Mammalian Gastrointestinal Tract Research Articles

Acute and repeated exposure to social stress reduces gut microbiota diversity in Syrian hamsters

Mood and anxiety disorders are strongly associated with somatic symptoms such as gastrointestinal distress (Bekhuis et al., 2014, Felice et al., 2015), and a high co-morbidity exists between stress-related neuropsychiatric symptoms and gastrointestinal disorders such as irritable bowel syndrome (Kanuri et al., 2016, Kennedy et al., 2012, Qin et al., 2014). One possibility is that stress impacts brain function and mental health via its effect on the gastrointestinal tract (for review see Dinan & Cryan, 2012, Dinan et al., 2015, Parashar & Udayabanu, 2016). Given that the available treatment strategies for a variety of stress-related neuropsychiatric disorders are inadequate for many, expanding our knowledge of a broader range of potential etiologic factors might lead to novel, more effective therapeutics (Culpepper et al., 2015, Haddad et al., 2015, Nestler et al., 2002). The mammalian gastrointestinal tract houses over 100 trillion microorganisms (Eckburg et al., 2005), which are critical for vital functions such as processing and digestion of food, synthesis of vitamins, inhibition of pathogens, and immune system development and maturation (Ramakrishna, 2013). Thus, a stable and symbiotic relationship exists between these microorganisms, referred to as gut microbiota, and the host gastrointestinal system (Mayer et al., 2015). These microbiota are essential to homeostasis, and abrupt dysbiosis or absence of this vibrant community can compromise the physical and mental health of the host (Chang et al., 2008, Cryan, 2016, Luczynski et al., 2016, Turnbaugh et al., 2006). Recently, it has been demonstrated that there is bi-directional communication, referred to as the gut-brain axis, between the central nervous system and the gastrointestinal tract, and altering the gut microbiota during early development or adulthood changes both stress-related behavior and responsivity of the stress axis (Desbonnet et al., 2014, Diaz et al., 2011, Collins et al., 2013, Sudo et al., 2004). Many neuropsychiatric disorders and symptoms that are associated with gastrointestinal dysfunction are also caused or exacerbated by exposure to stress (Agid et al., 2000, Kessler, 1997, Saveanu & Nemeroff, 2012), and stress has been associated with significant alterations in the gut microbial community in mammals, including humans (Lyte et al., 2011). These stress-induced alterations are associated with consequences ranging from inflammation to increased anxiety-like behavior (Bailey & Coe, 1999, Bailey et al., 2011). Exposure to social stress, in particular, can cause or exacerbate disabling neuropsychiatric disorders, including depression and PTSD (Bjorkqvist et al., 2001, Qiao et al., 2016). Relatively little is known, however, about the direct impact of social stress on the gut microbial community and how these microbes, in turn, may affect behavior. Bailey et al. (2011) demonstrated that group-housed mice exposed to 6, 2 hr bouts of social disruption stress exhibited alterations of the gut microbial community characterized by a reduction in microbial diversity and richness. A similar response was observed in mice that were exposed to a more severe, 10-day social defeat procedure (Bharwani et al., 2016). There is even some evidence that a single, 2 hr exposure to a social defeat stressor in mice impacts gut microbiota (Galley et al., 2014), suggesting that even acute social stress might have effects on the gut. The current study utilizes a well-characterized resident-intruder model in Syrian hamsters (Jasnow et al., 2001, Potegal et al., 1993) to investigate whether exposure to social stress affects the commensal gut microbiota and, in particular, whether it does so differently in individuals that “win” a social conflict (i.e., become dominant) versus those that “lose” (i.e., become subordinate). Syrian hamsters are ideal candidates for the study of social stress because when weight- and age-matched conspecifics are paired, they readily produce aggressive and territorial behavior that rapidly results in the formation of a stable dominance relationship (Albers et al., 2002). This allows a direct comparison of commensal bacteria in dominants and subordinates. This comparison is not possible in mice because conspecifics generally do not fight; defeated mice are produced using a larger, more aggressive heterospecific (e.g., C57J/BL6 defeated by a CD-I mouse). An additional benefit of using hamsters is that their agonistic behavior during brief encounters is highly ritualized and rarely results in any tissue damage, allowing us to focus on the psychological, as opposed to physical, aspects of social stress (Huhman & Jasnow, 2005). Furthermore, no studies have examined whether the baseline composition of the gut microbiota alters behavioral responses to social stress. Thus, we also measured whether the baseline gut microbiota composition can predict whether an animal becomes dominant or subordinate after a subsequent agonistic encounter.

Causal effects of the microbiota on immune-mediated diseases.

The mammalian immune system has evolved in the presence of a complex community of indigenous microorganisms that constitutively colonize all barrier surfaces. This intimate relationship has resulted in the development of a vast array of reciprocal interactions between the microbiota and the host immune system, particularly in the intestine, where the density and diversity of indigenous microbes are greatest. Alterations in the gut microbiota have been correlated with almost every known immunological disease, but in most cases, it remains unclear whether these changes are a cause or effect of the disease or merely a reflection of epidemiological differences between groups. Here, we review recent efforts to demonstrate a causal role for the microbiota in health and disease, outline experimental advances that have made these studies possible, and highlight how changes in microbial composition may influence immune system function.

Multifaceted Defense against Listeria monocytogenes in the Gastro-Intestinal Lumen

Listeria monocytogenes is a foodborne pathogen that can cause febrile gastroenteritis in healthy subjects and systemic infections in immunocompromised individuals. Despite the high prevalence of L. monocytogenes in the environment and frequent contamination of uncooked meat and poultry products, infections with this pathogen are relatively uncommon, suggesting that protective defenses in the general population are effective. In the mammalian gastrointestinal tract, a variety of defense mechanisms prevent L. monocytogenes growth, epithelial penetration and systemic dissemination. Among these defenses, colonization resistance mediated by the gut microbiota is crucial in protection against a range of intestinal pathogens, including L. monocytogenes. Here we review defined mechanisms of defense against L. monocytogenes in the lumen of the gastro-intestinal tract, with particular emphasis on protection conferred by the autochthonous microbiota. We suggest that selected probiotic species derived from the microbiota may be developed for eventual clinical use to enhance resistance against L. monocytogenes infections.

Frontline defenders: goblet cell mediators dictate host-microbe interactions in the intestinal tract during health and disease

Goblet cells (GCs) are the predominant secretory epithelial cells lining the luminal surface of the mammalian gastrointestinal (GI) tract. Best known for their apical release of mucin 2 (Muc2), which is critical for the formation of the intestinal mucus barrier, GCs have often been overlooked for their active contributions to intestinal protection and host defense. In part, this oversight reflects the limited tools available to study their function but also because GCs have long been viewed as relatively passive players in promoting intestinal homeostasis and host defense. In light of recent studies, this perspective has shifted, as current evidence suggests that Muc2 as well as other GC mediators are actively released into the lumen to defend the host when the GI tract is challenged by noxious stimuli. The ability of GCs to sense and respond to danger signals, such as bacterial pathogens, has recently been linked to inflammasome signaling, potentially intrinsic to the GCs themselves. Moreover, further work suggests that GCs release Muc2, as well as other mediators, to modulate the composition of the gut microbiome, leading to both the expansion as well as the depletion of specific gut microbes. This review will focus on the mechanisms by which GCs actively defend the host from noxious stimuli, as well as describe advanced technologies and new approaches by which their responses can be addressed. Taken together, we will highlight current insights into this understudied, yet critical, aspect of intestinal mucosal protection and its role in promoting gut defense and homeostasis.

Microbiome-driven allergic lung inflammation is ameliorated by short-chain fatty acids.

The mammalian gastrointestinal tract harbors a microbial community with metabolic activity critical for host health, including metabolites that can modulate effector functions of immune cells. Mice treated with vancomycin have an altered microbiome and metabolite profile, exhibit exacerbated T helper type 2 cell (Th2) responses, and are more susceptible to allergic lung inflammation. Here we show that dietary supplementation with short-chain fatty acids (SCFAs) ameliorates this enhanced asthma susceptibility by modulating the activity of T cells and dendritic cells (DCs). Dysbiotic mice treated with SCFAs have fewer interleukin-4 (IL4)-producing CD4+ T cells and decreased levels of circulating immunoglobulin E (IgE). In addition, DCs exposed to SCFAs activate T cells less robustly, are less motile in response to CCL19 in vitro, and exhibit a dampened ability to transport inhaled allergens to lung draining nodes. Our data thus demonstrate that gut dysbiosis can exacerbate allergic lung inflammation through both T cell- and DC-dependent mechanisms that are inhibited by SCFAs.

Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets

The gut microbiota generates a huge pool of unknown metabolites, and their identification and characterization is a key challenge in metabolomics. However, there are still gaps on the studies of gut microbiota and their chemical structures. In this investigation, an unusual class of bacterial sulfonolipids (SLs) is detected in mouse cecum, which was originally found in environmental microbes. We have performed a detailed molecular level characterization of this class of lipids by combining high-resolution mass spectrometry and liquid chromatography analysis. Eighteen SLs that differ in their capnoid and fatty acid chain compositions were identified. The SL called “sulfobacin B” was isolated, characterized, and was significantly increased in mice fed with high-fat diets. To reveal bacterial producers of SLs, metagenome analysis was acquired and only two bacterial genera, i.e., Alistipes and Odoribacter, were revealed to be responsible for their production. This knowledge enables explaining a part of the molecular complexity introduced by microbes to the mammalian gastrointestinal tract and can be used as chemotaxonomic evidence in gut microbiota.

Comprehensive review on toxicity of persistent organic pollutants from petroleum refinery waste and their degradation by microorganisms

Control and prevention of environmental pollution has become a worldwide issue of concern. Aromatic hydrocarbons including benzene, toluene, ethyl benzene, xylene (BTEX) and polyaromatic hydrocarbons (PAHs) are persistent organic pollutants (POPs), released into the environment mainly by exploration activities of petroleum industry. These pollutants are mutagenic, carcinogenic, immunotoxic and teratogenic to lower and higher forms of life i.e. microorganisms to humans. According to the International Agency for Research on Cancer (IARC) and United States Environmental Protection Agency (U.S. EPA), Benzo[a]pyrene (BaP) is carcinogenic in laboratory animals and humans. Aromatic hydrocarbons are highly lipid soluble and thus readily absorbed from environment in gastrointestinal tract of mammals. Treatment and remediation of petroleum refinery waste have been shown either to reduce or to eliminate genotoxicity of these pollutants. Bioremediation by using microorganisms to treat this waste is showing a promising technology as it is safe and cost-effective option among various technologies tested. The main aim of this review is to provide contemporary information on variety of aromatic hydrocarbons present in crude oil (with special focus to mono- and poly-aromatic hydrocarbons), exposure routes and their adverse effects on humans. This review also provides a synthesis of scientific literature on remediation technologies available for aromatic hydrocarbons, knowledge gaps and future research developments in this field.

Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes.

The community of microorganisms in the mammalian gastrointestinal tract, referred to as the gut microbiota, influences host physiology and immunity. The last decade of microbiome research has provided significant advancements for the field and highlighted the importance of gut microbes to states of both health and disease. Novel molecular techniques have unraveled the tremendous diversity of intestinal symbionts that potentially influence the host, many proof-of-concept studies have demonstrated causative roles of gut microbial communities in various pathologies, and microbiome-based approaches are beginning to be implemented in the clinic for diagnostic purposes or for personalized treatments. However, several challenges for the field remain: purely descriptive reports outnumbering mechanistic studies and slow translation of experimental results obtained in animal models into the clinics. Moreover, there is a dearth of knowledge regarding how gut microbes, including novel species that have yet to be identified, impact host immune responses. The sheer complexity of the gut microbial ecosystem makes it difficult, in part, to fully understand the microbiota-host networks that regulate immunity. In the present manuscript, we review key findings on the interactions between gut microbiota members and the immune system. Because culturing microbes allows performing functional studies, we have emphasized the impact of specific taxa or communities thereof. We also highlight underlying molecular mechanisms and discuss opportunities to implement minimal microbiome-based strategies.

Antigen-specific regulatory T-cell responses to intestinal microbiota.

The mammalian gastrointestinal tract can harbor both beneficial commensal bacteria important for host health, but also pathogenic bacteria capable of intestinal damage. It is therefore important that the host immune system mount the appropriate immune response to these divergent groups of bacteria-promoting tolerance in response to commensal bacteria and sterilizing immunity in response to pathogenic bacteria. Failure to induce tolerance to commensal bacteria may underlie immune-mediated diseases such as human inflammatory bowel disease. At homeostasis, regulatory T (Treg) cells are a key component of the tolerogenic response by adaptive immunity. This review examines the mechanisms by which intestinal bacteria influence colonic T-cells and B-cell immunoglobulin A (IgA) induction, with an emphasis on Treg cells and the role of antigen-specificity in these processes. In addition to discussing key primary literature, this review highlights current controversies and important future directions.

A review on early gut maturation and colonization in pigs, including biological and dietary factors affecting gut homeostasis

During the prenatal, neonatal and post-weaning periods, the mammalian gastrointestinal tract undergoes various morphological and physiological changes alongside with an expansion of the immune system and microbial ecosystem. This review focuses on the time period before weaning and summarizes the current knowledge regarding i) structural and functional aspects ii) the development of the immune system, and iii) the establishment of the gut ecosystem of the porcine intestine. Structural and functional maturation of the gastrointestinal tract gradually progress with age. In the neonatal period colostrum induces gut closure, leads to an increase in intestinal weight, absorptive area and brush border enzyme activities. During the first weeks of life, an increased secretion of stomach and pancreatic enzymes and an increased uptake of monosaccharides and amino acids are observed. The development in digestive function coincides with development in both the adaptive and innate immune system. This secures a balanced immune response to the ingested milk-derived macromolecules, and colonizing bacteria. Husbandry and dietary interventions in early life appear to affect the development of multiple components of the mucosal immune system. Furthermore, the composition of the intestinal microbial communities seems to be affected by the early postnatal environment, which might also contribute to gut maturation, metabolic and immune development. Understanding the interplay between morphological, functional and immunological maturation, as influenced by early microbial colonization and ingestion of dietary factors, is of utmost importance to identify management and feeding strategies to optimize intestinal health. We discuss some possible implications related to intrauterine growth restriction, and preterm delivery as these both dramatically increase the risk of mortality and morbidity. In addition, some nutritional interventions during the perinatal period in both sows and piglets will be discussed in the light of possible health consequences early in life and later on.

Microbiota-Based Therapies for Clostridium difficile and Antibiotic-Resistant Enteric Infections.

Bacterial pathogens are increasingly antibiotic resistant, and development of clinically effective antibiotics is lagging. Curing infections increasingly requires antimicrobials that are broader spectrum, more toxic, and more expensive, and mortality attributable to antibiotic-resistant pathogens is rising. The commensal microbiota, comprising microbes that colonize the mammalian gastrointestinal tract, can provide high levels of resistance to infection, and the contributions of specific bacterial species to resistance are being discovered and characterized. Microbiota-mediated mechanisms of colonization resistance and pathogen clearance include bactericidal activity, nutrient depletion, immune activation, and manipulation of the gut's chemical environment. Current research is focusing on development of microbiota-based therapies to reduce intestinal colonization with antibiotic-resistant pathogens, with the goal of reducing pathogen transmission and systemic dissemination.

Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal.

The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L. salivarius using bioinformatic techniques. The main aim of the study was to describe intra-species diversity and to determine how this diversity is spread across the replicons. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Additionally, the presence of extra linear and circular megaplasmids is noted in several strains, while small plasmids are not always present. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters and several clustered regularly interspaced short palindromic repeats-associated systems show a lot of variation on the chromosome. Overall, despite its reputation as a mammalian gastrointestinal tract specialist, the intra-specific variation of L. salivarius reveals potential strain-dependant effects on human health.

The human microbiome and metabolomics: Current concepts and applications

ABSTRACTThe mammalian gastrointestinal tract has co-developed with a large number of microbes in a symbiotic relationship over millions of years. Recent studies indicate that indigenous bacteria are intimate with the intestine and play essential roles in health and disease. In the quest to maintain a stable niche, these prokaryotes influence multiple host metabolic pathways, resulting from an interactive host–microbiota metabolic signaling and impacting strongly on the metabolic phenotypes of the host. Since dysbiosis of the gut bacteria result in alteration in the levels of certain microbial and host co-metabolites, identifying these markers could enhance early detection of diseases. Also, identification of these metabolic fingerprints could give us clues as to how to manipulate the microbiome to promote health or treat diseases. This review provides an overview of our current knowledge of the microbiome and metablomics, applications and the future perspectives.

Use of genetically modified bacteria for drug delivery in humans: Revisiting the safety aspect

The use of live, genetically modified bacteria as delivery vehicles for biologics is of considerable interest scientifically and has attracted significant commercial investment. We have pioneered the use of the commensal gut bacterium Bacteroides ovatus for the oral delivery of therapeutics to the gastrointestinal tract. Here we report on our investigations of the biological safety of engineered B. ovatus bacteria that includes the use of thymineless death as a containment strategy and the potential for the spread of transgenes in vivo in the mammalian gastrointestinal tract. We demonstrate the ability of GM-strains of Bacteroides to survive thymine starvation and overcome it through the exchange of genetic material. We also provide evidence for horizontal gene transfer in the mammalian gastrointestinal tract resulting in transgene-carrying wild type bacteria. These findings sound a strong note of caution on the employment of live genetically modified bacteria for the delivery of biologics.

The Rhomboid Protease GlpG Promotes the Persistence of Extraintestinal Pathogenic Escherichia coli within the Gut.

ABSTRACTExtraintestinal pathogenic Escherichia coli (ExPEC) strains are typically benign within the mammalian gut but can disperse to extraintestinal sites to cause diseases like urinary tract infections and sepsis. As occupation of the intestinal tract is often a prerequisite for ExPEC-mediated pathogenesis, we set out to understand how ExPEC colonizes this niche. A screen using transposon sequencing (Tn-seq) was performed to search for genes within ExPEC isolate F11 that are important for growth in intestinal mucus, which is thought to be a major source of nutrients for E. coli in the gut. Multiple genes that contribute to ExPEC fitness in mucus broth were identified, with genes that are directly or indirectly associated with fatty acid beta-oxidation pathways being especially important. One of the identified mucus-specific fitness genes encodes the rhomboid protease GlpG. In vitro, we found that the disruption of glpG had polar effects on the downstream gene glpR, which encodes a transcriptional repressor of factors that catalyze glycerol degradation. Mutation of either glpG or glpR impaired ExPEC growth in mucus and on plates containing the long-chain fatty acid oleate as the sole carbon source. In contrast, in a mouse gut colonization model in which the natural microbiota is unperturbed, the disruption of glpG but not glpR significantly reduced ExPEC survival. This work reveals a novel biological role for a rhomboid protease and highlights new avenues for defining mechanisms by which ExPEC strains colonize the mammalian gastrointestinal tract.

Microbiota-induced peritrophic matrix regulates midgut homeostasis and prevents systemic infection of malaria vector mosquitoes.

Manipulation of the mosquito gut microbiota can lay the foundations for novel methods for disease transmission control. Mosquito blood feeding triggers a significant, transient increase of the gut microbiota, but little is known about the mechanisms by which the mosquito controls this bacterial growth whilst limiting inflammation of the gut epithelium. Here, we investigate the gut epithelial response to the changing microbiota load upon blood feeding in the malaria vector Anopheles coluzzii. We show that the synthesis and integrity of the peritrophic matrix, which physically separates the gut epithelium from its luminal contents, is microbiota dependent. We reveal that the peritrophic matrix limits the growth and persistence of Enterobacteriaceae within the gut, whilst preventing seeding of a systemic infection. Our results demonstrate that the peritrophic matrix is a key regulator of mosquito gut homeostasis and establish functional analogies between this and the mucus layers of the mammalian gastrointestinal tract.

Ethanolamine Metabolism in the Mammalian Gastrointestinal Tract: Mechanisms, Patterns, and Importance.

Nutritional exchanges and cooperation between bacteria in the gastrointestinal tract and the mammalian host play an important role in health and disease. Ethanolamine is an essential dietary lipid nutrient for animals and is abundant in both intestinal and bacterial cell membranes. Ethanolamine can be utilized by intestinal eukaryotic cells via the cytidine phosphoethanolamine pathway for de novo synthesis of phosphatidylethanolamine, and certain bacteria are able to catabolize it as a major carbon and/or nitrogen source with the help of ethanolamine utilization proteins. In addition, ethanolamine utilization dramatically affects lipid metabolism and short-chain fatty acid biosynthesis. Ethanolamine metabolism plays a significant role in the renewal and proliferation of intestinal cells and intestinal inflammation, and ethanolamine may be a nutritional target to diagnose or treat diseases such as inflammatory bowel disease. This review summarizes the mechanisms of ethanolamine metabolism in the mammalian gastrointestinal tract and its influence on intestinal health and immunity, thus providing a theoretical reference for further studies on mammalian nutrition and disease.

Dietary metabolites derived from gut microbiota: critical modulators of epigenetic changes in mammals.

The mammalian gastrointestinal tract harbors trillions of commensal microorganisms, collectively known as the microbiota. The microbiota is a critical source of environmental stimuli and, thus, has a tremendous impact on the health of the host. The microbes within the microbiota regulate homeostasis within the gut, and any alteration in their composition can lead to disorders that include inflammatory bowel disease, allergy, autoimmune disease, diabetes, mental disorders, and cancer. Hence, restoration of the gut flora following changes or imbalance is imperative for the host. The low-molecular-weight compounds and nutrients such as short-chain fatty acids, polyamines, polyphenols, and vitamins produced by microbial metabolism of nondigestible food components in the gut actively participate in various epigenomic mechanisms that reprogram the genome by altering the transcriptional machinery of a cell in response to environmental stimuli. These epigenetic modifications are caused by a set of highly dynamic enzymes, notably histone acetylases, deacetylases, DNA methylases, and demethylases, that are influenced by microbial metabolites and other environmental cues. Recent studies have shown that host expression of histone acetylases and histone deacetylases is important for regulating communication between the intestinal microbiota and the host cells. Histone acetylases and deacetylases influence the molecular expression of genes that affect not only physiological functions but also behavioral shifts that occur via neuroepigenetic modifications of genes. The underlying molecular mechanisms, however, have yet to be fully elucidated and thus provide a new area of research. The present review provides insights into the current understanding of the microbiota and its association with mammalian epigenomics as well as the interaction of pathogens and probiotics with host epigenetic machinery.

Complete Genome Sequence of the Original Escherichia coli Isolate, Strain NCTC86.

ABSTRACTEscherichia coli is the most well-studied bacterium and a common colonizer of the lower mammalian gastrointestinal tract. We report here the complete genome sequence of the original Escherichia coli isolate, strain NCTC86, which was described by Theodor Escherich, for whom the genus is named.

Influences of the Gut Microbiota on DNA Methylation and Histone Modification

The gut microbiota is a vast ensemble of microorganisms inhabiting the mammalian gastrointestinal tract that can impact physiologic and pathologic processes. However, our understanding of the underlying mechanism for the dynamic interaction between host and gut microbiota is still in its infancy. The highly evolved epigenetic modifications allow hosts to reprogram the genome in response to environmental stimuli, which may play a key role in triggering multiple human diseases. In spite of increasing studies in gut microbiota and epigenetic modifications, the correlation between them has not been well elaborated. Here, we review current knowledge of gut microbiota impacts on epigenetic modifications, the major evidence of which centers on DNA methylation and histone modification of the immune system.