Sean M. Kearney

Microbial reprogramming inhibits Western diet-associated obesity.

A recent epidemiological study showed that eating ‘fast food’ items such as potato chips increased likelihood of obesity, whereas eating yogurt prevented age-associated weight gain in humans. It was demonstrated previously in animal models of obesity that the immune system plays a critical role in this process. Here we examined human subjects and mouse models consuming Westernized ‘fast food’ diet, and found CD4+ T helper (Th)17-biased immunity and changes in microbial communities and abdominal fat with obesity after eating the Western chow. In striking contrast, eating probiotic yogurt together with Western chow inhibited age-associated weight gain. We went on to test whether a bacteria found in yogurt may serve to lessen fat pathology by using purified Lactobacillus reuteri ATCC 6475 in drinking water. Surprisingly, we discovered that oral L. reuteri therapy alone was sufficient to change the pro-inflammatory immune cell profile and prevent abdominal fat pathology and age-associated weight gain in mice regardless of their baseline diet. These beneficial microbe effects were transferable into naïve recipient animals by purified CD4+ T cells alone. Specifically, bacterial effects depended upon active immune tolerance by induction of Foxp3+ regulatory T cells (Treg) and interleukin (Il)-10, without significantly changing the gut microbial ecology or reducing ad libitum caloric intake. Our finding that microbial targeting restored CD4+ T cell balance and yielded significantly leaner animals regardless of their dietary ‘fast food’ indiscretions suggests population-based approaches for weight management and enhancing public health in industrialized societies.

Microbial symbionts accelerate wound healing via the neuropeptide hormone oxytocin.

Wound healing capability is inextricably linked with diverse aspects of physical fitness ranging from recovery after minor injuries and surgery to diabetes and some types of cancer. Impact of the microbiome upon the mammalian wound healing process is poorly understood. We discover that supplementing the gut microbiome with lactic acid microbes in drinking water accelerates the wound-healing process to occur in half the time required for matched control animals. Further, we find that Lactobacillus reuteri enhances wound-healing properties through up-regulation of the neuropeptide hormone oxytocin, a factor integral in social bonding and reproduction, by a vagus nerve-mediated pathway. Bacteria-triggered oxytocin serves to activate host CD4+Foxp3+CD25+ immune T regulatory cells conveying transplantable wound healing capacity to naive Rag2-deficient animals. This study determined oxytocin to be a novel component of a multi-directional gut microbe-brain-immune axis, with wound-healing capability as a previously unrecognized output of this axis. We also provide experimental evidence to support long-standing medical traditions associating diet, social practices, and the immune system with efficient recovery after injury, sustained good health, and longevity.

Salt-responsive gut commensal modulates TH17 axis and disease

A Western lifestyle with high salt consumption can lead to hypertension and cardiovascular disease. High salt may additionally drive autoimmunity by inducing T helper 17 (TH17) cells, which can also contribute to hypertension. Induction of TH17 cells depends on gut microbiota; however, the effect of salt on the gut microbiome is unknown. Here we show that high salt intake affects the gut microbiome in mice, particularly by depleting Lactobacillus murinus. Consequently, treatment of mice with L. murinus prevented salt-induced aggravation of actively induced experimental autoimmune encephalomyelitis and salt-sensitive hypertension by modulating TH17 cells. In line with these findings, a moderate high-salt challenge in a pilot study in humans reduced intestinal survival of Lactobacillus spp., increased TH17 cells and increased blood pressure. Our results connect high salt intake to the gut–immune axis and highlight the gut microbiome as a potential therapeutic target to counteract salt-sensitive conditions.

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles

The healthy microbiome protects against the development of Clostridium difficile infection (CDI), which typically develops following antibiotics. The microbiome metabolises primary to secondary bile acids, a process if disrupted by antibiotics, may be critical for the initiation of CDI.

Two dynamic regimes in the human gut microbiome

The gut microbiome is a dynamic system that changes with host development, health, behavior, diet, and microbe-microbe interactions. Prior work on gut microbial time series has largely focused on autoregressive models (e.g. Lotka-Volterra). However, we show that most of the variance in microbial time series is non-autoregressive. In addition, we show how community state-clustering is flawed when it comes to characterizing within-host dynamics and that more continuous methods are required. Most organisms exhibited stable, mean-reverting behavior suggestive of fixed carrying capacities and abundant taxa were largely shared across individuals. This mean-reverting behavior allowed us to apply sparse vector autoregression (sVAR)—a multivariate method developed for econometrics—to model the autoregressive component of gut community dynamics. We find a strong phylogenetic signal in the non-autoregressive co-variance from our sVAR model residuals, which suggests niche filtering. We show how changes in diet are also non-autoregressive and that Operational Taxonomic Units strongly correlated with dietary variables have much less of an autoregressive component to their variance, which suggests that diet is a major driver of microbial dynamics. Autoregressive variance appears to be driven by multi-day recovery from frequent facultative anaerobe blooms, which may be driven by fluctuations in luminal redox. Overall, we identify two dynamic regimes within the human gut microbiota: one likely driven by external environmental fluctuations, and the other by internal processes.

Maternal Gut Microbes Control Offspring Sex and Survival

Sex outcome and maternal investment in progeny are important predictors of reproductive success. While environmental factors appear to influence these processes, there is little evidence to date of a direct role for gut commensals. Here we show that the reproductive outcomes (sex and survival) of mouse litters depend on signals conveyed through the microbiome. We discover that transient treatment of mouse mothers with specific microorganisms increases the absolute survival of offspring and skews offspring sex ratios via an endocrine-dependent mechanism requiring the neurophysiological hormone oxytocin. The implication of maternal oxytocin levels suggests that commensal microbes may have a broad role in modulating host endocrine and neurological pathways.

Designing synbiotics for improved human health

A synbiotic is the combination of a microorganism shown (or thought) to have some beneficial effect when consumed (i.e. a probiotic) and a compound that specifically favours its growth (i.e. a prebiotic), having a synergistic effect when paired together. Many probiotic supplements are currently marketed as synbiotics. These products typically contain a combination of Bifidobacterium, Lactobacillus or Streptococcus species, and a carbon substrate (e.g. lactose, lactulose or inulin) supporting growth of these organisms. Historical use of probiotics in foods and beverages and marketing towards digestive health has favoured food companies as producers of these products. The largest market share for probiotics comes from companies like Danone, Nestl e and General Mills, which are currently investing in R&D to expand their probiotic and prebiotic portfolios. Examples of growing interest in probiotics can be found among recent patents, containing claims of probiotics for reduction of belly fat (Grompone et al., 2014) or prebiotic fibre formulations for the treatment of inflammatory bowel disease (Boileau et al., 2015). In coming years, focus on the microbiome may shift the market share of probiotics towards pharmaceutical companies, which have infrastructure and revenue models to accommodate clinical trials. Indeed, both existing pharmaceutical companies (e.g. Johnson and Johnson, Merck, Pfizer and Novartis) and recent start-ups (e.g. Vedanta, Eligo Biosciences, Finch Therapeutics) have begun to target probiotics from the human microbiota for treatment of a broad range of diseases. Currently available probiotics sample a limited diversity of bacteria that does not include most dominant gut microorganisms positively associated with host health. The use of these established probiotics stems from their historical association with improved digestive health. Today, probiotic, prebiotic and synbiotic products are marketed towards use in gynaecology, urology, anti-ageing, gastroenterology, immunology, cardiology, skin care, dietetics and oral care. The broad applications of this limited clique of organisms suggest that there is a need for more extensive clinical and epidemiological evaluation of probiotics and their efficacies in the treatment of a variety of conditions. In general, for probiotics to be marketed as pharmaceutical products, the burden of proof for efficacy will be much greater than for similar formulations marketed as functional food products, similar to vitamins or other over-the-counter supplements. For well-studied probiotic species, we have some understanding of the mechanisms by which they impact host health. Some Lactobacillus species, in particular, are thought to deplete systemic pro-inflammatory Th17 immune cells through the production of tryptophan metabolites, which activate the aryl hydrocarbon receptor (AHR; Zelante et al., 2013). Many of their other downstream effects on host health have yet to be elucidated, but there are indications that certain Lactobacillus species may affect brain (Bravo et al., 2011), reproductive (Linhares et al., 2011) and epithelial barrier function (Levkovich et al., 2013). Ongoing research on the diverse and understudied members of the human gut microbiota likely will propel pharmaceutical investment in clinically relevant probiotics and synbiotics. By contrast, food and probiotics companies will likely invest in formulations that incorporate well-studied, previously identified probiotics to promote their non-clinical use in different settings. Recent studies analysing the effects of introduced bacteria on the host suggest that several commensals have generic and redundant effects on immunity (GevaZatorsky et al., 2017). However, these effects may change in the presence of an intact microbial community and likely interact with diet and host health (MaldonadoG omez et al., 2016). Some of these interactions may be desirable: e.g., some probiotics show competitive exclusion of pathogenic organisms (Caballero et al., 2017), support the growth of native bacteria helpful for host health (Belzer et al., 2017; Caballero et al., 2017) and provision nutrients from the diet otherwise inaccessible to the host (Marcobal and Sonnenburg, 2012). The

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host’s microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient’s microbiota.