Strain identifier

BacDive ID: 7498

Type strain: Yes

Species: Humibacter albus

Strain Designation: SC-083

Strain history: LMG 23996 <-- C. M. Manaia SC-083 <-- I. Vaz-Moreira et al..

NCBI tax ID(s): 1121952 (strain), 427754 (species)

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General

@ref: 7819

BacDive-ID: 7498

DSM-Number: 18994

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

description: Humibacter albus SC-083 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sewage sludge compost.

NCBI tax id

NCBI tax idMatching level
427754species
1121952strain

strain history

@refhistory
7819<- C. M. Manaia <- I. Vaz-Moreira; SC-083
67770LMG 23996 <-- C. M. Manaia SC-083 <-- I. Vaz-Moreira et al..

doi: 10.13145/bacdive7498.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Humibacter
  • species: Humibacter albus
  • full scientific name: Humibacter albus Vaz-Moreira et al. 2008

@ref: 7819

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Humibacter

species: Humibacter albus

full scientific name: Humibacter albus Vaz-Moreira et al. 2008

strain designation: SC-083

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32289positive1.3 µm0.59 µmrod-shapedyes
69480positive100

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_18994_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18994_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18994_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18994_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_18994_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 7819
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: 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

@refgrowthtypetemperaturerange
7819positivegrowth28mesophilic
19775positiveoptimum28mesophilic
32289positivegrowth22-36
32289positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
32289positivegrowth5.5-8
32289positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32289
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

halophily

@refsaltgrowthtested relationconcentration
32289NaClpositivegrowth<3 %
32289NaClpositiveoptimum<1 %

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3228922599arabinose+carbon source
3228918403L-arabitol+carbon source
3228917057cellobiose+carbon source
3228928757fructose+carbon source
3228928260galactose+carbon source
3228917234glucose+carbon source
3228917716lactose+carbon source
3228917306maltose+carbon source
3228929864mannitol+carbon source
3228937684mannose+carbon source
3228928053melibiose+carbon source
32289506227N-acetylglucosamine+carbon source
3228926546rhamnose+carbon source
3228917814salicin+carbon source
3228917992sucrose+carbon source
3228927082trehalose+carbon source
3228918222xylose+carbon source
322894853esculin+hydrolysis
3228917632nitrate+reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
32289catalase+1.11.1.6
32289urease+3.5.1.5
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19775--+--+++++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19775--+-++---+-++-+++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
7819sewage sludge compostPortoPortugalPRTEurope
60222Compost,municipal sewage sludgePorto ?PortugalPRTEurope2005
67770Sewage sludge compostPortoPortugalPRTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Waste#Sewage sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_4741.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2066;97_2857;98_3554;99_4741&stattab=map
  • Last taxonomy: Humibacter albus subclade
  • 16S sequence: AM494541
  • Sequence Identity:
  • Total samples: 161
  • soil counts: 41
  • aquatic counts: 51
  • animal counts: 49
  • plant counts: 20

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78191Risk group (German classification)
197751Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7819
  • description: Humibacter albus partial 16S rRNA gene, type strain SC-083T
  • accession: AM494541
  • length: 1488
  • database: ena
  • NCBI tax ID: 1121952

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Humibacter albus DSM 189941121952.3wgspatric1121952
66792Humibacter albus DSM 189942523533583draftimg1121952
67770Humibacter albus DSM 18994GCA_000421825contigncbi1121952

GC content

@refGC-contentmethod
781967.6
3228968
6777067.4-67.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno85no
motileno93.829no
flagellatedno98.387no
gram-positiveyes92.175yes
anaerobicno99.447yes
halophileno89.65no
spore-formingno91.244no
thermophileno97.772yes
glucose-utilyes86.297yes
aerobicyes87.949yes
glucose-fermentno88.101yes

External links

@ref: 7819

culture collection no.: DSM 18994, CCUG 54538, LMG 23996, JCM 16029, KACC 20986, NBRC 106151

straininfo link

  • @ref: 76944
  • straininfo: 294507

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18398211Humibacter albus gen. nov., sp. nov., isolated from sewage sludge compost.Vaz-Moreira I, Nobre MF, Ferreira AC, Schumann P, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.65266-02008Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, Fatty Acids/metabolism, Genes, Bacterial, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiology, Species Specificity, Terminology as Topic, Vitamin K 2/metabolismMetabolism
Phylogeny23838446Humibacter antri sp. nov., an actinobacterium isolated from a natural cave, and emended description of the genus Humibacter.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.050708-02013Actinomycetales/*classification/genetics/isolation & purification, Antineoplastic Combined Chemotherapy Protocols, Base Composition, Caves/*microbiology, Cell Wall/chemistry, Cyclophosphamide, DNA, Bacterial/genetics, Doxorubicin, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, Podophyllotoxin, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Vincristine, Vitamin K 2/chemistryGenetics
Phylogeny35816438Humibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity isolated from activated sludge.Choi GM, Lee YW, Choe H, Kim SY, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0054422022*Actinomycetales, Alanine/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ginsenosides, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage, Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7819Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18994)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18994
19775Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18994.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32289Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2852928776041
60222Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54538)https://www.ccug.se/strain?id=54538
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
76944Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294507.1StrainInfo: A central database for resolving microbial strain identifiers