Biology subjects

Lerma, A. I.

Publications and source records attributed to Lerma, A. I..

4 recordsLinked to original sources

bioRxiv2025

Evaluating effects of antibiotics across preclinical models of the human gastrointestinal microbiota

While antibiotics play important roles in treating infections, disruption of the gastrointestinal microbiota during antibiotic treatment can lead to negative health consequences. However, for many antibiotics, the spectrum of activity has been determined for select isolates rather than for the range of microbes that populate the gastrointestinal tract. Here, we examined the response of communities of gastrointestinal microbes to antibiotics using two different model systems, human fecal minibioreactors and human microbiota associated mice. Communities established in minibioreactors using 12 different fecal donors were exposed to 12 different classes of antibiotics. Samples from three fecal donors were used to colonize germ-free mice from three different genetic backgrounds; progeny mice were then exposed to 6 of 12 antibiotics tested in minibioreactors. Initial bacterial community diversity was dependent on both the fecal donor and model system. Antibiotics affected a wide range of taxa across the phylogenetic spectrum, with many taxa similarly affected across treatments with different classes of antibiotics. Vancomycin, typically administered to treat Gram-positive bacterial infections, decreased the abundance of diverse taxa, including Gram-negative Bacteroidota species. Effects on some taxa were restricted by model system, indicating the importance of environmental context on antibiotic susceptibility. Altogether, these results indicate the complex interrelationships between microbiota composition and environmental context on antibiotic susceptibility and demonstrate strengths and weaknesses of each pre-clinical model system for evaluating effects of new antibiotics and other compounds with potential to disrupt the microbiota.

microbiology↗

bioRxiv2024

Clostridioides difficile colonization is not mediated by bile salts and requires Stickland fermentation of proline in an in vitro model of infection

Treatment with antibiotics is a major risk factor for Clostridioides difficile infection, likely due to depletion of the gastrointestinal microbiota. Two microbiota-mediated mechanisms thought to limit C. difficile colonization include conversion of conjugated primary bile salts into secondary bile salts toxic to C. difficile growth, and competition between the microbiota and C. difficile for limiting nutrients. Using a continuous flow model that simulates the nutrient conditions of the distal colon, we investigated how treatment with six clinically-used antibiotics influenced susceptibility to C. difficile infection in 12 different microbial communities cultivated from healthy individuals. Antibiotic treatment reduced microbial richness; disruption varied by antibiotic class and microbiota composition, but did not correlate with C. difficile susceptibility. Antibiotic treatment also disrupted microbial bile salt metabolism, increasing levels of the primary bile salt, cholate. However, changes in bile salt did not correlate with increased C. difficile susceptibility. Further, bile salts were not required to inhibit C. difficile colonization. We tested whether amino acid fermentation contributed to persistence of C. difficile in antibiotic- treated communities. C. difficile mutants unable to use proline as an electron acceptor in Stickland fermentation due to disruption of proline reductase (prdB-) had significantly lower levels of colonization than wild-type strains in four of six antibiotic-treated communities tested. Inability to ferment glycine or leucine as electron acceptors, however, was not sufficient to limit colonization in any communities. This data provides further support for the importance of bile salt-independent mechanisms in regulating colonization of C. difficile. IMPORTANCEC. difficile is one of the leading causes of hospital-acquired infections and antibiotic-associated diarrhea. Several potential mechanisms through which the microbiota can limit C. difficile infection have been identified and are potential targets for new therapeutics. However, it is unclear which mechanisms of C. difficile inhibition represent the best targets for development of new therapeutics. These studies demonstrate that in a complex in vitro model of C. difficile infection, colonization resistance is independent of microbial bile salt metabolism. Instead, the ability of C. difficile to colonize is dependent upon its ability to metabolize proline, although proline-dependent colonization is context-dependent and is not observed in all disrupted communities. Altogether, these studies support the need for further work to understand how bile- independent mechanisms regulate C. difficile colonization.

microbiology↗

bioRxiv2023

Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile

Mucins are glycoproteins which can be found in host cell membranes and as a gelatinous surface formed from secreted mucins. Mucosal surfaces in mammals form a barrier to invasive microbes, particularly bacteria, but are a point of attachment for others. Clostridioides difficile is anaerobic bacterium which colonizes the mammalian GI tract and is a common cause of acute GI inflammation leading to a variety of negative outcomes. Although C. difficile toxicity stems from secreted toxins, colonization is a prerequisite for C. difficile disease. While C. difficile is known to associate with the mucus layer and underlying epithelium, the mechanisms underlying these interactions that facilitate colonization are less well-understood. To understand the molecular mechanisms by which C. difficile interacts with mucins, we used ex vivo mucosal surfaces to test the ability of C. difficile to bind to mucins from different mammalian tissues. We found significant differences in C. difficile adhesion based upon the source of mucins, with highest levels of binding observed to mucins purified from the human colonic adenocarcinoma line LS174T and lowest levels of binding to porcine gastric mucin. We also observed that defects in adhesion by mutants deficient in flagella, but not type IV pili. These results imply that interactions between host mucins and C. difficile flagella facilitate the initial host attachment of C. difficile to host cells and secreted mucus.

microbiology↗

bioRxiv2020

Identification of simplified microbial communities that inhibit Clostridioides difficile infection through dilution/extinction

The gastrointestinal microbiome plays an important role in limiting susceptibility to infection with Clostridioides difficile. To better understand the ecology of bacteria important for C. difficile colonization resistance, we developed an experimental platform to simplify complex communities of fecal bacteria through dilution and rapidly screen for their ability to inhibit C. difficile in vitro. We simplified complex communities from six fecal donors and found that 17% of simplified communities inhibited C. difficile growth when initially isolated and when re-cultured from frozen stocks. Composition varied between simplified communities based upon fecal donor used for dilution; complexity ranged from 19-67 OTUs. One simplified community could be further simplified through dilution and retain the ability to inhibit C. difficile. We tested efficacy of seven simplified communities in a humanized microbiota mouse model and found that four communities were able to significantly reduce the severity of the initial C. difficile infection and limit susceptibility to disease relapse. Analysis of fecal microbiomes from treated mice demonstrated that simplified communities accelerated recovery of endogenous bacteria and led to stable engraftment of at least 20% of bacteria from simplified communities. Overall, the insights gained through the identification and characterization of these simplified communities increase our understanding of the microbial dynamics of C. difficile infection and recovery. ImportanceClostridioides difficile is the leading cause of antibiotic-associated diarrhea and a significant healthcare burden. While fecal microbiota transplantation is highly effective at treating recurrent C. difficile disease, uncertainties about the undefined composition of fecal material and potential long-term unintended health consequences have motivated studies to identify new communities of simple microbes that will be effective at treating disease. This work describes a platform for rapidly identifying and screening new simplified communities of microbes for efficacy in treating C. difficile infection and identifies four new simplified communities of microbes with potential for development of new therapies to treat C. difficile disease in humans. While this platform was developed and validated to model infection with C. difficile, the underlying principles described in the paper could be easily modified to develop therapeutics to treat other gastrointestinal diseases.

microbiology↗