Clostridium difficile is a leading cause of antibiotic-associated diarrhea. The mechanisms underlying C. difficile expansion after microbiota disturbance are just emerging. We assessed the gene ...expression profile of C. difficile within the intestine of gnotobiotic mice to identify genes regulated in response to either dietary or microbiota compositional changes. In the presence of the gut symbiont Bacteroides thetaiotaomicron, C. difficile induces a pathway that metabolizes the microbiota fermentation end-product succinate to butyrate. The low concentration of succinate present in the microbiota of conventional mice is transiently elevated upon antibiotic treatment or chemically induced intestinal motility disturbance, and C. difficile exploits this succinate spike to expand in the perturbed intestine. A C. difficile mutant compromised in succinate utilization is at a competitive disadvantage during these perturbations. Understanding the metabolic mechanisms involved in microbiota-C. difficile interactions may help to identify approaches for the treatment and prevention of C. difficile-associated diseases.
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•Biassociation with a gut symbiont induces a C. difficile succinate-utilization operon•Succinate accumulates in the gut upon antibiotic treatment or motility disturbance•Succinate utilization enables C. difficile expansion in the perturbed gut•A C. difficile mutant compromised in succinate utilization is colonization defective
Nutrient resource partitioning by gut microbes is typically efficient. Ferreyra et al. demonstrate that upon antibiotic treatment or motility disturbance, succinate, an interspecies metabolic intermediate, transiently spikes to high levels. C. difficile induces a succinate-to-butyrate conversion pathway to take advantage of the succinate spike and expand during these gut perturbations.
The gut microbiome engenders colonization resistance against the diarrheal pathogen
but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut ...microbiome-produced metabolites important for colonization resistance against
is short-chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of
and is correlated with
-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in
occurs under conditions where
also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into
cells and is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (
)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of a butyrogenic pathway(s) in
coincides with alterations in toxin release and sporulation. Together, this work highlights butyrate as a marker of a
-inhospitable environment to which
responds by releasing its diarrheagenic toxins and producing environmentally resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how
growth is inhibited by butyrate and how butyrate alters
virulence in the face of a highly competitive and dynamic gut environment.IMPORTANCEThe gut microbiome engenders colonization resistance against the diarrheal pathogen
but the molecular basis of this colonization resistance is incompletely understood, which hinders the development of novel therapeutic interventions for
infection (CDI). We investigated how
responds to butyrate, an end-product of gut microbiome community metabolism which inhibits
growth. We show that exogenously produced butyrate is internalized into
, which inhibits
growth by interfering with its own butyrate production. This growth inhibition coincides with increased toxin release from
cells and the production of environmentally resistant spores necessary for transmission between hosts. Future work to disentangle the molecular mechanisms underlying these growth and virulence phenotypes will likely lead to new strategies to restrict
growth in the gut and minimize its pathogenesis during CDI.
Clostridioides difficile
is an opportunistic diarrheal pathogen responsible for significant morbidity and mortality worldwide. A disrupted (dysbiotic) gut microbiome, commonly engendered by ...antibiotic treatment, is the primary risk factor for
C
.
difficile
infection, highlighting that
C
.
difficile
–microbiome interactions are critical for determining the fitness of this pathogen. Here, we review short chain fatty acids (SCFAs): a major class of metabolites present in the gut, their production by the gut microbiome, and their impacts on the biology of the host and of
C
.
difficile
. We use these observations to illustrate a conceptual model whereby
C
.
difficile
senses and responds to SCFAs as a marker of a healthy gut and tunes its virulence accordingly in order to maintain dysbiosis. Future work to learn the molecular mechanisms and genetic circuitry underlying the relationships between
C
.
difficile
and SCFAs will help to identify precision approaches, distinct from antibiotics and fecal transplant, for mitigating disease caused by
C
.
difficile
and will inform similar investigations into other gastrointestinal pathogens.
The human gut microbiota produces dozens of metabolites that accumulate in the bloodstream, where they can have systemic effects on the host. Although these small molecules commonly reach ...concentrations similar to those achieved by pharmaceutical agents, remarkably little is known about the microbial metabolic pathways that produce them. Here we use a combination of genetics and metabolic profiling to characterize a pathway from the gut symbiont Clostridium sporogenes that generates aromatic amino acid metabolites. Our results reveal that this pathway produces twelve compounds, nine of which are known to accumulate in host serum. All three aromatic amino acids (tryptophan, phenylalanine and tyrosine) serve as substrates for the pathway, and it involves branching and alternative reductases for specific intermediates. By genetically manipulating C. sporogenes, we modulate serum levels of these metabolites in gnotobiotic mice, and show that in turn this affects intestinal permeability and systemic immunity. This work has the potential to provide the basis of a systematic effort to engineer the molecular output of the gut bacterial community.
The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of lysogeny, these viruses ...demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals.
Here we show that rapid phase variation of alternate capsular polysaccharides in Bacteroides intestinalis cultures plays an important role in a dynamic equilibrium between phage sensitivity and resistance, allowing phage and bacteria to multiply in parallel. The data also suggests the role of a concomitant phage persistence mechanism associated with delayed lysis of infected cells, similar to carrier state infection. From an ecological and evolutionary standpoint, this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other "benign" forms of phage infection when the host is stably present at high abundance.
Long-term persistence of bacteriophage and host could result from mutually beneficial mechanisms driving bacterial strain-level diversity and phage survival in complex environments.
Sepsis is a deleterious immune response to infection that leads to organ failure and is the 11th most common cause of death worldwide. Despite plaguing humanity for thousands of years, the host ...factors that regulate this immunological response and subsequent sepsis severity and outcome are not fully understood. Here we describe how the Western diet (WD), a diet high in fat and sucrose and low in fiber, found rampant in industrialized countries, leads to worse disease and poorer outcomes in an LPS-driven sepsis model in WD-fed mice compared with mice fed standard fiber-rich chow (SC). We find that WD-fed mice have higher baseline inflammation (metaflammation) and signs of sepsis-associated immunoparalysis compared with SC-fed mice. WD mice also have an increased frequency of neutrophils, some with an “aged” phenotype, in the blood during sepsis compared with SC mice. Importantly, we found that the WD-dependent increase in sepsis severity and higher mortality is independent of the microbiome, suggesting that the diet may be directly regulating the innate immune system through an unknown mechanism. Strikingly, we could predict LPS-driven sepsis outcome by tracking specific WD-dependent disease factors (e.g., hypothermia and frequency of neutrophils in the blood) during disease progression and recovery. We conclude that the WD is reprogramming the basal immune status and acute response to LPS-driven sepsis and that this correlates with alternative disease paths that lead to more severe disease and poorer outcomes.
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies ...IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of “hot spots” in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.
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•Insertion sequence (IS) element database and pipeline identify IS insertions•Intestinal bacteria have diverse IS insertions maintained over long timescales•IS insertions are enriched in accessory genes, such as susCD/tonB transporters•IS insertion activity is sensitive to perturbation (e.g., nutrients and phage)
Insertion sequence (IS) elements are small transposons found in the genomes of bacteria. Leveraging an assembled database of IS elements, Kirsch et al. developed a computational pipeline that reveals the presence, abundance, and dynamics of IS insertions in the human intestinal microbiota with high resolution.
As we learn about the sophisticated and far-reaching impacts that our resident microbiomes have on our biology, it is apparent that the tools we have for managing our microbiomes are rudimentary at ...best. For example, though antibiotics rid our microbiomes of bacterial pathogens, they target pathogens and commensals alike. Additional approaches, such as fecal microbiome transplant, seem to restore a healthy microbiome in some applications, but the mechanisms underlying this treatment and its long-term effects are poorly understood. Here, I discuss my laboratory's research, which uses two major drivers of gut microbiome ecology, diet and bacteriophages, as tools to develop new concepts and approaches for managing microbiomes. I speculate on the anticipated impacts of this research and how it will influence the way that we treat the kaleidoscope of microbe-microbe and microbe-host interactions central to our health.
Background Diarrheal disease is a leading cause of morbidity and mortality globally, especially in low- and middle-income countries. High-throughput and low-cost approaches to identify etiologic ...agents are needed to guide public health mitigation. Nanoliter-qPCR (nl-qPCR) is an attractive alternative to more expensive methods yet is nascent in application and without a proof-of-concept among hospitalized patients. Methods A census-based study was conducted among diarrheal patients admitted at two government hospitals in rural Bangladesh during a diarrheal outbreak period. DNA was extracted from stool samples and assayed by nl-qPCR for common bacterial, protozoan, and helminth enteropathogens as the primary outcome. Results A total of 961 patients were enrolled; stool samples were collected from 827 patients. Enteropathogens were detected in 69% of patient samples; More than one enteropathogen was detected in 32%. Enteropathogens most commonly detected were enteroaggregative Escherichia coli (26.0%), Shiga toxin-producing E.coli (18.3%), enterotoxigenic E. coli (15.5% heat stable toxin positive, 2.2% heat labile toxin positive), Shigella spp. (14.8%), and Vibrio cholerae (9.0%). Geospatial analysis revealed that the median number of pathogens per patient and the proportion of cases presenting with severe dehydration were greatest amongst patients residing closest to the study hospitals." Conclusions This study demonstrates a proof-of-concept for nl-qPCR as a high-throughput low-cost method for enteropathogen detection among hospitalized patients.
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