representative bacterial strains  (ATCC)

Journal: Cancer Research Communications

Article Title: The Tumor Microbiome Reacts to Hypoxia and Can Influence Response to Radiation Treatment in Colorectal Cancer

doi: 10.1158/2767-9764.CRC-23-0367

Figure Lengend Snippet: The presence of certain microbes in ORIEN tumors correlates with worse outcomes after radiotherapy. A, List of strains whose interactions with hypoxia in the tumor are significantly associated with survival outcomes in ORIEN patients who received radiation treatment. B, Kaplan–Meier survival curve showing an association between the presence of F. canifelinum and patient outcome. A risk table for this result is available as Supplementary Table S6. C, Model CT26 tumors grown in immune-deficient mice and inoculated with Fusobacterium show no increase in tumor growth delay after radiotherapy. D, Similarly, model tumors inoculated with several other bacterial strains show significant increases in tumor growth delay after radiotherapy. The strains included are Lactobacillus (Lacto), a mixed population from a healthy donor (Gut Mix), bacterial growth medium (GAM), Streptococcus (Strepto), and Akkermansia (AKK). Error bars are ±SEM. P values were calculated against GAM using the t test. *, P < 0.05.

Article Snippet: Representative bacterial strains Akkermansia muciniphila (ATCC ® BAA-835), Lactobacillus acidophilus (ATCC ® 4356), Streptococcus thermophilus (ATCC ® 19258), Bacteroides ovatus (ATCC ® 8483), and Dorea formicigenerans (ATCC ® 27755) were obtained from ATCC.

Techniques:

Journal: Nature microbiology

Article Title: Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota.

doi: 10.1038/s41564-024-01737-3

Figure Lengend Snippet: Fig. 6 | Impacts on tryptophan metabolism mediated by dietary fibre and substrate. In the gut, multiple bacterial species require tryptophan for their metabolism and produce bioactive molecules important for host health. E. coli catabolizes tryptophan into indole to generate pyruvate, while C. sporogenes regenerates NAD+ and produces ILA and IPA through the Stickland fermentation reductive pathway. The fibre degrader B. thetaiotaomicron degrades pectin and thereby releases monosaccharides available to E. coli. The monosaccharides repress expression of the E. coli tnaA gene encoding tryptophanase, thereby making more tryptophan available to Stickland fermenters in the gut environment. Blue arrows show events occurring in the absence of fibre, while green arrows

Article Snippet: Representative bacterial strains C. sporogenes (DSM 795), P. anaerobius (DSM 2949), B. thetaiotaomicron (DSM 2079) and E. coli K12-MG1655 (DSM 18039) were purchased from DSMZ (German Collection of Microorganisms and Cell Cultures).

Techniques: Expressing

Journal: bioRxiv

Article Title: Substrate availability and dietary fibre regulate metabolism of tryptophan by human gut microbes

doi: 10.1101/2023.06.05.543658

Figure Lengend Snippet: (a) Tryptophan, ILA and IPA accumulation in the culture supernatant of C. sporogenes grown in mGAM medium supplemented with final concentrations of 0.02, 0.05, 0.1 or 0.2 % free tryptophan. The left Y axis represents values for tryptophan (Trp) and for indolepropionic acid (IPA) whereas the right Y axis represents indolelactic acid (ILA). (b) Tryptophan metabolites in the culture supernatant of P. anaerobius grown in mGAM medium supplemented with final concentration of 0.02, 0.05, 0.1 or 0.2 % free tryptophan. (c) Normalized tryptophan metabolites in the culture supernatant of faecal microbiotas. Six infant faecal microbiotas were cultured either in YCFA medium or YCFA supplemented with 0.05 or 0.1 or 0.2 % of free tryptophan. Specific metabolite concentrations are normalized to the basal level of the given metabolite in the growth medium without tryptophan supplementation. Absolute values of individual faecal cultures are shown in the Supplementary figure 2.

Article Snippet: Representative bacterial strains Clostridium sporogenes (DSM 795), Peptostreptococcus anaerobius (DSM 2949), Bacteroides thetaiotaomicron (DSM 2079) and Escherichia coli K12-MG1655 (DSM 18039) were purchased from DSMZ (German Collection of Microorganisms and Cell Cultures GmbH, Germany).

Techniques: Concentration Assay, Cell Culture

Journal: bioRxiv

Article Title: Substrate availability and dietary fibre regulate metabolism of tryptophan by human gut microbes

doi: 10.1101/2023.06.05.543658

Figure Lengend Snippet: (a) Schematic representation of the bacterial species comprising the defined community. E. coli was selected as major indole producer, B. theta was selected as fibre degrader and C. sporogenes to produce Stickland fermentation products. (b) Tryptophan metabolites in the supernatant of the defined community cultured in mGAM medium supplemented with either 0.02 or 0.05 % free tryptophan. Both low and high tryptophan media were further supplemented with either no apple pectin or 0.5 % apple pectin. (c) RT-qPCR targeting tnaA mRNA in E. coli in response to pectin supplementation. (d) RT-qPCR targeting mRNAs of arabinose utilizing genes ( araA and araF ), rhamnose utilizing genes ( rhaA and rhaT ) and xylose utilizing genes ( xylA and xylG ) in E. coli in response to pectin supplementation. Total RNA was extracted from early stationary phase cultures (∼ 1 OD) and mRNA levels were measured as described in methods. Results are mean ± SD of three independent experiments. Statistical analysis was done using Welch’s ANOVA test in panel b. *P < 0.05, **P < 0.01, ***P < 0.001.

Article Snippet: Representative bacterial strains Clostridium sporogenes (DSM 795), Peptostreptococcus anaerobius (DSM 2949), Bacteroides thetaiotaomicron (DSM 2079) and Escherichia coli K12-MG1655 (DSM 18039) were purchased from DSMZ (German Collection of Microorganisms and Cell Cultures GmbH, Germany).

Techniques: Cell Culture, Quantitative RT-PCR

Journal: bioRxiv

Article Title: Substrate availability and dietary fibre regulate metabolism of tryptophan by human gut microbes

doi: 10.1101/2023.06.05.543658

Figure Lengend Snippet: (a) Schematic representation of experimental plan to evaluate the effect of dietary tryptophan and pectin on tryptophan metabolite production in vivo . Germ free mice were placed in four groups (N=5 per group), and fed a diet containing 2 g/kg tryptophan and 50 g/kg pectin for seven days for adaptation. They were then orally gavaged with a mixed culture of E. coli , B. theta and C. sporogenes in equal amounts (OD 600 ) and remained for another seven days on the same diet for stabilization. Diets were then changed and mice were fed either a diet with either 2 g/kg or 16 g/kg tryptophan, with or without 50 g/kg pectin for two more weeks. Samples were collected as shown in the scheme. (b) 16S rRNA gene sequencing profiles show the composition of the defined community in caeca of the four groups, overlaid indole values measured in the individual caeca. (c) Absolute caecal indole concentrations. (d) Indole concentration in the caeca, normalized to the relative abundance of E. coli . (e) Absolute concentrations of tryptophan, ILA, IAcrA and IPA in serum. (f) Serum tryptophan metabolites (ILA, IAcrA and IPA) normalized to C. sporogenes relative abundance in cecum. For plots in panel b-f, lines and error bars indicate median and IQR. Statistical analysis was done across groups within each metabolite measured using One-way ANOVA (panel c) or Kruskal Wallis tests (panel d-f), using uncorrected Fisher’s LSD or Dunn’s posthoc tests to compare between individual groups. *P < 0.05, **P < 0.01, ***P < 0.001. For panel e and f, one value for tryptophan and ILA was excluded as an extreme outlier (Grubbs test, alpha < 0.01).

Article Snippet: Representative bacterial strains Clostridium sporogenes (DSM 795), Peptostreptococcus anaerobius (DSM 2949), Bacteroides thetaiotaomicron (DSM 2079) and Escherichia coli K12-MG1655 (DSM 18039) were purchased from DSMZ (German Collection of Microorganisms and Cell Cultures GmbH, Germany).

Techniques: In Vivo, Sequencing, Concentration Assay

Journal: bioRxiv

Article Title: Substrate availability and dietary fibre regulate metabolism of tryptophan by human gut microbes

doi: 10.1101/2023.06.05.543658

Figure Lengend Snippet: In the gut, multiple bacterial species require tryptophan for their metabolism, and produce bioactive molecules important for host health. Escherichia coli catabolises tryptophan into indole to generate pyruvate, while C. sporogenes regenerates NAD+ and produces indolelactic acid (ILA) and indolepropionic acid (IPA) through the Stickland fermentation reductive pathway. The fibre degrader B. thetaiotaomicron degrades pectin, and thereby release monosaccharides available to E. coli . The monosaccharides represses expression of the E. coli tnaA gene encoding tryptophanase, thereby making more tryptophan available to Stickland fermenters in the gut environment. Black arrows show events occurring in the absence of fibre, while green arrows designate events preferentially occurring in the presence of fibre. Thick and thin arrows depict enhanced and reduced flow of tryptophan, respectively.

Article Snippet: Representative bacterial strains Clostridium sporogenes (DSM 795), Peptostreptococcus anaerobius (DSM 2949), Bacteroides thetaiotaomicron (DSM 2079) and Escherichia coli K12-MG1655 (DSM 18039) were purchased from DSMZ (German Collection of Microorganisms and Cell Cultures GmbH, Germany).

Techniques: Expressing