The interplay between Blastocystis and human gut microbiota.

Manipulation of the Microbiota for Treatment of IBS and IBD—Challenges and Controversies

The Gut Microbiome in Health and Disease

The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders

Risk of Probiotics: Functional Gastrointestinal Symptoms in Patients With Inflammatory Bowel Disease

Covering the Cover

Probiotics in Perspective

As an important part of ecosystem, microbes are widely distributed in various habitats. In recent years, more and more attention has been paid to the study on gut microbiota. The gut microbiota and their metabolites influence human and animal nutrition processing, metabolic balance, immune function, gastrointestinal development and other physiological activities. With the deepening of studies on human and animal gut microbiota, it has been found that some factors, such as diet, age, gender, and living environment, impacting on the composition of gut microbiota, while the differences among animal species have more significant influence on the gut microbiota composition. In relatively primitive grassland ecosystems, soil microbes interact with human and animal activities. On the one hand, microbes in the soil environment are the driving forces for the transformation and circulation of organic matter and nutrients. The improvement of soil microbial community diversity is beneficial for the soil fertility. On the other hand, human and animal activities will affect the diversity of soil microbial community. Although there are a lot of researches on soil microbiota, animal and human gut microbiota, their differences in diversity and composition within the same environment have not been studied. The advent of sequencing technology provides an effective mean for the accurate and comprehensive understanding of microbes, especially for the study of uncultivable microorganisms. The PacBio single-molecule real-time (SMRT) technology is advantageous in producing long sequence reads with high accuracy. Based on sequencing the full length 16S rRNA genes, the microbiota composition can be identified to the species level. Therefore, it is an effective approach for studying microbial diversity. We collected 56 stool and soil samples from Xilinguole, including 6, 10, 11, 9, and 10 stool samples from human, goat, cattle, horse, and sheep, respectively, as well as 10 soil samples. Genomic DNA was extracted from the samples. After DNA extraction and quality check, the 16S rRNA genes of all samples were amplified from the genomic DNA. The PCR products were sequenced using the PacBio RS II instrument. The QIIME software (V1.7) was used to analyze the sequencing data, and the R software (version 3.5.0) was used to further analyze and visualize the results. Firstly, it was found that the gut microbiota diversity of human was significantly lower than other samples ( P 0.01). The overall composition of the human and animal gut microbiota were dominated by the Firmicutes and Bacteroidetes phyla. However, the soil microbiota was dominated by Proteobacteria and Acidobacteria. At the genus level, the sheep, goat and cattle gut microbiota were dominated by Clostridium , Bacteroides , and Oscillibacter , while the horse gut microbiota was mainly composed of Clostridium , Eubacterium , and Treponema . The soil microbiota was composed mainly of Blastocatella and Bacillus . The human gut microbiota comprised much of Veillonella , Clostridium , Escherichia/Shigella . At the species level, the human gut microbiota mainly contained Escherichia/Shigella , dysenteriae , Streptococcus salivarius . The sheep, goat, cattle, and horse gut microbiota were dominated by Oscillibacter valericigenes and Eubacterium coprostanoligenes . The major species in soil were Blastocatella fastidiosa and Bacillus longiquaesitum . Moreover, principal coordinate analysis (PCoA) and hierarchical clustering analysis showed some differences in the microbiota structure among human gut, animal gut and soil samples. The gut microbiota structure was similar among cattle, goats and sheep. They were more different from the samples collected from human, horse and soil. We classified all samples into four clusters. Cluster 1 only included human samples; cluster 2 comprised the horse samples; cluster 3 was consisted of the sheep, goat, and cattle samples; while cluster 4 contained only the soil samples. Lastly, we identified the discriminatory OTUs and assigned them taxonomically to the species level. In conclusion, there were significant differences between animal gut microbiota and soil microbiota. The soil microbiota was more complex. As an omnivore, human gut microbiota diversity was significantly lower than other herbivorous animal (namely cattle, goat, horse and sheep). Although cattle, sheep, goat and horses are all herbivorous animals, the distinct features of the digestive systems could contribute to the difference in gut microbiota composition of horse from those of sheep, goat and cattle. This study revealed the differences of gut microbiota diversity between human and other animals, as well as from the soil microbial community. This work has laid a theoretical foundation for further studies on microbial diversity in different habitats.

The human gastrointestinal (GI) microbiota is a rich and dynamic community inhabited by approximately 1014 bacteria, most of which have not yet been cultivated in the laboratory (Zoetendal et al, 2006). The GI microbiota has been suggested as one of the etiological factors in irritable bowel syndrome (IBS), with a putative role in the development and maintenance of IBS symptoms (for a review, see Bolino & Bercik, 2010). The worldwide prevalence of IBS is 10-20% among adults and adolescents, depending on the diagnostic criteria applied (Longstreth et al, 2006). Abdominal pain or discomfort, irregular bowel movements and constipation or diarrhoea are common symptoms of IBS. Symptoms outside the GI tract, such as fatigue, anxiety and depression, are also often encountered. At its worst, IBS can cause significant effects on patients’ well-being, but it is not known to predispose to any severe illnesses. Patients can be grouped into three subtypes according to bowel habits: diarrhoea-predominant (IBS-D), constipation-predominant (IBS-C) or mixed-subtype (IBSM). However, the symptom subtype of each patient may vary over time (Longstreth et al, 2006). Compared to non-IBS controls, subjects with IBS have been associated with a greater temporal instability of the GI microbiota and quantitative changes have been detected within several distinct bacterial groups or species-like phylotypes, which are defined based solely on sequence data (see Table 1 for references). In analyses covering the overall microbial community, IBS subjects have shown a tendency to cluster apart from the healthy control subjects (Ponnusamy et al, 2011; Rajilic-Stojanovic, 2007). Moreover, the IBS symptom-subgroups IBS have been proposed to differ from each other according to the GI microbiota of subjects within these groups (Lyra et al, 2009; Malinen et al, 2005; RajilicStojanovic, 2007). The most distinctive symptom sub-type is IBS-D, which could also be a result of the impact of the diarrhoea on the microbial environment in the gut. In addition, comparatively low quantities of bifidobacteria, which are generally considered beneficial to health, have been detected in several IBS studies (Balsari et al, 1982; Enck et al, 2009; Kerckhoffs et al, 2009; Krogius-Kurikka et al, 2009; Si et al, 2004). This finding, though still preliminary, encourages development of probiotic and prebiotic therapies for IBS. On the other hand, elevated numbers of Proteobacteria and Firmicutes, including Ruminococcus – like phylotypes, Lactobacillus sp. and Veillonella sp., have been reported. Quantitative and qualitative microbial alterations in the GI tract of IBS subjects may have a functional role in the syndrome aetiology or merely reflect the status of the gut, but still have diagnostic or prognostic value in clinical practise and research (Kassinen, 2009;

Human gut microbiota is the complex community of microorganisms that live in the digestive tracts, including bacteria, archaea, virus, fungi and protists. These microorganisms coevolved together with human body for a long history, forming a balanced micro-ecosystem. Recent researches discovered the close association between gut microbiota and human health. The gut microbiota was thought to be the biggest endocrine organ, which keeps and restores human health by regulating the its composition and structure. Dysregulation in the composition and diversity of microbiota (dysbiosis) is closely associated with diverse metabolism and immune disorders, such as diabetes, allergy, autoimmunity, and gastrointestinal inflammatory disorders. Thus, a balanced network between gut microbiota and human body will be of great help for diagnosis, treatment and prognosis in the field of precision medicine. Gut microbiota also interacts with diet to degrade nutrients and provide additional nutrients. Meanwhile, faecal bacteria can exert a fundamental role in modulating energy metabolism. Studies have shown that in obesity individuals, the gut microbiota composition can be significantly different from that of lean individuals, and that modifications of gut microbiota composition can be associated with increases or reductions of body weight and body mass index. On the other hand, gut bacterial was related with nutrients absorption. Such as, decreased abundance of Lactobacillus maybe relate with iron (Fe) deficiency, which indicated the intimate connection between gut microbiota and nutrients. Development of nutriology has contributed greatly to human health. A well-balanced diet is the basis for a healthy life. Both the western diet and special diets can have a relevant impact on the microbiome and promote the development of various diseases. An increasing in food-related disorders in recent years, largely associated with dramatic changes in food consumption trends and main nutrients. Nutrition has a very special influence on the microbiome as it is an important factor throughout age. Gut bacteria are specialized in the fermentation of various substrates, thus, complex diets can lead to a number of metabolic products, especially vitamins and SCFAs, which are important to human health. Dietary-associated changes in compositional and functional microbiota traits should be correlated with the health status for the future development of dietary recommendations and potential clinical interventions. We have realized the close relationship between human body, gut microbiota, nutrients and immunity, which will bring an unprecedented opportunity for developing precision nutrition. This review will focus on the gut microbiota, nutrition and health. Due to rapid advances in this inter-discipline, we here only choose several facets to discuss.

Gastrointestinal disorders, although clinically heterogeneous, share pathogenic mechanisms, including genetic susceptibility, impaired gut barrier function, altered microbiota, and environmental triggers (infections, social and behavioral factors, epigenetic control, and diet). Gut microbiota has been studied for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) in either children or adults, while modifiable gut microbiota features, acting as risk and premorbid factors along the childhood-adulthood transition, have not been thoroughly investigated so far. Indeed, the relationship between variations of the entire host/microbiota/environmental scenario and clinical phenotypes is still not fully understood. In this respect, tracking gut dysbiosis grading may help deciphering host phenotype-genotype associations and microbiota shifts in an integrated top-down omics-based approach within large-scale pediatric and adult case-control cohorts. Large-scale gut microbiota signatures and host inflammation patterns may be integrated with dietary habits, under genetic and epigenetic constraints, providing gut dysbiosis profiles acting as risk predictors of IBD or IBS in preclinical cases. Tracking dysbiosis supports new personalized/stratified IBD and IBS prevention programmes, generating Decision Support System tools. They include (1) high risk or flare-up recurrence -omics-based dysbiosis profiles; (2) microbial and molecular biomarkers of health and disease; (3) -omics-based pipelines for laboratory medicine diagnostics; (4) health apps for self-management of score-based dietary profiles, which can be shared with clinicians for nutritional habit and lifestyle amendment; (5) -omics profiling data warehousing and public repositories for IBD and IBS profile consultation. Dysbiosis-related indexes can represent novel laboratory and clinical medicine tools preventing or postponing the disease, finally interfering with its natural history.

The Tuning of the Gut Nervous System by Commensal Microbiota

Probiotics in irritable bowel syndrome: Has the time arrived?

Inflammatory Bowel Disease: An Update on the Fundamental Biology and Clinical Management

The human gut microbiota has been widely studied due to the possibility of high-throughput sequencing. Humans are distinctly inhabited by normal flora and symbiotic microbial flora, with bacteria accounting for the vast bulk of the component microorganisms. These organisms can be found in a variety of locations throughout the body, including the oral cavity, vagina, skin and stomach. Microbe types and abundance vary in different organs of the same person, but they may also differ between persons. They are very important for human health and also affect the immune system by altering its metabolism and behavior. Conditions such as malnutrition, Crohn’s disease, inflammatory bowel disease and colon colitis, in addition to metabolic disorders including type II diabetes and obesity, have all been associated with the gut microbiota. Several studies in recent years have emphasized the relevance and involvement of commensal bacteria in the development of a variety of disorders, including autoimmune diseases. Autoimmune diseases, Such as Graves’ disease, systemic erythematosus lupus (SLE), and irritable bowel syndrome (IBS), are commonly known for their loss of self-tolerance, a hyperactive reaction against the body’s own tissue. Autoimmune diseases are triggered by the immune system targeting self-tissues, and their global frequency is estimated to be between 3 and 5%. This review reaffirms the links between autoimmune disorders and gut bacteria. The precise pathophysiology is unknown; however, environmental factors (such as lifestyle, diet, medications, and infections) and specific genetic conditions have been expected. The gut microbiota is important in autoimmunity because changes in microbial composition can trigger immunological tolerance loss.

Bugs, Stool, and the Irritable Bowel Syndrome: Too Much Is as Bad as Too Little?