Bb Finlay

Antibiotic exposure disrupts enteric pathogen colonization resistance, yet how antibiotics reshape pathogen population dynamics, infection bottlenecks, and strain-level heterogeneity in the gut remains poorly understood. Here, we combine high-resolution pathogen barcoding, transcriptomic, and metabolomic analyses to quantify how short-term vancomycin perturbation alters infection ecology in vivo . We use Citrobacter rodentium as a model for human infection by pathogenic Escherichia coli –an antimicrobial resistance priority group–to demonstrate that just two days of vancomycin pre-treatment profoundly reshapes infection trajectories, driving rapid, global gut colonization, a dramatic increase in pathogen founding population size, and preservation of strain diversity across intestinal sites. Notably, vancomycin eliminated the hallmark heterogeneity of C. rodentium infection, resulting in fully reproducible colonization across hosts. Population-level analysis revealed that antibiotic treatment relaxes competitive constraints both with the resident microbiota and among clonal pathogen lineages, allowing early-established founders to persist and expand. Despite accelerated pathogen engraftment and tissue pathology, transcriptomic analysis revealed reduced virulence gene expression. Instead, antibiotic-induced metabolic restructuring of the gut created permissive conditions for pathogen expansion. Interactions with a vancomycin-altered microbiota, dominated by Akkermansia and Bacteroides , further promoted nutrient cross-feeding and influenced epithelial attachment. Together, we illustrate how short-term antibiotic exposure reshapes enteric infection by removing ecological bottlenecks that normally constrain strain diversity and infection outcomes. These findings have implications for antibiotic use, antimicrobial resistance transmission, and therapeutic strategies that rely on competition-driven dynamics, such as strain replacement.

Bile acids modulate the intestinal microbiota and serve as key signaling molecules in host physiology. Bile acid dysregulation has been implicated in nutritional and inflammatory diseases; however, data on the pool of bile acids present in stunted children or children suffering of environmental enteric dysfunction (EED) is limited, particularly in the upper intestinal compartment where disease phenotypes are most relevant. In this study, we performed a targeted metabolomics approach on 75 bile acids and their derivatives, including gastric and duodenal aspirates and fecal samples from almost 1000 children from two Sub-Saharan cities. We found that levels of secondary bile acids, especially lithocholic acid, are significantly lower in the feces of stunted and EED children, while ursocholic acid and its derivatives are significantly higher. Levels of primary and sulfated bile acids are also increased in the feces of children with EED. Microbiota sequencing revealed that high lithocholic acid levels are positively associated with butyrate-producing bacteria, while negatively associated with oral taxa like Streptococcus and Veillonella . In vitro tests on a panel of reference strains showed that oral bacteria bioaccumulate and are inhibited by a variety of bile acids, while lithocholic and chenodeoxycholic acids modulate the growth of several butyrate-producing bacteria. This effect was even stronger with tauro- or glycol-conjugated bile acids. Exposing stool-derived in vitro communities from children in Afribiota to these bile acids confirmed their positive impact on butyrate producers and negative effect on overgrowing oral taxa. Our findings suggest that secondary bile acids, reduced in stunting and EED, modulate the growth of butyrate-producing bacteria while suppressing harmful oral taxa, highlighting their potential as tools to modulate microbiota composition.

Enteropathogenic Escherichia coli (EPEC), a major cause of diarrheal disease, produces plasma membrane pedestals that promote colonization of host cells. Critical for pedestal formation is EPEC’s type III secretion system, which injects ∼ 20 effector proteins into human cells. One of these effectors is Tir, which inserts into the host plasma membrane and stimulates the assembly of actin filaments essential for pedestal generation. To date, actin polymerization is the only host process known to contribute to pedestal formation. Here we report that EPEC co-opts the membrane trafficking pathway of polarized exocytosis, which acts together with actin polymerization to allow the efficient production of pedestals. Polarized exocytosis is mediated by the exocyst — a human octameric complex that uses intracellular vesicles to expand the plasma membrane. We found that EPEC stimulated exocytosis at sites of pedestal formation in a manner dependent on the exocyst. The bacterial effector EspH recruited the exocyst and promoted exocytosis. Genetic inactivation of espH or RNA interference (RNAi)-induced depletion of exocyst components reduced both the frequency and size of pedestals. Additional RNAi experiments indicated that the exocyst is dispensable for actin filament assembly in pedestals. Co-depletion of components of the exocyst and the Arp2/3 complex showed that exocytosis and actin polymerization make additive contributions to pedestal formation. Collectively, these results indicate that exocyst-mediated expansion of the plasma membrane acts together with actin polymerization to optimize the generation of pedestals. IMPORTANCE: Enteropathogenic E. coli (EPEC) induces the formation of host cell plasma membrane protrusions called “pedestals” that mediate tight adherence to intestinal epithelial cells. Substantial evidence indicates that the generation of pedestals requires bacterial-induced polymerization of the host cell actin cytoskeleton. However, it remains unknown if EPEC manipulates other human processes to augment the efficiency of pedestal generation. The significance of this research is to demonstrate that EPEC co-opts a second host process called polarized exocytosis to increase the frequency of pedestals and the size of these structures. EPEC induces exocytosis by using its effector protein EspH to recruit the human exocyst complex, which mediates the insertion of membrane at sites of bacterial attachment. Our results demonstrate EPEC’s ability to coordinate host membrane trafficking with cytoskeletal changes to enhance infection. Remarkably, EPEC shares this strategy with the intracellular bacterial pathogens Listeria monocytogenes and Shigella flexneri .

The gut microbiota is highly dynamic during the first year of life and plays a crucial role in immune development. Breastfeeding is known to support infant health, but the contributions of the numerous breastmilk components to gut microbiota and immune maturation remain unclear. Secretory IgA (SIgA), the most abundant antibody in human milk, is a key modulator of gut microbiota composition. We have shown previously that mouse milk SIgA protects against asthma by limiting segmented filamentous bacteria in mice. The present study uncovers a similar mechanism in humans. Using human milk from the CHILD Cohort Study, we define a relationship between human milk SIgA and infant gut microbiota composition. This leads to the identification of Erysipelatoclostridium ramosum as a key player in immune development, which is controlled by milk SIgA. Cell culture modeling demonstrates that SIgA restricts the capacity of E. ramosum to adhere to the intestinal epithelium and to induce Th17 responses, which are implicated in allergic and other chronic diseases.

BACKGROUND: Both Mediterranean and ketogenic diets have been proposed as nutritional interventions in Parkinson’s disease (PD). Combined approaches may offer maximal benefits. OBJECTIVE: Assess the feasibility, safety and exploratory efficacy of two Mediterranean-ketogenic dietary interventions in individuals with PD (PwP). METHODS: In this Phase II, random-order crossover study, PwP followed two 8-week dietary interventions, separated by an 8-week washout: 1) a high-fat, low-carbohydrate Mediterranean diet (MeDi-KD) and 2) a standard Mediterranean diet supplemented with medium chain triglycerides (MeDi-MCT). RESULTS: Of 52 participants randomized, 48 started the trial. Forty-one (79%) participants completed at least one and 33 (63%) completed both intervention phases. There were no intervention-related serious adverse events, nor any significant changes in plasma lipid profiles. Seventy-three percent and 92% of participants reported deviating from the MeDi-KD and MeDi-MCT no more than a few times per month, respectively. Moderate Mediterranean Diet Adherence Scores of 6.7 (SD: 1.6) and 7.2 (SD: 2.3) were achieved during the MeDi-KD and MeDi-MCT, respectively, out of a maximum of 14. Fifty percent of participants were in nutritional ketosis (BHB >0.5 mM) at follow-up for the MeDi-KD, as compared with only 1 (3%) participant following the MeDi-MCT. MDS-UPDRS Part II and IV scores decreased by a mean of -1.4 (SD: 4.2; p=0.039) and -1.0 (SD: 3.0; p=0.044) points, respectively, following the MeDi-MCT. CONCLUSIONS: Mediterranean-ketogenic interventions appear safe and potentially beneficial in PwP. Behavioral strategies to optimize adherence should be employed in future phase III trials. TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov: NCT05469997 . PLAIN LANGUAGE SUMMARY: Many patients want to know what the best diet is to follow for their Parkinson’s disease. Previous studies have suggested benefits of both ketogenic diets, which are high in fats and low in carbohydrates, and Mediterranean-style diets. Combining these two approaches could offer maximal advantages, while reducing the challenges of following a strict ketogenic diet. The aim of this study was to test whether so-called “Mediterranean-ketogenic” diets would be safe and practical for patients with Parkinson’s disease to follow. Early indicators of potential clinical benefit were also assessed. Fifty-two participants were randomly assigned to follow two types of Mediterranean-ketogenic diets for eight weeks each, with an eight-week break in between. The two interventions were: 1) A high-fat, low carbohydrate version of a Mediterranean diet (MeDi-KD) and 2) A Mediterranean diet administered with a ketogenic supplement, medium-chain triglyceride oil (MeDi-MCT). Forty-eight people started the study, 41 completed at least one diet intervention phase and 33 completed both intervention phases. No serious side effects were reported. Although most participants felt they followed the diets closely, objective measures of adherence suggested room for improvement. The MeDi-MCT diet led to small but significant improvements in patient-reported motor activities of daily living and motor complications. Longer-term studies are needed to validate these findings. Future trials should incorporate behavioral coaching techniques to better help participants follow the diets.

The central, mortality-associated hallmark of cancer is the process of metastasis. It is increasingly recognized that bacteria influence multiple facets of cancer progression, but the extent to which tumor microenvironment-associated bacteria control metastasis in cancer is poorly understood. To identify tumor-associated bacteria and their role in metastasis, we utilized established murine models of non-metastatic and metastatic breast tumors to identify bacteria capable of driving metastatic disease. We found several species of the Bacillus genus that were unique to metastatic tumors, and found that breast tumor cells cultured with a Bacillus bacterium isolated from metastatic tumors, Bacillus thermoamylovorans , produced nearly 3× the metastatic burden as control cells or cells cultured with bacteria from non-metastatic breast tumors. We then performed targeted metabolomics on tumor cells cultured with different bacterial species and found that B. thermoamylovorans differentially regulated tumor cell metabolite profiles compared to bacteria isolated from non-metastatic tumors. Using these bacteria, we performed de novo sequencing and tested for the presence of genes that were unique to the bacterium isolated from metastatic tumors in a patient population to provide a proof-of-concept for identifying how specific bacterial functions are associated with the metastatic process in cancer independent of bacterial species. Together, our data directly demonstrate the ability of specific bacteria to promote metastasis through interaction with cancer cells. IMPORTANCE: Metastasis is a major barrier to long-term survival for cancer patients, and therapeutic options for patients with aggressive, metastatic forms of breast cancer remain limited. It is therefore critical to understand the differences between non-metastatic and metastatic disease to identify potential methods for slowing or even stopping metastasis. In this work, we identify a bacterial species present with metastatic breast tumors capable of increasing the metastatic capabilities of tumor cells. We isolated and sequenced this bacteria, as well as a control species which failed to promote metastasis, and identified specific bacterial genes that were unique to the metastasis-promoting species. We tested for the presence of these bacterial genes in patient tumor samples and found they were more likely to be associated with mortality. We also identified enrichment of specific bacterial functions, providing insight into possible sources of bacteria-driven increases in the metastatic potential of multiple cancer types.

Secretory Immunoglobulin A (SIgA) is the dominant mucosal antibody and a key regulator of the gut microbiota. In early life, infants rely on breastmilk as their primary source of SIgA, but the role of milk-derived SIgA in early life microbiota colonization dynamics remains incompletely understood. Here, we show that species-specific SIgA in milk is antigen-inducible and discriminates between closely related but immunologically diverging microbes in the neonatal gut. More specifically, milk species-specific SIgA promotes colonization by an anti-inflammatory Escherichia coli strain while restricting the expansion of pro-inflammatory Proteus mirabilis. These findings uncover a dual role of maternal milk SIgA in actively sculpting the early life gut microbiota with species-level precision.

In addition to numerous clinical studies, research using experimental models have contributed extensive evidence to the link between antibiotic exposure and atopic disease. A number of mouse models of allergy have been developed and used to uncover the specific effects of various microbiota members and perturbations on allergy development. Studies in mice that lack microbes entirely have also demonstrated the various components of the immune system that require microbial exposure. The importance of the early-life period and the mechanisms by which atopy “protective” species identified in human cohorts promote immune development have been elucidated in mice. Finally, non-animal models involving human-derived cells shed light on specific effects of bacteria on human epithelial and immune responses. When considered alongside clinical cohort studies, experimental model systems have provided crucial evidence for the link between the neonatal gut microbiota and allergic disease, immensely supporting the stewardship of antibiotic administration in infants. The following review aims to describe the range of experimental models used for studying factors that affect the relationship between the gut microbiota and allergic disease and summarize key findings that have come from research in animal and in vitro models.