Biology subjects

Chanin, R. B.

Publications and source records attributed to Chanin, R. B..

4 recordsLinked to original sources

bioRxiv2026

Capsular polysaccharide can sensitize bacteria to non-antibiotic drugs

Medications administered over long durations, such as phenothiazine antipsychotics, accumulate in the gut at concentrations that affect microbial growth. However, the bacterial features influencing sensitivity to these non-antibiotics remain poorly understood. Bacterial capsular polysaccharides (CPSs) typically confer protection against environmental stressors, including chemical, viral, and immunological pressures within the gut. But their roles under non-antibiotic drug pressure are unknown. Here, we show that the K5 CPS of Escherichia coli Nissle 1917 (EcN) sensitizes it to thioridazine (TDZ) and related antipsychotics. Among a panel of E. coli strains grown in minimal medium, EcN exhibited the highest sensitivity to TDZ. Experimentally evolving EcN under gut-relevant TDZ concentrations selected for resistant populations with convergent variants affecting the CPS locus, and TDZ-resistant clones correspondingly had lower CPS expression than their drug-susceptible counterparts. Genetic, transcriptomic, and phenotypic analyses confirmed that the K5 CPS enhances, rather than mitigates, TDZ sensitivity. These findings demonstrate that canonically protective surface structures can become vulnerabilities under non-antibiotic pharmaceutical pressure. Human medications may therefore inadvertently shape the expression and evolution of bacterial surface structures in the gastrointestinal tract, challenging presumptions of CPS-mediated environmental protection.

microbiology↗

bioRxiv2025

Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics

Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that [~]5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.

microbiology↗

bioRxiv2023

Intragenic DNA inversions expand bacterial coding capacity

Bacterial populations that originate from a single bacterium are not strictly clonal. Often, they contain subgroups with distinct phenotypes. Bacteria can generate heterogeneity through phase variation: a preprogrammed, reversible mechanism that alters gene expression levels across a population. One well studied type of phase variation involves enzyme-mediated inversion of specific intergenic regions of genomic DNA. Frequently, these DNA inversions flip the orientation of promoters, turning ON or OFF adjacent coding regions within otherwise isogenic populations. Through this mechanism, inversion can affect fitness, survival, or group dynamics. Here, we develop and apply bioinformatic approaches to discover thousands of previously undescribed phase-variable regions in prokaryotes using long-read datasets. We identify intragenic invertons, a surprising new class of invertible elements found entirely within genes, in bacteria and archaea. To date, inversions within single genes have not been described. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We experimentally characterize specific intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, presenting a roadmap for investigating this new gene-diversifying phenomenon. One-Sentence SummaryIntragenic DNA inversions, identified using long-read sequencing datasets, are found in many phyla across the prokaryotic tree of life.

microbiology↗

bioRxiv2019

Shigella flexneri adherence factor expression in in vivo-like conditions

The Shigella species are Gram-negative, facultative intracellular pathogens that invade the colonic epithelium and cause significant diarrheal disease. Despite extensive research on the pathogen, comprehensive understanding of how Shigella initiates contact with epithelial cells remains unknown. Shigella maintains many of the same Escherichia coli adherence gene operons; however, at least one critical gene component in each operon is currently annotated as a pseudogene in reference genomes. These annotations, coupled with a lack of structures upon microscopic analysis following growth in laboratory media, have led the field to hypothesize that Shigella is unable to produce fimbriae or other \"traditional\" adherence factors. Nevertheless, our previous analyses have demonstrated that a combination of bile salts and glucose induce both biofilm formation and adherence to colonic epithelial cells. Through a two-part investigation, we first utilized various transcriptomic analyses to demonstrate that S. flexneri strain 2457T adherence gene operons are transcribed. Subsequently, we performed mutation, electron microscopy, biofilm, infection, and proteomic analyses to characterize three of the structural genes. In combination, these studies demonstrate that despite the gene annotations, S. flexneri 2457T uses adherence factors to initiate biofilm formation as well as epithelial cell contact. Furthermore, host factors, namely glucose and bile salts in the small intestine, offer key environmental stimuli required for proper adherence factor expression in S. flexneri. This research may have a significant impact on vaccine development for Shigella and further highlights the importance of utilizing in vivo-like conditions to study bacterial pathogenesis.\n\nImportanceBacterial pathogens have evolved to regulate virulence gene expression at critical points in the colonization and infection processes to successfully cause disease. The Shigella species infect the epithelial cells lining the colon to result in millions of cases of diarrhea and a significant global health burden. As antibiotic resistance rates increase, understanding the mechanisms of infection are vital to ensure successful vaccine development. Despite significant gains in our understanding of Shigella infection, it remains unknown how the bacteria initiate contact with the colonic epithelium. Most pathogens harbor multiple adherence factors to facilitate this process, but Shigella was thought to have lost the ability to produce these factors. Interestingly, we have identified conditions that mimic some features of gastrointestinal transit and enable Shigella to express adherence factors. This work highlights aspects of genetic regulation for Shigella adherence factors and may have a significant impact on future vaccine development.

microbiology↗