Biology subjects

Seekatz, A. M.

Publications and source records attributed to Seekatz, A. M..

6 recordsLinked to original sources

bioRxiv2025

Reduced carbohydrate complexity alters gut microbial structure independent of total carbohydrate intake

Dietary habits have dramatically altered over recent decades, yet the impact of simplified carbohydrate intake on the gut microbiomes complexity and function remains poorly understood. This study investigates how the variety of dietary carbohydrates--not just their amount--shapes gut microbial diversity and resilience in C57BL/6 mice. Over eight weeks, mice consumed diets varying in carbohydrate complexity but matched for total carbohydrate content. Using 16S rRNA sequencing, we found that reduced carbohydrate diversity led to significant declines in microbial diversity and taxonomic redundancy among important bacterial groups, such as unclassified Lachnospiraceae, Ruminococcaceae, and Muribaculaceae, despite no immediate changes in host physiology. Concurrently, Akkermansia increased under low-complexity diets, suggesting a shift toward mucin degradation when complex polysaccharides are scarce. These changes indicate that loss of carbohydrate complexity narrows microbial niches, potentially disrupting metabolic interactions and functional stability of the gut ecosystem. Given the widespread adoption of processed, low-fiber diets in modern societies, these findings emphasize the importance of macronutrient complexity in maintaining gut microbial health. While short-term host effects were minimal, the microbial shifts observed could presage long-term consequences for gut resilience and disease susceptibility. This study underscores the need to consider carbohydrate diversity in dietary recommendations and microbial ecology research to safeguard gut health in the face of global dietary simplification.

microbiology↗

bioRxiv2025

Diversity and prevalence of Anaerostipes in the human gut microbiota

Members of the class Clostridia, a polyphyletic group of Gram-positive, spore-forming anaerobes in the Bacillota (Firmicutes) phylum, are prevalent and commonly associated with beneficial functions, such as providing colonization resistance against pathogens. Despite a demonstrated value in maintaining Clostridial populations in the gut, the functional and strain diversity of most commensal Clostridial species remains understudied. Here, we isolated and characterized Clostridial isolates, focusing on the genomic diversity of Anaerostipes, a prevalent butyrate-producing genus within the gut microbiota. We conducted a genomic comparison across 21 Anaerostipes strains isolated from healthy human fecal samples (n = 5) and publicly available genomes (n = 105). Whole genome comparisons across the Anaerostipes genus demonstrated 12 species bins, clustering into three major functionally distinct clusters correlating with host origin. One cluster (representing mostly A. caccae genomes) was distinguished by possessing a complete vitamin B12 biosynthesis pathway. Variability in carbohydrate and amino acid metabolism was demonstrated within dominant species of the human microbiota (A. hadrus, A. caccae, and A. hominis). Collectively, these data indicate metabolic variance across Anaerostipes species that may influence coexistence within the gut environment and variably influence health. IMPORTANCEAnaerostipes is a genus containing species known to produce butyrate upon fermenting lactate. Despite their association with health across studies using 16S rRNA gene-based analyses, little is known about genomic variability within and across species. Our study represents one of the first analyses to define strain variability across the Anaerostipes genus, identifying three functional clusters and close phylogenetic distance within species found in the human gut. Major variability within species prevalent in the human gut included variable carbohydrate and amino acid metabolism genes, suggesting the ability to coexist in the gut environment.

microbiology↗

bioRxiv2024

Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice

Colonization resistance provided by the gut microbiota is essential for resisting both initial Clostridioides difficile infection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearing C. difficile compared to a mouse-derived microbiota, despite successful microbial engraftment and recovery of bacterial functional potential. Metabolomic analysis revealed deficits in secondary metabolites, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors involved in FMT-based recovery from rCDI. ImportanceClostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain largely underexplored. This study reveals that effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for CDI and other conditions.

microbiology↗

bioRxiv2023

Butyrate enhances Clostridioides difficile sporulation in vitro

Short chain fatty acids (SCFAs) are products of bacterial fermentation that help maintain important gut functions such as the intestinal barrier, signaling, and immune homeostasis. The main SCFAs acetate, propionate, and butyrate have demonstrated beneficial effects for the host, including importance in combatting infections caused by pathogens such as Clostridioides difficile. Despite the potential role of SCFAs in mitigating C. difficile infection, their direct effect on C. difficile remains unclear. Through a set of in vitro experiments, we investigated how SCFAs influence C. difficile growth, sporulation, and toxin production. Similar to previous studies, we observed that butyrate decreased growth of C. difficile strain 630 in a dose-dependent manner. The presence of butyrate also increased C. difficile sporulation, with minimal increases in toxin production. RNA-Seq analysis validated our experimental results, demonstrating increased expression of sporulation-related genes in conjunction with alternative metabolic and related C. difficile regulatory pathways, such as the carbon catabolite repressor, CcpA. Collectively, these data suggest that butyrate may signal alternative C. difficile metabolic pathways, thus modifying its growth and virulence to persist in the gut environment. IMPORTANCESeveral studies suggest that butyrate may be important in alleviating gut infections, such as reducing inflammation caused by the healthcare-associated Clostridioides difficile. While studies in both animal models and human studies correlate high levels of butyrate with reduced C. difficile burden, the direct impact of butyrate on C. difficile remains unclear. Our study demonstrates that butyrate directly influences C. difficile by increasing its sporulation and modifying its metabolism, potentially using butyrate as a biomarker to shift survival strategies in a changing gut environment. These data point to additional therapeutic approaches to combat C. difficile in a butyrate-directed manner.

microbiology↗

bioRxiv2022

Diversity and prevalence of Clostridium innocuum in the human gut microbiota

Clostridia are a polyphyletic group of Gram-positive, spore-forming anaerobes in the Firmicutes phylum that significantly impact metabolism and functioning of human gastrointestinal tract. Recently, Clostridia were divided into two separate classes, Clostridia and Erysipelotrichia, based on phenotypic and 16S rRNA gene-based differences. While Clostridia include many well-known pathogenic bacteria, Erysipelotrichia remain relatively uncharacterized, particularly regarding their role as a pathogen vs. commensal. Despite wide recognition as a commensal, the Erysipelotrichial species, Clostridium innocuum, has recently been associated with various disease states. To further understand the ecological and potential virulent role of C. innocuum, we conducted a genomic comparison across 38 C. innocuum isolates and 75 publicly available genomes. Based on colony morphology, we isolated multiple C. innocuum cultivars from the feces of healthy human volunteers (n=5). Comparison of the 16S rRNA gene of our isolates against publicly available microbiota datasets in healthy individuals suggests a high prevalence of C. innocuum across the human population (> 80%). Analysis of single nucleotide polymorphisms (SNPs) across core genes and average nucleotide identify (ANI) revealed the presence of 4 clades among all available unique genomes (n=108 total). Investigation of carbohydrate and protein utilization pathways, including comparison against the carbohydrate-activating-enzyme (CAZyme) database, demonstrated inter-and intra-clade differences that were further substantiated in vitro. Collectively, these data indicate genetic variance within the C. innocuum species that may help clarify its role in human disease and health. IMPORTANCEClostridia are a group of medically important anaerobes as both commensals and pathogens. Recently, a new class of Erysipelotrichia containing a number of re-assigned Clostridial species has emerged, including Clostridium innocuum. Recent studies have implicated C. innocuum as a potential causative agent of diarrhea in patients from whom Clostridioides difficile could not be isolated. Using genomic and in vitro comparison, this study sought to characterize C. innocuum in the healthy human gut. Our analyses suggest that C. innocuum is a highly prevalent and diverse species, demonstrating clade-specific differences in metabolism and potential virulence. Collectively, this study is the first investigation into a broader description of C. innocuum as a human gut inhabitant.

microbiology↗

bioRxiv2021

Gut microbiome features are associated with sepsis onset and outcomes

BackgroundEpidemiologic studies have linked antibiotic exposure to subsequent sepsis, suggesting that microbiome disruption may be in the causal pathway and an independent risk factor. This study tests whether variation in the gut microbiota associates with risk of sepsis onset and its outcomes. MethodsUsing a validated surveillance definition, patients with an archived rectal swab from intensive care and hematology units were screened for sepsis. After confirmation by chart review, cases were matched to controls in a 1:2 ratio based on age, gender, and collection date. Relative taxon abundance was measured by sequence analysis of 16S rRNA gene amplicons; total bacterial abundance was measured by qPCR of the 23S rRNA gene. Conditional logistic regression identified clinical and microbiota variables associated with sepsis. ResultsThere were 103 sepsis cases matched to 206 controls. In a final model adjusting for exposure to broad-spectrum antibiotics and indwelling vascular catheters, high relative abundance (RA) of Enterococcus (Odds Ratio (OR) 1.36 per 10% increase, P=.016) and high total bacterial abundance (OR 1.50 per 10-fold increase in 23S copies/L, P =.001) were independently associated with sepsis. Decreased RA of butyrate-producing bacteria also independently associated with sepsis (OR 1.20 for 10% decrease in RA, P =.041), and mortality in unadjusted analysis (OR=1.47 for 10% decrease in RA, P=.034). ConclusionsThis study indicates that the microbiota is altered at sepsis onset. The decreased RA of butyrate-producing bacteria in sepsis also associates with mortality, suggesting a therapeutic role for prebiotics and probiotics in the prevention and treatment of sepsis. ImportanceEarly detection of patients at risk for sepsis could enable interventions to prevent or rapidly treat this life-threatening condition. Prior antibiotic treatment is associated with sepsis, suggesting that disruption of the bacterial population in the gut (the intestinal microbiome) could be an important step leading to disease. To investigate this theory, we matched hospitalized patients with and without sepsis and characterized the patients microbiomes close to or at onset of sepsis. We found that several microbiome alterations, including having more total bacteria in the gut was associated with onset, regardless of prior antibiotic treatment. This signature of microbiome disruption brings us closer to identifying the biological causes of sepsis and could be used to develop new diagnostic tests to identify patients at risk of sepsis.

microbiology↗