Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology

An emerging role for the gut microbiome in tauopathy

Tauopathies constitute a group of neurodegenerative diseases characterized by abnormal aggregation of the protein tau, progressive neuronal and synaptic loss, and eventual cognitive and motor impairment. In this review, we will highlight the latest efforts investigating the intricate interplay between the gut microbiome and tauopathies. We discuss the physiological interactions between the microbiome and the brain as well as clinical and experimental evidence that suggests that the presence of tauopathy alters the composition of gut microbiota. We explore both animal and human studies that define causative relationships between the gut microbiome and tauopathy by directly manipulating or transferring gut microbiota. This review highlights future directions into identifying and mechanistically elucidating microbial species causally linked to tauopathies, with an ultimate goal of devising therapeutic targets towards the gut microbiome to treat tauopathies.

MIR-21 regulating distribution of intestinal flora through TNF-α promotes progression of ulcerative colitis

Background

To study the changes in intestinal flora in patients with ulcerative colitis (UC), and to explore its correlations with micro ribonucleic acid (miR)-21 and serum tumor necrosis factor-a (TNF-α).

Methods

A total of 150 patients with UC were selected and divided into remission group and seizure group according to the severity of disease. At the same time, 150 healthy people receiving physical examination in the hospital during the same period were selected as control group. The levels of fecal miR-21 and TNF-α in all subjects were determined via reverse transcription-polymerase chain reaction (RT-PCR). The correlation between miR-21 and TNF-α and their associations with the changes in intestinal bacteria in UC were analyzed using Pearson correlation analysis. The risk factors affecting the occurrence of UC were explored via multivariate logistic regression analysis.

Dietary fiber pectin: challenges and potential anti-inflammatory benefits for preterms and newborns

Pectins, a class of dietary fibers abundant in vegetables and fruits, have drawn considerable interest due to their potential anti-inflammatory properties. Numerous studies have indicated that incorporating pectins into infant formula could be a safe strategy for alleviating infant regurgitation and diarrhea. Moreover, pectins have been shown to modulate cytokine production, macrophage activity, and NF-kB expression, all contributing to their anti-inflammatory effects. Despite this promising evidence, the exact mechanisms through which pectins exert these functions and how their structural characteristics influence these processes remain largely unexplored. This knowledge is particularly significant in the context of gut inflammation in developing preterm babies, a critical aspect of necrotizing enterocolitis (NEC), and in children and adults dealing with inflammatory bowel disease (IBD). Our mini review aims to provide an up-to-date compilation of relevant research on the effects of pectin on gut immune responses, specifically focusing on preterms and newborns. By shedding light on the underlying mechanisms and implications of pectin-mediated anti-inflammatory properties, this review seeks to advance our knowledge in this area and pave the way for future research and potential therapeutic interventions.

Sterility testing of germ-free mouse colonies

In biomedical research, germ-free and gnotobiotic mouse models enable the mechanistic investigation of microbiota-host interactions and their role on (patho)physiology. Throughout any gnotobiotic experiment, standardized and periodic microbiological testing of defined gnotobiotic housing conditions is a key requirement. Here, we review basic principles of germ-free isolator technology, the suitability of various sterilization methods, and the use of sterility testing methods to monitor germ-free mouse colonies. We also discuss their effectiveness and limitations, and share the experience with protocols used in our facility. In addition, possible sources of isolator contamination are discussed and an overview of reported contaminants is provided.

Secretory-IgA binding to intestinal microbiota attenuates inflammatory reactions as the intestinal barrier of preterm infants matures

Previous work has shown that Secretory-IgA (SIgA) binding to the intestinal microbiota is variable and may regulate host inflammatory bowel responses. Nevertheless, the impact of the SIgA functional binding to the microbiota remains largely unknown in preterm infants whose immature epithelial barriers make them particularly susceptible to inflammation. Here, we investigated SIgA binding to intestinal microbiota isolated from stools of preterm infants <33 weeks gestation with various levels of intestinal permeability. We found that SIgA binding to intestinal microbiota attenuates inflammatory reactions in preterm infants. We also observed a significant correlation between SIgA affinity to the microbiota and the infant's intestinal barrier maturation. Still, SIgA affinity was not associated with developing host defenses, such as the production of mucus and inflammatory calprotectin protein, but it depended on the microbiota shifts as the intestinal barrier matures. In conclusion, we reported an association between the SIgA functional binding to the microbiota and the maturity of the preterm infant's intestinal barrier, indicating that the pattern of SIgA coating is altered as the intestinal barrier matures.

Towards the generation of gnotobiotic larvae as a tool to investigate the influence of the microbiome on the development of the amphibian immune system

The immune equilibrium model suggests that exposure to microbes during early life primes immune responses for pathogen exposure later in life. While recent studies using a range of gnotobiotic (germ-free) model organisms offer support for this theory, we currently lack a tractable model system for investigating the influence of the microbiome on immune system development. Here, we used an amphibian species (Xenopus laevis) to investigate the importance of the microbiome in larval development and susceptibility to infectious disease later in life. We found that experimental reductions of the microbiome during embryonic and larval stages effectively reduced microbial richness, diversity and altered community composition in tadpoles prior to metamorphosis. In addition, our antimicrobial treatments resulted in few negative effects on larval development, body condition, or survival to metamorphosis. However, contrary to our predictions, our antimicrobial treatments did not alter susceptibility to the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) in the adult life stage. While our treatments to reduce the microbiome during early development did not play a critical role in determining susceptibility to disease caused by Bd in X. laevis, they nevertheless indicate that developing a gnotobiotic amphibian model system may be highly useful for future immunological investigations. This article is part of the theme issue 'Amphibian immunity: stress, disease and ecoimmunology'.

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.

Decreased Enterobacteriaceae translocation due to gut microbiota remodeling mediates the alleviation of premature aging by a high-fat diet

Aging-associated microbial dysbiosis exacerbates various disorders and dysfunctions, and is a major contributor to morbidity and mortality in the elderly, but the underlying cause of this aging-related syndrome is confusing. SIRT6 knockout (SIRT6 KO) mice undergo premature aging and succumb to death by 4 weeks, and are therefore useful as a premature aging research model. Here, fecal microbiota transplantation from SIRT6 KO mice into wild-type (WT) mice phenocopies the gut dysbiosis and premature aging observed in SIRT6 KO mice. Conversely, an expanded lifespan was observed in SIRT6 KO mice when transplanted with microbiota from WT mice. Antibiotic cocktail treatment attenuated inflammation and cell senescence in KO mice, directly suggesting that gut dysbiosis contributes to the premature aging of SIRT6 KO mice. Increased Enterobacteriaceae translocation, driven by the overgrowth of Escherichia coli, is the likely mechanism for the premature aging effects of microbiome dysregulation, which could be reversed by a high-fat diet. Our results provide a mechanism for the causal link between gut dysbiosis and aging, and support a beneficial effect of a high-fat diet for correcting gut dysbiosis and alleviating premature aging. This study provides a rationale for the integration of microbiome-based high-fat diets into therapeutic interventions against aging-associated diseases.

Regulation of sleep disorders in patients with traumatic brain injury by intestinal flora based on the background of brain-gut axis

OBJECTIVE

This study investigates whether people with sleep disorders following traumatic brain injury exhibit altered intestinal flora. The changes may allow us to gain a better understanding of the role of intestinal flora in patients with sleep disorders after traumatic brain injury, which may give us insights into curing the sleep disorder after traumatic brain injury (TBI).

METHOD

We analyzed the intestinal microbial colony structure in the feces of the 28 patients in the normal sleep group and the sleep disorder group by 16SrDNAsequencing technology. The bioinformatics method was used to analyze the intestinal flora change in the v3-v4 region of patients with biorhythm disorder and to observe the difference between the two groups.

RESULTS

Group grouping comparison and analysis of the evolutionary cladistic map showed the intestinal flora of patients with normal sleep after TBI was mainly Bacilli and Lactobacillales, while that of patients with sleep disorders was mainly Lachnospiraceae and Bacteroidales. The histogram of group value distribution by grouping comparison and analysis showed that Lachnospiraceae, Bacteroidales, Bacteroidia, and Bacteroidetes were dominant in the sleep disorder group. A relative abundance map of species with significant differences by group grouping comparison showed the main manifestations of intestinal flora are Firmicutes, Bacilli, Lactobacillales, Streptococcaceae, and Bacteroidetes. The normal sleep group was dominated by Bacilli, Lactobacillales, Streptococcus, and Veillonella, while in the sleep disorder group, Lachnospiraceae, Bacteroidales, Bacteroidia, and Bacteroidetes were the main species. It was found that there were also significant differences in intestinal flora abundance between the two groups after TBI. After statistics processing, it was compared with the normal sleep group, Lactobacillus, Streptococcus, Oribacterium and Rothia, Actinomyces, Streptophyta, TM7-3 bacteria, and Serratia, showing a significant reduction in the sleep disorder group (P < 0.05). However, Odoribacter, Lachnospiraceae, and Bilophila increased significantly (P < 0.05).

CONCLUSION

The sleep disorders of patients after TBI can be closely related to intestinal flora disturbance, and its internal mechanism needs further study. Intestinal flora has the potential to be a new therapeutic target.

Association of SARS-CoV-2 and Polypharmacy with Gut-Lung Axis: From Pathogenesis to Treatment

SARS-CoV-2 is a novel infectious contagion leading to COVID-19 disease. The virus has affected the lives of millions of people across the globe with a high mortality rate. It predominantly affects the lung (respiratory system), but it also affects other organs, including the cardiovascular, psychological, and gastrointestinal (GIT) systems. Moreover, elderly and comorbid patients with compromised organ functioning and pre-existing polypharmacy have worsened COVID-19-associated complications. Microbiota (MB) of the lung plays an important role in developing COVID-19. The extent of damage mainly depends on the predominance of opportunistic pathogens and, inversely, with the predominance of advantageous commensals. Changes in the gut MB are associated with a bidirectional shift in the interaction among the gut with a number of vital human organs, which leads to severe disease symptoms. This review focuses on dysbiosis in the gut-lung axis, COVID-19-induced worsening of comorbidities, and the influence of polypharmacy on MB.

Probiotic Oxalate-Degrading Bacteria: New Insight of Environmental Variables and Expression of the oxc and frc Genes on Oxalate Degradation Activity

Oxalate, a compound produced by many edible plants and as a terminal metabolite in the liver of mammals, is a toxin that has a detrimental role to human health. Humans and other mammals do possess enzymatic systems to degrade oxalate. Moreover, numerous oxalate-degrading bacteria reside in the mammalian gut and, thus, provide an important function for hosts. The current review focuses on the environmental factors that influence the efficacy of probiotic oxalate-degrading bacteria, relative to oxalate metabolism. We describe the mechanism of oxalate catabolism and its consumption by obligate and facultative anaerobic oxalate-degrading bacteria, in both in vitro and in vivo environments. We also explore the environmental variables that impact oxalate degradation. Studies on single species degrade oxalate have not shown a strong impact on oxalate metabolism, especially in high oxalate conditions such as consumption of foods high in oxalate (such as coffee and chocolate for humans or halogeton in animal feed). Considering effective variables which enhance oxalate degradation could be used in application of effective probiotic as a therapeutic tool in individuals with hyperoxaluria. This study indicates probiotics can be considered a good source of naturally occurring oxalate degrading agent in human colon.

Intestinal Barrier Dysfunction in Fatty Liver Disease: Roles of Microbiota, Mucosal Immune System, and Bile Acids

Nonalcoholic fatty liver disease (NAFLD) describes a spectrum of progressive liver diseases ranging from simple steatosis to steatohepatitis and fibrosis. Globally, NAFLD is the leading cause of morbidity and mortality associated with chronic liver disease, and NAFLD patients are at a higher risk of developing cirrhosis and hepatocellular carcinoma. While there is a consensus that inflammation plays a key role in promoting NAFLD progression, the underlying mechanisms are not well understood. Recent clinical and experimental evidence suggest that increased hepatic translocation of gut microbial antigens, secondary to diet-induced impairment of the intestinal barrier may be important in driving hepatic inflammation in NAFLD. Here, we briefly review various endogenous and exogenous factors influencing the intestinal barrier and present recent advances in our understanding of cellular and molecular mechanisms underlying intestinal barrier dysfunction in NAFLD.

The Game for Three: Salmonella–Host–Microbiota Interaction Models

Colonization of the gastrointestinal (GI) tract by enteric pathogens occurs in a context strongly determined by host-specific gut microbiota, which can significantly affect the outcome of infection. The complex gameplay between the trillions of microbes that inhabit the GI tract, the host, and the infecting pathogen defines a specific triangle of interaction; therefore, a complete model of infection should consider all of these elements. Many different infection models have been developed to explain the complexity of these interactions. This review sheds light on current knowledge, along with the strengths and limitations of in vitro and in vivo models utilized in the study of Salmonella–host–microbiome interactions. These models range from the simplest experiment simulating environmental conditions using dedicated growth media through in vitro interaction with cell lines and 3-D organoid structure, and sophisticated “gut on a chip” systems, ending in various animal models. Finally, the challenges facing this field of research and the important future directions are outlined.

The Role of the Microbiota in Regeneration-Associated Processes

The microbiota, the set of microorganisms associated with a particular environment or host, has acquired a prominent role in the study of many physiological and developmental processes. Among these, is the relationship between the microbiota and regenerative processes in various organisms. Here we introduce the concept of the microbiota and its involvement in regeneration-related cellular events. We then review the role of the microbiota in regenerative models that extend from the repair of tissue layers to the regeneration of complete organs or animals. We highlight the role of the microbiota in the digestive tract, since it accounts for a significant percentage of an animal microbiota, and at the same time provides an outstanding system to study microbiota effects on regeneration. Lastly, while this review serves to highlight echinoderms, primarily holothuroids, as models for regeneration studies, it also provides multiple examples of microbiota-related interactions in other processes in different organisms.

Influenza: Toward understanding the immune response in the young

Annually influenza causes a global epidemic resulting in 290,000 to 650,000 deaths and extracts a massive toll on healthcare and the economy. Infants and children are more susceptible to infection and have more severe symptoms than adults likely mitigated by differences in their innate and adaptive immune responses. While it is unclear the exact mechanisms with which the young combat influenza, it is increasingly understood that their immune responses differ from adults. Specifically, underproduction of IFN-γ and IL-12 by the innate immune system likely hampers viral clearance while upregulation of IL-6 may create excessive damaging inflammation. The infant's adaptive immune system preferentially utilizes the Th-2 response that has been tied to γδ T cells and their production of IL-17, which may be less advantageous than the adult Th-1 response for antiviral immunity. This differential immune response of the young is considered to serve as a unique evolutionary adaptation such that they preferentially respond to infection broadly rather than a pathogen-specific one generated by adults. This unique function of the young immune system is temporally, and possibly mechanistically, tied to the microbiota, as they both develop in coordination early in life. Additional research into the relationship between the developing microbiota and the immune system is needed to develop therapies effective at combating influenza in the youngest and most vulnerable of our population.

MICROBIOME AND UVEITIDES. A REVIEW

Microorganisms inhabiting all surfaces of mucous membranes and skin and forming a complex ecosystem with the host is called microbiota. The term microbiome is used for the aggregate genome of microbiota. The microbiota plays important role in the mechanisms of number of physiological and pathological processes, especially of the hosts immune system. The origin and course of autoimmune diseases not only of the digestive tract, but also of the distant organs, including the eye, are significantly influenced by intestinal microbiota. The role of microbiota and its changes (dysbiosis) in the etiopathogenesis of uveitis has so far been studied mainly in experimental models. Reduction of severity of non-infectious intraocular inflammation in germ-free mice or in conventional mice treated with broad-spectrum antibiotics was observed in both the induced experimental autoimmune uveitis model (EAU) and the spontaneous R161H model. Studies have confirmed that autoreactive T cell activation occurs in the intestinal wall in the absence of retinal antigen. Recent experiments focused on the effect of probiotic administration on the composition of intestinal microbiota and on the course of autoimmune uveitis. Our study group demonstrated significant prophylactic effect of the administration of the probiotic Escherichia coli Nissle 1917 on the intensity of inflammation in EAU. To date, only a few studies have been published investigating intestinal dysbiosis in patients with uveitis (e.g., in Behcets disease or Vogt-Koyanagi-Harada syndrome). The results of preclinical studies will be presumably used in clinical practice, mainly in the sense of prophylaxis and therapy, such as change in the lifestyle, diet and especially the therapeutic use of probiotics or the transfer of faecal microbiota.

Polyphenols-Gut Microbiota Interrelationship: A Transition to a New Generation of Prebiotics

The present review summarizes the studies carried out on this topic in the last five years. According to the new definitions, among all the compounds included in the group of prebiotics, polyphenols are probably the most important secondary metabolites produced by the plant kingdom. Many of these types of polyphenols have low bioavailability, therefore reaching the colon in unaltered form. Once in the colon, these compounds interact with the intestinal microbes bidirectionally by modulating them and, consequently, releasing metabolites. Despite much research on various metabolites, little is known about the chemistry of the metabolic routes used by different bacteria species. In this context, this review aims to investigate the prebiotic effect of polyphenols in preclinical and clinical studies, highlighting that the consumption of polyphenols leads to an increase in beneficial bacteria, as well as an increase in the production of valuable metabolites. In conclusion, there is much evidence in preclinical studies supporting the prebiotic effect of polyphenols, but further clinical studies are needed to investigate this effect in humans.

Improving the Gut Microbiota with Probiotics and Faecal Microbiota Transplantation

Probiotics are “live strains of strictly selected microorganisms which, when administered in adequate amounts, confer a health benefit on the host”. After birth, our intestine is colonized by microbes like Escherichia coli, Clostridium spp., Streptococcus spp., Lactobacillus spp., Bacteroides spp., and Bifidobacterium spp. Our intestine is an extremely complex living system that participates in the protection of host through a strong defence against external aggregations. The microbial ecosystem of the intestine includes many native species of Bacteroides and Firmicutes that permanently colonize the gastrointestinal tract. The composition of flora changes over time depending upon diet and medical emergencies which leads to the diseased condition. Probiotics exert their mode of action by altering the local environment of the gut by competing with the pathogens, bacteriocins production, H2O2 production etc. Obesity is one of the major health problems and is considered as the most prevalent form of inappropriate nutrition. Probiotics like Lactobacillus Sp., Bifidobacterium Sp., Streptococcus Sp. are successfully used in the treatment of obesity proved in clinical trials. Faecal microbiota transplant (FMT), also known as a stool transplant, is the process of transplantation of Faecal bacteria from a healthy donor into a recipient’s gut to restore normal flora in the recipient. The therapeutic principle on which FMT works is microbes and their functions and metabolites produced by them which are used to treat a variety of diseases. The present review focuses on the role of gastrointestinal microbiome, probiotic selection criteria, their applications and FMT to treat diseases.

The microbiome and rodent models of immune mediated diseases

Over the last six decades production of laboratory rodents have been refined with the aim of eliminating all pathogens, which could influence research results. This has, however, also created rodents with little diversity in their microbiota. Until 10 years ago the impact of the microbiota on the outcome of rodent studies was ignored, but today it is clear that the phenotype of rodent models differs essentially in relation to the environment of origin, i.e. different breeders or different rooms. In this review, we outline the mechanisms behind gut bacterial impact on rodent models of immune mediated diseases, and how differences in environment of origin leads to phenotypic model differences within research areas such as infectious diseases and vaccine development, the metabolic syndrome, gut immunity and inflammation, autoimmunity and allergy. Finally, we sum up some tools to handle this impact to increase reproducibility and translatability of rodent models.

Effects of ammonia on growth performance, lipid metabolism and cecal microbial community of rabbits

This study was designed to investigate the effect of ammonia on growth performance, lipid metabolism and intestinal flora of rabbits. A total of 150 female IRA rabbits (35-days-old) were randomly divided into three groups including 0 ppm (CG), 10 ppm (LAC) and 30 ppm ammonia (HAC) groups for a period of 28 days. The average daily weight gain (ADG) of rabbits was significantly reduced in LAC (-17.11%; p < 0.001) and HAC groups (-17.46%; p < 0.001) as compared with the CG. Serum concentration of high density lipoprotein (HDL) and glucose (Glu) were increased in LAC (+80.95%; +45.99; p < 0.05) and HAC groups (+219.05%; +45.89; p < 0.001), while apolipoprotein A1 (apoA1) was decreased in LAC (-58.49%; p < 0.001) and HAC groups (-36.92%; p < 0.001). The structural integrity of cecum was damaged, and the thickness of mucosa and serosa were significantly decreased in LAC and HAC. The acetate, butyrate and propionate level of cecal chyme were reduced in HAC group (-21.67%; -19.82%; -30.81%; p < 0.05). Microbial diversity and burden of Firmicutes were significantly decreased, while that of pathogenic bacteria, such as Bacteroidetes, Clostridium and Proteobacteria were increased in ammonia treated groups. Spearman's correlation confirmed that burden of Ruminococcaceae_NK4A214_group showed significantly negative correlation with acetic acid (r = -0.67; p < 0.001) while Barnesiellaceae_unclassified showed significantly positive correlation with propionic acid (r = 0.50; p < 0.001). In conclusion, ammonia treatment was responsible for an imbalance of intestinal flora, which affected lipid metabolism and damaged intestinal barrier of rabbits, resulting in low growth performance due to lipid metabolism dysfunction.

Role of germ-free animal models in understanding interactions of gut microbiota to host and environmental health: A special reference to zebrafish

Numerous pieces of evidence documented the importance of gut microbiota in regulating human health and evaluating the toxicity of environmental pollutants, which are closely related to the host health in various aspects, including nutrition, energy translation, metabolism, pathogen resistance, and immune function. A variety of environmental factors can disrupt gut microbiota and their functions, and inevitably cause immune diseases, obesity and diabetes. However, deciphering the inner mechanisms involved in the functional interaction of gut microbes with host health is still needed extensive investigations. This review focused on the essential roles of intestinal microbes in host-related diseases and highlighted the development and applications of germ-free (GF) animal models, mainly zebrafish. Moreover, the generation, immunity characters, advantages and challenges of GF zebrafish models were also summarized. Importantly, the composition and isolation of zebrafish gut bacteria for further application and toxicity evaluation of aquatic environmental pollutants were also discussed. In conclusion, GF zebrafish play irreplaceable roles in understanding the potential functions and responses of customized microbiota towards human and environmental health implications.

FFAR from the Gut Microbiome Crowd: SCFA Receptors in T1D Pathology

The gut microbiome has emerged as a novel determinant of type 1 diabetes (T1D), but the underlying mechanisms are unknown. In this context, major gut microbial metabolites, short-chain fatty acids (SCFAs), are considered to be an important link between the host and gut microbiome. We, along with other laboratories, have explored how SCFAs and their cognate receptors affect various metabolic conditions, including obesity, type 2 diabetes, and metabolic syndrome. Though gut microbiome and SCFA-level changes have been reported in T1D and in mouse models of the disease, the role of SCFA receptors in T1D remains under explored. In this review article, we will highlight the existing and possible roles of these receptors in T1D pathology. We conclude with a discussion of SCFA receptors as therapeutic targets for T1D, exploring an exciting new potential for novel treatments of glucometabolic disorders.

Effects of Pediococcus pentosaceus LI05 on immunity and metabolism in germ-free rats

Many Pediococcus spp. have health-promoting benefits, and Pediococcus pentosaceus LI05 is one such species that was proved to be beneficial in previous studies. Our research aimed to determine the immune and metabolic effects of P. pentosaceus LI05 on germ-free rats. Germ-free rats were gavaged with P. pentosaceus LI05 suspensions (1 × 10⁹ CFU) for 2 weeks, and 3 weeks later, blood, spleen, intestine and liver samples were gathered for metabolome, intestine morphology, immunity, and transcriptomics analyses. Oral gavage of P. pentosaceus LI05 reduced the bodyweight of rats, which manifested as increased fecal carbohydrate concentrations, decreased intestinal fat intake and the hepatic fat synthesis gene expression, and accelerated fat-to-glycogen conversion. In addition, P. pentosaceus LI05 exhibited an anti-inflammatory ability, reducing serum proinflammatory cytokine levels and increasing intestinal subepidermal CD4⁺ cell levels. Furthermore, administration of P. pentosaceus LI05 increased the antimicrobial ability and enhanced the liver detoxification function. These results indicate that as a probiotic, P. pentosaceus LI05 ameliorates the hampered immune response of GF animals and improves the metabolism of fat and toxic substances.

Dysbiosis From a Microbial and Host Perspective Relative to Oral Health and Disease

The significance of microbiology and immunology with regard to caries and periodontal disease gained substantial clinical or research consideration in the mid 1960's. This enhanced emphasis related to several simple but elegant experiments illustrating the relevance of bacteria to oral infections. Since that point, the understanding of oral diseases has become increasingly sophisticated and many of the original hypotheses related to disease causality have either been abandoned or amplified. The COVID pandemic has reminded us of the importance of history relative to infectious diseases and in the words of Churchill "those who fail to learn from history are condemned to repeat it." This review is designed to present an overview of broad general directions of research over the last 60 years in oral microbiology and immunology, reviewing significant contributions, indicating emerging foci of interest, and proposing future directions based on technical advances and new understandings. Our goal is to review this rich history (standard microbiology and immunology) and point to potential directions in the future (omics) that can lead to a better understanding of disease. Over the years, research scientists have moved from a position of downplaying the role of bacteria in oral disease to one implicating bacteria as true pathogens that cause disease. More recently it has been proposed that bacteria form the ecological first line of defense against "foreign" invaders and also serve to train the immune system as an acquired host defensive stimulus. While early immunological research was focused on immunological exposure as a modulator of disease, the "hygiene hypothesis," and now the "old friends hypothesis" suggest that the immune response could be trained by bacteria for long-term health. Advanced "omics" technologies are currently being used to address changes that occur in the host and the microbiome in oral disease. The "omics" methodologies have shaped the detection of quantifiable biomarkers to define human physiology and pathologies. In summary, this review will emphasize the role that commensals and pathobionts play in their interaction with the immune status of the host, with a prediction that current "omic" technologies will allow researchers to better understand disease in the future.

Characterization of Lactobacillus species proposed as probiotics

An isolated Lactobacillus from several various sources were identified depending on morphological, microscopically and biochemical tests in vitro analysis of probiotic properties that included: an ability to tolerate in different concentration of bile salt, survival in acidic conditions, their antimicrobial activity, and S-layer characterizations were carried out. It was noticed that isolates of Lactobacillus rhamnosus and L. delbrueckii have a broad activity of antimicrobial and found the isolate L. rhamnosus represented with a survival percentage 6.9% at pH 4.5 and 5.1% at pH 2.0) also L. rhamnosus (5.7% at pH 4.5 and 4.9% at pH 2.0) tolerated acidic media, Lactobacillus spp. has antimicrobial activity against all gram-positive and negative tested isolates. 70 kDa of S-layer protein bands were detected with whole-cell SDS-PAGE analysis, and it's predominant in cells of isolates which grown in MRS broth anaerobically. It was noticed that the collected Lactobacillus isolates could be used as probiotic.

Differential analysis of gut microbiota and the effect of dietary Enterococcus faecium supplementation in broiler breeders with high or low laying performance

The difference in microbiota was examined for breeders with different egg-laying rates, and the impact of dietary Enterococcus faecium (EF) was also determined in the present study. A total of 256 Arbor Acres broiler breeders (48-wk-old) were used in a 2 × 2 factorial design, which encompassed 2 egg-laying rate levels [average (average egg laying: AP, 80.45 ± 0.91%) and low (lower egg laying: LP, 70.61 ± 1.16%)] and 2 different dietary groups [control (no additive), 6 × 10⁸ cfu/kg EF]. The results showed that the AP breeders presented a lower egg weight, feed conversion ratio, abdominal fat rate, and serum leptin level (P_(laying) ≤ 0.05) as well as a higher egg-laying rate (P_(laying) < 0.01) than the LP breeders. Dietary supplementation with EF improved the egg weight (P_(EF) = 0.03) and had a higher concentration of follicle-stimulating hormone (FSH) in the serum (P_(EF) = 0.04). The relative expression of Caspase 9, Bax, AMHR, BMP15, and GATA4 in the ovary of AP breeders was lower, whereas the FSHR and BMPR1B expression was higher than that measured in LP breeders (P_(laying) ≤ 0.05). LP increased the abundance of Bacteroidetes (phylum), Firmicutes (phylum), Bacteroidia (class), Clostridia (class), Bacteroidales (order), Clostridiales (order), and Lachnospiraceae (family), whereas the AP promoted the enrichment of Proteobacteria (phylum) and Gammaproteobacteria (class) (P_(laying) < 0.05). The genera Bacillus, Rhodanobacter, and Streptomyces were positively correlated with the egg-laying rate and BMPR1B expression (P < 0.05) but negatively correlated with the abdominal fat rate (P < 0.05) and Caspase 9 (P < 0.05). These findings indicate that the low reproductive performance breeders had lower microbiota diversity and higher Firmicutes, which triggers the energy storage that led to higher fat deposition. Besides, increases in the abdominal fat rate, leptin level, and apoptosis (Caspase 9, Bax) and reproduction-related gene (BMP15, AMHR, BMPR1B, and GATA4) expression would possibly be the potential mechanisms under which breeders have different reproductive performance. Dietary EF increased the egg weight and serum FSH level and decreased the Bacteroidetes (phylum) in low reproductive breeders.

Exploring the impact of intestinal ion transport on the gut microbiota

The gut microbiota and the host are intimately connected. The host physiology dictates the intestinal environment through regulation of pH, ion concentration, mucus production, etc., all of which exerts a selective pressure on the gut microbiota. Since different regions of the gastrointestinal tract are characterized by their own physicochemical conditions, distinct microbial communities are present in these locations. While it is widely accepted that the intestinal microbiome influences the host (tight junctions, cytokine/immune responses, diarrhea, etc.), the reciprocal interaction of the host on the microbiome is under-explored. This review aims to address these gaps in knowledge by focusing on how the host intestinal ion transport influences the luminal environment and thereby modulates the gut microbiota composition.

Gut Microbiota in Intestinal and Liver Disease

It is known that the gut microbiota, the numerically vast and taxonomically diverse microbial communities that thrive in a symbiotic fashion within our alimentary tract, can affect the normal physiology of the gastrointestinal tract and liver. Further, disturbances of the microbiota community structure from both endogenous and exogenous influences as well as the failure of host responsive mechanisms have been implicated in a variety of disease processes. Mechanistically, alterations in intestinal permeability and dysbiosis of the microbiota can result in inflammation, immune activation, and exposure to xenobiotic influences. Additionally, the gut and liver are continually exposed to small molecule products of the microbiota with proinflammatory, gene regulatory, and oxidative properties. Long-term coevolution has led to tolerance and incorporation of these influences into normal physiology and homeostasis; conversely, changes in this equilibrium from either the host or the microbial side can result in a wide variety of immune, inflammatory, metabolic, and neoplastic intestinal and hepatic disorders.

Innate Lymphoid Cells in Crohn's Disease

Innate lymphoid cells (ILCs) are a large family of cells of the immune system that performs various functions in immune defense, inflammation, and tissue remodeling. As a part of the innate immune system, ILCs are a distinct form of lymphocytes different from T and B cells. ILCs can provide host defense against the source of infection and initiate the repair and remodeling processes to restore and maintain host body homeostasis. The number of patients with Crohn’s disease (CD) worldwide has continued to increase in recent years and this disease has brought sickness and death to many families. Numerous studies have found that ILCs also undergo a series of alternations during the development of CD and contribute to this disease. Despite this, the pathogenesis of CD is still not fully explained. So, we keep researching and exploring. In this review, we have closely linked the latest progress on ILCs and CD, and introduced, in detail, the specific roles of four different types of ILCs in CD. We also describe new progress in the pathogenesis of CD, with particular emphasis on the plasticity of ILC3s in this disease. These new studies and findings may provide new insights and breakthrough points for the treatment of CD.

Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents

Development of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity of dairy cattle. The role of early microbial colonization on GIT development in neonatal cattle and the associated molecular changes remain largely unknown, particularly for the small intestine. In this study, we performed artificial dosing of exogenous rumen fluid during the early life of the calf, starting at birth through the weaning transition at 8 wk. Six calves were included in this study. At 8 wk of age, tissue from the ileum was collected and subjected to host transcriptome and microbial metatranscriptome analysis using RNA sequencing. A total of 333 genes showed significant differential expression (DE) (fold-change ≥2; adjusted P < 0.1, mean read-count ≥10) between the treated and control calves. Gene ontology analysis indicated that these DE genes are predominantly associated with processes related to the host immune response (P < 0.0001). Association analysis between the host gene expression and the microbial genus abundance identified 57 genes as having significant correlation with the ileum microbial genera (P < 0.0001). Of these, three genes showed significant association with six microbial genera: lysozyme 2 (LYZ2), fatty acid binding protein 5 (FABP5), and fucosyltransferase (FUT1). Specifically, the profound increase in expression of LYZ2 in treated calves suggests the initiation of antibacterial activity and innate response from the host. Despite the limitation of a relatively small sample size, this study sheds light on the potential impact of early introduction of microbes on the small intestine of calves.

Gut microbiota and metabolites in the pathogenesis of endocrine disease

Type 1 diabetes (T1D) and Hashimoto's thyroiditis (HT) are the two most common autoimmune endocrine diseases that have rising global incidence. These diseases are caused by the immune-mediated destruction of hormone-producing endocrine cells, pancreatic beta cells and thyroid follicular cells, respectively. Both genetic predisposition and environmental factors govern the onset of T1D and HT. Recent evidence strongly suggests that the intestinal microbiota plays a role in accelerating or preventing disease progression depending on the compositional and functional profile of the gut bacterial communities. Accumulating evidence points towards the interplay between the disruption of gut microbial homeostasis (dysbiosis) and the breakdown of host immune tolerance at the onset of both diseases. In this review, we will summarize the major recent findings about the microbiome alterations associated with T1D and HT, and the connection of these changes to disease states. Furthermore, we will discuss the potential mechanisms by which gut microbial dysbiosis modulates the course of the disease, including disruption of intestinal barrier integrity and microbial production of immunomodulatory metabolites. The aim of this review is to provide broad insight into the role of gut microbiome in the pathophysiology of these diseases.

Diet and the Human Gut Microbiome: An International Review

This review summarizes the key results of recently published studies on the effects of dietary change and nutritional intervention on the human microbiome from around the world, focusing on the USA, Canada, Europe, Asia, and Africa. It first explores mechanisms that might explain the ability of fiber-rich foods to suppress the incidence and mortality from westernized diseases, notably cancers of the colon, breast, liver, cardiovascular, infectious, and respiratory diseases, diabetes, and obesity (O'Keefe in Lancet Gastroenterol Hepatol 4(12):984-996, 2019; Am J Clin Nutr 110:265-266, 2019). It summarizes studies from Africa which suggest that disturbance of the colonic microbiome may exacerbate chronic malnutrition and growth failure in impoverished communities and highlights the importance of breast feeding. The American section discusses the role of the microbiome in the swelling population of patients with obesity and type 2 diabetes and examines the effects of race, ethnicity, geography, and climate on microbial diversity and metabolism. The studies from Europe and Asia extoll the benefits of whole foods and plant-based diets. The Asian studies examine the worrying changes from low-fat, high-carbohydrate diets to high-fat, low-carbohydrate ones and the increasing appearance of westernized diseases as in Africa and documents the ability of high-fiber traditional Chinese diets to reverse type 2 diabetes and control weight loss. In conclusion, most of the studies reviewed demonstrate clear changes in microbe abundances and in the production of fermentation products, such as short-chain fatty acids and phytochemicals following dietary change, but the significance of the microbiota changes to human health, with the possible exception of the stimulation of butyrogenic taxa by fiber-rich foods, is generally implied and not measured. Further studies are needed to determine how these changes in microbiota composition and metabolism can improve our health and be used to prevent and treat disease.

The effectiveness of a dietary direct-fed microbial and mannan oligosaccharide on ultrastructural changes of intestinal mucosa of turkey poults infected with Salmonella and Campylobacter

Salmonella and Campylobacter are considered major public health burdens worldwide, and poultry are known to be one of the main reservoirs for these zoonotic pathogens. This study was conducted to evaluate the effect of a commercial probiotic or direct-fed microbial (DFM) Calsporin (CSP), and prebiotic or mannan oligosaccharide (MOS) (IMW50) on ultrastructural changes and the villous integrity of intestinal mucosa in turkey poults challenged with Salmonella and Campylobacter. A 21-day battery cage study was conducted using 4 dietary treatments including a basal diet (corn and soybean-based) nonsupplemented and uninfected as a negative control (NC); basal diet supplemented with 0.05% DFM (CSP); basal diet supplemented with 0.05% MOS (IMW50); and basal diet supplemented with 0.05% mixture of DFM and MOS at equal proportions. Female large white turkey poults aged 336 days were obtained from a local commercial hatchery and randomly distributed in electrically heated battery cages with 12 treatments of 4 replicates per treatment containing 7 poults per pen. The first 16 pens were not infected with bacteria, poults in pens 17-32 were orally challenged at day 7 with 105 cfu Salmonella Heidelberg, and the poults in pens 33-48 were orally challenged at day 7 with 105 cfu Campylobacter jejuni. Feed and water were provided ad libitum throughout the study. At day 21, ileal tissue samples from 1 bird per cage were collected for intestinal integrity and ultrastructural examination by scanning and electron microscopy. DFM and MOS supplementation was effective in both challenged and nonchallenged (not infected with Salmonella and Campylobacter) birds. Goblet cells and mucus were increased, with the presence of large numbers of segmented filamentous bacteria in DFM- and MOS-supplemented groups compared with birds in control treatments. The number and size of villi were reduced in poults exposed to Salmonella and Campylobacter. Results show that CSP and IMW50 provide protection of ileal mucosal integrity in poults exposed to Salmonella or Campylobacter.

Whole Grains, Dietary Fibers and the Human Gut Microbiota: A Systematic Review of Existing Literature

BACKGROUND

The health benefits of dietary fibers have been proved for a long time. The importance of microbiota has been identified in human health and there is a growing interest to study the factors affecting it.

OBJECTIVE

This systematic review aimed to investigate the impact of fiber and whole grains (WGs) on human gut microbiota in a patent-based review.

METHODS

All related clinical trials were systematically searched on PubMed and Scopus search engines from inception up to Feb 2020. Interventional human studies reporting changes in microbiota by using any type of grains/fibers were included. The following information was extracted: date of the publication, location and design of the study, sample size, study population, demographic characteristics, the amount of dietary WGs/fiber, the duration of intervention, the types of grains or fibers, and changes in the composition of the microbiota.

RESULTS

Of 138 studies which were verified, 35 studies with an overall population of 1080 participants, met the inclusion criteria and entered the systematic review. The results of interventional trials included in this review suggest some beneficial effects of consuming different amounts and types of WGs and fibers on the composition of intestinal microbiota. Most included studies showed that the intake of WGs and fibers increases bifidobacteria and lactobacilli and reduces the pathogenic bacteria, such as Escherichia coli and clostridia in the human gut.

CONCLUSION

The consumption of WGs/fibers may modify the intestinal microbiota and promote the growth of bifidobacteria and lactobacilli. Nevertheless, further research is warranted in different populations and pathological conditions.

Development of an Index Score for Intestinal Inflammation-Associated Dysbiosis Using Real-World Stool Test Results

BACKGROUND

Gut microbiota play an important role in human health. However, the application of gut microbiome in regular clinical practice is limited by interindividual variations and complexity of test results.

HYPOTHESIS

It is possible to address interindividual variation by using large data-based exploratory-pattern analysis.

METHODS

The current study was conducted using a large data set (n = 173,221) of nonselective incoming patients' test results from a stool test. The data set included assays for the detection of 24 selected commensal microorganisms and multiple biomarkers in feces. Patients were grouped based on their levels of inflammation biomarkers such as calprotectin, eosinophil protein X, and IgA. Group mean values of biomarkers and commensal microbes were used in an exploratory-pattern analysis for association from which an index score for intestinal inflammation-associated dysbiosis (IAD) was developed. The IAD score was evaluated in one questionnaire-based study (n = 7263) and one prospective case series study (n = 122) with patients of inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), and celiac disease.

RESULTS

We identified a microbial profile strongly associated with fecal inflammation biomarkers. Developed on the pattern of the microbial profile, the IAD score demonstrated a strong association with fecal inflammation biomarkers and was significantly different between patients with IBD and those with IBS or celiac disease.

CONCLUSION

Using real-world data, we have developed a method to predict gut dysbiosis associated with different GI disease conditions. It may help clinicians simplify the process of interpreting gut microbial status and provide gut health assessment and treatment evaluation.

Autism and Gut-Brain Axis: Role of Probiotics

Characterized by a wide range of behavioural, social and language problems, autism is a complex developmental disability that affects an individual's capacity to communicate and interact with others. Although the real causes that lead to the development of autism are still unclear, the gastrointestinal tract has been found to play a major role in the development of autism. Alterations in macrobiotic compositions have been reported in autistic children. Irregularities in carbohydrate digestion and absorption could also explain some of the gastrointestinal problems reported in autistic patients, although their role in the neurological and behavioural problems remains uncertain. A relationship between improved gut health and decrease of symptoms in autism has been reported as well. Studies done to evaluate the gluten-free diets, casein-free diets, pre- and probiotic and multivitamin supplementation have shown promising results. Probiotics have been thought to alleviate the progression of autism and reduce cognitive and behavioural deficits.

Rectal Microbiome Composition Correlates with Humoral Immunity to HIV-1 in Vaccinated Rhesus Macaques

There is considerable effort directed toward evaluating HIV-1 vaccine platforms to select the most promising candidates for enhancing mucosal HIV-1 antibody. The most successful thus far, the RV144 trial provided partial protection due to waning HIV-1 antibody titers. In order to develop an effective HIV vaccine, it may therefore be important to understand how biological factors, such as the microbiome, modulate host immune responses. Furthermore, as intestinal microbiota antigens may generate antibodies cross-reactive to the HIV-1 envelope glycoprotein, understanding the relationship between gut microbiota composition and HIV-1 envelope antibody responses after vaccination is important. Here, we demonstrate for the first time in rhesus macaques that the rectal microbiome composition can influence HIV-1 vaccine immunogenicity, and we report temporal changes in the mucosal microbiome profile following HIV-1 vaccination. Our results could inform findings from the HIV Vaccine Trials Network (HVTN) vaccine studies and contribute to an understanding of how the microbiome influences HIV-1 antibody responses.

The microbiome is an integral and dynamic component of the host and is emerging as a critical determinant of immune responses; however, its influence on vaccine immunogenicity is largely not well understood. Here, we examined the pivotal relationship between the mucosal microbiome and vaccine-induced immune responses by assessing longitudinal changes in vaginal and rectal microbiome profiles after intradermal immunization with a human immunodeficiency virus type 1 (HIV-1) DNA vaccine in adult rhesus macaques that received two prior DNA primes. We report that both vaginal and rectal microbiomes were dominated by Firmicutes but were composed of distinct genera, denoting microbiome specialization across mucosal tissues. Following immunization, the vaginal microbiome was resilient, except for a transient decrease in Streptococcus. In contrast, the rectal microbiome was far more responsive to vaccination, exhibiting an increase in the ratio of Firmicutes to Bacteroidetes. Within Bacteroidetes, multiple genera were significantly decreased, including Prevotella, Alloprevotella, Bacteroides, Acetobacteroides, Falsiporphyromonas, and Anaerocella. Decreased abundance of Prevotella correlated with induction of gut-homing α₄β₇⁺ effector CD4 T cells. Prevotella abundance also negatively correlated with rectal HIV-1 specific IgG levels. While rectal Lactobacillus was unaltered following DNA vaccination, baseline Lactobacillus abundance showed strong associations with higher rectal HIV-1 gp140 IgA induced following a protein boost. Similarly, the abundance of Clostridium in cluster IV was associated with higher rectal HIV-1 gp140 IgG responses. Collectively, these data reveal that the temporal stability of bacterial communities following DNA immunization is site dependent and highlight the importance of host-microbiome interactions in shaping HIV-1 vaccine responses. Our findings have significant implications for microbial manipulation as a strategy to enhance HIV vaccine-induced mucosal immunity.

IMPORTANCE There is considerable effort directed toward evaluating HIV-1 vaccine platforms to select the most promising candidates for enhancing mucosal HIV-1 antibody. The most successful thus far, the RV144 trial provided partial protection due to waning HIV-1 antibody titers. In order to develop an effective HIV vaccine, it may therefore be important to understand how biological factors, such as the microbiome, modulate host immune responses. Furthermore, as intestinal microbiota antigens may generate antibodies cross-reactive to the HIV-1 envelope glycoprotein, understanding the relationship between gut microbiota composition and HIV-1 envelope antibody responses after vaccination is important. Here, we demonstrate for the first time in rhesus macaques that the rectal microbiome composition can influence HIV-1 vaccine immunogenicity, and we report temporal changes in the mucosal microbiome profile following HIV-1 vaccination. Our results could inform findings from the HIV Vaccine Trials Network (HVTN) vaccine studies and contribute to an understanding of how the microbiome influences HIV-1 antibody responses.

Bridging intestinal immunity and gut microbiota by metabolites

The gastrointestinal tract is the site of nutrient digestion and absorption and is also colonized by diverse, highly mutualistic microbes. The intestinal microbiota has diverse effects on the development and function of the gut-specific immune system, and provides some protection from infectious pathogens. However, interactions between intestinal immunity and microorganisms are very complex, and recent studies have revealed that this intimate crosstalk may depend on the production and sensing abilities of multiple bioactive small molecule metabolites originating from direct produced by the gut microbiota or by the metabolism of dietary components. Here, we review the interplay between the host immune system and the microbiota, how commensal bacteria regulate the production of metabolites, and how these microbiota-derived products influence the function of several major innate and adaptive immune cells involved in modulating host immune homeostasis.

Obesity and cancer: A mechanistic overview of metabolic changes in obesity that impact genetic instability

Obesity, defined as a state of positive energy balance with a body mass index exceeding 30 kg/m2 in adults and 95th percentile in children, is an increasing global concern. Approximately one-third of the world's population is overweight or obese, and in the United States alone, obesity affects one in six children. Meta-analysis studies suggest that obesity increases the likelihood of developing several types of cancer, and with poorer outcomes, especially in children. The contribution of obesity to cancer risk requires a better understanding of the association between obesity-induced metabolic changes and its impact on genomic instability, which is a major driving force of tumorigenesis. In this review, we discuss how molecular changes during adipose tissue dysregulation can result in oxidative stress and subsequent DNA damage. This represents one of the many critical steps connecting obesity and cancer since oxidative DNA lesions can result in cancer-associated genetic instability. In addition, the by-products of the oxidative degradation of lipids (e.g., malondialdehyde, 4-hydroxynonenal, and acrolein), and gut microbiota-mediated secondary bile acid metabolites (e.g., deoxycholic acid and lithocholic acid), can function as genotoxic agents and tumor promoters. We also discuss how obesity can impact DNA repair efficiency, potentially contributing to cancer initiation and progression. Finally, we outline obesity-related epigenetic changes and identify the gaps in knowledge to be addressed for the development of better therapeutic strategies for the prevention and treatment of obesity-related cancers.

Diverse Mechanisms Underlie Enhancement of Enteric Viruses by the Mammalian Intestinal Microbiota

Over the past two decades, there has been tremendous progress in understanding the impact of the intestinal microbiota on mammalian metabolism, physiology, and immune development and function. There has also been substantial advancement in elucidating the interplay between commensal and pathogenic bacteria. Relatively more recently, researchers have begun to investigate the effect of the intestinal microbiota on viral pathogenesis. Indeed, a growing body of literature has reported that commensal bacteria within the mammalian intestinal tract enhance enteric virus infections through a variety of mechanisms. Commensal bacteria or bacterial glycans can increase the stability of enteric viruses, enhance virus binding to host receptors, modulate host immune responses in a proviral manner, expand the numbers of host cell targets, and facilitate viral recombination. In this review, we will summarize the current literature exploring these effects of the intestinal microbiota on enteric virus infections.

Mechanisms and consequences of gut commensal translocation in chronic diseases

Humans and other mammalian hosts have evolved mechanisms to control the bacteria colonizing their mucosal barriers to prevent invasion. While the breach of barriers by bacteria typically leads to overt infection, increasing evidence supports a role for translocation of commensal bacteria across an impaired gut barrier to extraintestinal sites in the pathogenesis of autoimmune and other chronic, non-infectious diseases. Whether gut commensal translocation is a cause or consequence of the disease is incompletely defined. Here we discuss factors that lead to translocation of live bacteria across the gut barrier. We expand upon our recently published demonstration that translocation of the gut pathobiont Enterococcus gallinarum can induce autoimmunity in susceptible hosts and postulate on the role of Enterococcus species as instigators of chronic, non-infectious diseases.

The influence of maternal and infant nutrition on cardiometabolic traits: novel findings and future research directions from four Canadian birth cohort studies

A mother's nutritional choices while pregnant may have a great influence on her baby's development in the womb and during infancy. There is evidence that what a mother eats during pregnancy interacts with her genes to affect her child's susceptibility to poor health outcomes including childhood obesity, pre-diabetes, allergy and asthma. Furthermore, after what an infant eats can change his or her intestinal bacteria, which can further influence the development of these poor outcomes. In the present paper, we review the importance of birth cohorts, the formation and early findings from a multi-ethnic birth cohort alliance in Canada and summarise our future research directions for this birth cohort alliance. We summarise a method for harmonising collection and analysis of self-reported dietary data across multiple cohorts and provide examples of how this birth cohort alliance has contributed to our understanding of gestational diabetes risk; ethnic and diet-influences differences in the healthy infant microbiome; and the interplay between diet, ethnicity and birth weight. Ongoing work in this birth cohort alliance will focus on the use of metabolomic profiling to measure dietary intake, discovery of unique diet-gene and diet-epigenome interactions, and qualitative interviews with families of children at risk of metabolic syndrome. Our findings to-date and future areas of research will advance the evidence base that informs dietary guidelines in pregnancy, infancy and childhood, and will be relevant to diverse and high-risk populations of Canada and other high-income countries.

CD4+ T Cells Play a Critical Role in Microbiota-Maintained Anti-HBV Immunity in a Mouse Model

The ability of the host to clear hepatitis B virus (HBV) is closely correlated to the establishment of commensal microbiota. However, how microbiota affects anti-HBV immunity is still unclear. Using a well-known hydrodynamical HBV transfection mouse model and treatment with antibiotics (Atb), we explored the change in adaptive immunity (CD4⁺ cells, germinal center B cells and anti-HBs Ab). In our setting, normal mice exhibited complete clearance of HBV within 6 weeks post-hydrodynamic injection (HDI) of HBV-containing plasmid, whereas Atb-treated mice lost this capacity, showing high serum level of hepatitis B surface antigen (HBsAg) without hepatitis B surface antibodies (anti-HBs), similar as what happened in Rag1^−/− mice or CD4^−/− mice, suggesting that microbiota may influence the function of CD4⁺ T cells. Furthermore, the numbers of splenic and hepatic effector CD4⁺ T cells (CD44^hiCD62L⁻CD4⁺ T cells) both decreased with impaired function (IFN-γ synthesis), resulting in lower frequency of germinal center B cells and CD4⁺ follicular helper T cells, and impaired anti-HBs production. We further tried to find the bacterial species responsible for maintaining anti-HBV immunity, and found that each antibiotic alone could not significantly influence HBV clearance compared to antibiotic combination, suggesting that global commensal microbial load is critical for promoting HBV clearance. We also confirmed that TLRs (e.g., TLR2, 4, 9) are not major players in immune clearance of HBV using their agonists and knock-out mice. These results suggest that commensal microbiota play an important role in maintaining CD4⁺ T cell immunity against HBV infection.

Cross-Domain and Viral Interactions in the Microbiome

The importance of the microbiome to human health is increasingly recognized and has become a major focus of recent research. However, much of the work has focused on a few aspects, particularly the bacterial component of the microbiome, most frequently in the gastrointestinal tract. Yet humans and other animals can be colonized by a wide array of organisms spanning all domains of life, including bacteria and archaea, unicellular eukaryotes such as fungi, multicellular eukaryotes such as helminths, and viruses. As they share the same host niches, they can compete with, synergize with, and antagonize each other, with potential impacts on their host. Here, we discuss these major groups making up the human microbiome, with a focus on how they interact with each other and their multicellular host.

Purification of Capsular Polysaccharide Complex from Gram-Negative Bacteria

Capsular polysaccharides are a dominant class of antigens from bacteria, both pathogenic and symbiotic or commensal. With the rise of awareness for the influence of the microbiota over immune system development and immune homeostasis, analysis of the antigens is more important than ever. Here we describe a method for the isolation of capsular polysaccharide from gram-negative bacteria, with the purification of polysaccharide from the commensal bacterium Bacteroides fragilis serving as an example. The method efficiently removes all detectable endotoxins and other lipid components, proteins, and nucleic acids, providing a source of capsular polysaccharide for immunologic study.

Metabolomics and Lipidomics Approaches in the Science of Probiotics: A Review

The intestinal microflora plays important roles in the health of the host, such as nutrient processing and the modulation of intestinal immune responses. The constituents of the diet greatly affect the composition of the microbiota and its metabolites. The human intestinal microbiota is made up of around 100 trillion microbial cells encompassing at least 300 species. Consuming probiotics may lead to changes in the intestinal microflora that influence host health. Metabolomics is a powerful tool for revealing metabolic changes in biofluids, tissues, and organs of hosts induced by the consumption of probiotics, and lipidomics in particular is a technical approach that focuses on the analysis of lipids in various cells and biofluids. Metabolomics and lipidomics have been used to investigate intracellular and extracellular metabolites as well as for the nontargeted profiling and fingerprinting of metabolites. Based on metabolomics and lipidomics investigations, we reviewed the effects of consuming probiotics on metabolic profiles in controlled intestinal environments. We also discuss the associations between metabolic changes and human diseases after consuming probiotics in uncontrolled intestinal environments. In addition, we review the metabolic changes that take place within the food matrix during probiotic fermentation.

Chronic features of allergic asthma are enhanced in the absence of resistin-like molecule-beta

Asthma is characterized by inflammation and architectural changes in the lungs. A number of immune cells and mediators are recognized as initiators of asthma, although therapeutics based on these are not always effective. The multifaceted nature of this syndrome necessitate continued exploration of immunomodulators that may play a role in pathogenesis. We investigated the role of resistin-like molecule-beta (RELM-β), a gut antibacterial, in the development and pathogenesis of Aspergillus-induced allergic airways disease. Age and gender matched C57BL/6J and Retnlb^−/− mice rendered allergic to Aspergillus fumigatus were used to measure canonical markers of allergic asthma at early and late time points. Inflammatory cells in airways were similar, although Retnlb^−/− mice had reduced tissue inflammation. The absence of RELM-β elevated serum IgA and pro-inflammatory cytokines in the lungs at homeostasis. Markers of chronic disease including goblet cell numbers, Muc genes, airway wall remodelling, and hyperresponsiveness were greater in the absence RELM-β. Specific inflammatory mediators important in antimicrobial defence in allergic asthma were also increased in the absence of RELM-β. These data suggest that while characteristics of allergic asthma develop in the absence of RELM-β, that RELM-β may reduce the development of chronic markers of allergic airways disease.

Gut Microbiota and Host Juvenile Growth

Good genes, good food, good friends. That is what parents hope will sustain and nurture the harmonious growth of their children. The impact of the genetic background and nutrition on postnatal growth has been in the spot light for long, but the good friends have come to the scene only recently. Among the good friends perhaps the most crucial ones are those that we are carrying within ourselves. They comprise the trillions of microbes that collectively constitute each individual's intestinal microbiota. Indeed, recent epidemiological and field studies in humans, supported by extensive experimental data on animal models, demonstrate a clear role of the intestinal microbiota on their host's juvenile growth, especially under suboptimal nutrient conditions. Genuinely integrative approaches applicable to invertebrate and vertebrate systems combine tools from genetics, developmental biology, microbiology, nutrition, and physiology to reveal how gut microbiota affects growth both positively and negatively, in healthy and pathological conditions. It appears that certain natural or engineered gut microbiota communities can positively impact insulin/IGF-1 and steroid hormone signaling, thus contributing to the host juvenile development and maturation.