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Introduction: The environmentally acquired aerobic spore-forming (EAS-Fs) bacteria that are ubiquitous in nature (e.g., soil) are transient colonisers of the mammalian gastro-intestinal tract. Without regular exposure, their numbers quickly diminish. These species of bacteria have been suggested to be essential to the normal functioning of metabolic and immunogenic health. The modern Western lifestyle restricts exposure to these EAS-Fs, possibly explaining part of the pathogenesis of many Western diseases. To date, the only animal studies that address specific microbiome modelling are based around germ-free animals. We have designed a new animal model that specifically restricts exposure to environmental sources of bacteria. Methodology: A new protocol, termed Super Clean, which involves housing mice in autoclaved individually ventilated cages (IVCs), with autoclaved food/water and strict ascetic handling practice was first experimentally validated. The quantification of EAS-Fs was assessed by heat-treating faecal samples and measuring colony-forming units (CFUs). This was then compared to mice in standard conditions. Mice were housed in their respective groups from birth until 18 months. Stool samples were taken throughout the experiment to assess for abundance in transiently acquired environmental bacteria. Clinical, biochemical, histological, and gene expression markers were analysed for diabetes, hypercholesterolaemia, obesity, inflammatory bowel disease, and non-alcoholic fatty liver disease (the "diseases of the West"). Results: Our results show that stringent adherence to the Super Clean protocol produces a significantly decreased abundance of aerobic spore-forming Bacillota after 21 days. This microbiomic shift was correlated with significantly increased levels of obesity and impaired glucose metabolism. There was no evidence of colitis, liver disease or hypercholesterolaemia. Conclusions: This new murine model successfully isolates EAS-Fs and has potential utility for future research, allowing for an investigation into the clinical impact of living in relative hygienic conditions. [ABSTRACT FROM AUTHOR]

In mariculture facilities, bacterial infections pose significant production challenges, with potentially catastrophic impacts on fish species. Bacterial co-infections are a widespread phenomenon in the natural marine environment, although their impact on aquatic organisms remains poorly investigated. This study aimed to detail the pathological findings associated with a natural bacterial co-infection caused by three different pathogens, namely Photobacterium damselae subsp. piscicida, Tenacibaculum maritimum and Vibrio sp., as the cause of mass mortality in European sea bass. The fish had been reared in open-net cages in Sicily and later transferred for experimental research purposes to a user establishment after immunization with an inactivated vaccine. Macroscopic, cytological and histopathological examinations were performed on 109 animals, and bacterial species were identified by the 16S rRNA gene. Overall, ulcerative skin lesions, necrotizing myositis and tail rot with occasional tail loss were associated with tenacibaculosis and vibriosis, while P. damselae subsp. piscicida mainly caused granulomatous inflammation in the spleen and head kidney. Finally, an injection site reaction due to the oil-adjuvanted vaccine administered intraperitoneally was observed in the abdominal fat. Understanding the impact of bacterial pathogens is essential to manage the health and welfare of farmed fish, and the importance of a good health monitoring program cannot be overstated to avoid outbreaks and the possible emergence of new pathogens due to the intensification of the production systems, antibiotic resistance and climate changes. The study would also highlight the importance of the quarantine period when animals supplied for research come from aquaculture farms and how the main goal in the near future should be to better define the procedures to provide completely pathogen-free animals. [ABSTRACT FROM AUTHOR]

OBJECTIVE To cohouse cats experimentally infected with Bartonella clarridgeiae (Bc) with naive cats in a flea-free environment or with Ctenocephalides felis, Bartonella henselae (Bh), Mycoplasma haemofelis, and Candidatus Mycoplasma haemominutum to determine which flea could be a vector and to assess whether transmission of the infectious agents could be blocked by fipronil and (S)-methoprene. ANIMALS Specific pathogen-free cats (n = 34). METHODS In experiment 1, Bc was inoculated in 1 cat that was housed with 9 naive cats without C felis. In experiment 2, the 2 cats inoculated with Bc were housed with 6 other cats (2 inoculated with Bh, 2 inoculated with M haemofelis, and 2 inoculated with Candidatus M haemominutum) in the center (enclosure 2) of 3 housing enclosures separated by mesh walls that allow passage of fleas but precludes fighting. C felis were placed only on cats in enclosure 2 (5 times). Cats in enclosures 1 (n = 8) and 2 (8) were untreated, and cats in enclosure 3 (8) were administered fipronil and (S)-methoprene. Blood was collected from all cats for PCR assays for the pathogens. RESULTS None of the cats housed with the cat inoculated with Bc became PCR positive in the absence of C felis. All cats in enclosure 2 became Bc DNA positive. While 2 of 8 cats in enclosure 1 became Bc PCR positive, none of the treated cats in enclosure 3 became infected. CLINICAL RELEVANCE The study demonstrated that C felis can be a vector for Bc. The results support the recommendation that flea control products can reduce the risk of transmission of flea-borne pathogens. [ABSTRACT FROM AUTHOR]

Summary: Commensal microbes have the capacity to affect development and severity of autoimmune diseases. Germ‐free (GF) animals have proven to be a fine tool to obtain definitive answers to the queries about the microbial role in these diseases. Moreover, GF and gnotobiotic animals can be used to dissect the complex symptoms and determine which are regulated (enhanced or attenuated) by microbes. These include disease manifestations that are sex biased. Here, we review comparative analyses conducted between GF and Specific‐Pathogen Free (SPF) mouse models of autoimmunity. We present data from the B6;NZM‐Sle1NZM2410/AegSle2NZM2410/AegSle3NZM2410/Aeg−/LmoJ (B6.NZM) mouse model of systemic lupus erythematosus (SLE) characterized by multiple measurable features. We compared the severity and sex bias of SPF, GF, and ex‐GF mice and found variability in the severity and sex bias of some manifestations. Colonization of GF mice with the microbiotas taken from B6.NZM mice housed in two independent institutions variably affected severity and sexual dimorphism of different parameters. Thus, microbes regulate both the severity and sexual dimorphism of select SLE traits. The sensitivity of particular trait to microbial influence can be used to further dissect the mechanisms driving the disease. Our results demonstrate the complexity of the problem and open avenues for further investigations. [ABSTRACT FROM AUTHOR]

The drug response phenotype is determined by a combination of genetic and environmental factors. The high clinical conversion failure rate of gene‐targeted drugs might be attributed to the lack of emphasis on environmental factors and the inherent individual variability in drug response (IVDR). Current evidence suggests that environmental variables, rather than the disease itself, are the primary determinants of both gut microbiota composition and drug metabolism. Additionally, individual differences in gut microbiota create a unique metabolic environment that influences the in vivo processes underlying drug absorption, distribution, metabolism, and excretion (ADME). Here, we discuss how gut microbiota, shaped by both genetic and environmental factors, affects the host's ADME microenvironment within a new evaluation system for drug–microbiota interactions. Furthermore, we propose a new top‐down research approach to investigate the intricate nature of drug–microbiota interactions in vivo. This approach utilizes germ‐free animal models, providing foundation for the development of a new evaluation system for drug–microbiota interactions. Highlights: Shaped by both genetic and environmental factors, gut microbiota significantly influences the host's drug absorption, distribution, metabolism, and excretion (ADME) microenvironment, highlighting the need for a new evaluation system for drug‐microbiome interactions.To investigate the intricate nature of interactions between gut microbiota and drugs in vivo, a novel top‐down research approach utilizing germ‐free animal models is proposed. [ABSTRACT FROM AUTHOR]

Background: Gut microbiota is significantly influenced by altitude. However, the dynamics of gut microbiota in relation to altitude remains undisclosed. Methods: In this study, we investigated the microbiome profile of 610 healthy young men from three different places in China, grouped by altitude, duration of residence, and ethnicity. We conducted widely targeted metabolomic profiling and clinical testing to explore metabolic characteristics. Results: Our findings revealed that as the Han individuals migrated from low altitude to high latitude, the gut microbiota gradually converged towards that of the Tibetan populations but reversed upon returning to lower altitude. Across different cohorts, we identified 51 species specifically enriched during acclimatization and 57 species enriched during deacclimatization to high altitude. Notably, Prevotella copri was found to be the most enriched taxon in both Tibetan and Han populations after ascending to high altitude. Furthermore, significant variations in host plasma metabolome and clinical indices at high altitude could be largely explained by changes in gut microbiota composition. Similar to Tibetans, 41 plasma metabolites, such as lactic acid, sphingosine-1-phosphate, taurine, and inositol, were significantly elevated in Han populations after ascending to high altitude. Germ-free animal experiments demonstrated that certain species, such as Escherichia coli and Klebsiella pneumoniae, which exhibited altitude-dependent variations in human populations, might play crucial roles in host purine metabolism. Conclusions: This study provides insights into the dynamics of gut microbiota and host plasma metabolome with respect to altitude changes, indicating that their dynamics may have implications for host health at high altitude and contribute to host adaptation. 88DwbBo5LkUszxYCpXiUg_ Video Abstract [ABSTRACT FROM AUTHOR]

In vitro diagnostic methods face non-specific interactions increasing their background level and influencing the efficacy and reproducibility. Currently, the most important and employed blocker of non-specific interactions is bovine serum albumin (BSA), an animal product with some disadvantages like its batch-to-batch variability and contamination with RNases. Herein, we developed amphiphilic water-soluble synthetic copolymers based on the highly biocompatible, non-immunogenic and nontoxic N-2-(hydroxypropyl)methacrylamide (HPMA)-based copolymers or poly(oxazoline)s as highly effective synthetic blockers of non-specific interactions and an effective BSA alternative. The highest blocking capacity was observed for HPMA-based polymers containing two hydrophobic anchors taking advantage of the combination of two structurally different hydrophobic molecules. Polymers prepared by free radical polymerisation with broader dispersity were slightly better in terms of surface covering. The sandwich ELISA evaluating human thyroid-stimulating Hormone in patient samples revealed that the designed polymers can fully replace BSA without compromising the assay results. Importantly, as a fully synthetic material, the developed polymers are fully animal pathogen-free; thus, they are highly important materials for further development. [ABSTRACT FROM AUTHOR]

Over the last two decades, it has become clear that the human gut microbiota, a complex community of bacteria, archaea, fungi and viruses, are a critical determinant of human health and disease. Microbiota-derived metabolites provide the host with energy, protect against pathogens, modulate immune and endocrine systems as well as the level of reactive oxygen species in the gut. It has come with no surprise that the human gut microbiota is also linked to the production, utilisation and regulation of host hormones. This implies that the gut microbiota is capable of influencing human behaviour, appetite regulation and metabolism as well as development and immunity. Many of the advances in the field of crosstalk between the gut microbiota and host health, disease and behaviours are generally based on DNA analyses of microbial populations and transplantation of monocultured commensal species to germfree animals. Recent reports on the activity of the gut microbiota in gastrointestinal diseases such as inflammatory bowel disease and colorectal cancer have highlighted two important points. First, microbial DNA-based abundance does not always correlate with their level of activity and secondly, that metabolism of the complex gut microbiota is regulated by host health status, including the production and metabolism of several human hormones. In this review, we will discuss the lessons learnt from studying the activity and metabolism of the human gut microbiota in health and across gastrointestinal diseases, and how these findings can shape future research on the microbiome--gut--endocrine axis. [ABSTRACT FROM AUTHOR]

Transplantation of faecal microbiota (FMT) is generally considered a safe therapeutic procedure with few adverse effects. The main factors that limit the spread of the use of FMT therapy for idiopathic inflammatory bowel disease (IBD) are the necessity of minimising the risk of infection and transfer of another disease. Obtaining the animal model of UC (ulcerative colitis) by exposure to DSS (dextran sodium sulphate) depends on many factors that significantly affect the result. Per os intake of DSS with water is individual for each animal and results in the development of a range of various forms of induced UC. For this reason, the aim of our study was to evaluate the modulation and regenerative effects of FMT on the clinical and histopathological responses and the changes in the bowel microenvironment in pseudo germ-free (PGF) mice of the BALB/c line subjected to chemical induction of mild, moderate and serious forms of UC. The goal was to obtain new data related to the safety and effectiveness of FMT that can contribute to its improved and optimised use. The animals with mild and moderate forms of UC subjected to FMT treatment exhibited lower severity of the disease and markedly lower damage to the colon, including reduced clinical and histological disease index and decreased inflammatory response of colon mucosa. However, FMT treatment failed to achieve the expected therapeutic effect in animals with the serious form of UC activity. The results of our study indicated a potential safety risk involving development of bacteraemia and also translocation of non-pathogenic representatives of bowel microbiota associated with FMT treatment of animals with a diagnosed serious form of UC. [ABSTRACT FROM AUTHOR]

Inflammatory Bowel Disease (IBD) is characterized by prolonged inflammation of the gastrointestinal tract, which is thought to occur due to dysregulation of the immune system allowing the host’s cells to attack the GI tract and cause chronic inflammation. IBD can be caused by numerous factors such as genetics, gut microbiota, and environmental influences. In recent years, emphasis on commensal bacteria as a critical player in IBD has been at the forefront of new research. Each individual harbors a unique bacterial community that is influenced by diet, environment, and sanitary conditions. Importantly, it has been shown that there is a complex relationship among the microbiome, activation of the immune system, and autoimmune disorders. Studies have shown that not only does the microbiome possess pathogenic roles in the progression of IBD, but it can also play a protective role in mediating tissue damage. Therefore, to improve current IBD treatments, understanding not only the role of harmful bacteria but also the beneficial bacteria could lead to attractive new drug targets. Due to the considerable diversity of the microbiome, it has been challenging to characterize how particular microorganisms interact with the host and other microbiota. Fortunately, with the emergence of next-generation sequencing and the increased prevalence of germ-free animal models there has been significant advancement in microbiome studies. By utilizing human IBD studies and IBD mouse models focused on intraepithelial lymphocytes and innate lymphoid cells, this review will explore the multifaceted roles the microbiota plays in influencing the immune system in IBD. [ABSTRACT FROM AUTHOR]

Interleukin-17A (IL-17) is a pro-inflammatory cytokine involved in the immune response to many pathogens playing also a role in certain chronic and autoimmune diseases. The presented study focused on the early postnatal development of IL-17 producing cells in swine. In agreement with previous studies, ab T-helper (CD3+CD4+) and gd T (CD3+TCRgd+) cells were found to be the major producers of IL-17. In newborn conventional piglets, ab T-helper cells positive for IL-17 were almost undetectable, but their frequency increased markedly with age in all issues examined, i.e., blood, spleen, and mesenteric lymph nodes (MLN). Additional analyses of CD8 and CD27 expression showed that the main ab T-helper producers of IL-17 has CD8+CD27- phenotype in all tissues. IL-17 positive CD8+CD27+ ab T-helper subpopulation was found only in blood and spleen. The production of IL17 in CD8- CD27+ ab T-helper cells was always minor. In contrast, gd T cells positive for IL-17 did not show a similar agedependent increase in blood and spleen, whereas they increased in MLN. Because of the age-dependent increase in conventional animals, we included a comparison with germ-free piglets to show that the increase in IL-17 positive cells was clearly depended on the presence of the microbiota as the production in germ-free animals was negligible without any age-dependent increase. [ABSTRACT FROM AUTHOR]

Background: Typically, animal models studying gastrointestinal microbiotas compromised in early life have employed either germ-free animals or mice treated with a cocktail of antibiotics. Such studies intend to mimic scenarios of infants born by caesarean section and/or subjected to antibiotic treatment. However, the antibiotics used in these studies are rarely prescribed to infants. Therefore, an early life model was developed in which the murine gastrointestinal microbiota was severely disrupted by clindamycin treatment. Results: In this mouse model, we investigated the extent supplementation with a synbiotic mixture of prebiotics, being scGOS/lcFOS with the human milk oligosaccharide 2'-Fucosyllactose (2'-FL), in combination with or without single strain or mix of "infant type" bifidobacteria, can rescue an antibiotic-compromised microbiota. Shotgun metagenomic sequencing showed that the microbiota was severely disrupted by the clindamycin challenge. No recovery was observed 3 weeks post-challenge in the scGOS/lcFOS/2'FL group, while the group that received the synbiotic treatment of scGOS/lcFOS/2'-FL with Bifidobacterium breve NRBB01 showed partial recovery. Strikingly in the scGOS/lcFOS/2'-FL group receiving the mixture of bifidobacteria resulted in a recovery of the microbiota disruption. Histological analyses showed that the clindamycin-treated animals at the end of the experiment still suffered from mild oedema and villi/colonic crypt irregularities which was ameliorated by the synbiotic intervention. Conclusion: Our study demonstrates that supplementation of synbiotic mixture of scGOS/lcFOS/2'-FL in combination with a specific mix of infant-type bifidobacterial strains is able to partially revive an antibiotic-perturbed gastrointestinal microbiota. DqAiaRikLfonWr824rkSor Video Abstract [ABSTRACT FROM AUTHOR]

• Review of the role of the enteric nervous system (ENS) in autism spectrum disorders. • Key neuroimmune interactions within the ENS may influence intestinal homeostasis. • Zebrafish are an ideal model to assess cellular interactions. • State of the art methods can help uncover complex mechanisms of cell interactions. Autism spectrum disorders (ASD) affect about 1% of the population and are strongly associated with gastrointestinal diseases creating shortcomings in quality of life. Multiple factors contribute to the development of ASD and although neurodevelopmental deficits are central, the pathogenesis of the condition is complex and the high prevalence of intestinal disorders is poorly understood. In agreement with the prominent research establishing clear bidirectional interactions between the gut and the brain, several studies have made it evident that such a relation also exists in ASD. Thus, dysregulation of the gut microbiota and gut barrier integrity may play an important role in ASD. However, only limited research has investigated how the enteric nervous system (ENS) and intestinal mucosal immune factors may impact on the development of ASD-related intestinal disorders. This review focuses on the mechanistic studies that elucidate the regulation and interactions between enteric immune cells, residing gut microbiota and the ENS in models of ASD. Especially the multifaceted properties and applicability of zebrafish (Danio rerio) for the study of ASD pathogenesis are assessed in comparison to studies conducted in rodent models and humans. Advances in molecular techniques and in vivo imaging, combined with genetic manipulation and generation of germ-free animals in a controlled environment, appear to make zebrafish an underestimated model of choice for the study of ASD. Finally, we establish the research gaps that remain to be explored to further our understanding of the complexity of ASD pathogenesis and associated mechanisms that may lead to intestinal disorders. [ABSTRACT FROM AUTHOR]

Autoreactive encephalitogenic T cells exist in the healthy immune repertoire but need a trigger to induce CNS inflammation. The underlying mechanisms remain elusive, whereby microbiota were shown to be involved in the manifestation of CNS autoimmunity. Here, we used intravital imaging to explore how microbiota affect the T cells as trigger of CNS inflammation. Encephalitogenic CD4+ T cells transduced with the calcium-sensing protein Twitch-2B showed calcium signaling with higher frequency than polyclonal T cells in the small intestinal lamina propria (LP) but not in Peyer’s patches. Interestingly, nonencephalitogenic T cells specific for OVA and LCMV also showed calcium signaling in the LP, indicating a general stimulating effect of microbiota. The observed calcium signaling was microbiota and MHC class II dependent as it was significantly reduced in germfree animals and after administration of anti-MHC class II antibody, respectively. As a consequence of T cell stimulation in the small intestine, the encephalitogenic T cells start expressing Th17-axis genes. Finally, we show the migration of CD4+ T cells from the small intestine into the CNS. In summary, our direct in vivo visualization revealed that microbiota induced T cell activation in the LP, which directed T cells to adopt a Th17-like phenotype as a trigger of CNS inflammation. [ABSTRACT FROM AUTHOR]

This systematic review aimed to highlight the newest information on the effects of non-lactic acid probiotics on the foodborne pathogens. Following the PRISMA-P guidelines, electronic databases (PubMed, Medline, Cochrane Central, Web of Science, Scopus) was searched from their inception up to September 23, 2019. 83 studies met the inclusion criteria after the full-text analysis of 558 articles. Results demonstrated that the majority of the studies focused on spore-forming bacteria and species-specific direct antagonism as the mechanism of action. Nevertheless, further research with in-vivo experimental setups with gnotobiotic animals regarding immunomodulating effects and inhibition of biofilm formation is required. [ABSTRACT FROM AUTHOR]

The close association between animals and their associated microbiota is usually beneficial for both partners. Here, we used a simple marine model invertebrate, the flatworm Macrostomum lignano, to characterize the host-microbiota interaction in detail. This analysis revealed that the different developmental stages each harbor a specific microbiota. Studies with gnotobiotic animals clarified the physiological significance of the microbiota. While no fitness benefits were mediated by the microbiota when food was freely available, animals with microbiota showed significantly increased fitness with a reduced food supply. The microbiota of M. lignano shows circadian rhythmicity, affecting both the total bacterial load and the behavior of specific taxa. Moreover, the presence of the worm influences the composition of the bacterial consortia in the environment. In summary, the Macrostomum-microbiota system described here can serve as a general model for host-microbe interactions in marine invertebrates. A circadian rhythm and the capacity to manage fitness during limited food availability is identified in the microbiome of the marine flatworm. [ABSTRACT FROM AUTHOR]

A germ-free animal is an experimental animal with no live microorganisms and parasites in its body. It is a powerful experimental tool for the study of the relationship between microbiota and host health. We reviewed the development history of germ-free animals and provide an overview of their application in medical research, such as intestinal microbiota, immunology and oncology. We provide references for research on microbe-related diseases. [ABSTRACT FROM AUTHOR]

Metabolites produced by the gut microbiota play an important role in the cross-talk with the human host. Many microbial metabolites are biologically active and can pass the gut barrier and make it into the systemic circulation, where they form the gut microbial exposome, i.e. the totality of gut microbial metabolites in body fluids or tissues of the host. A major difficulty faced when studying the microbial exposome and its role in health and diseases is to differentiate metabolites solely or partially derived from microbial metabolism from those produced by the host or coming from the diet. Our objective was to collect data from the scientific literature and build a database on gut microbial metabolites and on evidence of their microbial origin. Three types of evidence on the microbial origin of the gut microbial exposome were defined: (1) metabolites are produced in vitro by human faecal bacteria; (2) metabolites show reduced concentrations in humans or experimental animals upon treatment with antibiotics; (3) metabolites show reduced concentrations in germ-free animals when compared with conventional animals. Data was manually collected from peer-reviewed publications and inserted in the Exposome-Explorer database. Furthermore, to explore the chemical space of the microbial exposome and predict metabolites uniquely formed by the microbiota, genome-scale metabolic models (GSMMs) of gut bacterial strains and humans were compared. A total of 1848 records on one or more types of evidence on the gut microbial origin of 457 metabolites was collected in Exposome-Explorer. Data on their known precursors and concentrations in human blood, urine and faeces was also collected. About 66% of the predicted gut microbial metabolites (n = 1543) were found to be unique microbial metabolites not found in the human GSMM, neither in the list of 457 metabolites curated in Exposome-Explorer, and can be targets for new experimental studies. This new data on the gut microbial exposome, freely available in Exposome-Explorer (http://exposome-explorer.iarc.fr/), will help researchers to identify poorly studied microbial metabolites to be considered in future studies on the gut microbiota, and study their functionalities and role in health and diseases. [ABSTRACT FROM AUTHOR]

Consumers' need to prefer pathogen-free animal products has led nutritionists to increasingly look for alternatives to synthetic additives, of which garlic has been considered as a natural additive. Therefore, a 12-week feeding trial was conducted to determine the potential of the dietary allicin-rich extract on the performance of laying hens. Eight hundred and forty (840) 28 weeks old Bovans Brown laying hens were randomly allotted to two experiments; the first study had four dietary treatments with 6 replicates and 20 birds and the second study had three treatments with 6 replicates and 20 birds per pen using a completely randomised design. The dietary treatments consisted of a negative control (Ncon./C, standard diet without antibiotics), positive control (Pcon./C+, standard diet + 1.0 g/l oxytetracycline), allicin-rich extract with low concentration (AEL, Ncon. + 0.5 ml/kg), allicin-rich extract with high concentration (AEH, Ncon. + 1.0 ml/kg) and allicinrich extract in drinking water (AE/C- + 1.0 ml/l of fresh drinking water). No statistical differences (P > 0.05) were observed in feed consumption and egg weight among all the treatments but egg production, egg mass and feed conversion ratio were significantly improved (P < 0.05) by the addition of allicin-rich extract at 0.50 ml/kg. Albumen was significantly superior (P < 0.05) in the AE group compared to the positive control group. With age, viable total coliform, E. coli and Clostridium perfringens were significantly lower (P < 0.05) in the experimental groups compared to the negative control group. Significantly lower (P < 0.05) concentrations of total cholesterol, triglycerides and low-density lipoprotein were recorded in the AE group. It can be concluded that the incorporation of dietary allicin-rich extract reduced pathogenic bacteria and boosted feed efficiency, egg production and blood lipid depending on the mode of application. [ABSTRACT FROM AUTHOR]

Mounting evidence highlights the pivotal role of enteric microbes as a dynamic interface with the host. Indeed, the gut microbiota, located in the lumen of the gastrointestinal (GI) tract, influence many essential physiological processes that are evident in both healthy and pathological states. A key signaling molecule throughout the body is serotonin (5‐hydroxytryptamine; 5‐HT), which acts in the GI tract to regulate numerous gut functions including intestinal motility and secretion. The gut microbiota can modulate host 5‐HT systems both directly and indirectly. Direct actions of gut microbes, evidenced by studies using germ‐free animals or antibiotic administration, alter the expression of key 5‐HT‐related genes to promote 5‐HT biosynthesis. Indirectly, the gut microbiota produce numerous microbial metabolites, whose actions can influence host serotonergic systems in a variety of ways. This review summarizes the current knowledge regarding mechanisms by which gut bacteria act to regulate host 5‐HT and 5‐HT‐mediated gut functions, as well as implications for 5‐HT in the microbiota–gut–brain axis. [ABSTRACT FROM AUTHOR]

Recently, influence of bacteria colonization on development and maturation of gut wall is getting more into the focus of gastrointestinal research. For years, the main interest and research were aimed to the development and maturation of gut wall and its functional properties in normal conditions, less attention has been paid on the germ-free animals. Germ-free (GF) piglets have clear microbiological background and are reared in sterile environment. GF piglets are regarded as clinically relevant models for studying of human diseases, as these piglets' manifest similar clinical symptoms to humans. In this study we briefly summarised the main characteristics in the distribution of goblet cells in the wall of jejunum and colon of GF piglets as healthy control (HC) group and piglets, which were experimentally infected by E. coli O149:K88 as ECK group. Neutral mucins were stained with periodic acid-Shiff (PAS) whereas acidic mucins are stained with Alcian blue. Numbers of goblet cells containing total acidic mucins in both, the jejunum and colon, differed significantly between HC and ECK piglets and in the colon, a similar trend was also observed. In the ECK piglets, jejunal goblet cells exhibited decrease in neutral mucins. This change in mucin profile in response to bacterial colonization suggests a potential role as a protective mechanism against pathogenic invasion of the intestinal mucosa during of gut mucosa development in piglets. [ABSTRACT FROM AUTHOR]

New Findings: What is the topic of this review?The importance of the early life gut microbiome, with a focus on preterm infants and microbially related diseases. Current techniques to study the preterm gut microbiome are appraised, and the potential of recent methodological advancements is discussed.What advances does it highlight?Recent findings in the field achieved by the application of advanced technologies, the applicability of intestinally derived organoid models to study host–microbiome interactions in the preterm gut, and recent developments in enhancing the physiological relevance of such models. Preterm intestinally derived organoids may provide novel insights into the mechanisms underlying preterm disease, as well as diagnosis and treatment opportunities. These models have huge translational potential, offering a step towards precision medicine. Accumulating evidence affirms the importance of the gut microbiome in both health and disease. In early life, there exists a critical period in which the composition of gut microbes is particularly malleable and subject to a wide range of influencing factors. Disturbances to microbial communities during this time may be beneficial or detrimental to short and long‐term health outcomes. For infants born prematurely, naïve immune systems, immature gastrointestinal tracts and additional clinical needs put this population at high risk of abnormal microbial colonisation, resulting in increased susceptibility to diseases including necrotising enterocolitis (NEC) and late‐onset sepsis (LOS). Traditional cell culture methods, gnotobiotic animals, molecular sequencing techniques (16S rRNA gene sequencing and metagenomics) and advanced 'omics' technologies (transcriptomics, proteomics and metabolomics) have been fundamental in exploring the associations between diet, gut microbes, microbial functions and disease. Despite significant investment and ongoing research efforts, prevention and treatment strategies in NEC and LOS remain limited. Recent endeavours have focused on searching for new, more physiologically relevant models to simulate the preterm intestine. Preterm intestinally derived organoids represent a promising in vitro approach in the study of host–microbiome interactions in the preterm infant gut, offering new and exciting possibilities in this field. [ABSTRACT FROM AUTHOR]

The human mucus layer plays a vital role in maintaining health by providing a physical barrier to pathogens. This biological hydrogel also provides the microenvironment for commensal bacteria. Common models used to study host–microbe interactions include gnotobiotic animals or mammalian–microbial co-culture platforms. Many of the current in vitro models lack a sufficient mucus layer to host these interactions. In this study, we engineered a mucus-like hydrogel Consisting of a mixed alginate-mucin (ALG-MUC) hydrogel network by using low concentration calcium chloride (CaCl2) as crosslinker. We demonstrated that the incorporation of ALG-MUC hydrogels into an aqueous two-phase system (ATPS) co-culture platform can support the growth of a mammalian monolayer and pathogenic bacteria. The ALG-MUC hydrogels displayed selective diffusivity against macromolecules and stability with ATPS microbial patterning. Additionally, we showed that the presence of mucin within hydrogels contributed to an increase in antimicrobial resistance in ATPS patterned microbial colonies. By using common laboratory chemicals to generate a mammalian–microbial co-culture system containing a representative mucus microenvironment, this model can be readily adopted by typical life science laboratories to study host–microbe interaction and drug discovery. [ABSTRACT FROM AUTHOR]

As one of the most metabolically complex systems in the body, the liver ensures multi-organ homeostasis and ultimately sustains life. Nevertheless, during early postnatal development, the liver is highly immature and takes about 2 years to acquire and develop almost all of its functions. Different events occurring at the environmental and cellular levels are thought to mediate hepatic maturation and function postnatally. The crosstalk between the liver, the gut and its microbiome has been well appreciated in the context of liver disease, but recent evidence suggests that the latter could also be critical for hepatic function under physiological conditions. The gut-liver crosstalk is thought to be mediated by a rich repertoire of microbial metabolites that can participate in a myriad of biological processes in hepatic sinusoids, from energy metabolism to tissue regeneration. Studies on germ-free animals have revealed the gut microbiome as a critical contributor in early hepatic programming, and this influence extends throughout life, mediating liver function and body homeostasis. In this seminar, we describe the microbial molecules that have a known effect on the liver and discuss how the gut microbiome and the liver evolve throughout life. We also provide insights on current and future strategies to target the gut microbiome in the context of hepatology research. [ABSTRACT FROM AUTHOR]

Observational studies reveal substantial variability in microbiome composition across individuals. Targeted studies in gnotobiotic animals underscore this variability by showing that some bacterial strains colonize deterministically, while others colonize stochastically. While some of this variability can be explained by external factors like environmental, dietary, and genetic differences between individuals, in this paper we show that for the model organism Drosophila melanogaster, interactions between bacteria can affect the microbiome assembly process, contributing to a baseline level of microbiome variability even among isogenic organisms that are identically reared, housed, and fed. In germfree flies fed known combinations of bacterial species, we find that some species colonize more frequently than others even when fed at the same high concentration. We develop an ecological technique that infers the presence of interactions between bacterial species based on their colonization odds in different contexts, requiring only presence/absence data from two-species experiments. We use a progressive sequence of probabilistic models, in which the colonization of each bacterial species is treated as an independent stochastic process, to reproduce the empirical distributions of colonization outcomes across experiments. We find that incorporating context-dependent interactions substantially improves the performance of the models. Stochastic, contextdependent microbiome assembly underlies clinical therapies like fecal microbiota transplantation and probiotic administration and should inform the design of synthetic fecal transplants and dosing regimes. [ABSTRACT FROM AUTHOR]

The human intestine harbors a huge number of diverse microorganisms where a variety of complex interactions take place between the microbes as well as the host and gut microbiota. Significant long-term variations in the gut microbiota (dysbiosis) have been associated with a variety of health conditions including inflammatory bowel disease (IBD). Conventional fecal microbiota transplantations (FMTs) have been utilized to treat IBD and have been proved promising. However, various limitations such as transient results, pathogen transfer, storage, and reproducibility render conventional FMT less safe and less sustainable. Defined synthetic microbial communities (SynCom) have been used to dissect the host-microbiota-associated functions using gnotobiotic animals or in vitro cell models. This review focuses on the potential use of SynCom in IBD and its advantages and relative safety over conventional FMT. Additionally, this review reinforces how various technological advances could be combined with SynCom to have a better understanding of the complex microbial interactions in various gut inflammatory diseases including IBD. Some technological advances including the availability of a gut-on-a-chip system, intestinal organoids, ex vivo intestinal cultures, AI-based refining of the microbiome structural and functional data, and multiomic approaches may help in making more practical in vitro models of the human host. Additionally, an increase in the cultured diversity from gut microbiota and the availability of their genomic information would further make the design and utilization of SynCom more feasible. Taken together, the combined use of the available knowledge of the gut microbiota in health and disease and recent technological advances and the development of defined SynCom seem to be a promising, safe, and sustainable alternative to conventional FMT in treating IBD. [ABSTRACT FROM AUTHOR]

Germ-free animals (GF) are those without a microbiome since birth. This particular biological model has become one of special interest with the growing evidence of importance of the microbiome in the life, development, adaptation, and immunity of humans and animals in the environments in which they live. Anatomical differences observed in GF compared with conventionally-reared animals (CV) has given rise to the question of the influence of commensal microflora on the development of structure and function (even immunological) of the bowel. Only recently, thanks to achievements in microscopy and associated methods, structural differences can be better evaluated and put in perspective with the immunological characteristics of GF vs. CV animals. This study, using a GF rat model, describes for the first time the possible influence that the presence of commensal microflora, continuously stimulating mucosal immunity, has on the collagen scaffold organization of the colon mucosa. Significant differences were found between CV and GF mucosa structure with higher complexity in the CV rats associated to a more activated immune environment. The immunological data suggest that, in response to the presence of a microbiome, an effective homeostatic regulation in developed by the CV rats in healthy conditions to avoid inflammation and maintain cytokine levels near the spontaneous production found in the GF animals. The results indicated that collagen scaffold adapted to the immune microenvironment; therefore, it is apparent that the microbiome was able to condition the structure of the colon mucosa. [ABSTRACT FROM AUTHOR]

The gut microbiome produces vitamins, nutrients, and neurotransmitters, and helps to modulate the host immune system—and also plays a major role in the metabolism of many exogenous compounds, including drugs and chemical toxicants. However, the extent to which specific microbial species or communities modulate hazard upon exposure to chemicals remains largely opaque. Focusing on the effects of collateral dietary exposure to the widely used herbicide atrazine, we applied integrated omics and phenotypic screening to assess the role of the gut microbiome in modulating host resilience in Drosophila melanogaster. Transcriptional and metabolic responses to these compounds are sex-specific and depend strongly on the presence of the commensal microbiome. Sequencing the genomes of all abundant microbes in the fly gut revealed an enzymatic pathway responsible for atrazine detoxification unique to Acetobacter tropicalis. We find that Acetobacter tropicalis alone, in gnotobiotic animals, is sufficient to rescue increased atrazine toxicity to wild-type, conventionally reared levels. This work points toward the derivation of biotic strategies to improve host resilience to environmental chemical exposures, and illustrates the power of integrative omics to identify pathways responsible for adverse health outcomes. Brown et al. apply integrated omics and phenotypic screening to assess the role of the gut microbiome in modulating host resilience in Drosophila melanogaster. They find that Acetobacter tropicalis in gnotobiotic animals, is sufficient to rescue increased atrazine toxicity, which could pave the way for biotic strategies to improve host resilience to environmental chemical exposure. [ABSTRACT FROM AUTHOR]

The use of axenic animal models in experimental research has exponentially grown in the past few years and the most reliable way for confirming their axenic status remains unclear. It is especially the case when using individual ventilated positive-pressure cages such as the Isocage. This type of cage are at a greater risk of contamination and expose animals to a longer handling process leading to more potential stress when opened compared to isolators. The aim of this study was to propose simple ways to detect microbial contaminants with Isocages type isolator resulting by developing, validating and optimizing three different methods (culture, microscopy, and molecular). These three approaches were also tested in situ by spiking 21 axenic mice with different microorganisms. Our results suggest that the culture method can be used for feces and surface station (IBS) swabs exclusively (in Brain Heart Infusion for 7 days at 25°C and 37°C in aerobic conditions, and at 30°C in anaerobic conditions), while microscopy (wet mounts) and molecular method (quantitative PCR) were only suitable for fecal matter analyses. In situ results suggests that the culture and molecular methods can detect up to 100% of bacterial contamination events while the microscopy approach generates many erroneous results when not performed by a skilled microscopist. In situ results also suggest that when an axenic mouse is contaminated by a microbial agent, the microorganism will colonize the mouse to such an extent that detection is obvious in 4 days, in average. This report validates simple but complimentary tests that can be used for optimal detection of contaminants in axenic animal facilities using Isocage type isolators. [ABSTRACT FROM AUTHOR]

Background: Lactobacillus rhamnosus GG (LGG) is the most widely used probiotic, but the mechanisms underlying its beneficial effects remain unresolved. Previous studies typically inoculated LGG in hosts with established gut microbiota, limiting the understanding of specific impacts of LGG on host due to numerous interactions among LGG, commensal microbes, and the host. There has been a scarcity of studies that used gnotobiotic animals to elucidate LGG-host interaction, in particular for gaining specific insights about how it modifies the metabolome. To evaluate whether LGG affects the metabolite output of pathobionts, we inoculated with LGG gnotobiotic mice containing Propionibacterium acnes, Turicibacter sanguinis, and Staphylococcus aureus (PTS). Results: 16S rRNA sequencing of fecal samples by Ion Torrent and MinION platforms showed colonization of germ-free mice by PTS or by PTS plus LGG (LTS). Although the body weights and feeding rates of mice remained similar between PTS and LTS groups, co-associating LGG with PTS led to a pronounced reduction in abundance of P. acnes in the gut. Addition of LGG or its secretome inhibited P. acnes growth in culture. After optimizing procedures for fecal metabolite extraction and metabolomic liquid chromatography-mass spectrometry analysis, unsupervised and supervised multivariate analyses revealed a distinct separation among fecal metabolites of PTS, LTS, and germ-free groups. Variables-important-in-projection scores showed that LGG colonization robustly diminished guanine, ornitihine, and sorbitol while significantly elevating acetylated amino acids, ribitol, indolelactic acid, and histamine. In addition, carnitine, betaine, and glutamate increased while thymidine, quinic acid and biotin were reduced in both PTS and LTS groups. Furthermore, LGG association reduced intestinal mucosal expression levels of inflammatory cytokines, such as IL-1α, IL-1β and TNF-α. Conclusions: LGG co-association had a negative impact on colonization of P. acnes, and markedly altered the metabolic output and inflammatory response elicited by pathobionts. [ABSTRACT FROM AUTHOR]

The functional ecology of the gastrointestinal tract impacts host physiology, and its dysregulation is at the center of various diseases. The immune system, and specifically innate immunity, plays a fundamental role in modulating the interface of host and microbes in the gut. While humans remain a primary focus of research in this field, the use of diverse model systems help inform us of the fundamental principles legislating homeostasis in the gut. Invertebrates, which lack vertebrate-style adaptive immunity, can help define conserved features of innate immunity that shape the gut ecosystem. In this context, we previously proposed the use of a marine invertebrate, the protochordate Ciona robusta , as a novel tractable model system for studies of host-microbiome interactions. Significant progress, reviewed herein, has been made to fulfill that vision. We examine and review discoveries from Ciona that include roles for a secreted immune effector interacting with elements of the microbiota, as well as chitin-rich mucus lining the gut epithelium, the gut-associated microbiome of adults, and the establishment of a large catalog of cultured isolates with which juveniles can be colonized. Also discussed is the establishment of methods to rear the animals germ-free, an essential technology for dissecting the symbiotic interactions at play. As the foundation is now set to extend these studies into the future, broadening our comprehension of how host effectors shape the ecology of these microbial communities in ways that establish and maintain homeostasis will require full utilization of "multi-omics" approaches to merge computational sciences, modeling, and experimental biology in hypothesis-driven investigations. [ABSTRACT FROM AUTHOR]

The study of the gut microbiota-brain axis has become an intriguing field, attracting attention from both gastroenterologists and neurobiologists. The hippocampus is the center of learning and memory, and plays a pivotal role in neurodegenerative diseases, such as Alzheimer's disease (AD). Previous studies using diet administration, antibiotics, probiotics, prebiotics, germ-free mice, and fecal analysis of normal and specific pathogen-free animals have shown that the structure and function of the hippocampus are affected by the gut microbiota. Furthermore, hippocampal pathologies in AD are positively correlated with changes in specific microbiota. Genomic and neurochemical analyses revealed significant alterations in genes and amino acids in the hippocampus of AD subjects following a remarkable shift in the gut microbiota. In a recent study, when young animals were transplanted with fecal microbiota derived from AD patients, the recipients showed significant impairment of cognitive behaviors, AD pathologies, and changes in neuronal plasticity and cytokines. Other studies have demonstrated the side effects of antibiotic administration along with the beneficial effects of probiotics, prebiotics, and specific diets on the composition of the gut microbiota and hippocampal functions, but these have been mostly preliminary with unclear mechanisms. Since some specific gut bacteria are positively or negatively correlated to the structure and function of the hippocampus, it is expected that specific gut bacteria administration and other microbiota-based interventions could be potentially applied to prevent or treat hippocampus-based memory impairment and neuropsychiatric disorders such as AD. [ABSTRACT FROM AUTHOR]

The majority of microbiome studies focused on understanding mechanistic relationships between the host and the microbiota have used mice and other rodents as the model of choice. However, the domestic pig is a relevant model that is currently underutilized for human microbiome investigations. In this study, we performed a direct comparison of the engraftment of fecal bacterial communities from human donors between human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. Analysis of 16S rRNA genes using amplicon sequence variants (ASVs) revealed that with the exception of early microbiota from infants, the more mature microbiotas tested established better in the HMA piglets compared to HMA mice. Of interest was the greater transplantation success of members belonging to phylum Firmicutes in the HMA piglets compared to the HMA mice. Together, these results provide evidence for the HMA piglet model potentially being more broadly applicable for donors with more mature microbiotas while the HMA mouse model might be more relevant for developing microbiotas such as those of infants. This study also emphasizes the necessity to exercise caution in extrapolating findings from HMA animals to humans, since up to 28% of taxa from some donors failed to colonize either model. Aluthge et al. evaluated the establishment of human fecal bacterial communities in human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. They find that human fecal bacterial communities from mature microbiotas establish more successfully in the HMA porcine model than mice, suggesting the broader applicability of the piglet model for human microbiome studies. [ABSTRACT FROM AUTHOR]

Chronic psychiatric patients with schizophrenia and related disorders are frequently treatment-resistant and may require higher doses of psychotropic drugs to remain stable. Prolonged exposure to these agents increases the risk of weight gain and cardiometabolic disorders, leading to poorer outcomes and higher medical cost. It is well-established that obesity has reached epidemic proportions throughout the world, however it is less known that its rates are two to three times higher in mentally ill patients compared to the general population. Psychotropic drugs have emerged as a major cause of weight gain, pointing to an urgent need for novel interventions to attenuate this unintended consequence. Recently, the gut microbial community has been linked to psychotropic drugs-induced obesity as these agents were found to possess antimicrobial properties and trigger intestinal dysbiosis, depleting Bacteroidetes phylum. Since germ-free animals exposed to psychotropics have not demonstrated weight gain, altered commensal flora composition is believed to be necessary and sufficient to induce dysmetabolism. Conversely, not only do psychotropics disrupt the composition of gut microbiota but the later alter the metabolism of the former. Here we review the role of gut bacterial community in psychotropic drugs metabolism and dysbiosis. We discuss potential biomarkers reflecting the status of Bacteroidetes phylum and take a closer look at nutritional interventions, fecal microbiota transplantation, and transcranial magnetic stimulation, strategies that may lower obesity rates in chronic psychiatric patients. [ABSTRACT FROM AUTHOR]

Background: Recent research has revealed that the community of microorganisms inhabiting the gut affects brain development, function and behaviour. In particular, disruption of the gut microbiome during critical developmental windows can have lasting effects on host physiology. Both antibiotic exposure and germ-free conditions impact the central nervous system and can alter multiple aspects of behaviour. Social impairments are typically displayed by antibiotic-treated and germ-free animals, yet there is a lack of understanding of the underlying neurobiological changes. Since the μ-opioid, oxytocin and vasopressin systems are key modulators of mammalian social behaviour, here we investigate the effect of experimentally manipulating the gut microbiome on the expression of these pathways.Results: We show that social neuropeptide signalling is disrupted in germ-free and antibiotic-treated mice, which may contribute to the behavioural deficits observed in these animal models. The most notable finding is the reduction in neuroreceptor gene expression in the frontal cortex of mice administered an antibiotic cocktail post-weaning. Additionally, the changes observed in germ-free mice were generally in the opposite direction to the antibiotic-treated mice.Conclusions: Antibiotic treatment when young can impact brain signalling pathways underpinning social behaviour and pain regulation. Since antibiotic administration is common in childhood and adolescence, our findings highlight the potential adverse effects that antibiotic exposure during these key neurodevelopmental periods may have on the human brain, including the possible increased risk of neuropsychiatric conditions later in life. In addition, since antibiotics are often considered a more amenable alternative to germ-free conditions, our contrasting results for these two treatments suggest that they should be viewed as distinct models. [ABSTRACT FROM AUTHOR]

Over the past decade, metagenomics has become the preferred method for exploring complex microbiota such as human gut microbiota. However, several bias affecting the results of microbiota composition, such as those due to DNA extraction, have been reported. These bias have been confirmed with the development of culturomics technique. In the present study, we report the contamination of a gnotobiotic mice unit with a bacterium first detected by gram staining. Scanning electron microscopy and transmission electron microscopy permitted to detect a bacterium with a thick cell wall. However, in parallel, the first attempt to identify and culture this bacterium by gene amplification and metagenomics of universal 16S rRNA failed. Finally, the isolation in culture of a fastidious bacterium not detected by using universal PCR was successfully achieved by using a BCYE agar plate with CO2 atmosphere at 30 °C. We performed genome sequencing of this bacterium using a strong extraction procedure. The genomic comparison allowed us to classify this bacterium as Klenkia terrae. And finally, it was also detected in the stool and kibble that caused the contamination by using specific qPCR against this bacterium. The elucidation of this contamination provides additional evidence that DNA extraction could be a bias for the study of the microbiota. Currently, most studies that strive to analyze and compare the gut microbiota are based on metagenomics. In a gnotobiotic mice unit contaminated with the fastidious Actinobacteria Klenkia terrae, standard culture, 16S rRNA gene amplification and metagenomics failed to identify the micro-organism observed in stools by gram-staining. Only a procedure based on culturomics allowed us to identify this bacterium and to elucidate the mode of contamination of the gnotobiotic mice unit through diet. [ABSTRACT FROM AUTHOR]

The composition of the intestinal microbiota influences the outcome of enteric infections in human and mice. However, the role of specific members and their metabolites contributing to disease severity is largely unknown. Using isogenic mouse lines harboring distinct microbiota communities, we observed highly variable disease kinetics of enteric Citrobacter rodentium colonization after infection. Transfer of communities from susceptible and resistant mice into germ-free mice verified that the varying susceptibilities are determined by microbiota composition. The strongest differences in colonization were observed in the cecum and could be maintained in vitro by coculturing cecal bacteria with C. rodentium. Cohousing of animals as well as the transfer of cultivable bacteria from resistant to susceptible mice led to variable outcomes in the recipient mice. Microbiome analysis revealed that a higher abundance of butyrate-producing bacteria was associated with the resistant phenotype. Quantification of short-chain fatty acid (SCFA) levels before and after infection revealed increased concentrations of acetate, butyrate and propionate in mice with delayed colonization. Addition of physiological concentrations of butyrate, but not of acetate and/or propionate strongly impaired growth of C. rodentium in vitro. In vivo supplementation of susceptible, antibiotic-treated and germ-free mice with butyrate led to the same level of protection, notably only when cecal butyrate concentration reached a concentration higher than 50 nmol/mg indicating a critical threshold for protection. In the recent years, commensal-derived primary and secondary bacterial metabolites emerged as potent modulators of hosts susceptibility to infection. Our results provide evidence that variations in SCFA production in mice fed fibre-rich chow-based diets modulate susceptibility to colonization with Enterobacteriaceae not only in antibiotic-disturbed ecosystems but even in undisturbed microbial communities. These findings emphasise the need for microbiota normalization across laboratory mouse lines for infection experiments with the model-pathogen C. rodentium independent of investigations of diet and antibiotic usage. Author summary: The distinct composition of the gut microbiota in each individual results in variable metabolic activity and output of these communities, which influences the host, including resistance to enteric pathogens. Lack of reproducibility in biomedical research is nowadays frequently attributed to the microbiota, but little is known about which specific members and metabolites contribute to disease severity. Here, we use genetically identical mouse lines with variable microbiota compositions on a standardized diet and observed highly variable colonization with the enteric pathogen Citrobacter rodentium without antibiotics intervention. We found the same differences in formerly germfree animals harbouring the respective donors microbiota and also in vitro by coculturing cecal bacteria from resistant and susceptible animals with C. rodentium showing that the phenotype is fully dependent on differences in the microbiota. We analysed the microbiome composition and found a higher abundance of butyrate-producing bacteria as well as increased levels of butyrate in resistant mice. By supplementation of susceptible and germ-free animals with butyrate, we could significantly lower the levels of colonization highlighting that commensal-derived primary and secondary bacterial metabolites are highly variable between laboratory animals from different vendors and are potent modulators of hosts susceptibility to infection with C. rodentium. [ABSTRACT FROM AUTHOR]

A healthy gut is predominantly occupied by bacteria which play a vital role in nutrition and health. Any change in normal gut homeostasis imposes gut dysbiosis. So far, efforts have been made to mitigate the gastrointestinal symptoms using modern day probiotics. The majority of the probiotics strains used currently belong to the genera Lactobacillus, Clostridium, Bifidobacterium and Streptococcus. Recent advancements in culturomics by implementing newer techniques coupled with the use of gnotobiotic animal models provide a subtle ground to develop novel host specific probiotics therapies. In this review article, the recent advances in the development of microbe-based therapies which can now be implemented to treat a wide spectrum of diseases have been discussed. However, these probiotics are not classified as drugs and there is a lack of stringent law enforcement to protect the end users against the pseudo-probiotic products. While modern probiotics hold strong promise for the future, more rigorous regulations are needed to develop genuine probiotic products and characterize novel probiotics using the latest research and technology. This article also highlights the possibility of reducing antibiotic usage by utilizing probiotics developed using the latest concepts of syn and ecobiotics. [ABSTRACT FROM AUTHOR]

The human intestine harbours a complex and diverse bacterial community called the gut microbiota. This microbiota, stable during the lifetime, is specific of each individual despite the existence of a phylogenetic core shared by the majority of adults. The influence of the gut microbiota on host's physiology has been largely studied using germfree animals and studies using these animal models have revealed that the effects of lipids on host physiology are microbiota-dependent. Studies in mice have also shown that a high-fat diet rapidly and reproducibly alters the gut microbiome. In humans, dietary fat interventions did not lead to strong and consistent modifications of the microbiota composition. Nevertheless, an association between total fat intake and the reduction of the microbiota richness has been repeatedly found. Interestingly, different types of fat exert different or even opposite effects on the microbiota. Concurrently, the gut microbiota is able to convert the lipids entering the colon, including fatty acids or cholesterol, leading to the production of metabolites with potential health effects. [ABSTRACT FROM AUTHOR]

Nitric oxide (NO) is a key signalling molecule in the regulation of cardiometabolic function and impaired bioactivity is considered to play an important role in the onset and progression of cardiovascular and metabolic disease. Research has revealed an alternative NO-generating pathway, independent of NO synthase (NOS), in which the inorganic anions nitrate (NO 3 -) and nitrite (NO 2 -) are serially reduced to form NO. This work specifically aimed at investigating the role of commensal bacteria in bioactivation of dietary nitrate and its protective effects in a model of cardiovascular and metabolic disease. In a two-hit model, germ-free and conventional male mice were fed a western diet and the NOS inhibitor l -NAME in combination with sodium nitrate (NaNO 3) or placebo (NaCl) in the drinking water. Cardiometabolic parameters including blood pressure, glucose tolerance and body composition were measured after six weeks treatment. Mice in both placebo groups showed increased body weight and fat mass, reduced lean mass, impaired glucose tolerance and elevated blood pressure. In conventional mice, nitrate treatment partly prevented the cardiometabolic disturbances induced by a western diet and l -NAME. In contrast, in germ-free mice nitrate had no such beneficial effects. In separate cardiovascular experiments, using conventional and germ-free animals, we assessed NO-like signalling downstream of nitrate by administration of sodium nitrite (NaNO 2) via gavage. In this acute experimental setting, nitrite lowered blood pressure to a similar degree in both groups. Likewise, isolated vessels from germ-free mice robustly dilated in response to the NO donor sodium nitroprusside. In conclusion, our findings demonstrate the obligatory role of host-microbiota in bioactivation of dietary nitrate, thus contributing to its favourable cardiometabolic effects. Image 1 • Dietary nitrate has salutary effects on cardiometabolic function in a mouse model of metabolic syndrome. • These effects are absent in germ free mice. • Host bacteria are essential for bioactivation of dietary nitrate. [ABSTRACT FROM AUTHOR]

The activity of the commensal microbiota significantly impacts human health and has been linked to the development of many diseases, including cancer. Gnotobiotic animal models have shown that the microbiota has many effects on host physiology, including on the development and regulation of immune responses. More recently, evidence has indicated that the microbiota can more specifically influence the outcome of cancer immunotherapy. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes have shown promise in mouse studies. Ongoing endeavors are translating these pre-clinical findings to early stage clinical testing. In this review we summarize 1) basic methodologies and considerations for studies of host-microbiota interactions; 2) experimental evidence towards a causal link between gut microbiota composition and immunotherapeutic efficacy; 3) possible mechanisms governing the microbiota-mediated impact on immunotherapy efficacy. Moving forward, there is need for a deeper understanding of the underlying biological mechanisms that link specific bacterial strains to host immunity. Integrating microbiome effects with other tumor and host factors regulating immunotherapy responsiveness versus resistance could facilitate optimization of therapeutic outcomes. [ABSTRACT FROM AUTHOR]

Gut microbiota has a crucial role in the maintenance of health. Increasing evidence suggests that changes or disturbances in gut microbiota may be associated with various diseases. Therefore, preclinical and clinical studies related to gut microbiota are becoming increasingly important. Germ-free animal experimentation is one of the most important in vivo experimental models for preclinical studies on gut microbiota interactions. It represents a model to study effect of probiotic research and other experimental animal studies requiring careful control of outside contaminants that can affect the trial. Germ-free animals have defected immune systems, so they are used to model immune mediated metabolic, peripheral, and central diseases. In addition, gut–brain axis studies have recently increased. This minireview provides current information on this model and discusses the validity of its use in gut microbiota studies. [ABSTRACT FROM AUTHOR]

The gut microbiota influence host vascular physiology locally in the intestine, but also evoke remote effects that impact distant organ functions. Amongst others, the microbiota affect intestinal vascular remodeling, lymphatic development, cardiac output and vascular function, myelopoiesis, prothrombotic platelet function, and immunovigilance of the host. Experimentally, host-microbiota interactions are investigated by working with animals devoid of symbiotic bacteria, i.e., by the decimation of gut commensals by antibiotic administration, or by taking advantage of germ-free mouse isolator technology. Remarkably, some of the vascular effects that were unraveled following antibiotic treatment were not observed in the germ-free animal models and vice versa. In this review, we will dissect the manifold influences that antibiotics have on the cardiovascular system and their effects on thromboinflammation. [ABSTRACT FROM AUTHOR]

The wide diversity in gut microbiota that is found among individuals is affected by factors including environment, genetics, dietary habits, and lifestyle after birth. The gastrointestinal tract, the largest and most complicated in vivo ecosystem, is a natural habitat for microbe colonization. Gut microbiota acts as "metabolic organ" that interacts with the human host symbiotically and performs an important role in maintaining health. In addition to the above factors, microbiota distributions/proportions are affected by exercise and other forms of physical activity. However, diet, lifestyle, and nutritional supplementation may impede the actual analytic relationship in practice. Therefore, the purpose of this study is to understand the effects of several microbiota on physical fitness, exercise performance, energy metabolism, and biochemistries using the concept of gnotobiote based on a germ-free model. The microbes Eubacterium rectale, Lactobacillus plantarum TWK10 , and Clostridium coccoides were separately inoculated into gnotobiotic animal models. Fecal analysis was regularly done for the entire duration of the experiment. The exercise capacities were measured repeatedly with and without aerobic exercise training using an exhaustive swimming test. Various fatigue-associated biochemical variables, including lactate, ammonia, glucose, lactic dehydrogenase (LDH), and creatine kinase (CK) were also measured to assess physiological adaption. In addition, metabolic phenotype was applied to record basal metabolic rate, diet, behavior, and activities. Body composition, glycogen content, and histopathology were further evaluated to assess the gnotobiotic effects. E. rectale engendered capacities, physiological adaption, and physical activities that were significantly better than other two microbes, possible due to energy regulation and bioavailability. In addition, L. plantarum TWK10 and C. coccoides were found to significantly increase the basal metabolic rate and to alter the body compositions, although no exercise capacity benefit was found in the gnotobiotic models. The E. rectale and L. plantarum gnotobiotic animals all showed normal histological observations with the exception of the C. coccoides gnotobiote, which showed the pathological observation of hepatic necrosis. The gnotobiotic model directly demonstrates the interactions between microbes and hosts, which are especially relevant and applicable to the field of sports science. This study supports the development of beneficial microbiota for application to exercise and fitness, which is an emerging area of health promotion. [ABSTRACT FROM AUTHOR]