Taxonomic and functional characterization of human gut microbes involved in dietary plant lignan metabolism.

Abstract

Background: Dietary plant lignans, such as secoisolariciresinol diglucoside (SDG), are metabolized to the enterolignans, enterodiol (END) and enterolactone (ENL), by gut microbes. Evidence suggests that enterolignans may reduce risk of cardiovascular disease and several forms of cancer. Our aim was to characterize the microbial community involved in enterolignan production by using an in vitro batch culture system to enrich for lignan-metabolizing organisms. Methods: Stool samples from eight participants were incubated separately for ~1 week with a mineral salts media containing formate, acetate, glucose, and 6.55 μM SDG. Daily secoisolariciresinol (SECO), END, and ENL concentrations were measured using gas chromatography–mass spectrometry (GCMS). Microbial community in initial stool (Day 1) and in vitro-incubated fecal suspensions (final-day) was assessed via Illumina paired-end 16S rRNA gene amplicon and whole-metagenome shotgun sequencing. 16S rRNA gene sequences were taxonomically annotated using an in-house QIIME pipeline. Metagenomic shotgun sequences were taxonomically annotated using MetaPhlAn and functionally annotated using DIAMOND and HUMAnN. Annotation-based alpha diversity, organism abundance, and functional gene abundance were used to assess differences between Day 1 and final-day microbial community composition. Results: Stool of all 8 participants converted the majority of SDG to ENL by Day 6 (average ± standard deviation: 88.4% ± 6.9). In most incubations, Bacteroidetes:Firmicutes ratio increased; methanogenic, deglycosylating, and demethylating organisms were enriched; and KEGG Orthology gene families (KOs) corresponding to beta-glucosidases were present at high levels. In some incubations, Eubacterium limnosum, Akkermansia muciniphila, and KOs corresponding to demethylases, dehydroxylases, dehydrogenases, methane metabolism, the Wood-Ljungdahl pathway, and acetogenic bacterial O-demethylation were enriched. Conclusions: Organisms and functional genes identified or hypothesized to be involved in lignan metabolism were not unanimously enriched, but sample-specific. These findings may help further elucidate organisms, enzymes, and biochemical pathways involved in lignan metabolism. Future studies with larger sample sizes may help to confirm these results.