Abyssicoccus albus (DSM 29158, CCTCC AB 2014213, YIM M12140)

Name: Abyssicoccus albus (DSM 29158, CCTCC AB 2014213, YIM M12140)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132558

Type strain

Culture col. no. DSM 29158 CCTCC AB 2014213 YIM M12140 JCM 30296

NCBI tax ID(s) 1817405

Special Collections DSMZ JCM

History <- W.-J. Li, YIM; YIM M12140 <- J. Zhao W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM M12140.

Links

Abyssicoccus albus DSM 29158 is a mesophilic prokaryote that was isolated from deep sea sediment.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406210

DSM 29158

@ref 20215

Last LPSN update 2026-02-09 11:31:44

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Staphylococcaceae

Genus Abyssicoccus

Species Abyssicoccus albus

Full scientific name Abyssicoccus albus Jiang et al. 2016

Synonyms (1)

Auricoccus indicus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	91.989

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24347	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24347	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

Observation

67770

Observationquinones: MK-6, MK-7

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	lipoate biosynthesis	100	5 of 5
66794	peptidoglycan biosynthesis	100	15 of 15
66794	acetoin degradation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	vitamin B1 metabolism	92.31	12 of 13
66794	chorismate metabolism	88.89	8 of 9
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	pentose phosphate pathway	81.82	9 of 11
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	pyrimidine metabolism	73.33	33 of 45
66794	flavin biosynthesis	73.33	11 of 15
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	photosynthesis	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	methionine metabolism	69.23	18 of 26
66794	purine metabolism	69.15	65 of 94
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	heme metabolism	64.29	9 of 14
66794	ketogluconate metabolism	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	phenylalanine metabolism	61.54	8 of 13
66794	NAD metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	methylglyoxal degradation	60	3 of 5
66794	starch degradation	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	citric acid cycle	57.14	8 of 14
66794	degradation of sugar alcohols	56.25	9 of 16
66794	d-mannose degradation	55.56	5 of 9
66794	valine metabolism	55.56	5 of 9
66794	glutamate and glutamine metabolism	53.57	15 of 28
66794	cysteine metabolism	50	9 of 18
66794	butanoate fermentation	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	isoleucine metabolism	50	4 of 8
66794	biotin biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	oxidative phosphorylation	48.35	44 of 91
66794	proline metabolism	45.45	5 of 11
66794	alanine metabolism	44.83	13 of 29
66794	tryptophan metabolism	44.74	17 of 38
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	serine metabolism	44.44	4 of 9
66794	propanol degradation	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	propionate fermentation	40	4 of 10
66794	glycine metabolism	40	4 of 10
66794	urea cycle	38.46	5 of 13
66794	leucine metabolism	38.46	5 of 13
66794	metabolism of disaccharids	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	lipid metabolism	35.48	11 of 31
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	arginine metabolism	33.33	8 of 24
66794	polyamine pathway	30.43	7 of 23
66794	threonine metabolism	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	histidine metabolism	27.59	8 of 29
66794	ascorbate metabolism	27.27	6 of 22
66794	lysine metabolism	26.19	11 of 42
66794	degradation of pentoses	25	7 of 28
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Continent	Latitude	Longitude
24347	deep sea sediment	(81° 04.978' E, 1° 53.375' N, 4481 m depth)	Indian Ocean	Asia	1.8896	81.083 1.8896/81.083
67770	Sediment from the Indian Ocean (1° 53.375' N 81° 04.978' E) at a depth of 4,481 m

Taxonmaps

69479

Global distribution of 16S sequence KT935587 (>99% sequence identity) for Abyssicoccus albus subclade from Microbeatlas

Aquatic Samples	2483
Soil Samples	2286
Animal Samples	26548
Plant Samples	591
Total Samples	31908

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24347	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM381503v1 assembly for Abyssicoccus albus DSM 29158	scaffold	GCA_003815035	1817405.3	2786546168	1817405	72.27

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24347	Abyssicoccus albus strain LIPI11-2-Ac043 16S ribosomal RNA gene, partial sequence	KT935587	1576		1817405

GC content

@ref	GC-content (mol%)	Method
24347	42.4	high performance liquid chromatography (HPLC)
67770	41.3-43.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Abyssicoccus albus DSM 29158
NCBI: GCA_003815035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	81.60	no
125439	motility	BacteriaNetⓘ	yes	63.60	no
125439	gram_stain	BacteriaNetⓘ	positive	73.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	76.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Abyssicoccus albus strain DSM 29158
PATRIC: 1817405.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.99	no
125438	anaerobic	anaerobicⓘ	no	96.24	no
125438	spore-forming	spore-formingⓘ	no	80.06	no
125438	aerobic	aerobicⓘ	yes	65.75	no
125438	thermophilic	thermophileⓘ	no	93.66	yes
125438	flagellated	motile2+ⓘ	no	85.71	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Expanding the Genome-Editing Toolbox with Abyssicoccus albus Cas9 Using a Unique Protospacer Adjacent Motif Sequence.	Nakamura A, Yamamoto H, Yano T, Hasegawa R, Makino Y, Mitsuda N, Terakawa T, Ito S, Sugano SS.	CRISPR J	10.1089/crispr.2024.0013	2024
Phylogeny	Unification of Abyssicoccus albus Jiang et al. 2016 and Auricoccus indicus Prakash et al. 2017 and the status of the genus Auricoccus Prakash et al. 2017.	Dobritsa AP, Samadpour M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004479	2020
Phylogeny	Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae.	Madhaiyan M, Wirth JS, Saravanan VS.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004498	2020
	Indoor metabolites and chemicals outperform microbiome in classifying childhood asthma and allergic rhinitis.	Sun Y, Tang H, Du S, Chen Y, Ou Z, Zhang M, Chen Z, Tang Z, Zhang D, Chen T, Xu Y, Li J, Norback D, Hashim JH, Hashim Z, Shao J, Fu X, Zhao Z.	Eco Environ Health	10.1016/j.eehl.2023.08.001	2023
	Homology modeling, virtual screening, molecular docking, and dynamics studies for discovering Staphylococcus epidermidis FtsZ inhibitors.	Vemula D, Maddi DR, Bhandari V.	Front Mol Biosci	10.3389/fmolb.2023.1087676	2023
Genetics	Whole Genome Sequencing of Staphylococci Isolated From Bovine Milk Samples.	Fergestad ME, Touzain F, De Vliegher S, De Visscher A, Thiry D, Ngassam Tchamba C, Mainil JG, L'Abee-Lund T, Blanchard Y, Wasteson Y.	Front Microbiol	10.3389/fmicb.2021.715851	2021
Phylogeny	Abyssicoccus albus gen. nov., sp. nov., a novel member of the family Staphylococcaceae isolated from marine sediment of the Indian Ocean.	Jiang Z, Yuan CG, Xiao M, Tian XP, Khan IU, Kim CJ, Zhi XY, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0717-2	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 )
#24347	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29158
#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 )

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Abyssicoccus albus (DSM 29158, CCTCC AB 2014213, YIM M12140)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003815035

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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