High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans.

Autor: Creswell R; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA., Tan J; Kaleido Biosciences, Lexington, MA, 02421, USA., Leff JW; Kaleido Biosciences, Lexington, MA, 02421, USA., Brooks B; Kaleido Biosciences, Lexington, MA, 02421, USA.; Present Address: Prescient Metabiomics, Carlsbad, CA, 92008, USA., Mahowald MA; Kaleido Biosciences, Lexington, MA, 02421, USA.; Present Address: LEO Pharma A/S, Ballerup, Denmark., Thieroff-Ekerdt R; Kaleido Biosciences, Lexington, MA, 02421, USA.; Present Address: Sojournix Inc., 400 Tottenpond Rd, Waltham, MA, 02451, USA., Gerber GK; Department of Pathology, Brigham and Women's Hospital, 60 Fenwood Road, Boston, MA, 02115, USA. ggerber@bwh.harvard.edu.; Harvard Medical School, Boston, MA, 02115, USA. ggerber@bwh.harvard.edu.
Jazyk: angličtina
Zdroj: Genome medicine [Genome Med] 2020 Jul 03; Vol. 12 (1), pp. 59. Date of Electronic Publication: 2020 Jul 03.
DOI: 10.1186/s13073-020-00758-x
Abstrakt: Background: Dietary glycans, widely used as food ingredients and not directly digested by humans, are of intense interest for their beneficial roles in human health through shaping the microbiome. Characterizing the consistency and temporal responses of the gut microbiome to glycans is critical for rationally developing and deploying these compounds as therapeutics.
Methods: We investigated the effect of two chemically distinct glycans (fructooligosaccharides and polydextrose) through three clinical studies conducted with 80 healthy volunteers. Stool samples, collected at dense temporal resolution (~ 4 times per week over 10 weeks) and analyzed using shotgun metagenomic sequencing, enabled detailed characterization of participants' microbiomes. For analyzing the microbiome time-series data, we developed MC-TIMME2 (Microbial Counts Trajectories Infinite Mixture Model Engine 2.0), a purpose-built computational tool based on nonparametric Bayesian methods that infer temporal patterns induced by perturbations and groups of microbes sharing these patterns.
Results: Overall microbiome structure as well as individual taxa showed rapid, consistent, and durable alterations across participants, regardless of compound dose or the order in which glycans were consumed. Significant changes also occurred in the abundances of microbial carbohydrate utilization genes in response to polydextrose, but not in response to fructooligosaccharides. Using MC-TIMME2, we produced detailed, high-resolution temporal maps of the microbiota in response to glycans within and across microbiomes.
Conclusions: Our findings indicate that dietary glycans cause reproducible, dynamic, and differential alterations to the community structure of the human microbiome.
Databáze: MEDLINE
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