B. ovatus (ATCC 8483), B. caccae (ATCC 43185), B. thetaiotaomicron (VPI 5482), B. vulgatus (ATCC 8482), R. gnavus (ATCC 29149), C. bolteae (ATCC BAA-613), C. aerofaciens (ATCC 25986) and E. coli (K-12 MG1655), P. johnsonii (DSMZ 18315) and B. intestinalis (DSMZ 17393) were obtained from global repositories: the American Type Culture Collection (ATCC) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). Apart from E. coli, the bacterial strains were grown under anaerobic condition at 37°C in Brain Heart Infusion (BHI) medium supplemented with 0.5% yeast extract (Difco Laboratories), 0.4% monosaccharide mixture, 0.3% disaccharide mixture, L-cysteine (0.5 mg/ml; Sigma-Aldrich), malic acid (1 mg/ml; Sigma-Aldrich) and 5 μg/ml hemin. LB Broth Miller (EMD Chemicals, Inc.) was used for E. coli culture under aerobic conditions at 37°C. After bacterial cultures reached an OD600 of 1–2, glycerol was added to a final concentration of 15% (v/v). The mixture was aliquoted into glass vials with a crimped top and stored at −80°C freezer for further use.
B ovatus
Manufactured by American Type Culture Collection
B. ovatus is a strain of bacterium maintained by the American Type Culture Collection. It is a gram-negative, obligately anaerobic bacterium. The core function of this strain is to serve as a reference culture for research and identification purposes.
Automatically generated - may contain errors
Lab products found in correlation
B vulgatus, by American Type Culture Collection (5 mentions)
B caccae, by American Type Culture Collection (4 mentions)
B intestinalis, by American Type Culture Collection (3 mentions)
B finegoldii, by American Type Culture Collection (2 mentions)
B stercoris, by American Type Culture Collection (2 mentions)
B uniformis, by American Type Culture Collection (2 mentions)
B eggerthii, by American Type Culture Collection (2 mentions)
Malic acid, by Merck Group (1 mentions)
Yeast extract, by BD (1 mentions)
L cysteine, by Merck Group (1 mentions)
Platinum taq polymerase, by Thermo Fisher Scientific (1 mentions)
Qiamp dna stool mini kit, by Qiagen (1 mentions)
Parabacteroides distasonis, by American Type Culture Collection (1 mentions)
Qiamp dna mini kit, by Qiagen (1 mentions)
Bacteroides caccae, by American Type Culture Collection (1 mentions)
5 protocols using b ovatus
1
Cultivation and Cryopreservation of Gut Microbiota
2
Gut Microbiome Diversity Profiling
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The Bacteroides strains used were: B. thetaiotaomicron VPI-5482, B. fragilis NCTC9343, B. caccae ATCC43185, B. cellulosilyticus DSM14838, B. finegoldii DSM17565, B. vulgatus ATCC8483, B. ovatus ATCC8482, B. intestinalis DSM17393, and Akkermansia muciniphila ATCC BAA835/DSM22959.
3
Characterization of Bacteroides fragilis Strains
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Bacterial DNA from the 84 feces samples and 192 bacterial isolates was obtained
using, respectively, the commercial QIAmp DNA Stool Mini Kit and QIAmp DNA Mini Kit
(QIAGEN), according to the manufacturer's instructions. DNA was stored at −80 °C
until use.
The presence of B. fragilis in the fecal samples was detected by PCR
amplification with 16S rRNA primers. DNA from the bacterial isolates was amplified
with 16S-23S rRNA primers. All DNA samples positive for B. fragiliswere screened for the presence of ETBF and/or NTBF sequences. The oligonucleotide
pairs and amplification conditions used are described inTable 1 .
All PCR assays were performed as follows: 1X PCR buffer, 50 mM MgCl2, 0.2
mM dNTP mix, 0.4 mM each primer, 0.5 U of Platinum Taq polymerase
(Invitrogen), and 1 ng of DNA. PCR products were analyzed by 1% agarose gel
electrophoresis, stained with 0.5 μg/mL of ethidium bromide and photographed under UV
light.
B. fragilis ATCC 43858 (ETBF pattern I, bft+) and ATCC 25285 (NTBF pattern III, bft-) were used, respectively, as positive and negative controls. The other
strains used as controls were: B. thetaiotaomicron ATCC 29741,
B. vulgatus ATCC 8482, B. caccae ATCC 43185,
B. ovatus ATCC 8483, B. eggerthii ATCC 27754,
B. uniformis ATCC 8492, B. stercoris ATCC 43183,
Parabacteroides distasonis ATCC 8503, and P.
merdae ATCC 43184.
using, respectively, the commercial QIAmp DNA Stool Mini Kit and QIAmp DNA Mini Kit
(QIAGEN), according to the manufacturer's instructions. DNA was stored at −80 °C
until use.
The presence of B. fragilis in the fecal samples was detected by PCR
amplification with 16S rRNA primers. DNA from the bacterial isolates was amplified
with 16S-23S rRNA primers. All DNA samples positive for B. fragiliswere screened for the presence of ETBF and/or NTBF sequences. The oligonucleotide
pairs and amplification conditions used are described in
All PCR assays were performed as follows: 1X PCR buffer, 50 mM MgCl2, 0.2
mM dNTP mix, 0.4 mM each primer, 0.5 U of Platinum Taq polymerase
(Invitrogen), and 1 ng of DNA. PCR products were analyzed by 1% agarose gel
electrophoresis, stained with 0.5 μg/mL of ethidium bromide and photographed under UV
light.
B. fragilis ATCC 43858 (ETBF pattern I, bft+) and ATCC 25285 (NTBF pattern III, bft-) were used, respectively, as positive and negative controls. The other
strains used as controls were: B. thetaiotaomicron ATCC 29741,
B. vulgatus ATCC 8482, B. caccae ATCC 43185,
B. ovatus ATCC 8483, B. eggerthii ATCC 27754,
B. uniformis ATCC 8492, B. stercoris ATCC 43183,
Parabacteroides distasonis ATCC 8503, and P.
merdae ATCC 43184.
4
Anaerobic Culture of Bacteroides Species
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Bacteroides species were grown in Tryptone Yeast Glucose broth (TYG) [16 (link)] in an anaerobic chamber (37°C, 5% CO2, 5% H2 and 90% N2) and included B. caccae ATCC 43185T, B. dorei JCM 13471, B. eggerthii ATCC 27754, B. fragilis NCTC 9343, B. finegoldii JCM13345, B. intestinalis JCM 13265, P. merdae ATCC 43184, B. ovatus JCM 5824, B. sartorii A-C2-0, B. stercoris ATCC 43183, B. thetaiotaomicron VPI 5482, B. uniformis JCM 5828T, and B. vulgatus ATCC 8482. Non-Bacteroides species included Prevotella stercorea JCM 13469T grown using Peptone Yeast Glucose broth (PYG, DSMZ Medium 104) and Escherichia coli grown in Luria Bertani broth (LB, BD 244620).
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Bacteroides species were grown in Tryptone Yeast Glucose broth (TYG) [16 (link)] in an anaerobic chamber (37°C, 5% CO2, 5% H2 and 90% N2) and included B. caccae ATCC 43185T, B. dorei JCM 13471, B. eggerthii ATCC 27754, B. fragilis NCTC 9343, B. finegoldii JCM13345, B. intestinalis JCM 13265, P. merdae ATCC 43184, B. ovatus JCM 5824, B. sartorii A-C2-0, B. stercoris ATCC 43183, B. thetaiotaomicron VPI 5482, B. uniformis JCM 5828T, and B. vulgatus ATCC 8482. Non-Bacteroides species included Prevotella stercorea JCM 13469T grown using Peptone Yeast Glucose broth (PYG, DSMZ Medium 104) and Escherichia coli grown in Luria Bertani broth (LB, BD 244620).
5
Anaerobic Growth of Bacteroidetes on Arabinogalactan
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Bacteroidetes sp. were grown on a 2x defined minimal media (Table S1 ) under anaerobic conditions at 37 °C over 24 hours to assay growth on various carbon sources, including arabinogalactan. Strains used were Bacteroides caccae ATCC 43185, B. cellulosilyticus DSM 14838, B. dorei DSM 17855, B. finegoldii DSM 17565, B. intestinalis DSM 17393, B. nordii CL02T12C05, B. ovatus ATCC 8483, B. thetaiotaomicron VPI-5482, B. vulgatus ATCC 8482, B. xylanisolvens XB1A, Dysgonomonas gadei ATCC BAA-286, D. mossii DSM 22836, Parabacteroides gordonii DSM 23371, P. johnsonii DSM 18315. Escherichia coli and Pseudomonas aeruginosa PA7 ATCC 15692 strains were grown in lysogeny broth at 37 °C (unless otherwise specified). Mycobacterium smegmatis mc2155 ATCC 19420 was grown in Tryptic soy Broth at 37 °C with agitation.
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