The human gut microbiome and its dysfunctions

Probiotic-fermented traditional Chinese herbal medicine, a promising approach to maintaining the intestinal microecology

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional Chinese herbal medicines (TCHM) have been extensively used in China and other East and Southeast Asian countries. Due to the low content of bioactive components in most TCHM and the potential toxicity of some herbal ingredients to humans, researchers have turned to probiotic fermentation to enhance the efficacy, mitigate the toxic or side effects and improve the taste of TCHM. Both probiotics and certain TCHM benefit the intestinal microbiota and intestinal barrier of human body, demonstrating synergistic effects on in intestinal microecology.

AIM OF THE STUDY

This review aims to provide an overview of the development of fermentation technology, commonly used probiotic strains for TCHM fermentation, the advantages of probiotic fermentation and the challenges and limitations of probiotic-fermented TCHM. Additionally, it summarises and discusses the impact of probiotic-fermented TCHM on the intestinal barrier and microbiota, as well as the possible mechanisms involved.

MATERIALS AND METHODS

An extensive search of primary literature was conducted using various databases including PubMed, Google Scholar, Web of Science, Elsevier, SpringerLink, ScienceDirect, CNKI, and others. All the plant names have been checked with World Flora Online (http://www.worldfloraonline.org) on August 7, 2024.

RESULTS

The literature mentioned above was analyzed and summarized comprehensively. Probiotic-fermented TCHM can improve the intestinal barrier, modulate gut microbiota, and maintain homeostasis of the intestinal microecology. Modulating intestinal microecology by probiotic-fermented TCHM may be a crucial mechanism for its beneficial effects.

CONCLUSIONS

This article establishes a theoretical basis for further research on the relationship between probiotic-fermented TCHM and the intestinal microecology, with the hope of inspiring innovative concepts for the development of TCHM and exploring the potential of probiotic-fermented TCHM as a promising strategy for maintaining intestinal microecological balance.

Anti-obesogenic effect of lupin-derived protein hydrolysate through modulation of adiposopathy, insulin resistance and gut dysbiosis in a diet-induced obese mouse

The prevalence of obesity is increasingly widespread, resembling a global epidemic. Lifestyle changes, such as consumption of high-energy-dense diets and physical inactivity, are major contributors to obesity. Common features of this metabolic pathology involve an imbalance in lipid and glucose homeostasis including dyslipidemia, insulin resistance and adipose tissue dysfunction. Moreover, the importance of the gut microbiota in the development and susceptibility to obesity has recently been highlighted. In recent years, new strategies based on the use of functional foods, in particular bioactive peptides, have been proposed to counteract obesity outcomes. In this context, the present study examines the effects of a lupin protein hydrolysate (LPH) on obesity, dyslipidemia and gut dysbiosis in mice fed a high-fat diet (HFD). After 12 weeks of LPH treatment, mice gained less weight and showed decreased adipose dysfunction compared to the HFD-fed group. HFD-induced dyslipidemia (increased triglycerides, cholesterol and LDL concentration) and insulin resistance were both counteracted by LPH consumption. Discriminant analysis differentially distributed LPH-treated mice compared to non-treated mice. HFD reduced gut ecological parameters, promoted the blooming of deleterious taxa and reduced the abundance of commensal members. Some of these changes were corrected in the LPH group. Finally, correlation analysis suggested that changes in this microbial population could be responsible for the improvement in obesity outcomes. In conclusion, this is the first study to show the effect of LPH on improving weight gain, adiposopathy and gut dysbiosis in the context of diet-induced obesity, pointing to the therapeutic potential of bioactive peptides in metabolic diseases.

Association between gut microbiota and male infertility: a two-sample Mendelian randomization study

Previous research has confirmed the significant association between gut microbiota (GM) and male infertility (MI), but the causality between them remains unclear. This study aims to investigate the causal relationship between GM and MI using Mendelian randomization (MR) and provide supplementary information for the optimization of future randomized controlled trials (RCTs). Instrumental variables for 211 GM taxa were obtained from genome-wide association studies (GWAS), and inverse variance weighted (IVW) method was used as the main analysis method for two-sample MR analysis to assess the impact of GM on the risk of MI. Four methods were used to test for horizontal pleiotropy and heterogeneity of MR results to ensure the reliability of the MR findings. A total of 50 single-nucleotide polymorphisms (SNPs) closely related to GM were included, and ultimately identified 1 family and 4 general are causally associated with MI. Among them, Anaerotruncus (OR = 1.96, 95% CI 1.31-3.40, P = 0.016) is significantly associated with increased MI risk. Furthermore, we used four MR methods to evaluate the causality, and the results supported these findings. The leave-one-out analysis showed stable results with no instrumental variables exerting strong influence on the results. The causal direction indicated a positive effect, and the effects of heterogeneity and horizontal pleiotropy on the estimation of causal effect were minimized. We confirmed a causal relationship between GM taxa and MI, providing new insights into the mechanisms underlying GM-mediated MI.

The Human Gut Microbiota: A Dynamic Biologic Factory

The human body constitutes a living environment for trillions of microorganisms, which establish the microbiome and, the largest population among them, reside within the gastrointestinal tract, establishing the gut microbiota. The term "gut microbiota" refers to a set of many microorganisms [mainly bacteria], which live symbiotically within the human host. The term "microbiome" means the collective genomic content of these microorganisms. The number of bacterial cells within the gut microbiota exceeds the host's cells; collectively and their genes quantitatively surpass the host's genes. Immense scientific research into the nature and function of the gut microbiota is unraveling its roles in certain human health activities such as metabolic, physiology, and immune activities and also in pathologic states and diseases. Interestingly, the microbiota, a dynamic ecosystem, inhabits a particular environment such as the human mouth or gut. Human microbiota can evolve and even adapt to the host's unique features such as eating habits, genetic makeup, underlying diseases, and even personalized habits. In the past decade, biologists and bioinformaticians have concentrated their research effort on the potential roles of the gut microbiome in the development of human diseases, particularly immune-mediated diseases and colorectal cancer, and have initiated the assessment of the impact of the gut microbiome on the host genome. In the present chapter, we focus on the biological features of gut microbiota, its physiology as a biological factory, and its impacts on the host's health and disease status.

A polysaccharide from salviae miltiorrhizae radix inhibits weight gain of mice with high-fat diet via modulating intestinal bacteria

BACKGROUND

Obesity, a global chronic disease, has been recognized as a severe risk to health. In our study, a novel polysaccharide named ARS was isolated and purified from aerial part of salviae miltiorrhizae radix. Our aim is to investigate the weight-reducing effect of a polysaccharide from salviae miltiorrhizae radix on mice fed a high-fat diet.

RESULTS

The novel polysaccharide ARS mainly consisted of glucose and galactose with a molar ratio of 0.59:1.00. We found that treatment with ARS could inhibit weight gain of mice fed a high-fat diet via modulating the intestinal bacteria. Moreover, we surveyed its mechanism in mice, and the gut microbiota sequencing results demonstrated that ARS can reverse or resist high-fat-diet-induced significant weight gain or obesity by increasing the diversity of gut microbiota and optimizing the ratio of Firmicutes to Bacteroidetes. Phylum and species analysis of gut microbiota demonstrated that obesity caused by a high-fat diet was accompanied by significant changes in the microbial communities, but ARS could reverse the disturbance of gut microbiota induced by the high-fat diet to maintain homeostasis.

CONCLUSION

Overall, our findings suggested a new function of ARS in regulating gut microbiota, which provides a theoretical basis for the development of high-quality ARS functional foods and the application of dietary supplements. © 2023 Society of Chemical Industry.

Effect of Preoperative Oral Antibiotics and Mechanical Bowel Preparations on the Intestinal Flora of Patients Undergoing Laparoscopic Colorectal Cancer Surgery: A Single-Center Prospective Pilot Study

INTRODUCTION

 In the last few decades, considerable progress has been made in controlling surgical site infections (SSIs) using a combination of mechanical and oral antibiotic bowel preparation. However, the number of bacteria present after bowel preparation has not been clarified. In this study, we investigated the bacterial cultures of intestinal fluid samples from patients undergoing laparoscopic surgery for colorectal cancer after preoperative bowel preparation.

METHODS

This prospective observational study was designed as a pilot study at a single center. We enrolled 25 consecutive patients who underwent laparoscopic surgery for colorectal cancer between March 2021 and February 2022 at our institution.

RESULTS

The rate of bacterial culture positivity was 56.0%. The most abundant bacterium was Escherichia coli (44.0%). The positivity rates for E. coli on the right and left sides were 54.5% and 35.7%, respectively (P = 0.60). Moreover, there was a significant relationship between a low American Society of Anesthesiologists Physical Status score and E. coli positivity on the right side (P = 0.031). In the left-sided group, female sex and large tumor size were significantly associated with E. coli positivity (P = 0.036 and 0.049, respectively). Superficial SSI occurred in the patient in the left-sided group, but E. coli was negative.

CONCLUSION

This study emphasizes the importance of understanding intestinal fluid contamination and its relationship to infection risk. Future prospective multicenter studies should be conducted to determine the association between intestinal bacteria and different types of preoperative preparation.

Gut microbiota dependant trimethylamine N-oxide and hypertension

The human gut microbiota environment is constantly changing and some specific changes influence the host's metabolic, immune, and neuroendocrine functions. Emerging evidence of the gut microbiota's role in the development of cardiovascular disease (CVD) including hypertension is remarkable. There is evidence showing that alterations in the gut microbiota and especially the gut-dependant metabolite trimethylamine N-oxide is associated with hypertension. However, there is a scarcity of literature addressing the role of trimethylamine N-oxide in hypertension pathogenesis. In this review, we discuss the impact of the gut microbiota and gut microbiota dependant trimethylamine N-oxide in the pathogenesis of hypertension. We present evidence from both human and animal studies and further discuss new insights relating to potential therapies for managing hypertension by altering the gut microbiota.

Boundaries That Prevent or May Lead Animals to be Reservoirs of Escherichia coli O104:H4

Escherichia coli O104:H4, a hybrid serotype carrying virulence factors from enteroaggregative (EAEC) and Shiga toxin-producing (STEC) pathotypes, is the reported cause of a multicountry outbreak in 2011. Evaluation of potential routes of human contamination revealed that this strain is a foodborne pathogen. In contrast to STEC strains, whose main reservoir is cattle, serotype O104:H4 has not been commonly isolated from animals or related environments, suggesting an inability to naturally colonize the gut in hosts other than humans. However, contrary to this view, this strain has been shown to colonize the intestines of experimental animals in infectious studies. In this minireview, we provide a systematic summary of reports highlighting potential evolutionary changes that could facilitate the colonization of new reservoirs by these bacteria.

Faecal microbiota transplantation in patients with haematological malignancies undergoing cellular therapies: from translational research to routine clinical practice

The effect of the gut microbiota on patients' outcomes after allogeneic haematopoietic cell transplantation (HCT) is now well established. In particular, gut microbiota dysbiosis has been associated with acute graft-versus-host disease (GVHD). Furthermore, increasing data also suggest an effect of the gut microbiota on outcome after autologous HCT and CAR T cells. In fact, the bacterial gut microbiota interplays with the immune system and contributes to immunological complication and antitumour response to treatment. Therefore, faecal microbiota transplantation has been evaluated in patients with haematological malignancies for various indications, including Clostridioides difficile infection, eradication of multidrug-resistant bacteria, and steroid refractory acute GVHD. In addition, use of prophylactic faecal microbiota transplantation to restore the gut microbiota and improve patients' outcomes is being developed in the setting of allogeneic HCT, but also probably very soon in patients receiving autologous HCT or CAR T cells.

Helicobacter bilis Contributes to the Occurrence of Inflammatory Bowel Disease by Inducing Host Immune Disorders

Gut microbiota coevolve with humans to achieve a symbiotic relationship, which ultimately leads to physiological homeostasis. A variety of diseases can occur once this balance is disrupted. Helicobacter bilis (H. bilis) is an opportunistic pathogen in humans, triggering multiple diseases, including inflammatory bowel disease (IBD). IBD is a chronic immunologically mediated inflammation of the human gastrointestinal tract, and its occurrence is closely related to the gut microbiota. Several studies have demonstrated that H. bilis colonization is associated with IBD, and its mechanism is related to host immunity. However, few studies have investigated these mechanisms of action. Therefore, this article is aimed at reviewing these studies and summarizing the mechanisms of H. bilis-induced IBD from two perspectives: adaptive immunity and innate immunity. Furthermore, this study provides a preliminary discussion on treating H. bilis-related IBD. In addition, we also demonstrated that H. bilis played an important role in promoting the carcinogenesis of IBD and discussed its mechanism.

Peony seed oil decreases plasma cholesterol and favorably modulates gut microbiota in hypercholesterolemic hamsters

PURPOSE

Peony (Paeonia spp.) seed oil (PSO) contains a high amount of α-linolenic acid. The effects of PSO on hypercholesterolemia and gut microbiota remains unclear. The present study was to investigate effects of PSO supplementation on cholesterol metabolism and modulation of the gut microbiota.

METHODS

Male Golden Syrian hamsters (n = 40) were randomly divided into five groups (n = 8, each) fed one of the following diets namely low-cholesterol diet (LCD); high cholesterol diet (HCD); HCD with PSO substituting 50% lard (LPSO), PSO substituting 100% lard (HPSO) and HCD with addition of 0.5% cholestyramine (PCD), respectively, for 6 weeks.

RESULTS

PSO supplementation dose-dependently reduced plasma total cholesterol (TC) by 9-14%, non-high-density lipoprotein cholesterol (non-HDL-C) by 7-18% and triacylglycerols (TG) by 14-34% (p < 0.05). In addition, feeding PSO diets reduced the formation of plaque lesions by 49-61% and hepatic lipids by 9-19% compared with feeding HCD diet (p < 0.01). PSO also altered relative genus abundance of unclassified_f__Coriobacteriaceae, unclassified_f__Erysipelotrichaceae, Peptococcus, unclassified_f__Ruminococcaceae, norank_o__Mollicutes_RF9 and Christensenellaceae_R-7_group.

CONCLUSIONS

It was concluded that PSO was effective in reducing plasma cholesterol and hepatic lipids and favorably modulating gut microbiota associated with cholesterol metabolism.

Probiotics and Phytochemicals: Role on Gut Microbiota and Efficacy on Irritable Bowel Syndrome, Functional Dyspepsia, and Functional Constipation

Functional gastrointestinal disorders (FGIDs), such as irritable bowel syndrome, functional constipation, and functional dyspepsia, have had a high prevalence over the past few years. Recent evidence suggests that functional foods and bioactive compounds, such as probiotics and phytochemicals, may have a positive effect in treating the symptoms of the above diseases. In this systematic review study, 32 published studies were selected with the use of comprehensive scientific databases, according to PRISMA guidelines, with emphasis on recent interventional studies that reflect the effect of probiotics and selected phytochemicals on the improvement of FGID symptoms. The bioactive compounds in the selected studies were administered to patients either in capsule form or in enriched food products (yogurt, juice, etc.). According to the results, there is a correlation between the consumption of probiotics and phytochemicals, such as polyphenols, and the relief of symptoms in selected gastrointestinal disorders. Enriching foods that are regularly consumed by the population, such as fruit juices, yogurt, and cheese, with ingredients that may have a positive effect on gastrointestinal disorders, could be a possible novel goal for the management of these diseases. However, further evidence is required for the role of probiotics and phytochemicals in FGIDs to be fully understood.

The Association between the Oral-Gut Axis and the Outcomes of Severe COVID-19 Patients Receiving Extracorporeal Membrane Oxygenation: A Case-Control Study

The novel conceptual disease model, the oral–gut axis, which represents the immunomodulatory mutual relationship between oral and gut microbial compartments, has been attracting attention in relation to systemic health issues. We investigated whether this unique crosstalk influences the systemic condition of patients with COVID-19 infections who received extracorporeal membrane oxygenation (ECMO) in the intensive care unit (ICU) during April and December 2020. In this case-control study, patients were divided into two groups according to their survival (total entry size, n = 21; survivors, n = 13; non-survivors, n = 8). Patients were evaluated using the oral assessment guide from Fukuoka University (OAG-F) and the Bristol Stool Form Scale (BSFS) to examine the oral and fecal conditions. A blood-based inflammatory factor, the neutrophil-to-lymphocyte ratio (NLR), was used as an indicator of systemic immunity. The high total OAG-F scores were associated with both elevated BSFS and NLR values, and a mutually positive correlation between BSFS and NLR was observed. This indicated an interplay between oral deterioration, gut dysbiosis, and the impairment of immunity. Furthermore, oral deterioration was more frequently observed in non-survivors on day 14 of ICU admission. In addition, on days 7 and 21 of ICU admission, impaired immunity, reflected by an elevated NLR, was observed in non-survivors. However, the distribution of the gut microbiome—reflected by increased BSFS values—with the time it was examined was not directly observed in non-survivors. Taken together, these findings suggested that oral–gut health may be specifically associated with mortality in COVID-19 patients receiving ECMO in the ICU.

Microorganisms in chemotherapy for pancreatic cancer: An overview of current research and future directions

Pancreatic cancer is a malignant tumor of the digestive system with a very high mortality rate. While gemcitabine-based chemotherapy is the predominant treatment for terminal pancreatic cancer, its therapeutic effect is not satisfactory. Recently, many studies have found that microorganisms not only play a consequential role in the occurrence and progression of pancreatic cancer but also modulate the effect of chemotherapy to some extent. Moreover, microorganisms may become an important biomarker for predicting pancreatic carcinogenesis and detecting the prognosis of pancreatic cancer. However, the existing experimental literature is not sufficient or convincing. Therefore, further exploration and experiments are imperative to understanding the mechanism underlying the interaction between microorganisms and pancreatic cancer. In this review, we primarily summarize and discuss the influences of oncolytic viruses and bacteria on pancreatic cancer chemotherapy because these are the two types of microorganisms that are most often studied. We focus on some potential methods specific to these two types of microorganisms that can be used to improve the efficacy of chemotherapy in pancreatic cancer therapy.

The small intestine: barrier, permeability and microbiota

In recent years, there has been growing interest in the comprehension of the physiology of intestinal permeability and microbiota; and how these elements could influence the pathogenesis of diseases. The term intestinal permeability describes all the processes that allow the passage of molecules as water, electrolytes and nutrients through the intestinal barrier by the paracellular or the transcellular transport systems with several implications for self-tolerance and not-self immunity. An increased permeability might induce a more significant interaction of the immune system with unknown external antigens. This might favor the onset of several immune-related extra-intestinal diseases including coeliac disease, diabetes mellitus type 1, bronchial asthma and inflammatory bowel diseases. Furthermore, the intestinal permeability interacts every day with microbiota, the complex system of mutualistic inhabitants and commensal microorganisms living in the healthy gut. Microbiota is implicated in physiological functions by actively participating in digestion, absorption, synthesis of vitamins and protection from external aggressions. The critical site where these processes occur is the small intestine to which this updated review is dedicated. Understanding its anatomy, its barrier structure and permeability modulation and its microbiota composition is the essential skill to comprehend the complex pathogenesis of several - not only gastroenterological - diseases.

Antibiotics, cancer risk and oncologic treatment efficacy: a practical review of the literature

Antibiotics have been extensively used to treat infectious diseases over the past century and have largely contributed to increased life expectancy over time. However, antibiotic use can impose profound and protracted changes to the diversity of the microbial ecosystem, affecting the composition of up to 30% of the bacterial species in the gut microbiome. By modifying human microbiota composition, antibiotics alter the action of several oncologic drugs, potentially leading to decreased efficacy and increased toxicities. Whether antibiotics interfere with cancer therapies or even increase the risk of cancer development has been under investigation, and no randomised trials have been conducted so far. The aim of the current review is to describe the possible effects of antibiotic therapies on different oncologic treatments, especially immunotherapies, and to explore the link between previous antibiotics use and the development of cancer.

Lactobacilli Supplemented with Larch Arabinogalactan and Colostrum Stimulates an Immune Response towards Peripheral NK Activation and Gut Tolerance

Probiotics possibly affect local and systemic immune reactions and maintain the intestinal immune homeostasis in healthy individuals and patients with diseases such as irritable bowel syndrome (IBS). In this single-center, blinded trial, we enrolled 40 individuals (20 patients with IBS and 20 healthy individuals) whose blood and fecal samples were collected before and after a 21-day administration of a product comprising Lactobacillus spp., larch arabinogalactan, and colostrum. The percentage of HLA-DR+ natural killer (NK) cells was higher in healthy individuals (p = 0.03) than in patients with IBS after product supplementation. In the fecal samples of patients with IBS, we observed a decline in IL-6, IFN-γ, TNF-α, and secretory IgA levels and, simultaneously, an increase in IL-10 and IL-17A levels after supplementation, although non-significant, whereas, in healthy individuals, we observed a significant decline in IL-6 and IFN-γ levels after supplementation (p < 0.001). Nevertheless, we observed a clinical improvement of symptoms in 65–75% of patients with IBS and the complete resolution of the initial symptoms in five of the 20 patients. We also observed a possible prophylactic effect by the inducing system antiviral impact accompanied by a trend for local immune tolerance in the gut in healthy individuals, where it is the desirable state.

Connection between gut microbiome and the development of obesity

The potential role of the gut microbiota in various human diseases has attracted considerable attention worldwide. Here, we discuss the vital role of the intestinal microbiota in the development of obesity. First, we describe how the gut microbiota promotes fat accumulation. Additionally, a high-fat diet leads to structural instability among in the gut microbiota, further leading to an increase in endotoxins, which aggravates obesity. We then discuss how gut microbiota metabolites, including short-chain fatty acids and lipopolysaccharides, affect the host. Finally, we review several strategies for regulating the intestinal flora.

The Interplay between Immunity and Microbiota at Intestinal Immunological Niche: The Case of Cancer

The gut microbiota is central to the pathogenesis of several inflammatory and autoimmune diseases. While multiple mechanisms are involved, the immune system clearly plays a special role. Indeed, the breakdown of the physiological balance in gut microbial composition leads to dysbiosis, which is then able to enhance inflammation and to influence gene expression. At the same time, there is an intense cross-talk between the microbiota and the immunological niche in the intestinal mucosa. These interactions may pave the way to the development, growth and spreading of cancer, especially in the gastro-intestinal system. Here, we review the changes in microbiota composition, how they relate to the immunological imbalance, influencing the onset of different types of cancer and the impact of these mechanisms on the efficacy of traditional and upcoming cancer treatments.

No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases

Since the successful conquest of many acute, communicable (infectious) diseases through the use of vaccines and antibiotics, the currently most prevalent diseases are chronic and progressive in nature, and are all accompanied by inflammation. These diseases include neurodegenerative (e.g. Alzheimer's, Parkinson's), vascular (e.g. atherosclerosis, pre-eclampsia, type 2 diabetes) and autoimmune (e.g. rheumatoid arthritis and multiple sclerosis) diseases that may appear to have little in common. In fact they all share significant features, in particular chronic inflammation and its attendant inflammatory cytokines. Such effects do not happen without underlying and initially 'external' causes, and it is of interest to seek these causes. Taking a systems approach, we argue that these causes include (i) stress-induced iron dysregulation, and (ii) its ability to awaken dormant, non-replicating microbes with which the host has become infected. Other external causes may be dietary. Such microbes are capable of shedding small, but functionally significant amounts of highly inflammagenic molecules such as lipopolysaccharide and lipoteichoic acid. Sequelae include significant coagulopathies, not least the recently discovered amyloidogenic clotting of blood, leading to cell death and the release of further inflammagens. The extensive evidence discussed here implies, as was found with ulcers, that almost all chronic, infectious diseases do in fact harbour a microbial component. What differs is simply the microbes and the anatomical location from and at which they exert damage. This analysis offers novel avenues for diagnosis and treatment.

The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy

The mammalian gut is colonized by a large variety of microbes, collectively termed ‘the microbiome’. The gut microbiome undergoes rapid changes during the first few years of life and is highly variable in adulthood depending on various factors. With the gut being the largest organ of immune responses, the composition of the microbiome of the gut has been found to be correlated with qualitative and quantitative differences of mucosal and systemic immune responses. Animal models have been very useful to unravel the relationship between gut microbiome and immune responses and for the understanding of variations of immune responses to vaccination in different childhood populations. However, the molecular mechanisms underlying optimal immune responses to infection or vaccination are not fully understood. The gut virome and gut bacteria can interact, with bacteria facilitating viral infectivity by different mechanisms. Some gut bacteria, which have a beneficial effect on increasing immune responses or by overgrowing intestinal pathogens, are considered to act as probiotics and can be used for therapeutic purposes (as in the case of fecal microbiome transplantation).

Actinobacteria: A relevant minority for the maintenance of gut homeostasis

Actinobacteria are one the four major phyla of the gut microbiota and, although they represent only a small percentage, are pivotal in the maintenance of gut homeostasis. During the last decade many studies focused the attention on Actinobacteria, especially on their role both in gastrointestinal and systemic diseases and on their possible therapeutic use. In fact, classes of this phylum, especially Bifidobacteria, are widely used as probiotic demonstrating beneficial effects in many pathological conditions, even if larger in vivo studies are needed to confirm such encouraging results. This review aims to explore the current knowledge on their physiological functions and to speculate on their possible therapeutic role(s) in gastrointestinal and systemic diseases.

Drosophila Perpetuates Nutritional Mutualism by Promoting the Fitness of Its Intestinal Symbiont Lactobacillus plantarum

Facultative animal-bacteria symbioses, which are critical determinants of animal fitness, are largely assumed to be mutualistic. However, whether commensal bacteria benefit from the association has not been rigorously assessed. Using a simple and tractable gnotobiotic model- Drosophila mono-associated with one of its dominant commensals, Lactobacillus plantarum-we reveal that in addition to benefiting animal growth, this facultative symbiosis has a positive impact on commensal bacteria fitness. We find that bacteria encounter a strong cost during gut transit, yet larvae-derived maintenance factors override this cost and increase bacterial population fitness, thus perpetuating symbiosis. In addition, we demonstrate that the maintenance of the association is required for achieving maximum animal growth benefits upon chronic undernutrition. Taken together, our study establishes a prototypical case of facultative nutritional mutualism, whereby a farming mechanism perpetuates animal-bacteria symbiosis, which bolsters fitness gains for both partners upon poor nutritional conditions.

Steroids, stress and the gut microbiome-brain axis

It is becoming well established that the gut microbiome has a profound impact on human health and disease. In this review, we explore how steroids can influence the gut microbiota and, in turn, how the gut microbiota can influence hormone levels. Within the context of the gut microbiome-brain axis, we discuss how perturbations in the gut microbiota can alter the stress axis and behaviour. In addition, human studies on the possible role of gut microbiota in depression and anxiety are examined. Finally, we present some of the challenges and important questions that need to be addressed by future research in this exciting new area at the intersection of steroids, stress, gut-brain axis and human health.

Acid-Suppressive Therapy and Risk of Infections: Pros and Cons

This narrative review summarises the benefits, risks and appropriate use of acid-suppressing drugs (ASDs), proton pump inhibitors and histamine-2 receptor antagonists, advocating a rationale balanced and individualised approach aimed to minimise any serious adverse consequences. It focuses on current controversies on the potential of ASDs to contribute to infections-bacterial, parasitic, fungal, protozoan and viral, particularly in the elderly, comprehensively and critically discusses the growing body of observational literature linking ASD use to a variety of enteric, respiratory, skin and systemic infectious diseases and complications (Clostridium difficile diarrhoea, pneumonia, spontaneous bacterial peritonitis, septicaemia and other). The proposed pathogenic mechanisms of ASD-associated infections (related and unrelated to the inhibition of gastric acid secretion, alterations of the gut microbiome and immunity), and drug-drug interactions are also described. Both probiotics use and correcting vitamin D status may have a significant protective effect decreasing the incidence of ASD-associated infections, especially in the elderly. Despite the limitations of the existing data, the importance of individualised therapy and caution in long-term ASD use considering the balance of benefits and potential harms, factors that may predispose to and actions that may prevent/attenuate adverse effects is evident. A six-step practical algorithm for ASD therapy based on the best available evidence is presented.

Dysbiosis and Its Discontents

Dysbiosis is a key term in human microbiome research, especially when microbiome patterns are associated with disease states. Although some questions have been raised about how this term is applied, its use continues undiminished in the literature. We investigate the ways in which microbiome researchers discuss dysbiosis and then assess the impact of different concepts of dysbiosis on microbiome research. After an overview of the term's historical roots, we conduct quantitative and qualitative analyses of a large selection of contemporary dysbiosis statements. We categorize both short definitions and longer conceptual statements about dysbiosis. Further analysis allows us to identify the problematic implications of how dysbiosis is used, particularly with regard to causal hypotheses and normal-abnormal distinctions. We suggest that researchers should reflect carefully on the ways in which they discuss dysbiosis, in order for the field to continue to develop greater predictive scope and explanatory depth.

Models of microbiome evolution incorporating host and microbial selection

BACKGROUND

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation.

METHODS

In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts.

RESULTS

We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong parental contribution, when host-mediated selection acts on microbes concomitantly.

CONCLUSIONS

We present a computational framework that integrates different selective processes acting on the evolution of microbiomes. Our framework demonstrates that selection acting on microbes can have a strong effect on microbial diversities and fitnesses, whereas selection on hosts can have weaker outcomes.

INTESTINAL MICROBIOTA IN DIGESTIVE DISEASES

BACKGROUND

In recent years, especially after the development of sophisticated metagenomic studies, research on the intestinal microbiota has increased, radically transforming our knowledge about the microbiome and its association with health maintenance and disease development in humans. Increasing evidence has shown that a permanent alteration in microbiota composition or function (dysbiosis) can alter immune responses, metabolism, intestinal permeability, and digestive motility, thereby promoting a proinflammatory state. Such alterations can mainly impair the host's immune and metabolic functions, thus favoring the onset of diseases such as diabetes, obesity, digestive, neurological, autoimmune, and neoplastic diseases. This comprehensive review is a compilation of the available literature on the formation of the complex intestinal ecosystem and its impact on the incidence of diseases such as obesity, non-alcoholic steatohepatitis, irritable bowel syndrome, inflammatory bowel disease, celiac disease, and digestive neoplasms.

CONCLUSION:

Alterations in the composition and function of the gastrointestinal microbiota (dysbiosis) have a direct impact on human health and seem to have an important role in the pathogenesis of several gastrointestinal diseases, whether inflammatory, metabolic, or neoplastic ones.

Diversity and enterotype in gut bacterial community of adults in Taiwan

Background

Gastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medicine intake, and three enterotypes of the human gut microbiome were announced in 2011. These enterotypes are not significantly correlated with gender, age, or body weight but are influenced by long-term dietary habits. However, to date, only two enterotypes (predominantly consisting of Bacteroides and Prevotella) have shown these characteristics in previous research; the third enterotype remains ambiguous. Understanding the enterotypes can improve the knowledge of the relationship between microbiota and human health.

Results

We obtained 181 human fecal samples from adults in Taiwan. Microbiota compositions were analyzed using next-generation sequencing (NGS) technology, which is a culture-independent method of constructing microbial community profiles by sequencing 16S ribosomal DNA (rDNA). In these samples, 17,675,898 sequencing reads were sequenced, and on average, 215 operational taxonomic units (OTUs) were identified for each sample. In this study, the major bacteria in the enterotypes identified from the fecal samples were Bacteroides, Prevotella, and Enterobacteriaceae, and their correlation with dietary habits was confirmed. A microbial interaction network in the gut was observed on the basis of the amount of short-chain fatty acids, pH value of the intestine, and composition of the bacterial community (enterotypes). Finally, a decision tree was derived to provide a predictive model for the three enterotypes. The accuracies of this model in training and independent testing sets were 97.2 and 84.0%, respectively.

Conclusions

We used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3261-6) contains supplementary material, which is available to authorized users.

To flush or not to flush … that is a question

The human gut microflora has drawn a lot of attention as a potent therapeutic tool for many decades. More recently, efforts have been developed to devise efficient ways of complementing or replacing deficient intestinal microflora associated with intestinal diseases that are resistant to conventional medical treatments. Aside from the medical and industrial applications that emerged from the use of gut microbiota, the complex constitution of this ecosystem raises fascinating questions regarding host-cell communication and host response mechanisms to the ever changing environment. This brief comment also points to questions raised by some unexpected applications that have recently emerged from this field.

The Circadian Clock Mutation Promotes Intestinal Dysbiosis

BACKGROUND

Circadian rhythm disruption is a prevalent feature of modern day society that is associated with an increase in pro-inflammatory diseases, and there is a clear need for a better understanding of the mechanism(s) underlying this phenomenon. We have previously demonstrated that both environmental and genetic circadian rhythm disruption causes intestinal hyperpermeability and exacerbates alcohol-induced intestinal hyperpermeability and liver pathology. The intestinal microbiota can influence intestinal barrier integrity and impact immune system function; thus, in this study, we sought to determine whether genetic alteration of the core circadian clock gene, Clock, altered the intestinal microbiota community.

METHODS

Male Clock(Δ19) -mutant mice (mice homozygous for a dominant-negative-mutant allele) or littermate wild-type mice were fed 1 of 3 experimental diets: (i) a standard chow diet, (ii) an alcohol-containing diet, or (iii) an alcohol-control diet in which the alcohol calories were replaced with dextrose. Stool microbiota was assessed with 16S ribosomal RNA gene amplicon sequencing.

RESULTS

The fecal microbial community of Clock-mutant mice had lower taxonomic diversity, relative to wild-type mice, and the Clock(Δ19) mutation was associated with intestinal dysbiosis when mice were fed either the alcohol-containing or the control diet. We found that alcohol consumption significantly altered the intestinal microbiota in both wild-type and Clock-mutant mice.

CONCLUSIONS

Our data support a model by which circadian rhythm disruption by the Clock(Δ19) mutation perturbs normal intestinal microbial communities, and this trend was exacerbated in the context of a secondary dietary intestinal stressor.

Modulation of microbiota as treatment for intestinal inflammatory disorders: An uptodate

Alterations of intestinal microflora may significantly contribute to the pathogenesis of different inflammatory and autoimmune disorders. There is emerging interest on the role of selective modulation of microflora in inducing benefits in inflammatory intestinal disorders, by as probiotics, prebiotics, synbiotics, antibiotics, and fecal microbiota transplantation (FMT). To summarize recent evidences on microflora modulation in main intestinal inflammatory disorders, PubMed was searched using terms microbiota, intestinal flora, probiotics, prebiotics, fecal transplantation. More than three hundred articles published up to 2015 were selected and reviewed. Randomized placebo-controlled trials and meta-analysis were firstly included, mainly for probiotics. A meta-analysis was not performed because of the heterogeneity of these studies. Most of relevant data derived from studies on probiotics, reporting some efficacy in ulcerative colitis and in pouchitis, while disappointing results are available for Crohn's disease. Probiotic supplementation may significantly reduce rates of rotavirus diarrhea. Efficacy of probiotics in NSAID enteropathy and irritable bowel syndrome is still controversial. Finally, FMT has been recently recognized as an efficacious treatment for recurrent Clostridium difficile infection. Modulation of intestinal flora represents a very interesting therapeutic target, although it still deserves some doubts and limitations. Future studies should be encouraged to provide new understanding about its therapeutical role.

The Gut Microbiota in Immune-Mediated Inflammatory Diseases

The collection of microbes and their genes that exist within and on the human body, collectively known as the microbiome has emerged as a principal factor in human health and disease. Humans and microbes have established a symbiotic association over time, and perturbations in this association have been linked to several immune-mediated inflammatory diseases (IMID) including inflammatory bowel disease, rheumatoid arthritis, and multiple sclerosis. IMID is a term used to describe a group of chronic, highly disabling diseases that affect different organ systems. Though a cornerstone commonality between IMID is the idiopathic nature of disease, a considerable portion of their pathobiology overlaps including epidemiological co-occurrence, genetic susceptibility loci and environmental risk factors. At present, it is clear that persons with an IMID are at an increased risk for developing comorbidities, including additional IMID. Advancements in sequencing technologies and a parallel explosion of 16S rDNA and metagenomics community profiling studies have allowed for the characterization of microbiomes throughout the human body including the gut, in a myriad of human diseases and in health. The main challenge now is to determine if alterations of gut flora are common between IMID or, if particular changes in the gut community are in fact specific to a single disease. Herein, we review and discuss the relationships between the gut microbiota and IMID.

Potential role of the intestinal microbiota in programming health and disease

The composition of the microbiota varies according to prenatal events, delivery methods, infant feeding, infant care environment, and antibiotic use. Postnatal gut function and immune development are largely influenced by the intestinal microbiota. Emerging evidence has shown that early microbiota colonization may influence the occurrence of later diseases (microbial programming). The vast majority of microbial species (commensals) give rise to symbiotic host-bacterial interactions that are fundamental for human health. However, changes in the composition of the gut microbiota (dysbiosis) may be associated with several clinical conditions, including obesity and metabolic diseases, autoimmune diseases and allergy, acute and chronic intestinal inflammation, irritable bowel syndrome (IBS), allergic gastroenteritis (e.g., eosinophilic gastroenteritis and allergic IBS), and necrotizing enterocolitis. Based on recent advances, modulation of gut microbiota with probiotics, prebiotics, or fermented dairy products has been suggested as a treatment of, or prevention for, different disorders such as IBS, infectious diarrhea, allergic disease, and necrotizing enterocolitis.

Gut microbiota and obesity

The human intestine harbors a complex bacterial community called the gut microbiota. This microbiota is specific to each individual despite the existence of several bacterial species shared by the majority of adults. The influence of the gut microbiota in human health and disease has been revealed in the recent years. Particularly, the use of germ-free animals and microbiota transplant showed that the gut microbiota may play a causal role in the development of obesity and associated metabolic disorders, and lead to identification of several mechanisms. In humans, differences in microbiota composition, functional genes and metabolic activities are observed between obese and lean individuals suggesting a contribution of the gut microbiota to these phenotypes. Finally, the evidence linking gut bacteria to host metabolism could allow the development of new therapeutic strategies based on gut microbiota modulation to treat or prevent obesity.

Using bugs as drugs: Microbial ecosystem therapeutics

The human gut harbours a dense and highly diverse microbial ecosystem-the microbiota-that plays an important role in the maintenance of health. Modern lifestyle practices, including widespread antibiotic use, have degraded microbiota diversity, compromising the integrity of this vital ecosystem and creating susceptibility to diseases such as Clostridium difficile infection. Treatment of patients to restore the diversity of the gut microbiota offers a logical solution to disease. Although fecal microbial therapy (FMT) has started to gain traction as an effective method to effect this restoration, it is not without risks and there are significant barriers to its implementation in the clinic. Some of the risks and challenges with FMT are addressed by microbial ecosystem therapeutics (MET), an alternative approach to FMT that uses selected, defined microbial ecosystems to redress microbiota balance and functionality. The time has come for the use of bugs as drugs.

Dysbiosis: A Review Highlighting Obesity and Inflammatory Bowel Disease

There are microbes in and on many parts of the human body and all of the microbes that inhabit an ecosystem are the microbiota, which can be commensal, symbiotic, and pathogenic. Alterations in the homeostasis of the microbiota are considered dysbiosis. To determine how changes to the normal flora are associated with disease, we first need to identify normal gut flora. The gold standard for microbiota analysis is currently by 16S rRNA gene amplification techniques. The human diseases, obesity and inflammatory bowel disease, are prime examples of dysbiosis. Both diseases exhibit a decreased diversity of microorganisms and characteristic changes in bacterial phyla as well as evidence of abnormal gut bacterial translocation and inflammation. As standardization of techniques and longitudinal studies come together in multicenter observations of the gut microbiota, a blossoming understanding will inevitably allow us to better diagnose, treat, and possibly even prevent disease.

Clinical conundrums in management of sepsis in the elderly

In 2012, surviving sepsis campaign came out with updated international guidelines for management of severe sepsis and septic shock. Paradoxically, there are no specific guidelines for management of sepsis in the elderly, although the elderly are more predisposed to sepsis, and morbidity and mortality related to sepsis. Sepsis in the elderly is, more often than not, complicated by clinical conundrums such as congestive heart failure (CHF), atrial fibrillation (AF), chronic kidney disease (CKD), acute kidney injury (AKI), delirium, dementia, ambulatory dysfunction, polypharmacy, malglycemia, nutritional deficiencies, and antibiotic resistance. Also, with recurrent admissions to the hospital and widespread use of antibiotics, the elderly are more susceptible to Clostridium difficile colitis.

Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development

The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. 1H-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota "core" of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.

Effects of synbiotic on anthropometry, lipid profile and oxidative stress in obese children

Recent studies have suggested some beneficial effects of probiotics and/or prebiotics on obesity in adults; such experience is limited in children and adolescents. This study was an open-label, randomised, controlled study including children with primary obesity. The first group was treated with a standard method with a reduced calorie intake and increased physical activity. The second group received add-on daily synbiotic supplementation during one month. The aim of this study was to evaluate potential effects of a synbiotic on anthropometric measurements, lipid profile and oxidative stress parameters. One month of supplementation of the synbiotic resulted in a significant reduction of weight (P<0.001) and body mass index (P<0.01). Changes (% reduction comparing to baseline) in anthropometric measurements, were significantly higher in the children receiving the additional synbiotic supplement (P<0.05). The percentage of children with weight loss was higher in the synbiotic group, but not statistically significant (71.4 vs 64.2%, P>0.05). At the 30(th) day of synbiotic intervention, serum total cholesterol, low density lipoprotein cholesterol and total oxidative stress levels significantly declined (P<0.05). Changes in serum lipid levels were significantly higher in the synbiotic group (P<0.05). Changes in serum total oxidative stress levels before and after the intervention period, were significant in synbiotic group (P<0.01). In our study, changes in weight, body mass index, and triceps skinfold thickness were higher in the group receiving the one month synbiotic supplement thin in the standard method group. The supplement tested also had a beneficial effect on lipid profile and total oxidative stress. To the best of our knowledge, this is the first study showing the effects of synbiotics on oxidative stress in obese patients with an additional effect on weight loss regarding to previous studies.

Neutral Models of Microbiome Evolution

There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes). Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these microbiomes may have evolved. In this paper, we develop an agent-based framework to study the dynamics of microbiome evolution. Our framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled. Most importantly, our framework also incorporates a Wright-Fisher genealogical model of hosts, so that the dynamics of microbiome evolution is studied on an evolutionary timescale. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes: the greater the parental contribution, the less diverse the microbiomes. In contrast, even when there is only a very small contribution from a constant environmental pool, microbial communities can remain highly diverse. Finally, we show that our models may be used to construct hypotheses about the types of processes that operate to assemble microbiomes over evolutionary time.

Apples and cardiovascular health--is the gut microbiota a core consideration?

There is now considerable scientific evidence that a diet rich in fruits and vegetables can improve human health and protect against chronic diseases. However, it is not clear whether different fruits and vegetables have distinct beneficial effects. Apples are among the most frequently consumed fruits and a rich source of polyphenols and fiber. A major proportion of the bioactive components in apples, including the high molecular weight polyphenols, escape absorption in the upper gastrointestinal tract and reach the large intestine relatively intact. There, they can be converted by the colonic microbiota to bioavailable and biologically active compounds with systemic effects, in addition to modulating microbial composition. Epidemiological studies have identified associations between frequent apple consumption and reduced risk of chronic diseases such as cardiovascular disease. Human and animal intervention studies demonstrate beneficial effects on lipid metabolism, vascular function and inflammation but only a few studies have attempted to link these mechanistically with the gut microbiota. This review will focus on the reciprocal interaction between apple components and the gut microbiota, the potential link to cardiovascular health and the possible mechanisms of action.

The relevance of intestinal dysbiosis in liver transplant candidates

BACKGROUND

The gut microbial ecosystem plays an important role in the pathogenesis of liver diseases. However, the association of microbial community structure with the severity of liver dysfunction is not completely understood.

METHODS

Fecal microflora was assessed in 40 patients with liver cirrhosis listed for primary liver transplantation (LT). Independent associations between fecal microbial counts and serum bilirubin, serum creatinine, international normalized ratio (INR), and the Model for End-stage Liver Disease (MELD) score were established in multiple linear regression models.

RESULTS

Bifidobacterium (standardized regression coefficient [sβ] = -0.549; P < 0.001), Enterococcus (sβ = 0.369; P = 0.004), and yeast (sβ = 0.315; P = 0.018) numbers were independently associated with serum bilirubin, while Escherichia coli counts (sβ = 0.318; P = 0.046) correlated with INR, and Bifidobacterium counts (sβ = 0.410; P = 0.009) with serum creatinine. Only Bifidobacterium (sβ = -0.468; P = 0.003) and Enterococcus (sβ = 0.331; P = 0.029) counts were independent predictors of the MELD score. Bifidobacterium/Enterococcus ratio, proposed as a measure of pre-LT gut dysbiosis, was significantly related to the MELD score following the adjustment for the absolute Bifidobacterium (sβ = -0.333; P = 0.029) and Enterococcus (sβ = -0.966; P = 0.003) numbers. This pre-transplant dysbiosis ratio (PTDR) was significantly correlated with Enterococcus (R = -0.897; P < 0.001) but not with Bifidobacterium (R = 0.098; P = 0.546) counts. Among the other components of gut microflora, only hydrogen peroxide (H2 O2 )-producing Lactobacillus strains significantly influenced Enterococcus counts (sβ = 0.349; P = 0.028) and PTDR (sβ = -0.318; P = 0.046).

CONCLUSION

While the abundance of both Bifidobacterium and Enterococcus is related to liver dysfunction, the size of the Enterococcus population seems to be the most important determinant of pre-LT gut dysbiosis in cirrhotic patients. The H2 O2 -producing Lactobacillus strains potentially ameliorate this dysbiotic state.

The intestinal microbiota: its role in health and disease

The intestinal microbiota (previously referred to as "intestinal flora") has entered the focus of research interest not only in microbiology but also in medicine. Huge progress has been made with respect to the analysis of composition and functions of the human microbiota. An "imbalance" of the microbiota, frequently also called a "dysbiosis," has been associated with different diseases in recent years. Crohn's disease and ulcerative colitis as two major forms of inflammatory bowel disease, irritable bowel syndrome (IBS) and some infectious intestinal diseases such as Clostridium difficile colitis feature a dysbiosis of the intestinal flora. Whereas this is somehow expected or less surprising, an imbalance of the microbiota or an enrichment of specific bacterial strains in the flora has been associated with an increasing number of other diseases such as diabetes, metabolic syndrome, non-alcoholic fatty liver disease or steatohepatitis and even psychiatric disorders such as depression or multiple sclerosis. It is important to understand the different aspects of potential contributions of the microbiota to pathophysiology of the mentioned diseases.

CONCLUSION

With the present manuscript, we aim to summarize the current knowledge and provide an overview of the different concepts on how bacteria contribute to health and disease in animal models and-more importantly-humans. In addition, it has to be borne in mind that we are only at the very beginning to understand the complex mechanisms of host-microbial interactions.

The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts

The human gut microbiota is a complex microbial ecosystem that contributes an important component towards the health of its host. This highly complex ecosystem has been underestimated in its importance until recently, when a realization of the enormous scope of gut microbiota function has been (and continues to be) revealed. One of the more striking of these discoveries is the finding that the gut microbiota and the brain are connected, and thus there is potential for the microbiota in the gut to influence behavior and mental health. In this short review, we outline the link between brain and gut microbiota and urge the reader to consider the gut microbiota as an ecosystem ‘organ’ rather than just as a collection of microbes filling a niche, using the hypothesized role of the gut microbiota in autism spectrum disorder to illustrate the concept.

Intestinal barrier homeostasis in inflammatory bowel disease

The single-cell thick intestinal epithelial cell (IEC) lining with its protective layer of mucus is the primary barrier protecting the organism from the harsh environment of the intestinal lumen. Today it is clear that the balancing act necessary to maintain intestinal homeostasis is dependent on the coordinated action of all cell types of the IEC, and that there are no passive bystanders to gut immunity solely acting as absorptive or regenerative cells: Mucin and antimicrobial peptides on the epithelial surface are continually being replenished by goblet and Paneth's cells. Luminal antigens are being sensed by pattern recognition receptors on the enterocytes. The enteroendocrine cells sense the environment and coordinate the intestinal function by releasing neuropeptides acting both on IEC and inflammatory cells. All this while cells are continuously and rapidly being regenerated from a limited number of stem cells close to the intestinal crypt base. This review seeks to describe the cell types and structures of the intestinal epithelial barrier supporting intestinal homeostasis, and how disturbance in these systems might relate to inflammatory bowel disease.