Biology subjects

Chac, D.

Publications and source records attributed to Chac, D..

9 recordsLinked to original sources

bioRxiv2026

Orally available designed miniproteins inhibit enterotoxigenic Bacteroides fragilis pathology by blocking toxin receptor binding

Toxigenic bacterial infections in the gut are a significant contributor to the global burden of disease. Advanced tools for protein and live biotherapeutic engineering offer potentially transformative strategies for treating such diseases, while avoiding the collateral effects of traditional antibacterials. Here we used de novo protein design to identify inhibitors of the metzincin family protease Bacteroides fragilis toxin (BFT). These inhibitors, which bind distal to the active site, interfere with toxin-mediated E-cadherin cleavage and downstream proinflammatory signaling by blocking claudin-4 receptor binding. We tested the inhibitors as disulfide-stabilized variants administered directly to the cecum or in drinking water, as well as through in situ secretion by an engineered live biotherapeutic. Across these delivery modalities, the inhibitors successfully neutralized the toxin and effectively prevented BFT-associated gut pathology, including tumor formation. These results highlight the potential of de novo designed proteins as precise, non-antibiotic interventions to mitigate bacterial toxin-driven disease in the gut.

microbiology↗

bioRxiv2026

If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice

The microbiome-gut-brain axis is a mediator of stress-related disorders. The number of preclinical studies exploring the potential causal mechanism of this connection using fecal microbiota transplantation (FMT) is growing. However, the most common method for delivering fecal transplants in rodent models is still oral gavage, which creates an adverse experience that may confound stress-related outcomes. Here, we establish an alternative methodology for FMT that decreases stress induced by traditional experimental procedures. We first used preference and anxiety behavior assays to identify antibiotic therapies having maximal tolerability and minimal anxiolytic properties. We then collected feces from donor mice and homogenized them with a microbe-stabilizing buffer to create a slurry, which was frozen into pellets ("poopsicles") for subsequent FMT. Recipient mice voluntarily consumed the pellets, and blood was collected to compare corticosterone levels relative to traditional gavage FMT. Plasma corticosterone levels were found to be significantly lower in mice receiving FMT via pellets compared to oral gavage. Furthermore, relative to gavage FMT, microbial signatures of mice receiving FMT via pellets were more similar to those of the donor pellets at one week following final FMT and were sustained for up to six weeks, as assessed by comparing Bray-Curtis beta-diversity distances. Together, these results establish effective antibiotic and FMT methods that minimize treatment-induced stress, while effectively transplanting fecal microbes between murine conspecifics.

microbiology↗

bioRxiv2024

Prevalent chromosome fusion in Vibrio cholerae O1

Two circular chromosomes are a defining feature of the family Vibrionaceae, including the pathogen Vibrio cholerae, with rare reports of isolates with a single, fused chromosome. Here we report chromosome fusions in clinical V. cholerae O1 isolates, including several independent fusion events stable enough to be transmitted between patients within a household. Fusion occurs in a 12 kilobase-pair homologous sequence shared between the two chromosomes, which may lead to reversible chromosomal fusion.

microbiology↗

bioRxiv2024

The Role of Morphological Adaptability in Vibrio cholerae's Motility and Pathogenicity

Vibrio cholerae, the etiological agent of cholera, exhibits remarkable adaptability to different environmental conditions by undergoing morphological changes that significantly contribute to its pathogenicity and impact the epidemiology of the disease globally. This study investigates the morphological adaptability of the clinically isolated V. cholerae O1 strain, specifically focusing on the motility and pathogenicity differences between the filamentous and original comma-shaped forms within diverse viscosity conditions. Utilizing the El Tor strain of V. cholerae O1, we induced the transformation into the filamentous form and performed a comparative analysis with the canonical comma-shaped morphology. Our approach involved assessing motility patterns, swimming speeds, rotation rates, kinematics, and reversal frequencies through dark-field microscopy and high-speed imaging techniques. The findings reveal that filamentous V. cholerae cell retains enhanced motility in viscous environments. This suggests an evolutionary adaptation enabling survival across a range of habitats, notably the human gastrointestinal tract. Filamentous forms demonstrated increased reversal behavior at mucin interfaces, hinting at an advantage in penetrating the mucus layer. Rabbit intestinal loop assays further showed that both morphological forms exhibit similar fluid accumulation ratios, thus indicating comparable pathogenic potentials. These results underscore the significance of V. choleraes morphological flexibility in adapting to environmental viscosity changes, shedding light on the bacteriums intricate survival and infection strategies. Our study provides critical insights into the dynamics of cholera, underlining the importance of considering bacterial morphology in developing effective cholera control strategies.

microbiology↗

bioRxiv2024

Diversity of Vibrio cholerae O1 through the human gastrointestinal tract during cholera

Vibrio cholerae O1 causes the diarrheal disease cholera, and the small intestine is the site of active infection. During cholera, cholera toxin is secreted from V. cholerae and induces a massive fluid influx into the small intestine, which causes vomiting and diarrhea. Typically, V. cholerae genomes are sequenced from bacteria passed in stool, but rarely from vomit, a fluid that may more closely represents the site of active infection. We hypothesized that the V. cholerae O1 population bottlenecks along the gastrointestinal tract would result in reduced genetic variation in stool compared to vomit. To test this, we sequenced V. cholerae genomes from ten cholera patients with paired vomit and stool samples. Genetic diversity was low in both vomit and stool, consistent with a single infecting population rather than co-infection with divergent V. cholerae O1 lineages. The number of single nucleotide variants decreased between vomit and stool in four patients, increased in two, and remained unchanged in four. The number of genes encoded in the V. cholerae genome decreased between vomit and stool in eight patients and increased in two. Pangenome analysis of assembled short-read sequencing demonstrated that the toxin-coregulated pilus operon more frequently contained deletions in genomes from vomit compared to stool. However, these deletions were not detected by PCR or long-read sequencing, indicating that interpreting gene presence or absence patterns from short-read data alone may be incomplete. Overall, we found that V. cholerae O1 isolated from stool is genetically similar to V. cholerae recovered from the upper intestinal tract. IMPORTANCEVibrio cholerae O1, the bacterium that causes cholera, is ingested in contaminated food or water and then colonizes the upper small intestine and is excreted in stool. Shed V. cholerae genomes are usually studied, but V. cholerae isolated from vomit may be more representative of where V. cholerae colonizes in the upper intestinal epithelium. V. cholerae may experience bottlenecks, or large reductions in bacterial population sizes or genetic diversity, as it passes through the gut. Passage through the gut may select for distinct V. cholerae mutants that are adapted for survival and gut colonization. We did not find strong evidence for such adaptive mutations, and instead observed that passage through the gut results in modest reductions in V. cholerae genetic diversity, and only in some patients. These results fill a gap in our understanding of the V. cholerae life cycle, transmission, and evolution.

microbiology↗

bioRxiv2021

Polyunsaturated fatty acid arachidonic acid increases the virulence of gut pathogen, Yersinia enterocolitica

Food-borne illnesses are a major health concern worldwide. While 1 in 6 individuals are infected in the United States yearly, there is little research into which dietary factors can alter the risk of infection. Despite evidence suggesting a correlation between obesity and enteric infection, the few reported studies focus on the role of dietary factors and the impact on host tissues and susceptibility. The direct impact of dietary constituents on the virulence of a pathogen has largely been ignored. One component of the Western diet that has been correlated with increasing inflammatory diseases is increased consumption of omega-6 polyunsaturated fatty acids such as arachidonic acid. Here, we show that arachidonic acid directly alters the pathogenicity of the food-borne pathogen Yersinia enterocolitica. Using in vitro cellular adherence assays, proteomic peptide mass fingerprint profiles and in vivo mouse models, we show that arachidonic acid can alter the pathogenesis of Y. enterocolitica by increasing proliferation and intracellular invasion. These findings have major implications in more than food safety, potentially revealing how current dietary habits may increase the virulence of food-borne pathogens.

microbiology↗

bioRxiv2021

A Co-abundant Gene Analysis for Identification of Gut Microbial Strains Associated with Immune Responses to Oral Cholera Vaccine

The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. We used metagenomic sequencing of the microbiota at the time of vaccination, and then related microbial features to immune responses after OCV using a reference-independent gene-level analysis. We found that the presence of sphingolipid-producing bacteria was associated with the development of protective immune responses after OCV. We experimentally tested these results by stimulating human macrophages with Bacteroides xylanisolvens metabolites and found that sphingolipid-containing extracts increased innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identified that microbe-derived sphingolipids impact in vitro immune responses to OCV antigens.

microbiology↗

bioRxiv2021

Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement

Recent studies indicate that the human intestinal microbiota could impact the outcome of infection by Vibrio cholerae, the etiological agent of the diarrheal disease cholera. A commensal bacterium, Paracoccus aminovorans, was previously identified in high abundance in stool collected from individuals infected with V. cholerae when compared to stool from uninfected persons. However, if and how P. aminovorans interacts with V. cholerae has not been experimentally determined; moreover, whether any association between this bacterium alters the behaviors of V. cholerae to affect the disease outcome is unclear. Here we show that P. aminovorans and V. cholerae together form dual-species biofilm structures at the air-liquid interface, with previously uncharacterized novel features. Importantly, the presence of P. aminovorans within the murine small intestine enhances V. cholerae colonization in the same niche that is dependent on the Vibrio exopolysaccharide (VPS) and other major components of mature V. cholerae biofilm. These studies illustrate that dual-species biofilm formation is a plausible mechanism used by a gut microbe to increase the virulence of the pathogen, and this interaction may alter outcomes in enteric infections. Significance StatementWhile ample evidence suggests that the outcome of some enteric infections can be affected by the intestinal microbiota, how specific gut microbes change the behaviors of a pathogen is unclear. Here we characterize the interaction between Vibrio cholerae and Paracoccus aminovorans, a gut microbe known to increase in abundance in the intestines during active V. cholerae infection in humans. These two bacteria form a dual-species biofilm structure at the air-liquid interface, and the gut microbe increases the host colonization efficiency of V. cholerae. Importantly, our study identifies a previously unknown mechanism of gut microbe-pathogen interaction that has the potential to alter the disease outcome.

microbiology↗

bioRxiv2020

Proteomic changes in bacteria caused by exposure to environmental conditions can be detected by Matrix-Assisted Laser Desorption/Ionization - Time of Flight (MALDI-ToF) Mass Spectrometry

In the past decade, matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) has become a timely and cost-effective alternative to bacterial identification. The MALDI-ToF MS technique analyzes the total protein of culturable microorganisms at the species level and produces a mass spectra based on peptides which is compared to a database of identified profiles. Consequently, unique signatures of each microorganism are produced allowing identification at the species and, more importantly, strain level. Our present study proposes that the MALDI-ToF MS can be further used to screen functional and metabolic differences. While other studies applied the MALDI-ToF technique to identify subgroups within species, we investigated how various environmental factors could alter the unique bacterial signatures. We found that genetic and phenotypic differences between microorganisms belonging to the same species can be reflected in peptide-mass fingerprints generated by MALDI-ToF MS. These results suggest that MALDI-ToF MS can screen intra-species phenotypic differences of several microorganisms.

microbiology↗