Biology subjects

Radey, M.

Publications and source records attributed to Radey, M..

4 recordsLinked to original sources

bioRxiv2025

A conserved electron transport chain sensitizes Bacteroides to a pore-forming type VI secretion toxin

Data suggest that antagonism between bacteria is prevalent within the gut microbiome. Such antagonism could have profound consequences on the fitness of species; however, the susceptibility determinants to even the most pervasive antagonistic factors in this ecosystem remain incompletely understood. Here, we screened for genetic factors that impact the susceptibility of Bacteroides to type VI secretion system (T6SS)-delivered toxins. This revealed that the Bte2 family of pore-forming toxins, which are widespread in B. fragilis and other human gut-associated Bacteroidales, strictly require the H+/Na+-translocating ferredoxin:NAD+ reductase (Rnf) electron transport chain within target cells in order to intoxicate. In Bacteriodes, the precise metabolic role of the conserved Rnf pathway has not been defined. We establish that the Rnf complex is important for redox balancing within cells utilizing sugars derived from dietary fiber and is critical for fitness in vivo. Surprisingly, we find that while the intact Rnf membrane complex is required for Bte2 intoxication, Rnf-catalyzed electron transport is dispensable. We propose that the Rnf complex facilitates Bte2 membrane insertion, leading to intoxication via membrane depolarization. Our data suggest that T6SS toxins may avoid collateral damage within a complex ecosystem by recognizing discriminatory features of competitor species. SignificancePathways for interbacterial antagonism are prevalent in the gut microbiome. The breadth of targeting and specificity determinants of these systems remain largely uncharacterized. We discovered that a widespread pore-forming toxin produced by gut Bacteroidales requires the conserved Rnf protein complex in target organisms. Although this complex is dispensable during in vitro growth, we show it is required for Bacteroides fitness during colonization of the mammalian gut. Our data support a model in which transient interaction between the toxin and Rnf enables rearrangement of the protein, facilitating membrane insertion. Related toxins found in Proteobacteria lack the requirement for Rnf, suggesting that competition between Bacteroidales species in the gut may be driving specialization of their antibacterial toxins.

microbiology↗

bioRxiv2021

A Population-level Strain Genotyping Method to Study Pathogen Strain Dynamics in Human Infections

A hallmark of chronic bacterial infections is the long-term persistence of one or more pathogen species at the compromised site. Repeated detection of the same bacterial species can suggest that a single strain or lineage is continually present. However, infection with multiple strains of a given species, strain acquisition and loss, and changes in strain relative abundance can occur. Detecting strain-level changes and their effects on disease is challenging as most methods require labor intensive isolate-by-isolate analyses, thus, only a few cells from large infecting populations can be examined. Here we present a population-level method for enumerating and measuring the relative abundance of strains called "PopMLST". The method exploits PCR amplification of strain-identifying polymorphic loci, next-generation sequencing to measure allelic variants, and informatic methods to determine whether variants arise from sequencing errors or low abundance strains. These features enable PopMLST to simultaneously interrogate hundreds of bacterial cells that are either cultured en masse from patient samples, or are present in DNA directly extracted from clinical specimens without ex vivo culture. This method could be used to detect epidemic or super-infecting strains, facilitate understanding of strain dynamics during chronic infections, and enable studies that link strain changes to clinical outcomes.

microbiology↗

bioRxiv2019

Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing

While microbiome studies have focused on diversity on the species or higher level, bacterial species in microbiomes are represented by different, often multiple strains. These strains could be clonally and phenotypically very different, making assessment of strain content vital to a full understanding of microbiome function. This is especially important with respect to antibiotic resistant strains, the clonal spread of which may be dependent on competition between them and susceptible strains from the same species. The pandemic, multi-drug resistant, and highly pathogenic E. coli subclone ST131-H30 (H30) is of special interest, as it has already been found persisting in the gut and bladder of healthy people. In order to rapidly assess E. coli clonal diversity, we developed a novel method based on deep sequencing of two loci used for sequence typing, along with an algorithm for analysis of resulting data. Using this method, we assessed fecal and urinary samples from healthy women carrying H30, and were able to uncover considerable diversity, including strains with frequencies at <1% of the E. coli population. We also found that even in the absence of antibiotic use, H30 could complete dominate the gut and, especially, urine of healthy carriers. Our study offers a novel tool for assessing a species clonal diversity (clonobiome) within the microbiome, that could be useful in studying population structure and dynamics of multi-drug resistant and/or highly pathogenic strains in their natural environments.\n\nIMPORTANCEBacterial species in the microbiome are often represented by multiple genetically and phenotypically different strains, making insight into subspecies diversity critical to a full understanding of the microbiome, especially with respect to opportunistic pathogens. However, methods allowing efficient high-throughput clonal typing are not currently available. This study combines a conventional E. coli typing method with deep amplicon sequencing to allow analysis of many samples concurrently. While our method was developed for E. coli, it may be adapted for other species, allowing for microbiome researchers to assess clonal strain diversity in natural samples. Since assessment of subspecies diversity is particularly important for understanding the spread of antibiotic resistance, we applied our method to study of a pandemic multidrug-resistant E. coli clone. The results we present suggest that this clone could be highly competitive in healthy carriers, and that the mechanisms of colonization by such clones need to be studied.

microbiology↗

bioRxiv2017

The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition

While the composition of the human gut microbiome has been well defined, the forces governing its assembly are poorly understood. Recently, prominent members of this community from the order Bacteroidales were shown to possess the type VI secretion system (T6SS), which mediates contact-dependent antagonism between Gram-negative bacteria. However, the distribution of the T6SS in human gut microbiomes and its role have not yet been characterized. To address this challenge, we construct an extensive catalog of T6SS effector/immunity (E-I) genes from three genetic architectures (GA1-3) found in Bacteroidales genomes. We then use metagenomic analysis to assess the abundances of these genes across a large set of gut microbiome samples. We find that despite E-I diversity across reference strains, each individual microbiome harbors a limited set of E-I genes representing a single E-I genotype. Importantly, for GA1-2, these genotypes are not associated with a specific species, suggesting selection for compatibility. GA3, in contrast, is restricted to B. fragilis, and its low diversity reflects a single B. fragilis strain per sample. We further show that in infant microbiomes GA3 is enriched and B. fragilis strains are replaced over time, suggesting competition for dominance in developing microbiomes. Finally, we find a strong association between the presence of GA3 and increased abundance of Bacteroides, indicating that this system confers a selective advantage in vivo in Bacteroides rich ecosystems. Combined, our findings provide the first comprehensive characterization of the T6SS landscape in the human microbiome, implicating it in both intra- and inter-species interactions.

microbiology↗