Strain identifier
BacDive ID: 137143
Type strain:
Species: Bifidobacterium bifidum
Strain Designation: S28a
Strain history: CIP <- 1964, Lab. Ident. Inst. Pasteur, Paris, France <- M. Sebald, Inst. Pasteur, Paris, France <- H. Werner <- G. Reuter: strain S28a
NCBI tax ID(s): 1207542 (strain), 1681 (species)
General
@ref: 37007
BacDive-ID: 137143
keywords: genome sequence, Bacteria, anaerobe, mesophilic
description: Bifidobacterium bifidum S28a is an anaerobe, mesophilic bacterium that was isolated from Intestine of infant.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1207542 | strain |
1681 | species |
strain history
@ref | history |
---|---|
67770 | T. Mitsuoka IV-4 <-- G. Reuter S28a (Variant b). |
37007 | CIP <- 1964, Lab. Ident. Inst. Pasteur, Paris, France <- M. Sebald, Inst. Pasteur, Paris, France <- H. Werner <- G. Reuter: strain S28a |
doi: 10.13145/bacdive137143.20230509.8.1
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 bifidum
- full scientific name: Bifidobacterium bifidum (Tissier 1900) Orla-Jensen 1924 (Approved Lists 1980)
synonyms
@ref synonym 20215 Bacillus bifidus 20215 Bacterium bifidum
@ref: 37007
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Bifidobacteriales
family: Bifidobacteriaceae
genus: Bifidobacterium
species: Bifidobacterium bifidum
strain designation: S28a
type strain: no
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 94.466 | ||
69480 | 99.999 | positive | ||
37007 | no | positive | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | composition | link |
---|---|---|---|---|
37007 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml) | |
37007 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
37007 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
69480 | anaerobe | 98.243 |
37007 | anaerobe |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.99
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
37007 | 17632 | nitrate | - | reduction |
37007 | 16301 | nitrite | - | reduction |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | + | fermentation |
68379 | 17716 | lactose | + | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
68381 | 29016 | arginine | - | hydrolysis |
68381 | 16988 | D-ribose | - | builds acid from |
68381 | 16899 | D-mannitol | - | builds acid from |
68381 | 30911 | sorbitol | - | builds acid from |
68381 | 17716 | lactose | + | builds acid from |
68381 | 27082 | trehalose | - | builds acid from |
68381 | 16634 | raffinose | - | builds acid from |
68381 | 17992 | sucrose | - | builds acid from |
68381 | 30849 | L-arabinose | - | builds acid from |
68381 | 18333 | D-arabitol | - | builds acid from |
68381 | 40585 | alpha-cyclodextrin | - | builds acid from |
68381 | 606565 | hippurate | - | hydrolysis |
68381 | 28087 | glycogen | - | builds acid from |
68381 | 27941 | pullulan | - | builds acid from |
68381 | 17306 | maltose | - | builds acid from |
68381 | 28053 | melibiose | - | builds acid from |
68381 | 6731 | melezitose | - | builds acid from |
68381 | 320055 | methyl beta-D-glucopyranoside | - | builds acid from |
68381 | 16443 | D-tagatose | - | builds acid from |
68381 | 16199 | urea | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
37007 | 35581 | indole | no |
68380 | 35581 | indole | no |
68381 | 15688 | acetoin | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68381 | 15688 | acetoin | - | |
68380 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68381 | urease | - | 3.5.1.5 |
68381 | beta-mannosidase | - | 3.2.1.25 |
68381 | glycyl tryptophan arylamidase | - | |
68381 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68381 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68381 | beta-galactosidase | + | 3.2.1.23 |
68381 | Alanyl-Phenylalanyl-Proline arylamidase | + | |
68381 | alkaline phosphatase | - | 3.1.3.1 |
68381 | alpha-galactosidase | + | 3.2.1.22 |
68381 | beta-glucuronidase | - | 3.2.1.31 |
68381 | beta-glucosidase | - | 3.2.1.21 |
68381 | arginine dihydrolase | - | 3.5.3.6 |
68380 | serine arylamidase | + | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | + | |
68380 | glycin arylamidase | + | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | + | |
68380 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | phenylalanine arylamidase | + | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | + | 3.4.11.5 |
68380 | L-arginine arylamidase | + | |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68379 | catalase | - | 1.11.1.6 |
68379 | gelatinase | - | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | - | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
37007 | oxidase | - | |
37007 | catalase | - | 1.11.1.6 |
37007 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | Control | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
65639 | - | + | - | + | - | + | + | + | - | - | - | - | + | - | - | - | + | + | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
37007 | - | - | - | - | - | + | - | - | - | - | + | + | - | + | - | - | - | + | - | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
65639 | - | - | + | + | - | + | - | - | - | + | - | - | - | - | - | - | - | + | + | - | + | + | + | + | + | + | + | - | + |
API rID32STR
@ref | ADH Arg | beta GLU | beta GAR | beta GUR | alpha GAL | PAL | RIB | MAN | SOR | LAC | TRE | RAF | SAC | LARA | DARL | CDEX | VP | APPA | beta GAL | PyrA | beta NAG | GTA | HIP | GLYG | PUL | MAL | MEL | MLZ | Mbeta DG | TAG | beta MAN | URE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
65639 | - | - | + | - | + | - | - | - | - | + | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
67770 | Intestine of infant |
37007 | Human, Infant, intestine |
Safety information
risk assessment
- @ref: 37007
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bifidobacterium bifidum LMG 13195 JCM 7004 | GCA_003573955 | complete | ncbi | 1207542 |
66792 | Bifidobacterium bifidum LMG 13195 strain JCM 7004 | 1207542.9 | complete | patric | 1207542 |
66792 | Bifidobacterium bifidum JCM 7004 | 2859461767 | complete | img | 1681 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 86 | no |
motile | no | 93.622 | no |
flagellated | no | 96.037 | no |
gram-positive | yes | 92.094 | no |
anaerobic | yes | 97.89 | no |
aerobic | no | 96.193 | no |
halophile | no | 77.097 | no |
spore-forming | no | 96.332 | no |
glucose-util | yes | 88.305 | no |
thermophile | no | 97.88 | no |
glucose-ferment | yes | 85.882 | yes |
External links
@ref: 37007
culture collection no.: CIP 64.65, ATCC 15696, NCDO 2203, CCUG 45219, JCM 7004, BCRC 14614, CCUG 17358, KCTC 3418, LMG 10644
straininfo link
- @ref: 94106
- straininfo: 264229
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 7836576 | Growth and viability of Bifidobacterium bifidum in cheddar cheese. | Dinakar P, Mistry VV | J Dairy Sci | 10.3168/jds.S0022-0302(94)77225-8 | 1994 | Bifidobacterium/growth & development/*physiology, Cheese/*microbiology, Chromatography, High Pressure Liquid, Dietary Proteins/metabolism, Microscopy, Electron, Scanning, Taste, Time Factors | |
Pathogenicity | 8872711 | Growth characteristics of bifidobacteria in infant formulas. | Dubey UK, Mistry VV | J Dairy Sci | 10.3168/jds.S0022-0302(96)76468-8 | 1996 | Acetic Acid/metabolism, Animals, Bifidobacterium/cytology/*growth & development, Buffers, Caseins, Fats/analysis, Humans, Hydrogen-Ion Concentration, Infant Food/analysis/*microbiology, Infant, Newborn, Kinetics, Lactic Acid/biosynthesis, Milk, Protein Hydrolysates, Proteins/analysis, Soybeans | Enzymology |
Pathogenicity | 8872712 | Effect of bifidogenic factors on growth characteristics of bifidobacteria in infant formulas. | Dubey UK, Mistry VV | J Dairy Sci | 10.3168/jds.S0022-0302(96)76469-X | 1996 | Acetic Acid/metabolism, Bifidobacterium/*drug effects/*growth & development, Caseins, Colony Count, Microbial, Fructose/*pharmacology, Humans, Hydrogen-Ion Concentration, Infant, Infant Food/analysis/*microbiology, Lactic Acid/biosynthesis, Lactulose/*pharmacology, Oligosaccharides/*pharmacology, Protein Hydrolysates, Soybeans | Metabolism |
Metabolism | 12926870 | Andean yacon root (Smallanthus sonchifolius Poepp. Endl) fructooligosaccharides as a potential novel source of prebiotics. | Pedreschi R, Campos D, Noratto G, Chirinos R, Cisneros-Zevallos L | J Agric Food Chem | 10.1021/jf0344744 | 2003 | Asteraceae/*chemistry, Bifidobacterium/metabolism, Chromatography, Gel, Fermentation, Lactobacillus/metabolism, Lactobacillus acidophilus/metabolism, Oligosaccharides/*metabolism, Plant Roots/*chemistry, Probiotics/*metabolism | |
Metabolism | 15039348 | Probiotic bifidobacteria protect mice from lethal infection with Shiga toxin-producing Escherichia coli O157:H7. | Asahara T, Shimizu K, Nomoto K, Hamabata T, Ozawa A, Takeda Y | Infect Immun | 10.1128/IAI.72.4.2240-2247.2004 | 2004 | Acetic Acid/pharmacology, Animals, Bifidobacterium/*growth & development, Disease Models, Animal, Escherichia coli Infections/microbiology/*prevention & control, Escherichia coli O157/*pathogenicity, Escherichia coli Proteins/metabolism, Gene Expression Regulation, Bacterial, Humans, Hydrogen-Ion Concentration, Intestines/microbiology, Male, Mice, Mice, Inbred BALB C, *Probiotics, Shiga Toxin 1/genetics/*metabolism, Shiga Toxin 2/genetics/*metabolism | Pathogenicity |
Phylogeny | 26859305 | Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome. | Abdulkadir B, Nelson A, Skeath T, Marrs EC, Perry JD, Cummings SP, Embleton ND, Berrington JE, Stewart CJ | Neonatology | 10.1159/000442936 | 2016 | Bifidobacterium/isolation & purification, Case-Control Studies, *Dietary Supplements, Feces/microbiology, Female, *Gastrointestinal Microbiome, Humans, Infant, Infant, Newborn, *Infant, Premature, Lactobacillus/isolation & purification, Male, *Metabolome, Probiotics/*administration & dosage, RNA, Ribosomal, 16S/analysis | Enzymology |
Metabolism | 28814130 | Identification and characterization of a sulfoglycosidase from Bifidobacterium bifidum implicated in mucin glycan utilization. | Katoh T, Maeshibu T, Kikkawa KI, Gotoh A, Tomabechi Y, Nakamura M, Liao WH, Yamaguchi M, Ashida H, Yamamoto K, Katayama T | Biosci Biotechnol Biochem | 10.1080/09168451.2017.1361810 | 2017 | Acetylglucosaminidase/chemistry/genetics/*metabolism, Amino Acid Sequence, Bifidobacterium bifidum/*enzymology/genetics/metabolism, Gene Expression Regulation, Bacterial, Mucins/*metabolism, Polysaccharides/*metabolism | Enzymology |
Metabolism | 28974612 | Bifidobacterium bifidum Extracellular Sialidase Enhances Adhesion to the Mucosal Surface and Supports Carbohydrate Assimilation. | Nishiyama K, Yamamoto Y, Sugiyama M, Takaki T, Urashima T, Fukiya S, Yokota A, Okada N, Mukai T | mBio | 10.1128/mBio.00928-17 | 2017 | Animals, *Bacterial Adhesion, Bifidobacterium bifidum/drug effects/*enzymology/genetics/*physiology, *Carbohydrate Metabolism, Colon/microbiology, Epithelial Cells/microbiology, Humans, Mice, Mucins/metabolism, Neuraminidase/*metabolism, Oligosaccharides/chemistry/pharmacology, Polysaccharides/metabolism, Protein Binding, Recombinant Proteins/genetics/metabolism, Swine | Pathogenicity |
Metabolism | 30228375 | Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum. | Gotoh A, Katoh T, Sakanaka M, Ling Y, Yamada C, Asakuma S, Urashima T, Tomabechi Y, Katayama-Ikegami A, Kurihara S, Yamamoto K, Harata G, He F, Hirose J, Kitaoka M, Okuda S, Katayama T | Sci Rep | 10.1038/s41598-018-32080-3 | 2018 | Adult, Bacterial Proteins/genetics/*metabolism, Bifidobacteriales Infections/*metabolism/microbiology, Bifidobacterium/classification/genetics/*metabolism, Cells, Cultured, Child, Preschool, Dietary Supplements, Feces/*microbiology, Female, Gastrointestinal Microbiome, Genome, Bacterial, Humans, Infant, Male, Milk, Human/*metabolism, Oligosaccharides/*metabolism | Genetics |
Metabolism | 30683741 | Bifidobacterium bifidum ATCC 15696 and Bifidobacterium breve 24b Metabolic Interaction Based on 2'-O-Fucosyl-Lactose Studied in Steady-State Cultures in a Freter-Style Chemostat. | Centanni M, Ferguson SA, Sims IM, Biswas A, Tannock GW | Appl Environ Microbiol | 10.1128/AEM.02783-18 | 2019 | Batch Cell Culture Techniques, Bifidobacterium bifidum/genetics/*growth & development/*metabolism, Bifidobacterium breve/genetics/*growth & development/*metabolism, Coculture Techniques, Culture Media/chemistry, Ecosystem, Fucose/metabolism, Gastrointestinal Microbiome, Humans, Intestines/microbiology, Lactose/metabolism, Milk, Human/chemistry, Oligosaccharides/metabolism, Transcriptome, Trisaccharides/*metabolism | Pathogenicity |
Pathogenicity | 34794372 | Effectiveness of two probiotics in preventing necrotising enterocolitis in a cohort of very-low-birth-weight premature new-borns. | Uberos J, Campos-Martinez A, Fernandez-Marin E, Millan IC, Lopez AR, Blanca-Jover E | Benef Microbes | 10.3920/BM2021.0088 | 2021 | *Enterocolitis, Necrotizing/epidemiology/prevention & control, Humans, Infant, Newborn, Infant, Premature, Infant, Very Low Birth Weight, Lactobacillus acidophilus, *Probiotics/therapeutic use |
Reference
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
37007 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2064.65 | Collection of Institut Pasteur (CIP 64.65) | |
65639 | Curators of the CCUG | https://www.ccug.se/strain?id=45219 | Culture Collection University of Gothenburg (CCUG) (CCUG 45219) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68379 | Automatically annotated from API Coryne | |||
68380 | Automatically annotated from API rID32A | |||
68381 | Automatically annotated from API rID32STR | |||
68382 | Automatically annotated from API zym | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
94106 | Reimer, 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 identifiers | 10.60712/SI-ID264229.1 |