinicella alkaliphila DSM 100013	GCA_004345905	scaffold	GenBank ENA	1734049 tax ID
[Ref.: #66792]	Serpentinicella alkaliphila 3B	GCA_018141405	chromosome	GenBank ENA	1734049 tax ID	*
[Ref.: #66792]	Serpentinicella alkaliphila strain DSM 100013	1734049.3	wgs	PATRIC	1734049 tax ID	*
[Ref.: #66792]	Serpentinicella alkaliphila DSM 100013	2795386145	draft	JGI IMG/M	1734049 tax ID	*

[Ref.: #24469]

GC-content

33.2 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Serpentinicella alkaliphila strain DSM 100013 PATRIC: 1734049.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Serpentinicella alkaliphila 3B NCBI: GCA_018141405.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	63.824	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	85.085	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	96.782	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	76.87	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	76.953	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	78.142	no

Availability in culture collections External links

[Ref.: #24469]

Culture collection no.

DSM 100013, JCM 30645

[Ref.: #90988]

SI-ID 406320

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia.	Mei N, Postec A, Erauso G, Joseph M, Pelletier B, Payri C, Ollivier B, Quemeneur M	Int J Syst Evol Microbiol	10.1099/ijsem.0.001375	2016	*

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 )

#24469

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100013

#25025

N. P. Mei, A.,Erauso, G.,Joseph, M.,Pelletier, B.,Payri, C.,Ollivier, B.,Quéméneur, M.: Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia. IJSEM 66: 4464 - 4470 2016 ( DOI 10.1099/ijsem.0.001375 , PubMed 27499124 )

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

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

#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 )

#90988

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-ID406320.1 )

* 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 Serpentinicella alkaliphila in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Serpentinicella alkaliphila strain DSM 100013

Serpentinicella alkaliphila 3B

Change proposal

Change proposal