Yu, M. K. | Search bioRxiv

bioRxiv2021

Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut

Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments, and reveal taxon-independent markers of dysbiosis that may explain why widespread yet typically low abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.

microbiology↗

bioRxiv2020

Discovering plasmids in metagenomes based on genetic architecture

Despite their prevalence and impact on microbial lifestyles, ecological and evolutionary insights into naturally occurring plasmids are far from complete. Here we developed a machine learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes, and we organized them into 1,169 evolutionarily cohesive plasmid systems using our sequence containment-aware network partitioning algorithm, MobMess. Similar to microbial taxa, individuals from the same country tend to cluster together based on their plasmid diversity. However, we found no correlation between plasmid diversity and bacterial taxonomy. Individual plasmids were often country-specific, yet most plasmid systems spanned across geographically distinct human populations, revealing cargo genes that likely respond to environmental selection. Our study introduces powerful tools to recognize and organize plasmids, uncovers their tremendous diversity and intricate ecological and evolutionary patterns in naturally occurring habitats, and demonstrates that plasmids represent a dimension of ecosystems that is not explained by microbial taxonomy alone.

bioinformatics↗