Strain identifier
BacDive ID: 7274
Type strain:
Species: Agromyces lapidis
Strain Designation: CD55
Strain history: CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD55 <- I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0324
NCBI tax ID(s): 279574 (species)
General
@ref: 6423
BacDive-ID: 7274
DSM-Number: 16390
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Agromyces lapidis CD55 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from carved stone wall.
NCBI tax id
- NCBI tax id: 279574
- Matching level: species
strain history
@ref | history |
---|---|
6423 | <- I. Groth; HKI 0324 <- Ch. Weigel; CD55 |
67770 | I. Groth CD55 (=HKI 0324) <-- Ch. Weigel. |
120559 | CIP <- 2005, V. Jurado, CSIC, Sevilla, Spain: strain CD55 <- I. Groth, Hans Knöll Inst., Jena, Germany: strain HKI 0324 |
doi: 10.13145/bacdive7274.20230509.8.1
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 lapidis
- full scientific name: Agromyces lapidis Jurado et al. 2005
@ref: 6423
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Agromyces
species: Agromyces lapidis
full scientific name: Agromyces lapidis Jurado et al. 2005
strain designation: CD55
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|
31369 | positive | 0.5 µm | rod-shaped | no | |
69480 | positive | 100 | |||
120559 | positive | rod-shaped | no |
colony morphology
- @ref: 120559
pigmentation
- @ref: 31369
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6423 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: 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 |
6423 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | 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 |
37633 | MEDIUM 56 - for Micromonospora purpurea | yes | Distilled 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) | |
120559 | CIP Medium 56 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=56 | |
120559 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6423 | positive | growth | 28 | mesophilic |
31369 | positive | growth | 10-37 | |
31369 | positive | optimum | 28 | mesophilic |
37633 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31369 | positive | growth | 5-9.5 | alkaliphile |
31369 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31369 | aerobe |
120559 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.99 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31369 | NaCl | positive | growth | <4 % |
31369 | NaCl | positive | optimum | 2 % |
murein
- @ref: 6423
- murein short key: B07
- type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab
observation
- @ref: 67770
- observation: quinones: MK-12, MK-13
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31369 | 22599 | arabinose | + | carbon source |
31369 | 17057 | cellobiose | + | carbon source |
31369 | 33984 | fucose | + | carbon source |
31369 | 28260 | galactose | + | carbon source |
31369 | 17234 | glucose | + | carbon source |
31369 | 17754 | glycerol | + | carbon source |
31369 | 506227 | N-acetylglucosamine | + | carbon source |
31369 | 16634 | raffinose | + | carbon source |
31369 | 17814 | salicin | + | carbon source |
31369 | 17992 | sucrose | + | carbon source |
31369 | 17632 | nitrate | + | reduction |
120559 | 17632 | nitrate | + | reduction |
120559 | 16301 | nitrite | - | reduction |
120559 | 17632 | nitrate | - | respiration |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31369 | catalase | + | 1.11.1.6 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
120559 | oxidase | + | |
120559 | alcohol dehydrogenase | - | 1.1.1.1 |
120559 | catalase | + | 1.11.1.6 |
120559 | lysine decarboxylase | - | 4.1.1.18 |
120559 | ornithine decarboxylase | - | 4.1.1.17 |
120559 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120559 | - | - | + | + | - | + | + | + | - | - | + | + | + | + | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6423 | carved stone wall | Rome, Domitilla catacombs | Italy | ITA | Europe |
67770 | Stone wall of a tomb | Domitilla Catacombs, Rome | Italy | ITA | Europe |
120559 | Carved stone wall | Rome | Italy | ITA | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6423 | 1 | Risk group (German classification) |
120559 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6423
- description: Agromyces lapidis 16S ribosomal RNA gene, partial sequence
- accession: AY618217
- length: 1470
- database: ena
- NCBI tax ID: 279574
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Agromyces lapidis strain JCM 14321 | 279574.3 | wgs | patric | 279574 |
67770 | Agromyces lapidis JCM 14321 | GCA_009749405 | contig | ncbi | 279574 |
GC content
@ref | GC-content | method |
---|---|---|
6423 | 70.4 | |
67770 | 70.4 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 88.131 | no |
gram-positive | yes | 90.631 | no |
anaerobic | no | 99.688 | yes |
halophile | no | 91.238 | no |
spore-forming | no | 88.664 | no |
glucose-util | yes | 86.159 | no |
flagellated | no | 97.489 | yes |
aerobic | yes | 95.762 | yes |
thermophile | no | 99.413 | no |
glucose-ferment | no | 91.607 | no |
External links
@ref: 6423
culture collection no.: DSM 16390, NCIMB 14013, HKI 0324, JCM 14321, IAM 15275, CIP 108739
straininfo link
- @ref: 76725
- straininfo: 137994
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15774677 | Agromyces 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 C | Int J Syst Evol Microbiol | 10.1099/ijs.0.63414-0 | 2005 | Actinomycetales/*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 Specificity | Genetics |
Phylogeny | 35085062 | Agromyces agglutinans sp. nov., isolated from saline lake sediment. | Yi BF, Xia TT, Niu MM, Zhao ZY, Su QY, Ming H, Nie GX | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005208 | 2022 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Geologic Sediments/*microbiology, *Lakes/microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA, Vitamin K 2/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6423 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16390) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16390 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31369 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 27682 | 28776041 | |
37633 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6401 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
76725 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID137994.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120559 | Curators of the CIP | Collection of Institut Pasteur (CIP 108739) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108739 |