Halalkalibacter nanhaiisediminis (DSM 27953, CGMCC 1.10116, JCM 16507)

Name: Halalkalibacter nanhaiisediminis (DSM 27953, CGMCC 1.10116, JCM 16507)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23707

Type strain

Strain Designation NH3

Culture col. no. DSM 27953 CGMCC 1.10116 JCM 16507 NH3

NCBI tax ID(s) 688079

Special Collections DSMZ JCM Literature strains

History <- JCM <- J. Zhang; NH3 J. Zhang NH3.

Links

Halalkalibacter nanhaiisediminis NH3 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from sediment.

spore-forming Gram-positive motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 401112

JCM 16507,DSM 27953

@ref 20215

Last LPSN update 2026-02-09 11:23:47

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Halalkalibacter

Species Halalkalibacter nanhaiisediminis

Full scientific name Halalkalibacter nanhaiisediminis (Zhang et al. 2011) Joshi et al. 2022

Synonyms (2)

Alkalihalobacillus nanhaiisediminis
Bacillus nanhaiisediminis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
29877	positive	1.9 µm	0.6 µm	rod-shaped

Pigmentation

29877

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20435	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20435	positive	growth	30	mesophilic
29877	positive	growth	10-43
29877	positive	optimum	37	mesophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29877	positive	optimum	9
29877	positive	growth	6.5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29877	aerobe
125439	facultative anaerobe	90.2

Spore formation

29877

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29877	NaCl	positive	growth	0-11 %

Observation

@ref	Observation
29877	aggregates in clumps
67770	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29877	30089 ChEBI	acetate	+	carbon source
29877	22599 ChEBI	arabinose	+	carbon source
29877	17057 ChEBI	cellobiose	+	carbon source
29877	28260 ChEBI	galactose	+	carbon source
29877	5417 ChEBI	glucosamine	+	carbon source
29877	17234 ChEBI	glucose	+	carbon source
29877	17754 ChEBI	glycerol	+	carbon source
29877	17306 ChEBI	maltose	+	carbon source
29877	29864 ChEBI	mannitol	+	carbon source
29877	37684 ChEBI	mannose	+	carbon source
29877	28053 ChEBI	melibiose	+	carbon source
29877	17632 ChEBI	nitrate	+	reduction
29877	15361 ChEBI	pyruvate	+	carbon source
29877	16634 ChEBI	raffinose	+	carbon source
29877	26546 ChEBI	rhamnose	+	carbon source
29877	30911 ChEBI	sorbitol	+	carbon source
29877	30031 ChEBI	succinate	+	carbon source
29877	27082 ChEBI	trehalose	+	carbon source
29877	16199 ChEBI	urea	+	carbon source
29877	17151 ChEBI	xylitol	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29877	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
29877	35581 ChEBI	indole	+

Enzymes

@ref	Value	Activity	Ec
29877	catalase	+	1.11.1.6
29877	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	biotin biosynthesis	100	4 of 4
66794	ceramide biosynthesis	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	cyanate degradation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	ribulose monophosphate pathway	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	glycine betaine biosynthesis	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	aspartate and asparagine metabolism	100	9 of 9
66794	tetrahydrofolate metabolism	100	14 of 14
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	propionate fermentation	100	10 of 10
66794	aerobactin biosynthesis	100	1 of 1
66794	vitamin B1 metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	glutamate and glutamine metabolism	89.29	25 of 28
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	phenylalanine metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	1,4-dihydroxy-6-naphthoate biosynthesis	83.33	5 of 6
66794	flavin biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	purine metabolism	78.72	74 of 94
66794	heme metabolism	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	methionine metabolism	69.23	18 of 26
66794	urea cycle	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	arginine metabolism	66.67	16 of 24
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	tryptophan metabolism	65.79	25 of 38
66794	phenol degradation	65	13 of 20
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	oxidative phosphorylation	61.54	56 of 91
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	vitamin K metabolism	60	3 of 5
66794	starch degradation	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	cysteine metabolism	55.56	10 of 18
66794	lysine metabolism	54.76	23 of 42
66794	vitamin B6 metabolism	54.55	6 of 11
66794	ethanol fermentation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	myo-inositol biosynthesis	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	CMP-KDO biosynthesis	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	polyamine pathway	47.83	11 of 23
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	3-phenylpropionate degradation	40	6 of 15
66794	gallate degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	metabolism of disaccharids	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	tyrosine metabolism	35.71	5 of 14
66794	degradation of pentoses	35.71	10 of 28
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	nitrate assimilation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	cholesterol biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Continent
20435	sediment	South China Sea	Asia
67770	Sediment sample collected from the South China Sea

Taxonmaps

69479

Global distribution of 16S sequence GQ292773 (>99% sequence identity) for Alkalihalobacillus nanhaiisediminis subclade from Microbeatlas

Aquatic Samples	594
Soil Samples	517
Animal Samples	650
Plant Samples	79
Total Samples	1840

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20435	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM783018v1 assembly for Halalkalibacter nanhaiisediminis CGMCC 1.10116	scaffold	GCA_007830185	688079.3	2596583586	688079	73.27

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20435	Bacillus nanhaiisediminis 16S ribosomal RNA gene, partial sequence	GQ292773	1419		688079

GC content

@ref	GC-content (mol%)	Method
20435	40.3	thermal denaturation, midpoint method (Tm)
29877	40.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Halalkalibacter nanhaiisediminis CGMCC 1.10116
NCBI: GCA_007830185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	88.50	no
125439	motility	BacteriaNetⓘ	yes	75.10	no
125439	gram_stain	BacteriaNetⓘ	variable	70.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	90.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alkalihalobacillus nanhaiisediminis CGMCC 1.10116
NCBI: GCA_007830185.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	75.38	yes
125438	anaerobic	anaerobicⓘ	no	89.13	yes
125438	aerobic	aerobicⓘ	yes	82.79	yes
125438	spore-forming	spore-formingⓘ	yes	87.65	yes
125438	thermophilic	thermophileⓘ	no	87.25	yes
125438	flagellated	motile2+ⓘ	yes	86.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera.	Joshi A, Thite S, Karodi P, Joseph N, Lodha T.	Front Microbiol	10.3389/fmicb.2021.722369	2021
Phylogeny	Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils.	Dou G, Liu H, He W, Ma Y	Antonie Van Leeuwenhoek	10.1007/s10482-015-0616-y	2015
Phylogeny	Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea.	Zhu D, Tanabe SH, Xie C, Honda D, Sun J, Ai L	Int J Syst Evol Microbiol	10.1099/ijs.0.058610-0	2014
Phylogeny	Bacillus nanhaiisediminis sp. nov., an alkalitolerant member of Bacillus rRNA group 6.	Zhang J, Wang J, Song F, Fang C, Xin Y, Zhang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.023671-0	2010
Phylogeny	Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye.	Hirota K, Aino K, Yumoto I	Int J Syst Evol Microbiol	10.1099/ijsem.0.001015	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 )
#20435	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27953
#26251	IJSEM 1078 2011 ( DOI 10.1099/ijs.0.023671-0 , PubMed 20525818 )
#29877	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 #26251
#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 .
#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 )

Rate our new design

Content

About us

Halalkalibacter nanhaiisediminis (DSM 27953, CGMCC 1.10116, JCM 16507)

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

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_007830185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media