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Polyphenol Utilization Proteins in the Human Gut Microbiome.

Bo Zheng1,2, Yinchao He3,4, Pengxiang Zhang3

  • 1Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, Beijing, China.

Applied and Environmental Microbiology
|December 1, 2021
PubMed
Summary

Dietary polyphenols benefit health, but gut microbes control their use. This study created dbPUP, a database of polyphenol utilization proteins (PUPs) and their gene clusters, revealing their abundance in African microbiomes and offering new research avenues.

Keywords:
PUPPUP gene clustersgut microbiotamicrobiomepolyphenolpolyphenol utilization proteins

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Area of Science:

  • Microbiology
  • Biochemistry
  • Bioinformatics

Background:

  • Dietary polyphenols offer health benefits, but their bioavailability is modulated by gut microbiota.
  • Polyphenol utilization proteins (PUPs) are key enzymes in the human gut microbiome responsible for metabolizing these compounds.
  • Understanding PUPs is crucial for harnessing the full health potential of polyphenol-rich diets.

Purpose of the Study:

  • To create a comprehensive database of experimentally characterized and homologous polyphenol utilization proteins (PUPs).
  • To systematically classify PUPs and identify potential novel protein families involved in polyphenol metabolism.
  • To analyze the distribution and abundance of PUPs and their gene clusters across diverse human gut microbiomes.

Main Methods:

  • Manual curation of experimentally validated PUPs from scientific literature.
  • Database searches (UniProt, UHGP) to identify PUP homologs.
  • Classification of PUPs using Enzyme Commission (EC) numbers, Pfam domains, and sequence similarity networks.
  • Identification of physically linked PUP gene clusters (PGCs) within the UHGP database.
  • Metagenomic data analysis of human gut microbiomes from different geographical populations.

Main Results:

  • A curated dataset of 60 experimentally characterized PUPs ('seeds') and 107,851 homologs.
  • Systematic classification of PUPs into classes, families, and subfamilies, with identification of signature Pfam domains.
  • Discovery of 1,074 potentially functional PUP gene clusters (PGCs) in the human gut.
  • African gut microbiomes exhibit the highest abundance and prevalence of PUP homologs and PGCs.
  • A user-friendly web interface (dbPUP) was developed to provide online access to all data.

Conclusions:

  • The dbPUP database provides a valuable resource for studying polyphenol metabolism in the human gut.
  • Systematic classification and domain analysis facilitate the identification and annotation of novel PUPs.
  • Geographical variations in PUPs suggest a link between dietary polyphenol consumption and gut microbiome composition.
  • The dbPUP resource can accelerate research into the health benefits of dietary polyphenols and personalized nutrition.