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Fig. 2 | Microbiome

Fig. 2

From: Uncovering the trimethylamine-producing bacteria of the human gut microbiota

Fig. 2

TMA-producing communities of fecal samples revealed by gene-targeting assays. Panel a depicts gene abundances of cutC (red) and cntA (blue) relative to the total amount of 16S rRNA gene copies of a sample. Volunteers are sorted by descending quantity of cutC, and error bars represent standard deviation on triplicate measurements. The composition of cutC (b) and cntA (c) genes is presented as neighbor-joining trees comprising representative sequences derived from complete-linkage clustering on the nucleotide level using a 90% identity cutoff. Heatmaps are aligned with bars from panel a to illustrate the composition of each gene for all samples (relative abundances of clusters are shown). Clusters that contained reference sequences are indicated by name (Clostridium sp. AT5 (1720194.3.peg.1841); C. hathewayi (566550.8.peg.2440); Clostridium citroniae WAL19142 (742734.4.peg.3562)/Clostridium sp. FS41; Clostridium asparagiforme DSM 15981 (518636.5.peg.3238)/Clostridiales bacterium VE202-15 for cutC and Escherichia/Shigella (1169329.3.peg.2590); Citrobacter (742730.3.peg.4068); Klebsiella (1308539.3.peg.2257) for cntA; specific sequence IDs that were used to build the trees are given in brackets), whereas letters represent clusters that did not include any reference. CutC reference sequences that are closely related to representative sequences of clusters are displayed in the tree as well (Eubacterium sp. AB3007 (1392487.3.peg.725); Dorea sp. 52 (1235798.3.peg.5630); Clostridium clostridioforme AGR2157 (1280695.3.peg.868); Collinsella sp. MS5 (1499681.3.peg.1502); Desulfovibrio desulfuricans subsp. desulfuricans DSM 642 (1121445.4.peg.1354)). Bootstrap values ≥50 and ≥90% are indicated by circles. Only major clusters of highest abundances are shown representing 80 and 99% of all cutC and cntA sequences, respectively. Asterisks highlight the reference sequences belonging to Clostridium XIVa strains

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