Strain identifier
BacDive ID: 1601
Type strain:
Species: Phocaeicola vulgatus
Strain Designation: LRA 049 07 85
Strain history: CIP <- 1993, R. Mercier, bioMérieux, La Balme les Grottes, France: strain LRA 049 07 85 <- 1985, Analytab, Plainview, USA <- ATCC <- A.H. Eggerth
NCBI tax ID(s): 435590 (strain), 821 (species)
General
@ref: 769
BacDive-ID: 1601
DSM-Number: 1447
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped, human pathogen
description: Phocaeicola vulgatus LRA 049 07 85 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human faeces.
NCBI tax id
NCBI tax id | Matching level |
---|---|
821 | species |
435590 | strain |
strain history
@ref | history |
---|---|
769 | <- ATCC <- A.H. Eggerth |
67770 | ATCC 8482 <-- A. H. Eggerth. |
123893 | CIP <- 1993, R. Mercier, bioMérieux, La Balme les Grottes, France: strain LRA 049 07 85 <- 1985, Analytab, Plainview, USA <- ATCC <- A.H. Eggerth |
doi: 10.13145/bacdive1601.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Bacteroidia
- order: Bacteroidales
- family: Bacteroidaceae
- genus: Phocaeicola
- species: Phocaeicola vulgatus
- full scientific name: Phocaeicola vulgatus (Eggerth and Gagnon 1933) García-López et al. 2020
synonyms
- @ref: 20215
- synonym: Bacteroides vulgatus
@ref: 769
domain: Bacteria
phylum: Bacteroidetes
class: Bacteroidia
order: Bacteroidales
family: Bacteroidaceae
genus: Phocaeicola
species: Phocaeicola vulgatus
full scientific name: Phocaeicola vulgatus (Eggerth and Gagnon 1933) García-López et al. 2020
strain designation: LRA 049 07 85
type strain: yes
Morphology
cell morphology
- @ref: 123893
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
@ref | type of hemolysis | incubation period |
---|---|---|
769 | gamma | 1-2 days |
123893 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
769 | FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) | yes | https://mediadive.dsmz.de/medium/1203a | Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water |
769 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water |
769 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
34918 | 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) | |
123893 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
769 | positive | growth | 37 | mesophilic |
34918 | positive | growth | 37 | mesophilic |
44810 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
123893 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
769 | anaerobe |
44810 | anaerobe |
123893 | anaerobe |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
123893 | 4853 | esculin | - | hydrolysis |
123893 | 17632 | nitrate | - | reduction |
123893 | 16301 | nitrite | - | reduction |
123893 | 17632 | nitrate | + | respiration |
68380 | 16199 | urea | - | hydrolysis |
68380 | 16024 | D-mannose | + | fermentation |
68380 | 16634 | raffinose | + | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
antibiotic resistance
- @ref: 123893
- ChEBI: 6909
- metabolite: metronidazole
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
123893 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
769 | catalase | - | 1.11.1.6 |
769 | cytochrome-c oxidase | - | 1.9.3.1 |
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 |
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 | 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 | alpha-arabinosidase | + | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | urease | - | 3.5.1.5 |
123893 | oxidase | - | |
123893 | beta-galactosidase | + | 3.2.1.23 |
123893 | gelatinase | - | |
123893 | amylase | - | |
123893 | DNase | - | |
123893 | caseinase | + | 3.4.21.50 |
123893 | catalase | - | 1.11.1.6 |
123893 | tween esterase | - | |
123893 | lecithinase | - | |
123893 | lipase | - | |
123893 | protease | - | |
123893 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123893 | - | + | - | - | - | - | - | - | - | - | + | + | + | + | + | + | - | + | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
769 | - | - | + | + | - | + | - | + | - | + | + | + | - | + | - | - | + | - | - | + | - | - | - | - | + | + | - | + | - |
769 | - | - | + | + | +/- | + | - | + | +/- | + | + | + | - | + | - | - | + | - | - | + | - | - | - | - | + | + | - | + | - |
769 | - | + | + | + | - | + | - | + | - | + | + | + | - | + | - | - | + | - | - | + | - | - | - | - | + | + | - | + | - |
769 | - | - | + | + | - | + | - | + | +/- | + | + | + | - | + | - | - | + | - | - | + | - | - | - | - | + | + | - | + | - |
769 | - | - | + | + | - | + | - | + | + | + | + | + | - | + | - | - | - | - | - | + | - | - | - | - | + | + | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
769 | human faeces |
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Gastrointestinal tract | #Feces (Stool) |
taxonmaps
- @ref: 69479
- File name: preview.99_830.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_500;97_573;98_659;99_830&stattab=map
- Last taxonomy: Phocaeicola vulgatus subclade
- 16S sequence: AB510712
- Sequence Identity:
- Total samples: 152509
- soil counts: 881
- aquatic counts: 2761
- animal counts: 148487
- plant counts: 380
Safety information
risk assessment
@ref | pathogenicity human | biosafety level | biosafety level comment |
---|---|---|---|
769 | yes, in single cases | 1 | Risk group (German classification) |
123893 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bacteroides vulgatus 16S-23S rDNA intergenic spacer region | AF176693 | 426 | ena | 435590 |
20218 | Bacteroides vulgatus 16S rRNA gene, strain ATCC 8482 | AJ867050 | 1476 | ena | 435590 |
20218 | Bacteroides vulgatus strain DSM 1447 16S ribosomal RNA gene, partial sequence | HQ012024 | 931 | ena | 821 |
20218 | Bacteroides vulgatus 16S ribosomal RNA gene, partial sequence | M58762 | 1533 | ena | 821 |
769 | Bacteroides vulgatus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5826 | AB510712 | 1489 | ena | 821 |
67770 | Bacteroides vulgatus gene for 16S rRNA, partial sequence | AB050111 | 1397 | ena | 821 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Phocaeicola vulgatus ATCC 8482 | GCA_000012825 | complete | ncbi | 435590 |
66792 | Bacteroides vulgatus ATCC 8482 | 435590.9 | complete | patric | 435590 |
66792 | Bacteroides vulgatus ATCC 8482 strain Bacteroides vulgatus 81B11 | 435590.45 | wgs | patric | 435590 |
66792 | Phocaeicola vulgatus strain FDAARGOS_1098 | 821.4031 | complete | patric | 821 |
66792 | Phocaeicola vulgatus ATCC 8482 | 2886510283 | draft | img | 435590 |
66792 | Phocaeicola vulgatus ATCC 8482 | 2510065017 | draft | img | 435590 |
66792 | Bacteroides vulgatus ATCC 8482 | 640753008 | complete | img | 435590 |
66792 | Phocaeicola vulgatus ATCC 8482 | GCA_028538915 | contig | ncbi | 435590 |
GC content
@ref | GC-content | method |
---|---|---|
769 | 41.0 | thermal denaturation, midpoint method (Tm) |
769 | 42.2 | sequence analysis |
67770 | 41 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 92.573 | no |
flagellated | no | 96.829 | no |
gram-positive | no | 95.915 | no |
anaerobic | yes | 98.138 | yes |
halophile | no | 90.584 | no |
spore-forming | no | 94.139 | no |
thermophile | no | 99.193 | no |
glucose-util | yes | 89.899 | no |
aerobic | no | 96.897 | yes |
glucose-ferment | yes | 78.492 | no |
External links
@ref: 769
culture collection no.: DSM 1447, ATCC 8482, CCUG 4940, JCM 5826, BCRC 12903, CIP 103714, IAM 14520, IFO 14291, LMG 7956, NBRC 14291, NCTC 11154
straininfo link
- @ref: 71246
- straininfo: 9749
literature
Pubmed-ID | title | authors | journal | DOI | year | mesh | topic | topic2 |
---|---|---|---|---|---|---|---|---|
6837522 | Demonstration of bacteroides capsules by light microscopy and ultrastructural cytochemistry. | Strohm H, Payne CM, Ryan KJ | Am J Clin Pathol | 10.1093/ajcp/79.5.591 | 1983 | Bacteroides fragilis/analysis/*cytology/ultrastructure, Cell Membrane/analysis, Histocytochemistry, Ink, Polysaccharides, Bacterial/analysis | ||
8182163 | Growth stimulator for bifidobacteria produced by Propionibacterium freudenreichii and several intestinal bacteria. | Kaneko T, Mori H, Iwata M, Meguro S | J Dairy Sci | 10.3168/jds.S0022-0302(94)76965-4 | 1994 | Bacteroides/drug effects/growth & development, Bifidobacterium/*drug effects/*growth & development, Fatty Acids/pharmacology, Food Microbiology, Food Preservatives/pharmacology, Growth Substances/*biosynthesis/isolation & purification/pharmacology, Humans, In Vitro Techniques, Intestines/*microbiology, Propionibacterium/*metabolism | Pathogenicity | Biotechnology |
16825642 | Bacteroides dorei sp. nov., isolated from human faeces. | Bakir MA, Sakamoto M, Kitahara M, Matsumoto M, Benno Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.64257-0 | 2006 | Anaerobiosis, Bacterial Typing Techniques, Bacteroides/*classification/cytology/*isolation & purification/physiology, Bacteroides Infections/*microbiology, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Feces/*microbiology, Genes, rRNA, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial | Phylogeny | Pathogenicity |
20495039 | Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces. | Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijs.0.024026-0 | 2010 | Anaerobiosis, Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Base Composition, Chinchilla/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Phylogeny | Genetics |
21872662 | Structural characterization of BVU_3255, a methyltransferase from human intestine antibiotic resistant pathogen Bacteroides vulgatus. | Kumar V, Sivaraman J | J Struct Biol | 10.1016/j.jsb.2011.08.007 | 2011 | Bacterial Proteins/*chemistry, Bacteroides/*enzymology, Binding Sites, Catalytic Domain, Crystallography, X-Ray, Drug Resistance, Bacterial, Humans, Intestines/*microbiology, Methylation, Methyltransferases/*chemistry, Protein Folding, Protein Structure, Secondary, S-Adenosylhomocysteine/chemistry, S-Adenosylmethionine/chemistry, Ubiquinone/biosynthesis | Pathogenicity | Proteome |
24013960 | Utilization of major fucosylated and sialylated human milk oligosaccharides by isolated human gut microbes. | Yu ZT, Chen C, Newburg DS | Glycobiology | 10.1093/glycob/cwt065 | 2013 | Bacterial Proteins/metabolism, Bacteroides/growth & development/isolation & purification/metabolism, Bifidobacterium/growth & development/isolation & purification/metabolism, Clostridium/growth & development/isolation & purification/metabolism, Culture Media, Enterococcus faecalis/growth & development/isolation & purification/metabolism, Escherichia coli K12/growth & development/isolation & purification/metabolism, Fucose/metabolism, Gastrointestinal Tract/*microbiology, Glycosylation, Humans, Hydrogen-Ion Concentration, Lactobacillus delbrueckii/growth & development/isolation & purification/metabolism, *Microbiota, Milk, Human/*metabolism, Oligosaccharides/*metabolism, Sialic Acids/metabolism, Streptococcus thermophilus/growth & development/isolation & purification/metabolism, alpha-L-Fucosidase/metabolism | Metabolism | Phylogeny |
24026770 | Production of AI-2 is mediated by the S-ribosylhomocystein lyase gene luxS in Bacteroides fragilis and Bacteroides vulgatus. | Peixoto RJ, Miranda KR, Ferreira EO, de Paula GR, Rocha ER, Lobo LA, Domingues RM | J Basic Microbiol | 10.1002/jobm.201300311 | 2013 | Amino Acid Sequence, Bacterial Proteins/*genetics/metabolism, Bacteroides/*genetics/metabolism, Bacteroides fragilis/*genetics/metabolism, Biofilms/*growth & development, Carbon-Sulfur Lyases/*genetics/metabolism, Conserved Sequence, Escherichia coli/genetics/metabolism, *Gene Expression Regulation, Bacterial, Genetic Complementation Test, Homoserine/*analogs & derivatives/biosynthesis, Lactones, Molecular Sequence Data, Quorum Sensing, Recombinant Proteins/genetics/metabolism, Sequence Alignment, Signal Transduction | Metabolism | Genetics |
27040269 | Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium. | Li J, Mandal G, Rosen BP | Anaerobe | 10.1016/j.anaerobe.2016.03.012 | 2016 | Anaerobiosis/genetics, Arsenicals/*pharmacology, Bacterial Proteins/*genetics/metabolism, Bacteroides/*drug effects/genetics/isolation & purification/metabolism, Drug Resistance, Bacterial/*genetics, Gastrointestinal Microbiome/physiology, *Gene Expression Regulation, Bacterial, *Genome, Bacterial, Humans, Operon, Transcription, Genetic | Pathogenicity | Metabolism |
27071651 | Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk. | Lange A, Beier S, Steimle A, Autenrieth IB, Huson DH, Frick JS | Genome Biol Evol | 10.1093/gbe/evw070 | 2016 | Animals, Bacteroides/*genetics, Base Sequence, CRISPR-Cas Systems, DNA, Bacterial/genetics, *Evolution, Molecular, *Gene Transfer, Horizontal, *Genome, Bacterial, Intestines/microbiology, Mice/*microbiology, Phylogeny | Genetics | Phylogeny |
28397401 | Anaerobic utilization of Fe(III)-xenosiderophores among Bacteroides species and the distinct assimilation of Fe(III)-ferrichrome by Bacteroides fragilis within the genus. | Rocha ER, Krykunivsky AS | Microbiologyopen | 10.1002/mbo3.479 | 2017 | Anaerobiosis, Bacterial Proteins/genetics/metabolism, Bacteroides/genetics/*metabolism, Biological Transport, Enterobactin/analogs & derivatives/metabolism, Ferric Compounds/*metabolism, Ferrichrome/*metabolism, Gene Deletion, Genetic Complementation Test, Glucosides/metabolism, Membrane Transport Proteins/genetics/metabolism, Siderophores/*metabolism | Metabolism | |
28583864 | The gut bacterium and pathobiont Bacteroides vulgatus activates NF-kappaB in a human gut epithelial cell line in a strain and growth phase dependent manner. | O Cuiv P, de Wouters T, Giri R, Mondot S, Smith WJ, Blottiere HM, Begun J, Morrison M | Anaerobe | 10.1016/j.anaerobe.2017.06.002 | 2017 | Bacteroides/*immunology, Cell Line, Chemokine CCL2/biosynthesis, Chemokine CXCL10/biosynthesis, Epithelial Cells/*immunology/*microbiology, Gastrointestinal Tract/*immunology/*microbiology, Gene Expression, *Host-Pathogen Interactions, Humans, Interleukin-6/biosynthesis, Interleukin-8/biosynthesis, NF-kappa B/*metabolism, Protein Transport, Up-Regulation | Pathogenicity | Metabolism |
29535205 | The Biosynthesis of Lipooligosaccharide from Bacteroides thetaiotaomicron. | Jacobson AN, Choudhury BP, Fischbach MA | mBio | 10.1128/mBio.02289-17 | 2018 | Bacteroides thetaiotaomicron/*genetics/*metabolism, Biosynthetic Pathways/*genetics, Lipopolysaccharides/*biosynthesis/chemistry, Mutation, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization | Metabolism | |
31177942 | The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice. | Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR | Gut Microbes | 10.1080/19490976.2019.1618173 | 2019 | Animals, Bacteria, Anaerobic/*genetics/*metabolism, Bacteroides/genetics/metabolism, Bile Acids and Salts/*metabolism, Bilophila/genetics/metabolism, Cecum/*microbiology, Cholic Acids/metabolism, Clostridium/genetics/metabolism, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics, Germ-Free Life, Humans, *Metabolome, Mice, Mice, Inbred C57BL, Microbiota, Operon, RNA-Seq, *Transcriptome, Up-Regulation | Metabolism | Genetics |
31291601 | Binary interactions between the yeast Candida albicans and two gut-associated Bacteroides species. | Valentine M, Benade E, Mouton M, Khan W, Botha A | Microb Pathog | 10.1016/j.micpath.2019.103619 | 2019 | Anaerobiosis, Bacteroides/drug effects/*growth & development, Bacteroides fragilis/growth & development, Candida albicans/drug effects/*growth & development/metabolism, Cell Wall/chemistry, Chloramphenicol/pharmacology, Coculture Techniques, Culture Media/chemistry, Gastrointestinal Microbiome/*physiology, Humans, Mannans, Microbial Interactions/*physiology, Microbial Viability, Oxygen | Pathogenicity | Metabolism |
33148507 | Bacteroides vulgatus diminishes colonic microbiota dysbiosis ameliorating lumbar bone loss in ovariectomized mice. | Yuan S, Shen J | Bone | 10.1016/j.bone.2020.115710 | 2020 | Animals, Bacteroides, *Dysbiosis/drug therapy, Female, *Gastrointestinal Microbiome, Humans, Mice, NF-kappa B, Ovariectomy | Pathogenicity | |
34040330 | Gut microbiota dysbiosis in Chinese children with type 1 diabetes mellitus: An observational study. | Liu X, Cheng YW, Shao L, Sun SH, Wu J, Song QH, Zou HS, Ling ZX | World J Gastroenterol | 10.3748/wjg.v27.i19.2394 | 2021 | Bacteroides, Child, China/epidemiology, Clostridiales, *Diabetes Mellitus, Type 1/diagnosis, Dysbiosis, *Gastrointestinal Microbiome, Humans, RNA, Ribosomal, 16S/genetics | Pathogenicity | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
769 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1447) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1447 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
34918 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15542 | ||||
44810 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 4940) | https://www.ccug.se/strain?id=4940 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
71246 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID9749.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123893 | Curators of the CIP | Collection of Institut Pasteur (CIP 103714) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103714 |