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)

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General

@ref: 6422

BacDive-ID: 7275

DSM-Number: 16389

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

description: Agromyces humatus CD 5 is an aerobe, Gram-positive, rod-shaped 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/bacdive7275.20240916.9.1

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 shapemotilityconfidence
31369positive0.4 µmrod-shapedno
119981positiverod-shapedno
69480positive92.216
69480no92.5

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

@refgrowthtypetemperature
6422positivegrowth28
31369positivegrowth15-37
31369positiveoptimum28
37635positivegrowth30
67770positivegrowth28

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: nuccore
  • 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

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.216yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.557yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.21yes
69480spore-formingspore-formingAbility to form endo- or exosporesno71.905no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98no
69480flagellatedmotile2+Ability to perform flagellated movementno92.5yes

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
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)
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