Strain identifier

BacDive ID: 158314

Type strain: Yes

Species: Nocardioides houyundeii

Strain Designation: 78

Strain history: <- X. Wang, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infections Disease Prevention and Control, Beijing, P.R. China; 78

NCBI tax ID(s): 2045452 (species)

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General

@ref: 64990

BacDive-ID: 158314

DSM-Number: 106424

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

description: Nocardioides houyundeii 78 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from feces of the Tibetan antelope.

NCBI tax id

  • NCBI tax id: 2045452
  • Matching level: species

strain history

  • @ref: 64990
  • history: <- X. Wang, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infections Disease Prevention and Control, Beijing, P.R. China; 78

doi: 10.13145/bacdive158314.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides houyundeii
  • full scientific name: Nocardioides houyundeii Wang et al. 2018

@ref: 64990

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides houyundeii

full scientific name: Nocardioides houyundeii Wang et al. 2018

strain designation: 78

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66779positive1.0-2.5 µm0.6-1.2 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 66779
  • colony size: 1-2 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 5 days
  • medium used: BHI-5% sheep blood agar

multimedia

  • @ref: 64990
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_106424.jpg
  • caption: Medium 215 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64990BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
64990COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
64990TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
64990GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
66779BHI agarno
66779BHI-5% sheep blood agaryes
66779Reasoner's 2A agar (R2A)no
66779tryptic soy agar (TSA)no

culture temp

@refgrowthtypetemperaturerange
64990positivegrowth28mesophilic
66779positiveoptimum28mesophilic
66779positivegrowth14-32

culture pH

@refabilitytypepH
66779positiveoptimum7
66779positivegrowth6.5-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 66779
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.958
69481no92

halophily

  • @ref: 66779
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.5-1.5 %(w/v)

observation

  • @ref: 66779
  • observation: The predominant menaquinone is MK-8 (H4) and the polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and an unidentified lipid.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
667796731melezitose-builds acid from
6677912936D-galactose-builds acid from
6677915443inulin-builds acid from
6677915824D-fructose-builds acid from
6677915963ribitol-builds acid from
6677916024D-mannose-builds acid from
6677916634raffinose-builds acid from
6677916813galactitol-builds acid from
6677916899D-mannitol-builds acid from
6677917057cellobiose-builds acid from
6677917108D-arabinose-builds acid from
6677917113erythritol-builds acid from
6677917266L-sorbose-builds acid from
6677917268myo-inositol-builds acid from
6677917306maltose-builds acid from
6677917634D-glucose-builds acid from
6677917716lactose-builds acid from
6677917754glycerol-builds acid from
6677917814salicin-builds acid from
6677917924D-sorbitol-builds acid from
6677917992sucrose-builds acid from
6677918222xylose-builds acid from
6677918287L-fucose-builds acid from
6677918305arbutin-builds acid from
6677922605arabinitol-builds acid from
6677927082trehalose-builds acid from
6677927613amygdalin-builds acid from
6677928053melibiose-builds acid from
6677928087glycogen-builds acid from
6677928847D-fucose-builds acid from
6677930849L-arabinose-builds acid from
6677932032potassium gluconate-builds acid from
6677959640N-acetylglucosamine-builds acid from
6677962345L-rhamnose-builds acid from
6677965327D-xylose-builds acid from
6677974863methyl beta-D-xylopyranoside-builds acid from
6677916988D-ribose+builds acid from
66779320061methyl alpha-D-glucopyranoside+builds acid from
66779esculin ferric citrate+builds acid from

metabolite production

  • @ref: 66779
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66779acid phosphatase-3.1.3.2
66779alpha-chymotrypsin-3.4.21.1
66779alpha-fucosidase-3.2.1.51
66779alpha-galactosidase-3.2.1.22
66779beta-galactosidase-3.2.1.23
66779beta-glucosidase-3.2.1.21
66779beta-glucuronidase-3.2.1.31
66779beta-mannosidase-3.2.1.25
66779cystine arylamidase-3.4.11.3
66779cytochrome oxidase-1.9.3.1
66779gelatinase-
66779lipase (C 14)-
66779N-acetyl-beta-glucosaminidase-3.2.1.52
66779nitrate reductase-1.7.99.4
66779trypsin-3.4.21.4
66779urease-3.5.1.5
66779valine arylamidase-
66779alkaline phosphatase+3.1.3.1
66779alpha-glucosidase+3.2.1.20
66779catalase+1.11.1.6
66779esterase (C 4)+
66779esterase Lipase (C 8)+
66779leucine arylamidase+3.4.11.1
66779naphthol-AS-BI-phosphohydrolase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling dateenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
64990feces of the Tibetan antelopeqinghai province, haixi city, Kekexili (35° 21' 55.7'' N, 93° 26' 38'' E)ChinaCHNAsia35.365593.4439
66779faecal sample of Tibetan antelopeHoh Xil Nature Reserve, Qinghai-Tibet PlateauChinaCHNAsia35.365593.44392014brain-heart infusion (BHI) agarsupplemented with 5% sheep blood (per litre: 12.5 g brain infusion solids, 5 g beefheart infusion solids, 10 g proteose peptone, 5 g NaCl, 2 g glucose, 2.5 g disodium phosphate, 10 g agar and 50 ml sterile defibrinated sheep blood; pH 7.4)7 days28The faecal samples were processed as follows: the sample (1 g) was suspended in 200 µl of sterile water, 100 µl of the suspension was spread on brain-heart infusion (BHI) agar

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Caprinae (Sheep/Goat)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_87650.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2111;97_13208;98_60564;99_87650&stattab=map
  • Last taxonomy: Nocardioides houyundeii subclade
  • 16S sequence: MG209819
  • Sequence Identity:
  • Total samples: 2700
  • soil counts: 2082
  • aquatic counts: 162
  • animal counts: 286
  • plant counts: 170

Sequence information

16S sequences

  • @ref: 66779
  • description: Nocardioides sp. strain 78 16S ribosomal RNA gene, partial sequence
  • accession: MG209819
  • length: 1480
  • database: ena
  • NCBI tax ID: 35761

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides houyundeii 78GCA_002865585completencbi2045452
66792Nocardioides houyundeii 782775506984completeimg2045452

GC content

  • @ref: 66779
  • GC-content: 71.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
flagellatedno93.839yes
gram-positiveyes89.528yes
anaerobicno98.701yes
aerobicyes93.424yes
halophileno94.81no
spore-formingno79.23no
glucose-utilyes86.232no
thermophileno99.106yes
motileno76.864yes
glucose-fermentno89.405no

External links

@ref: 64990

culture collection no.: DSM 106424, CGMCC 4.7461

straininfo link

  • @ref: 111127
  • straininfo: 399542

literature

  • topic: Phylogeny
  • Pubmed-ID: 30362934
  • title: Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces.
  • authors: Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Zhang G, Huang Y, Zhu W, Wu X, Liang H, Xu J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003076
  • year: 2018
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sheep, Tibet
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
64990Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106424Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106424)
66779Xiaoxia Wang, Jing Yang, Shan Lu, Xin-He Lai, Dong Jin, Ji Pu, Gui Zhang, Ying Huang, Wentao Zhu, Xiaomin Wu, Hao Liang and Jianguo XuNocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces10.1099/ijsem.0.003076IJSEM 68: 3874-3880 201830362934
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111127Reimer, 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-ID399542.1