Strain identifier

BacDive ID: 140460

Type strain: Yes

Species: Abyssicoccus albus

Strain Designation: S31

Strain history: CIP <- 2019, CCUG <- 2016, R. Sharma, CSIR-IGIB, New Delhi, India <- S. Muduli, strain: S31

NCBI tax ID(s): 1817405 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 9.3 (current version)

General

@ref: 43178

BacDive-ID: 140460

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped, colony-forming

description: Abyssicoccus albus S31 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from skin samples from healthy human subjects.

NCBI tax id

  • NCBI tax id: 1817405
  • Matching level: species

strain history

  • @ref: 120087
  • history: CIP <- 2019, CCUG <- 2016, R. Sharma, CSIR-IGIB, New Delhi, India <- S. Muduli, strain: S31

doi: 10.13145/bacdive140460.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • 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

    • @ref: 20215
    • synonym: Auricoccus indicus

@ref: 43178

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Staphylococcaceae

genus: Auricoccus

species: Auricoccus indicus

strain designation: S31

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
43178positivecoccus-shapedno
125438positive90.608
120087positivecoccus-shapedno

colony morphology

  • @ref: 43178
  • colony size: 0.5 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Zobell marine agar (ZMA)

Culture and growth conditions

culture medium

@refnamegrowthlink
43178Zobell marine agar (ZMA)yes
43178tryptic soy agar (TSA)yes
43178nutritient agar (NA)yes
43178Reasoner's 2A agar (R2A)yes
43178Luria agar (LA)yes
43178MacConkey agarno
120087CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
43178positiveoptimum35
43178positivegrowth20-40
63681positivegrowth37

culture pH

@refabilitytypepHPH range
43178positivegrowth5-10alkaliphile
43178positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43178aerobe
63681aerobe

spore formation

  • @ref: 43178
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43178NaClpositivegrowth1-20 %
43178NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4317817992sucrose+builds acid from
4317817234glucose+
4317817234glucose-fermentation
4317816467L-arginine-assimilation
4317816199urea-
431784853esculin-
4317831605ferric citrate-
431785291gelatin-
431783557154-nitrophenyl beta-D-galactopyranoside-
4317830849L-arabinose-
4317816024D-mannose-
4317816899D-mannitol-
43178506227N-acetylglucosamine-
4317817306maltose-
4317832032potassium gluconate-
4317827689decanoate-
4317817128adipate-
4317825115malate-
4317853258sodium citrate-
4317818401phenylacetate-
4317816947citrate-carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.group ID
431782637amikacinyesyes30 µg (disc)
431782676amoxicillinyesyes10 µg (disc)
43178amoxicillinyesyes10 µg (disc)
43178204928cefotaximeyesyes30 µg (disc)
4317829007ceftriaxoneyesyes10 µg (disc)
43178100241ciprofloxacinyesyes5 µg (disc)
4317837943colistinyesyes10 µg (disc)
431785195furazolidoneyesyes50 µg (disc)
4317817833gentamicinyesyes10 µg (disc)
431787528netilmycinyesyes30 µg (disc)
43178100246norfloxacinyesyes10 µg (disc)
431789332sulfamethoxazoleyesyes25 µg (disc)26
4317845924trimethoprimyesyes25 µg (disc)26

metabolite production

@refChebi-IDmetaboliteproduction
4317835581indoleno
4317815688acetoinno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testcitrate test
4317817234glucose-
4317815688acetoin-
4317816947citrate-

enzymes

@refvalueactivityec
43178catalase+1.11.1.6
43178cytochrome oxidase+1.9.3.1
43178urease-3.5.1.5
43178gelatinase-
43178amylase-
43178nitrate reductase+1.7.99.4
43178alkaline phosphatase+3.1.3.1
43178esterase (C 4)+
43178esterase Lipase (C 8)+
43178acid phosphatase+3.1.3.2
43178naphthol-AS-BI-phosphohydrolase+
43178DNase-
43178chitinase-3.2.1.14
43178endo-1,4-beta-xylanase-3.2.1.8
43178tyrosinase-1.14.18.1
43178cellulase-3.2.1.4
43178lipase (C 14)-
43178leucine arylamidase-3.4.11.1
43178valine arylamidase-
43178cystine arylamidase-3.4.11.3
43178trypsin-3.4.21.4
43178alpha-chymotrypsin-3.4.21.1
43178alpha-galactosidase-3.2.1.22
43178beta-galactosidase-3.2.1.23
43178beta-glucuronidase-3.2.1.31
43178alpha-glucosidase-3.2.1.20
43178beta-glucosidase-3.2.1.21
43178N-acetyl-beta-glucosaminidase-3.2.1.52
43178alpha-mannosidase-3.2.1.24
43178alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43178C14:00.7
    43178C16:02.5
    43178C18:01.4
    43178C20:02.2
    43178C14:0 iso4.8
    43178C15:0 iso2.3
    43178C16:0 iso11.7
    43178C17:0 iso1.1
    43178C19:0 iso0.4
    43178C18:0 iso2.6
    43178C20:0 iso1.5
    43178C15:0 anteiso56.4
    43178C17:0 anteiso8.4
    43178C19:0 anteiso2.5
  • type of FA analysis: whole cell analysis
  • incubation medium: ZMA
  • agar/liquid: agar
  • incubation time: 2
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typeenrichment cultureenrichment culture durationenrichment culture temperaturesampling dategeographic locationcountryorigin.countrycontinentisolation date
43178skin samples from healthy human subjectsLuria Bertani (LB) agar3 days37
63681Healthy skin,human ear2012-01-29New Delhi,Sukhdev Vihar,CSIR-IGIBIndiaINDAsia
120087Human, Ear, healthy skinIndiaINDAsia2012-01-29

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_2905.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1534;97_1831;98_2246;99_2905&stattab=map
  • Last taxonomy: Abyssicoccus albus subclade
  • 16S sequence: KU302615
  • Sequence Identity:
  • Total samples: 31908
  • soil counts: 2286
  • aquatic counts: 2483
  • animal counts: 26548
  • plant counts: 591

Safety information

risk assessment

  • @ref: 120087
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 43178
  • description: Abyssicoccus albus strain S31 16S ribosomal RNA gene, partial sequence
  • accession: KU302615
  • length: 1507
  • database: nuccore
  • NCBI tax ID: 1849491

Genome sequences

  • @ref: 66792
  • description: Abyssicoccus albus S31
  • accession: GCA_001989575
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1817405

GC content

  • @ref: 43178
  • GC-content: 34
  • method: Thermal denaturation, fluorometry

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.608yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.342yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes66.636no
125438spore-formingspore-formingAbility to form endo- or exosporesno81.786yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.349yes
125438motile2+flagellatedAbility to perform flagellated movementno84.331yes

External links

@ref: 43178

culture collection no.: CCUG 69858, KCTC 33611, MCC 3027, CIP 111652

straininfo link

  • @ref: 96723
  • straininfo: 409408

literature

  • topic: Phylogeny
  • Pubmed-ID: 28086066
  • title: Description of Auricoccus indicus gen. nov., sp. nov., isolated from skin of human ear.
  • authors: Prakash O, Muduli S, Kumar R, Kumari C, Nimonkar Y, Shouche YS, Sharma R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001787
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Ear/*microbiology, Fatty Acids/chemistry, Gram-Positive Asporogenous Rods/*classification/genetics/isolation & purification, Humans, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Skin/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
43178Om Prakash, Suchismita Muduli, Rohit Kumar, Chanchal Kumari, Yogesh Nimonkar, Yogesh S. Shouche, Rakesh SharmaDescription of Auricoccus indicus gen. nov., sp. nov., isolated from skin of human ear10.1099/ijsem.0.001787IJSEM 67: 1212-1218 201728086066
63681Curators of the CCUGhttps://www.ccug.se/strain?id=69858Culture Collection University of Gothenburg (CCUG) (CCUG 69858)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João 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 betahttps://microbeatlas.org/
96723Reimer, 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 identifiers10.60712/SI-ID409408.1
120087Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111652Collection of Institut Pasteur (CIP 111652)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695