Strain identifier

BacDive ID: 132346

Type strain: Yes

Species: Bifidobacterium hapali

Strain Designation: MRM_8.14

Strain history: P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; MRM_8.14.

NCBI tax ID(s): 1630172 (species)

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General

@ref: 24135

BacDive-ID: 132346

DSM-Number: 100202

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

description: Bifidobacterium hapali MRM_8.14 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from faeces of baby common marmosets .

NCBI tax id

  • NCBI tax id: 1630172
  • Matching level: species

strain history

@refhistory
24135<- P. Mattarelli, Univ. Bologna, Italy; MRM_8.14 <- M. Modesto
67770P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; MRM_8.14.

doi: 10.13145/bacdive132346.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Bifidobacteriales
  • family: Bifidobacteriaceae
  • genus: Bifidobacterium
  • species: Bifidobacterium hapali
  • full scientific name: Bifidobacterium hapali Michelini et al. 2016

@ref: 24135

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Bifidobacteriales

family: Bifidobacteriaceae

genus: Bifidobacterium

species: Bifidobacterium hapali

full scientific name: Bifidobacterium hapali Michelini et al. 2016

strain designation: MRM_8.14

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
43839positiverod-shapedno
69480no95.024
69480positive100

colony morphology

  • @ref: 43839
  • type of hemolysis: gamma
  • colony size: 1.5-2.5 mm
  • colony color: White
  • colony shape: circular
  • incubation period: 2 days
  • medium used: TPY agar plates

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43839TPY agar platesyes
24135BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)yeshttps://mediadive.dsmz.de/medium/58Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

culture temp

@refgrowthtypetemperaturerange
43839positivegrowth25-42
43839positiveoptimum37mesophilic
24135positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
43839positivegrowth4.5-7.5
43839positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43839aerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
69481no100
69480no99.997

murein

  • @ref: 24135
  • murein short key: A11.11
  • type: A3alpha L-Lys(L-Orn)-L-Ala2-L-Ser

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43839168082-dehydro-D-gluconate-builds acid from
43839581435-dehydro-D-gluconate-builds acid from
4383927613amygdalin-builds acid from
4383918305arbutin-builds acid from
4383915963ribitol-builds acid from
4383917108D-arabinose-builds acid from
4383918333D-arabitol-builds acid from
4383928847D-fucose-builds acid from
4383912936D-galactose-builds acid from
4383962318D-lyxose-builds acid from
4383916899D-mannitol-builds acid from
4383916988D-ribose-builds acid from
4383917924D-sorbitol-builds acid from
4383916443D-tagatose-builds acid from
4383916813galactitol-builds acid from
4383917113erythritol-builds acid from
4383928066gentiobiose-builds acid from
4383924265gluconate-builds acid from
4383928087glycogen-builds acid from
4383917268myo-inositol-builds acid from
4383915443inulin-builds acid from
4383918403L-arabitol-builds acid from
4383962345L-rhamnose-builds acid from
4383917266L-sorbose-builds acid from
4383965328L-xylose-builds acid from
4383928053melibiose-builds acid from
43839320061methyl alpha-D-glucopyranoside-builds acid from
4383943943methyl alpha-D-mannoside-builds acid from
43839506227N-acetylglucosamine-builds acid from
4383928017starch-builds acid from
4383927082trehalose-builds acid from
4383932528turanose-builds acid from
4383917151xylitol-builds acid from
4383917632nitrate-reduction
4383917057cellobiose+builds acid from
4383915824D-fructose+builds acid from
4383917634D-glucose+builds acid from
4383916024D-mannose+builds acid from
4383917754glycerol+builds acid from
4383930849L-arabinose+builds acid from
4383917716lactose+builds acid from
4383917306maltose+builds acid from
4383974863methyl beta-D-xylopyranoside+builds acid from
4383916634raffinose+builds acid from
4383917992sucrose+builds acid from
438394853esculin+hydrolysis
4383965327D-xylose+/-builds acid from
438396731melezitose+/-builds acid from
4383917814salicin+/-builds acid from
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from

metabolite production

  • @ref: 43839
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43839catalase-1.11.1.6
43839cytochrome oxidase-1.9.3.1
43839urease+3.5.1.5
43839arginine dihydrolase+3.5.3.6
43839alkaline phosphatase+3.1.3.1
43839arginine arylamidase+
43839proline-arylamidase+3.4.11.5
43839phenylalanine arylamidase+
43839leucine arylamidase+3.4.11.1
43839pyroglutamic acid arylamidase+
43839tyrosine arylamidase+
43839alanine arylamidase+3.4.11.2
43839leucyl glycin arylamidase+3.4.11.1
43839histidine arylamidase+
43839serine arylamidase+
43839glutamyl-glutamate arylamidase+
43839lipase (C 14)-
43839valine arylamidase-
43839cystine arylamidase-3.4.11.3
43839alpha-chymotrypsin-3.4.21.1
43839alpha-galactosidase-3.2.1.22
43839beta-galactosidase-3.2.1.23
438396-phospho-beta-galactosidase-3.2.1.85
43839alpha-glucosidase-3.2.1.20
43839beta-glucosidase-3.2.1.21
43839alpha-arabinosidase-3.2.1.55
43839beta-glucuronidase-3.2.1.31
43839N-acetyl-beta-glucosaminidase-3.2.1.52
43839glutamate decarboxylase-4.1.1.15
43839alpha-fucosidase-3.2.1.51

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
24135----+-+--++++++/------+++/-+-+++/-+/-+++---+---++---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
24135faeces of baby common marmosets (Callithrix jacchus L.)Callithrix jacchusVeronaItalyITAEurope
43839The feaces of common marmosets (Callithrix jacchus L.)
67770Feces of a common marmosets

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Primates
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_160162.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_24;96_60314;97_78080;98_105433;99_160162&stattab=map
  • Last taxonomy: Bifidobacterium hapali subclade
  • 16S sequence: KP718961
  • Sequence Identity:
  • Total samples: 10364
  • soil counts: 73
  • aquatic counts: 98
  • animal counts: 10181
  • plant counts: 12

Safety information

risk assessment

  • @ref: 24135
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24135
  • description: Bifidobacterium hapali strain MRM_8.14 16S ribosomal RNA gene, partial sequence
  • accession: KP718961
  • length: 1381
  • database: ena
  • NCBI tax ID: 1630172

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bifidobacterium hapali DSM 100202GCA_002259755contigncbi1630172
66792Bifidobacterium hapali strain DSM 1002021630172.3wgspatric1630172
66792Bifidobacterium hapali DSM 1002022791355243draftimg1630172

GC content

@refGC-contentmethod
4383956.4
2413556.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.102no
gram-positiveyes92.645no
anaerobicyes93.566yes
aerobicno94.217no
halophileno89.121no
spore-formingno94.69no
glucose-utilyes87.452no
flagellatedno96.996yes
thermophileno96.188yes
glucose-fermentyes80.272no

External links

@ref: 24135

culture collection no.: DSM 100202, JCM 30799, MRM 8.14

straininfo link

  • @ref: 90692
  • straininfo: 401039

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26515885Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.).Michelini S, Oki K, Yanokura E, Shimakawa Y, Modesto M, Mattarelli P, Biavati B, Watanabe KInt J Syst Evol Microbiol10.1099/ijsem.0.0007082015Aldehyde-Lyases/metabolism, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Bifidobacterium/classification/genetics/isolation & purification, Callithrix/*microbiology, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Heat-Shock Proteins/genetics, Molecular Sequence Data, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny29395537Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov.Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura MSyst Appl Microbiol10.1016/j.syapm.2018.01.0022018Animals, Bacterial Typing Techniques, Base Sequence, Bifidobacterium/*classification/genetics, Callithrix/microbiology, Cricetinae/microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/*microbiology, Geese/microbiology, High-Throughput Nucleotide Sequencing, Italy, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rabbits/microbiology, Saguinus/microbiology, Sequence Analysis, DNATranscriptome

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
24135Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100202Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100202)
43839Samanta Michelini, Kaihei Oki, Emiko Yanokura, Yasuhisa Shimakawa, Monica Modesto, Paola Mattarelli, Bruno Biavati, Koichi WatanabeBifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.)10.1099/ijsem.0.000708IJSEM 66: 255-265 201626515885
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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
90692Reimer, 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-ID401039.1