Strain identifier

BacDive ID: 7275

Type strain: Yes

Species: Agromyces humatus

Strain Designation: CD 5, CD5

Strain history: CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD5 <- I. Groth: strain HKI 0327

NCBI tax ID(s): 279573 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6422

BacDive-ID: 7275

DSM-Number: 16389

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

description: Agromyces humatus CD 5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from wall of a tomb.

NCBI tax id

  • NCBI tax id: 279573
  • Matching level: species

strain history

@refhistory
6422<- I. Groth; HKI 0327 <- Ch. Weigel; CD 5
67770I. Groth CD5 (=HKI 0327) <-- Ch. Weigel.
119981CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD5 <- I. Groth: strain HKI 0327

doi: 10.13145/bacdive7275.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces humatus
  • full scientific name: Agromyces humatus Jurado et al. 2005

@ref: 6422

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces humatus

full scientific name: Agromyces humatus Jurado et al. 2005

strain designation: CD 5, CD5

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
31369positive0.4 µmrod-shapedno
119981positiverod-shapedno

colony morphology

  • @ref: 119981

pigmentation

  • @ref: 31369
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6422R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
6422TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
37635MEDIUM 56 - for Micromonospora purpureayesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (10.000g);Yeast extract (5.000 g);Starch maize (20.000 g);Calcium carbonate (1.000 g);Casamino acids (5.000 g)
119981CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
119981CIP Medium 56yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=56

culture temp

@refgrowthtypetemperaturerange
6422positivegrowth28mesophilic
31369positivegrowth15-37
31369positiveoptimum28mesophilic
37635positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31369positivegrowth5-9.5alkaliphile
31369positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31369aerobe
119981obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
31369NaClpositivegrowth<2 %
31369NaClpositiveoptimum1 %

murein

  • @ref: 6422
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-13, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3136922599arabinose+carbon source
3136928260galactose+carbon source
313695291gelatin+carbon source
3136917234glucose+carbon source
3136917754glycerol+carbon source
3136925115malate+carbon source
3136929864mannitol+carbon source
3136916634raffinose+carbon source
3136926546rhamnose+carbon source
3136930031succinate+carbon source
3136917992sucrose+carbon source
3136917632nitrate+reduction
11998117632nitrate+reduction
11998116301nitrite-reduction

enzymes

@refvalueactivityec
31369catalase+1.11.1.6
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
119981oxidase-
119981alcohol dehydrogenase-1.1.1.1
119981catalase+1.11.1.6
119981lysine decarboxylase-4.1.1.18
119981ornithine decarboxylase-4.1.1.17
119981urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119981-+++-++-+-+++++++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6422wall of a tombRome, Domitilla Catacombs, Little Apostle cubicleItalyITAEurope
67770Wall of a tomb located in the Little Apostle cubicleDomitilla Catacombs, RomeItalyITAEurope
119981Wall of a tombRomeItalyITAEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Built environment

taxonmaps

  • @ref: 69479
  • File name: preview.99_11964.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_852;97_3714;98_4708;99_11964&stattab=map
  • Last taxonomy: Agromyces
  • 16S sequence: AY618216
  • Sequence Identity:
  • Total samples: 4364
  • soil counts: 3011
  • aquatic counts: 192
  • animal counts: 261
  • plant counts: 900

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64221Risk group (German classification)
1199811Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6422
  • description: Agromyces humatus 16S ribosomal RNA gene, partial sequence
  • accession: AY618216
  • length: 1388
  • database: ena
  • NCBI tax ID: 279573

Genome sequences

  • @ref: 66792
  • description: Agromyces humatus JCM 14319
  • accession: GCA_021228295
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 279573

GC content

@refGC-contentmethod
642270.6
6777070.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.897yes
gram-positiveyes93.941no
anaerobicno99.625yes
aerobicyes94.121yes
halophileno89.379yes
spore-formingno91.985no
motileno90.594yes
thermophileno98.479yes
glucose-utilyes86.848no
glucose-fermentno87.94no

External links

@ref: 6422

culture collection no.: DSM 16389, NBRC 109085, NCIMB 14012, HKI 0327, JCM 14319, CIP 108741, IAM 15274

straininfo link

  • @ref: 76726
  • straininfo: 137992

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774677Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs.Jurado V, Groth I, Gonzalez JM, Laiz L, Schuetze B, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijs.0.63414-02005Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, History, Ancient, Italy, Molecular Sequence Data, *Mortuary Practice, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny26883212Agromyces insulae sp. nov., an actinobacterium isolated from a soil sample.Huang JR, Ming H, Li S, Meng XL, Zhang JX, Khieu TN, Tang Z, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0009782016Actinomycetales/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vietnam, Vitamin K 2/chemistryTranscriptome
Phylogeny36001366Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan.Fang BZ, Gao L, Jiao JY, Zhang ZT, Li MM, Mohamad OAA, Ahmed I, Li L, Liu YH, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0055032022*Actinomycetales, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6422Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16389)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16389
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
31369Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2768228776041
37635Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6403
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
76726Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID137992.1StrainInfo: A central database for resolving microbial strain identifiers
119981Curators of the CIPCollection of Institut Pasteur (CIP 108741)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108741