Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria
Nicholas A Pudlo1, Karthik Urs1, Ryan Crawford2
1Department of Microbiology and Immunology, University of Michigan Medical Schoolgrid.471406.0, Ann Arbor, Michigan, USA.
Msystems
|February 15, 2022
Summary
Gut bacteria like Bacteroidetes break down complex carbohydrates. This study reveals species-specific roles in nutrient utilization and gene transfer, impacting gut microbial ecology and dietary strategies.
Area of Science:
- Microbiology and Microbial Ecology
- Genomics and Bioinformatics
- Human Gut Microbiome Research
Background:
- Symbiotic gut bacteria are crucial for digesting complex carbohydrates in the human colon.
- Dietary polysaccharides significantly influence gut microbiota composition and function.
- Understanding nutrient utilization by specific microbes is key to diet-microbe interactions.
Purpose of the Study:
- To determine carbohydrate utilization profiles for 354 members of the dominant saccharolytic phylum, Bacteroidetes.
- To investigate the genomic basis and evolutionary dynamics of polysaccharide and mucin glycan utilization in Bacteroides species.
- To correlate microbial phenotypes with genomic architecture and identify potential gene transfer events.
Main Methods:
- Utilized a custom phenotyping array to assess carbohydrate utilization across a large collection of Bacteroidetes.
- Employed phenotype-based clustering to group bacteria by species and functional roles.
- Conducted pangenome reconstruction and global transcriptomic analyses on specific Bacteroides strains.
Main Results:
- Demonstrated significant variation in substrate degradation among individual bacteria, with species-level clustering indicating conserved functional roles.
- Observed a negative correlation between dietary polysaccharide and mucin glycan utilization, suggesting niche exclusion.
- Revealed a mosaic genome architecture in Bacteroides ovatus/Bacteroides xylanisolvens, with evidence of interspecies gene transfer and loss of mucin utilization capabilities in some lineages.
Conclusions:
- Bacteroidetes species exhibit diverse and characteristic carbohydrate metabolism, shaped by genomic plasticity and gene transfer.
- The ability to utilize dietary versus host-derived glycans represents distinct ecological niches with potential for competitive exclusion.
- Findings provide insights into microbial adaptation, the evolution of metabolic traits, and potential strategies for manipulating the gut microbiome through diet.
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