Beyond genetics. Influence of dietary factors and gut microbiota on type 1 diabetes

Gut microbiome in type 1 diabetes: the immunological perspective

INTRODUCTION

Type 1 diabetes (T1D) is a prevalent, and yet uncurable, autoimmune disease targeting insulin-producing pancreatic β-cells. Despite a known genetic component in T1D onset, genetics alone cannot explain the alarming worldwide rise in T1D incidence, which is attributed to a growing impact of environmental factors, including perturbations of the gut microbiome.

AREAS COVERED

Intestinal commensal bacteria plays a crucial role in host physiology in health and disease by regulating endocrine and immune functions. An aberrant gut microbiome structure and metabolic function have been documented prior and during T1D onset. In this review, we summarize and discuss the current studies depicting the taxonomic profile and role of the gut microbial communities in murine models of T1D, diabetic patients and human interventional trials.

EXPERT OPINION

Compelling evidence have shown that the intestinal microbiota is instrumental in driving differentiation and functions of immune cells. Therefore, any alterations in the intestinal microbiome composition or microbial metabolite production, particularly early in life, may impact disease susceptibility and amplify inflammatory responses and hence accelerate the course of T1D pathogenesis.

The effect of “moderately restricted carbohydrate” diet on gut microbiota composition and metabolic parameters in women with metabolic syndrome: a study protocol for a randomized controlled trial

Background

Metabolic syndrome (MetS) is a group of risk factors that increase the risk of death and a variety of chronic diseases. Recent studies have indicated that the imbalance of gut microbiota might contribute to development and progression of metabolic syndrome. Carbohydrate restriction in the diet has been proven to be one of the most effective methods in the management of metabolic syndrome, even in the absence of weight loss. However, no study has examined the effects of a carbohydrate-restricted diet on gut microbiota composition in metabolic syndrome patients. Thus, we will examine the effects of a “moderately restricted carbohydrate (MRC)” diet on gut microbiota, insulin resistance, and components of MetS among Iranian women. In addition, the stability of changes in dependent variables, including gut microbiota, will also be assessed.

Methods

This is a parallel randomized clinical trial in which 70 overweight or obese women aged 20–50 years with MetS will be randomly assigned to receive either MRC diet (42–45% carbohydrate, 35–40% fats) or a normal weight loss (NWL) diet (52–55% carbohydrate, 25–30% fats) for 3 months. Protein accounted for 15–17% of total energy in both diets. The quantity of gut microbiota including Firmicutes, Bacteroidetes, Bifidobacteria, Lactobacillus, Clostridium, Prevotella, Bacteroidetes, and Akkermansia muciniphila, as well as anthropometric, blood pressure, and metabolic parameters will be measured at study baseline and the end of trail. At the end of this phase, all participants will be placed on a weight maintenance diet for an additional 6 months. After following up study subjects in this duration, all dependent variables will be examined again to assess their stability over this period.

Discussion

To the best of our knowledge, this is the first randomized controlled trial investigating the effects of a moderately restricted carbohydrate diet on gut microbiota composition and several metabolic parameters during the weight loss and maintenance phases in women with MetS.

Trial registration

Iranian Registry of Clinical Trials (www.irct.ir, IRCT20210307050621N1). Registered on May 31, 2021.

MicrobiomeGWAS: A Tool for Identifying Host Genetic Variants Associated with Microbiome Composition

The microbiome is the collection of all microbial genes and can be investigated by sequencing highly variable regions of 16S ribosomal RNA (rRNA) genes. Evidence suggests that environmental factors and host genetics may interact to impact human microbiome composition. Identifying host genetic variants associated with human microbiome composition not only provides clues for characterizing microbiome variation but also helps to elucidate biological mechanisms of genetic associations, prioritize genetic variants, and improve genetic risk prediction. Since a microbiota functions as a community, it is best characterized by β diversity; that is, a pairwise distance matrix. We develop a statistical framework and a computationally efficient software package, microbiomeGWAS, for identifying host genetic variants associated with microbiome β diversity with or without interacting with an environmental factor. We show that the score statistics have positive skewness and kurtosis due to the dependent nature of the pairwise data, which makes p-value approximations based on asymptotic distributions unacceptably liberal. By correcting for skewness and kurtosis, we develop accurate p-value approximations, whose accuracy was verified by extensive simulations. We exemplify our methods by analyzing a set of 147 genotyped subjects with 16S rRNA microbiome profiles from non-malignant lung tissues. Correcting for skewness and kurtosis eliminated the dramatic deviation in the quantile–quantile plots. We provided preliminary evidence that six established lung cancer risk SNPs were collectively associated with microbiome composition for both unweighted (p = 0.0032) and weighted (p = 0.011) UniFrac distance matrices. In summary, our methods will facilitate analyzing large-scale genome-wide association studies of the human microbiome.

The Gut Microbiota (Microbiome) in Cardiovascular Disease and Its Therapeutic Regulation

In the last two decades, considerable interest has been shown in understanding the development of the gut microbiota and its internal and external effects on the intestine, as well as the risk factors for cardiovascular diseases (CVDs) such as metabolic syndrome. The intestinal microbiota plays a pivotal role in human health and disease. Recent studies revealed that the gut microbiota can affect the host body. CVDs are a leading cause of morbidity and mortality, and patients favor death over chronic kidney disease. For the function of gut microbiota in the host, molecules have to penetrate the intestinal epithelium or the surface cells of the host. Gut microbiota can utilize trimethylamine, N-oxide, short-chain fatty acids, and primary and secondary bile acid pathways. By affecting these living cells, the gut microbiota can cause heart failure, atherosclerosis, hypertension, myocardial fibrosis, myocardial infarction, and coronary artery disease. Previous studies of the gut microbiota and its relation to stroke pathogenesis and its consequences can provide new therapeutic prospects. This review highlights the interplay between the microbiota and its metabolites and addresses related interventions for the treatment of CVDs.

Impact of type 1 diabetes on the composition and functional potential of gut microbiome in children and adolescents: possible mechanisms, current knowledge, and challenges

Diabetes prevalence and incidence among youth have been increasing globally. Type 1 Diabetes (T1D) in children or adolescents accounts for 5-10% of all diagnosed cases of diabetes. Emerging evidence indicates that genetic factors, especially genes in the human leukocyte antigen region, are not the only factors involved in the predisposition of an individual to T1D. The pathogenesis and development of T1D is driven by both genetic predisposition and environmental factors. Studies indicate that gut microbiota is one of the potential environmental influencers involved in the pathophysiology of TID. Gut microbiota mediates the development of diabetes by altering intestinal permeability, modifying intestinal immunity, and molecular mimicry. The gut microbial diversity, taxonomic profile, and functional potential of gut microbes are significantly altered in individuals with T1D as compared to healthy individuals. However, studies are still needed to identify the specific microbes and microbial metabolites that are involved in the development and pathogenesis of T1D. This will help the development of microbiome-based therapeutic strategies for the prevention and treatment of T1D. The present review article highlights the following: (i) the current knowledge and knowledge gaps in understanding the association between T1D and gut microbiome specifically focusing on the composition and functional potential of gut microbiome in children and adolescents, (ii) the possible mechanisms involved in gut microbiome-mediated T1D pathogenesis, and (iii) challenges and future direction in this field.Abbreviations: B/F ratio: Bacteroidetes to Firmicutes ratio; F/B ratio: Firmicutes to Bacteroidetes ratio; FDR: First-degree relatives; GPR: G protein-coupled receptors; HLA: human leucocyte antigen; IL: interleukin; IFN- γ: interferon-γ; KEGG: Kyoto Encyclopedia of Genes and Genomes; LPS: lipopolysaccharide; mTOR: mammalian target of rapamycin; PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; SCFA: short chain fatty acids; T1D: Type 1 diabetes; T2D: Type 2 diabetes; TJ: tight junction; T_regs: regulatory T cells.

Fecal Bacteria as Non-Invasive Biomarkers for Colorectal Adenocarcinoma

Colorectal adenocarcinoma (CRC) ranks one of the five most lethal malignant tumors both in China and worldwide. Early diagnosis and treatment of CRC could substantially increase the survival rate. Emerging evidence has revealed the importance of gut microbiome on CRC, thus fecal microbial community could be termed as a potential screen for non-invasive diagnosis. Importantly, few numbers of bacteria genus as non-invasive biomarkers with high sensitivity and specificity causing less cost would be benefitted more in clinical compared with the whole microbial community analysis. Here we analyzed the gut microbiome between CRC patients and healthy people using 16s rRNA sequencing showing the divergence of microbial composition between case and control. Furthermore, ExtraTrees classifier was performed for the classification of CRC gut microbiome and heathy control, and 13 bacteria were screened as biomarkers for CRC. In addition, 13 biomarkers including 12 bacteria genera and FOBT showed an outstanding sensitivity and specificity for discrimination of CRC patients from healthy controls. This method could be used as a non-invasive method for CRC early diagnosis.

Association of diabetes and microbiota: An update

Diabetes is an emerging health condition globally and is suggested to have a direct connection with the gut microbiota that determine our metabolic outcomes. Sensitivity to insulin and glucose metabolism is normal in healthy people as compared to those people who cannot maintain their glucose metabolism. One of the reasons of the differences is that healthy people have different microbiome that leads to achieve more short chain fatty acids and make up more branched amino acids, while the gut microbiota of the other group of people are more likely to produce compounds that affects glucose metabolism. Herein, this review will present the research related to the impact of gut microbes on diabetes carried out in the past decade. The review focus on the relation between gut microbiota and Type-1 Diabetes (T1D), Type-2 Diabetes (T2D), and how gut microbiota could be an alternative therapy for treatment of diabetes.

CD101 as an indicator molecule for pathological changes at the interface of host-microbiota interactions

Intestinal microbiota signal to local and distant tissues in the body. Thus, they also regulate biochemical, metabolic and immunological processes in the gut and in the pancreas. Vice versa, eating habits or the immune system of the host shape the intraluminal microbiota. Disruptions of these versatile host-microbiota interactions underlie the pathogenesis of complex immune-mediated disorders such as inflammatory bowel disease (IBD) or type 1 diabetes (T1D). Consequently, dysbiosis and increased intestinal permeability associated with both disorders change the biology of underlying tissues, as evidenced, for example, by an altered expression of surface markers such as CD101 on immune cells located at these dynamic host-microbiota interfaces. CD101, a heavily glycosylated member of the immunoglobulin superfamiliy, is predominantly detected on myeloid cells, intraepithelial lymphocytes (IELs) and regulatory T cells (Tregs) in the gut. The expression of CD101 on both myeloid cells and T lymphocytes protects from experimental enterocolitis and T1D. The improved outcome of both diseases is associated with an anti-inflammatory cytokine profile and a reduced expansion of T cells. However, distinct bacteria suppress the expression of CD101 on myeloid cells, similar as does inflammation on T cells. Thus, the reduced CD101 expression in T1D and IBD patients might be a consequence of an altered composition of the intestinal microbiota, enhanced bacterial translocation and a subsequent primining of local and systemic inflammatory immune responses.

The crucial role of early-life gut microbiota in the development of type 1 diabetes

Early-life healthy gut microbiota has a profound implication on shaping the mucosal immune system as well as maintaining healthy status later in life, especially at the prenatal or neonatal stages, while intestinal dysbiosis in early life is associated with several autoimmune diseases, including type 1 diabetes (T1D). Since the gut microbiome is potentially modifiable, optimizing the intestinal bacterial composition in early life may be a novel option for T1D prevention. In this review, we will review current data depicting the crucial role of early-life intestinal microbiome in the development of T1D and discuss the possible mechanisms whereby early-life intestinal microbiome influences the T1D progression. We also summarize recent findings on environmental factors affecting gut microbiota colonization and interventions that may successfully alter microbial composition to discuss potential means of preventing T1D progression in at-risk children.

Gut Microbiota and Type 1 Diabetes Mellitus: The Effect of Mediterranean Diet

Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease resulting from a complex interplay between genetic susceptibility and environmental factors. Regarding the latter, gut microbiota has a pivotal role in the pathogenesis of T1DM, by affecting intestinal permeability, molecular mimicry, and modulating innate and adaptive immune system, as described in several previous studies. The composition of the gut microbiota is largely influenced by diet. Some observational studies have shown that a low fiber intake is associated with the development of many inflammatory and immune-mediated diseases. In this context, the Mediterranean diet (MD), which is based on high consumption of cereals (preferably as whole grains), legumes, nuts, vegetables, fruits, olive oil, and fish, could play a protective role. Many of the characteristic components of MD have functional characteristics with positive effects on health and well-being. Eating habits are the main significant determinants of the microbial multiplicity of the intestine and the food components influence both microbial populations and their metabolic activities from the early stages of life. Moreover, food metabolites influence the immune response. The intestine is considered the primary site where food metabolites mediate their effects, through epithelial integrity or mucosal immunity. The compromised epithelial integrity allows the translocation of bacteria and/or the diffusion of their products, such as food antigens and lipopolysaccharides, from the intestinal lumen to the tissues, which could enhance the stimulation of immune cells, contributing to the pathogenesis of autoimmune diseases, such as T1DM. The intake of a high amount of fiber and therefore of prebiotics with MD allows the microbiota to have a good microbial balance. Moreover, as more dietary fibers are ingested, a higher amount of short-chain fatty acids (SCFAs) is produced by anaerobic gut microbiota, promoting gut homeostasis, to which also contribute tryptophan metabolites and omega-3-fatty acids. Furthermore, the higher intake of polyunsaturated fatty acids and omega-3-fatty-acids contribute to a better metabolic control. In this review we report the relationship between gut microbiota and T1DM and we explore the effects of Mediterranean diet on microbiota as a potential therapeutic strategy, aimed at preventing or delaying progression of T1DM and its complications.

Involvement of Gut Microbiota, Microbial Metabolites and Interaction with Polyphenol in Host Immunometabolism

Immunological and metabolic processes are inextricably linked and important for maintaining tissue and organismal health. Manipulation of cellular metabolism could be beneficial to immunity and prevent metabolic and degenerative diseases including obesity, diabetes, and cancer. Maintenance of a normal metabolism depends on symbiotic consortium of gut microbes. Gut microbiota contributes to certain xenobiotic metabolisms and bioactive metabolites production. Gut microbiota-derived metabolites have been shown to be involved in inflammatory activation of macrophages and contribute to metabolic diseases. Recent studies have focused on how nutrients affect immunometabolism. Polyphenols, the secondary metabolites of plants, are presented in many foods and beverages. Several studies have demonstrated the antioxidant and anti-inflammatory properties of polyphenols. Many clinical trials and epidemiological studies have also shown that long-term consumption of polyphenol-rich diet protects against chronic metabolic diseases. It is known that polyphenols can modulate the composition of core gut microbiota and interact with the immunometabolism. In the present article, we review the mechanisms of gut microbiota and its metabolites on immunometabolism, summarize recent findings on how the interaction between microbiota and polyphenol modulates host immunometabolism, and discuss future research directions.

Exercise and Type 1 Diabetes

Diabetes mellitus (DM) is the most common endocrine and metabolic disease caused by absolute or insufficient insulin secretion. Under the context of an aging population worldwide, the number of diabetic patients is increasing year by year. Most patients with diabetes have multiple complications that severely threaten their survival and living quality. DM is mainly divided into type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM). T1DM is caused by absolute lack of insulin secretion, so the current treatment for T1DM patients is exogenous insulin replacement therapy. At present, exercise therapy has been widely recognized in the prevention and treatment of diabetes, and regular aerobic exercise has become an important part of T1DM treatment. At the same time, exercise therapy is also used in conjunction with other treatments in the prevention and treatment of diabetic complications. However, for patients with T1DM, exercise still has the risk of hypoglycemia or hyperglycemia. T1DM Patients and specialist physician need to fully understand the effects of exercise on metabolism and implement individualized exercise programs. This chapter reviews the related content of exercise and T1DM.

Recent Advances on Microbiota Involvement in the Pathogenesis of Autoimmunity

Autoimmune disorders derive from genetic, stochastic, and environmental factors that all together interact in genetically predisposed individuals. The impact of an imbalanced gut microbiome in the pathogenesis of autoimmunity has been suggested by an increasing amount of experimental evidence, both in animal models and humans. Several physiological mechanisms, including the establishment of immune homeostasis, are influenced by commensal microbiota in the gut. An altered microbiota composition produces effects in the gut immune system, including defective tolerance to food antigens, intestinal inflammation, and enhanced gut permeability. In particular, early findings reported differences in the intestinal microbiome of subjects affected by several autoimmune conditions, including prediabetes or overt disease compared to healthy individuals. The present review focuses on microbiota-host homeostasis, its alterations, factors that influence its composition, and putative involvement in the development of autoimmune disorders. In the light of the existing literature, future studies are necessary to clarify the role played by microbiota modifications in the processes that cause enhanced gut permeability and molecular mechanisms responsible for autoimmunity onset.

Oral LPS Dosing Induces Local Immunological Changes in the Pancreatic Lymph Nodes in Mice

Lacking the initial contact between the immune system and microbial-associated molecular patterns (MAMPs), such as lipopolysaccharides (LPS), early in life, may be regarded as one of the causal factors of the increasing global increase in the incidence of autoimmune diseases, such as type 1 diabetes (T1D). Previously, a reduced incidence of T1D accompanied by dramatically increased abundances of both the mucin-metabolising bacterium Akkermansia muciniphila, and LPS-carrying Proteobacteria was observed, when vancomycin was given to pups of nonobese diabetic (NOD) mice. While the T1D incidence reducing effect of A. muciniphila has been shown in further studies, little is known as to whether the increased abundance of LPS-carrying bacteria also has a protective effect. Therefore, we fed NOD pups with Eschericia coli LPS orally from birth to weaning, which decreased the gene expressions of TNFα, IL-10, IL-6, IFNγ, IL-1β, IL-2, IL-4, and FoxP3 in the pancreatic lymph nodes, while the same gene expression profile in the spleen was unaffected. However, no significant difference in the incidence of T1D, gut microbiota composition, or ileum expression of the genetic markers of gut permeability, Claudin8, Occludin, Zonulin-1 (Tjp1), Claudin15, Muc1, and Muc2 were observed in relation to LPS ingestion. It is, therefore, concluded that early life oral E. coli LPS has an impact on the local immune response, which, however, did not influence T1D incidence in NOD mice later in life.

Dietary Cows' Milk Protein A1 Beta-Casein Increases the Incidence of T1D in NOD Mice

The contribution of cows’ milk containing beta-casein protein A1 variant to the development of type 1 diabetes (T1D) has been controversial for decades. Despite epidemiological data demonstrating a relationship between A1 beta-casein consumption and T1D incidence, direct evidence is limited. We demonstrate that early life exposure to A1 beta-casein through the diet can modify progression to diabetes in non-obese diabetic (NOD) mice, with the effect apparent in later generations. Adult NOD mice from the F0 generation and all subsequent generations (F1 to F4) were fed either A1 or A2 beta-casein supplemented diets. Diabetes incidence in F0–F2 generations was similar in both cohorts of mice. However, diabetes incidence doubled in the F3 generation NOD mice fed an A1 beta-casein supplemented diet. In F4 NOD mice, subclinical insulitis and altered glucose handling was evident as early as 10 weeks of age in A1 fed mice only. A significant decrease in the proportion of non-conventional regulatory T cell subset defined as CD4⁺CD25⁻FoxP3⁺ was evident in the F4 generation of A1 fed mice. This feeding intervention study demonstrates that dietary A1 beta-casein may affect glucose homeostasis and T1D progression, although this effect takes generations to manifest.

Oral insulin does not alter gut microbiota composition of NOD mice

BACKGROUND

Oral insulin as a preventive strategy and/or treatment of type 1 diabetes has been the target of much research. Producing oral insulins is a complex and challenging task, with numerous pitfalls, due to physiological, physical, and biochemical barriers. Our aim was to determine the impact of oral insulin on the delicate gut microbiota composition.

METHODS

Female nonobese diabetic mice were given oral porcine insulin 2 times a week from 5 weeks of age for 4 weeks, and then subsequently once a week for 21 weeks, or until euthanized. The mice were divided into groups on a gluten-reduced diet or a standard diet. Gut microbiota composition was analysed based on faecal samples, and the type 1 diabetes incidence of the mice was monitored.

RESULTS

We observed no influence of the oral porcine insulin on the gut microbiota composition of mice on a gluten-reduced or a standard diet at 9 weeks of age. Also, the administration of oral insulin did not influence the incidence of type 1 diabetes at 30 weeks of age.

CONCLUSIONS

Oral porcine insulin does not alter the gut microbiota composition of nonobese diabetic mice on either a gluten-reduced diet or standard diet. Also, the oral porcine insulin did not influence the incidence of type 1 diabetes in the groups.

Javamide-II Found in Coffee Is Better than Caffeine at Suppressing TNF-α Production in PMA/PHA-Treated Lymphocytic Jurkat Cells

Recent studies have suggested positive benefits of coffee consumption on inflammation-related diseases, such as liver diseases and diabetes, where activated lymphocytes and TNF-α are critically implicated. Interestingly, some reports suggested that javamide-II found in coffee may have anti-inflammatory activity greater than that of caffeine, but there is limited information about its effect on TNF-α production by activated lymphocytes. Therefore, the inhibitory effect of javamide-II on TNF-α was investigated in PMA/PHA-treated lymphocytic Jurkat cells. At 5 μM, javamide-II, not caffeine, inhibited TNF-α production in the cells (45 ± 4%, P < 0.001). To elucidate the underlying mechanism, the phosphorylation of MAP kinases (ERK, p38, and JNK) was investigated in the Jurkat cells. Javamide-II had little effect on JNK or p38 phosphorylation, but javamide-II (<20 μM) decreased ERK phosphorylation, consequently reducing TNF-α mRNA expression in the cells ( P < 0.001). The involvement of ERK phosphorylation was also confirmed by an ERK1/2 inhibitor (SCH772984). Furthermore, javamide-II was also found to inhibit IL-2 production, which is up-regulated by ERK phosphorylation in cells ( P < 0.001). These data suggested that javamide-II may be a potent compound to suppress TNF-α production more efficiently than caffeine by inhibiting ERK phosphorylation in Jurkat cells.

Type 1 diabetes: Through the lens of human genome and metagenome interplay

Diabetes is a genetic- and epigenetic-related disease from which a large population worldwide suffers. Some genetic factors along with various mutations related to the immune system for disease mechanism(s) have contrastively been determined. However, sometimes mechanisms have not been fully managed for the clarification of the initiation and/or progression of diseases to help patients. In the recent years, due to familiarity with the role of gut microbiota in the health, it has been found that the changes of the microbial balance in the industrialized societies can cause a battery of modern diseases, for which we have no specific definition of how they emerge. This work aims to explore the relationship between the human gut microbiota and the immune system along with their possible role in avoiding/emerging of type 1 diabetes (T1D) accompanied with the relation between genome and metagenome and their imbalance in causing T1D. Moreover, it provides novel view on how to balance the intestinal microbiota by lifestyle to hinder the mechanisms leading to T1D.

On the pathogenesis of insulin-dependent diabetes mellitus: the role of microbiota

Type 1 diabetes (T1D) is an autoimmune disorder characterized by the selective destruction of insulin-producing β cells as result of a complex interplay between genetic, stochastic and environmental factors in genetically susceptible individuals. An increasing amount of experimental data from animal models and humans has supported the role played by imbalanced gut microbiome in T1D pathogenesis. The commensal intestinal microbiota is fundamental for several physiologic mechanisms, including the establishment of immune homeostasis. Alterations in its composition have been correlated to changes in the gut immune system, including defective tolerance to food antigens, intestinal inflammation and enhanced gut permeability. Early findings reported differences in the intestinal microbiome of subjects affected by prediabetes or overt disease compared to healthy individuals. The present review focuses on microbiota-host homeostasis, its alterations, factors that influence microbiome composition and discusses their putative correlation with T1D development. Further studies are necessary to clarify the role played by microbiota modifications in the processes that cause enhanced permeability and the autoimmune mechanisms responsible for T1D onset.

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota

BACKGROUND

Dysbiosis of the gut microbiota has been implicated in the pathogenesis of many autoimmune conditions including type 1 diabetes (T1D). It is unknown whether changes in the gut microbiota observed in T1D are due to environmental drivers, genetic risk factors, or both. Here, we have performed an analysis of associations between the gut microbiota and T1D genetic risk using the non-obese diabetic (NOD) mouse model of T1D and the TwinsUK cohort.

RESULTS

Through the analysis of five separate colonies of T1D susceptible NOD mice, we identified similarities in NOD microbiome that were independent of animal facility. Introduction of disease protective alleles at the Idd3 and Idd5 loci (IL2, Ctla4, Slc11a1, and Acadl) resulted in significant alterations in the NOD microbiome. Disease-protected strains exhibited a restoration of immune regulatory pathways within the gut which could also be reestablished using IL-2 therapy. Increased T1D disease risk from IL-2 pathway loci in the TwinsUK cohort of human subjects resulted in some similar microbiota changes to those observed in the NOD mouse.

CONCLUSIONS

These findings demonstrate for the first time that type 1 diabetes-associated genetic variants that restore immune tolerance to islet antigens also result in functional changes in the gut immune system and resultant changes in the microbiota.

The Impact of Diet Wheat Source on the Onset of Type 1 Diabetes Mellitus-Lessons Learned from the Non-Obese Diabetic (NOD) Mouse Model

Nutrition, especially wheat consumption, is a major factor involved in the onset of type 1 diabetes (T1D) and other autoimmune diseases such as celiac. While modern wheat cultivars possess similar gliadin proteins associated with the onset of celiac disease and T1D, alternative dietary wheat sources from Israeli landraces and native ancestral species may be lacking the epitopes linked with T1D, potentially reducing the incidence of T1D. The Non-Obese Diabetic (NOD) mouse model was used to monitor the effects of dietary wheat sources on the onset and development of T1D. The effects of modern wheat flour were compared with those from either T. aestivum, T. turgidum spp. dicoccoides, or T. turgidum spp. dicoccum landraces or a non-wheat diet. Animals which received wheat from local landraces or ancestral species such as emmer displayed a lower incidence of T1D and related complications compared to animals fed a modern wheat variety. This study is the first report of the diabetogenic properties of various dietary wheat sources and suggests that alternative dietary wheat sources may lack T1D linked epitopes, thus reducing the incidence of T1D.

Does infant feeding modulate the manifestation of celiac disease and type 1 diabetes?

PURPOSE OF REVIEW

The review aims to critically discuss the role of infant feeding in the development of celiac disease and type 1 diabetes (T1D).

RECENT FINDINGS

Prospective observational and randomized interventional studies show that breastfeeding (BF) or BF during gluten introduction does not reduce the risk of developing CD, but high gluten consumption before age 2 years increased the risk in Swedish children.Despite evidence from retrospective studies, prospective trials failed to find a protective effect of breastfeeding against the risk of T1D development. Nevertheless, breastfeeding at the time of cereal introduction decreases this risk. There is some evidence demonstrating that early exposure to sugar-sweetened beverages increases the risk of T1D in childhood, whereas the timing of gluten introduction, except if introduced very early, does not affect it.

SUMMARY

Breastfeeding and/or timing of gluten introduction does not influence celiac disease risk. Breastfeeding at the time of cereal introduction might be protective against T1D. The introduction of certain solid foods at an early age may be associated with the risk of T1D.

Where genes meet environment-integrating the role of gut luminal contents, immunity and pancreas in type 1 diabetes

The rise in new cases of type 1 diabetes (T1D) in genetically susceptible individuals over the past half century has been attributed to numerous environmental "triggers" or promoters such as enteroviruses, diet, and most recently, gut bacteria. No single cause has been identified in humans, likely because there are several pathways by which one can develop T1D. There is renewed attention to the role of the gut and its immune system in T1D pathogenesis based largely on recent animal studies demonstrating that altering the gut microbiota affects diabetes incidence. Although T1D patients display dysbiosis in the gut microbiome, it is unclear whether this is cause or effect. The heart of this question involves several moving parts including numerous risk genes, diet, viruses, gut microbiota, timing, and loss of immune tolerance to β-cells. Most clinical trials have addressed only one aspect of this puzzle using some form of immune suppression, without much success. The key location where our genes meet and deal with the environment is the gastrointestinal tract. The influence of all of its major contents, including microbes, diet, and immune system, must be understood as part of the integrative biology of T1D before we can develop durable means of preventing, treating, or curing this disease. In the present review, we expand our previous gut-centric model based on recent developments in the field.

The Genetic Architecture of Diabetes in Pregnancy: Implications for Clinical Practice

The genetic architecture of diabetes mellitus in general and in pregnancy is complex, owing to the multiple types of diabetes that comprise both complex/polygenic forms and monogenic (largely caused by a mutation in a single gene) forms such as maturity-onset diabetes of the young (MODY). Type 1 diabetes (T1D) and type 2 diabetes (T2D) have complex genetic etiologies, with over 40 and 90 genes/loci, respectively, implicated that interact with environmental/lifestyle factors. The genetic etiology of gestational diabetes mellitus has largely been found to overlap that of T2D. Genetic testing for complex forms of diabetes is not currently useful clinically, but genetic testing for monogenic forms, particularly MODY, has important utility for determining treatment, managing risk in family members, and pregnancy management. In particular, diagnosing MODY2, caused by GCK mutations, indicates that insulin should not be used, including during pregnancy, with the possible exception of an unaffected pregnancy during the third trimester to prevent macrosomia. A relatively simple method for identifying women with MODY2 has been piloted. MODY1, caused by HNF4A mutations, can paradoxically cause neonatal hyperinsulinemic hypoglycemia and macrosomia, indicating that detecting these cases is also clinically important. Diagnosing all MODY types provides opportunities for diagnosing other family members.

Microbial antigen mimics activate diabetogenic CD8 T cells in NOD mice

Both animal model and human studies indicate that commensal bacteria may modify type 1 diabetes (T1D) development. However, the underlying mechanisms by which gut microbes could trigger or protect from diabetes are not fully understood, especially the interaction of commensal bacteria with pathogenic CD8 T cells. In this study, using islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP)-reactive CD8 T cell receptor NY8.3 transgenic nonobese diabetic mice, we demonstrated that MyD88 strongly modulates CD8(+) T cell-mediated T1D development via the gut microbiota. Some microbial protein peptides share significant homology with IGRP. Both the microbial peptide mimic of Fusobacteria and the bacteria directly activate IGRP-specific NY8.3 T cells and promote diabetes development. Thus, we provide evidence of molecular mimicry between microbial antigens and an islet autoantigen and a novel mechanism by which the diabetogenicity of CD8(+) T cells can be regulated by innate immunity and the gut microbiota.

Microbiome Changes during Tuberculosis and Antituberculous Therapy

The critical role of commensal microbiota in the human body has been increasingly recognized, and our understanding of its implications in human health and disease has expanded rapidly. The lower respiratory tract contains diverse communities of microbes known as lung microbiota, which are present in healthy individuals and in individuals with respiratory diseases. The dysbiosis of the airway microbiota in pulmonary tuberculosis (TB) may play a role in the pathophysiological processes associated with TB disease. Recent studies of the lung microbiome have pointed out changes in lung microbial communities associated with TB and other lung diseases and have also begun to elucidate the profound effects that antituberculous drug therapy can have on the human lung microbiome composition. In this review, the potential role of the human microbiome in TB pathogenesis and the changes in the human microbiome with Mycobacterium tuberculosis infection and TB therapy are presented and discussed.

Whey protein stories - An experiment in writing a multidisciplinary biography

This is an experimental, dual-purpose article about whey protein and how to conduct interdisciplinary analyses and writings. On the one hand, this article is a multidisciplinary commodity biography, which consists of five descriptions of whey protein written by the five different research groups involved in the interdisciplinary research project CALM(Counteracting Age-related loss of Skeletal Muscle Mass). On the other hand, it is a meta-analysis, which aims to uncover and highlight examples of how the five descriptions contribute to each other with insights into the contextualisation of knowledge, contrasts between the descriptions and the new dimensions they bring to established fields of interest. The meta-analysis also contains a discussion of interdisciplinary study objects and the usefulness of the multidisciplinary commodity biography as a format for interdisciplinary publications. The article contributes to the field of food studies with a multidisciplinary biography of whey protein - including its sensory qualities and challenges, insights into its cultural history, its nutritional value and effects on the human body and an analysis of how it is perceived by people who consume it. The biography thereby expands upon existing understandings of whey protein while discussing the usefulness of employing the commodity biography format in interdisciplinary writing. Moreover, the article contributes to the field of interdisciplinary research by providing a practical example of a joint publication and reflections upon the existence, interaction and possibilities of monodisciplinary knowledge structures within interdisciplinary studies and publications.

A Review of Applied Aspects of Dealing with Gut Microbiota Impact on Rodent Models

The gut microbiota (GM) affects numerous human diseases, as well as rodent models for these. We will review this impact and summarize ways to handle this challenge in animal research. The GM is complex, with the largest fractions being the gram-positive phylum Firmicutes and the gram-negative phylum Bacteroidetes. Other important phyla are the gram-negative phyla Proteobacteria and Verrucomicrobia, and the gram-positive phylum Actinobacteria. GM members influence models for diseases, such as inflammatory bowel diseases, allergies, autoimmunity, cancer, and neuropsychiatric diseases. GM characterization of all individual animals and incorporation of their GM composition in data evaluation may therefore be considered in future protocols. Germfree isolator-housed rodents or rodents made virtually germ free by antibiotic cocktails can be used to study diverse microbial influences on disease expression. Through subsequent inoculation with selected strains or cocktails of microbes, new "defined flora" models can yield valuable knowledge on the impact of the GM, and of specific GM members and their interactions, on important disease phenotypes and mechanisms. Rodent husbandry and microbial quality assurance practices will be important to ensure and confirm appropriate and research relevant GM.

Current Understanding of Dysbiosis in Disease in Human and Animal Models

Inflammatory bowel disease (IBD) is an intestinal inflammatory condition that affects more than 2 million people in the United States. Although the etiology and pathogenesis of IBD are still largely unknown, dysregulated host/enteric microbial interactions are requisite for the development of IBD. So far, many researchers have tried to identify a precise relationship between IBD and an imbalance of the intestinal microbiota, termed "dysbiosis." Despite extensive efforts, it is still largely unknown about the interplay among microbes, their hosts, and their environments, and whether dysbiosis is a causal factor or an effect of IBD. Recently, deep-sequencing analyses of the microbiota in patients with IBD patients have been instrumental in characterizing the strong association between dysbiosis and IBD development, although it is still unable to identify specific-associated species level changes in most cases. Based on many recent reports, dysbiosis of the commensal microbiota is implicated in the pathogenesis of several diseases, including IBD, obesity, and allergic disorders, in both human and animal models. In this review article, the authors have focused on explaining the multiple types of dysbiosis, as well as dysbiosis-related diseases and potential treatments to apply this knowledge to understand a possible cause and potentially find therapeutic strategies for IBD as well as the other dysbiosis-related diseases.

Comparison of Predictive Models for the Early Diagnosis of Diabetes

OBJECTIVES

This study develops neural network models to improve the prediction of diabetes using clinical and lifestyle characteristics. Prediction models were developed using a combination of approaches and concepts.

METHODS

We used memetic algorithms to update weights and to improve prediction accuracy of models. In the first step, the optimum amount for neural network parameters such as momentum rate, transfer function, and error function were obtained through trial and error and based on the results of previous studies. In the second step, optimum parameters were applied to memetic algorithms in order to improve the accuracy of prediction. This preliminary analysis showed that the accuracy of neural networks is 88%. In the third step, the accuracy of neural network models was improved using a memetic algorithm and resulted model was compared with a logistic regression model using a confusion matrix and receiver operating characteristic curve (ROC).

RESULTS

The memetic algorithm improved the accuracy from 88.0% to 93.2%. We also found that memetic algorithm had a higher accuracy than the model from the genetic algorithm and a regression model. Among models, the regression model has the least accuracy. For the memetic algorithm model the amount of sensitivity, specificity, positive predictive value, negative predictive value, and ROC are 96.2, 95.3, 93.8, 92.4, and 0.958 respectively.

CONCLUSIONS

The results of this study provide a basis to design a Decision Support System for risk management and planning of care for individuals at risk of diabetes.

Cohort profile: the German Diabetes Study (GDS)

Background

The German Diabetes Study (GDS) is a prospective longitudinal cohort study describing the impact of subphenotypes on the course of the disease. GDS aims at identifying prognostic factors and mechanisms underlying the development of related comorbidities.

Study design and methods

The study comprises intensive phenotyping within 12 months after clinical diagnosis, at 5-year intervals for 20 years and annual telephone interviews in between. Dynamic tests, including glucagon, mixed meal, intravenous glucose tolerance and hyperinsulinemic clamp tests, serve to assess beta-cell function and tissue-specific insulin sensitivity. Magnetic resonance imaging and multinuclei spectroscopy allow quantifying whole-body fat distribution, tissue-specific lipid deposition and energy metabolism. Comprehensive analyses of microvascular (nerve, eye, kidney) and macrovascular (endothelial, cardiorespiratory) morphology and function enable identification and monitoring of comorbidities. The GDS biobank stores specimens from blood, stool, skeletal muscle, subcutaneous adipose tissue and skin for future analyses including multiomics, expression profiles and histology. Repeated questionnaires on socioeconomic conditions, patient-reported outcomes as quality of life, health-related behavior as physical activity and nutritional habits are a specific asset of GDS. This study will recruit 3000 patients and a group of humans without familiy history of diabetes. 237 type 1 and 456 type 2 diabetes patients have been already included.

Electronic supplementary material

The online version of this article (doi:10.1186/s12933-016-0374-9) contains supplementary material, which is available to authorized users.

Postnatal Hematopoiesis and Gut Microbiota in NOD Mice Deviate from C57BL/6 Mice

Neonatal studies in different mouse strains reveal that early life colonization affects the development of adaptive immunity in mice. The nonobese diabetic (NOD) mouse spontaneously develops autoimmune diabetes, but neonatal studies of NOD mice are lacking. We hypothesized that NOD mice deviate from another much used mouse strain, C57BL/6, with respect to postnatal microbiota and/or hematopoiesis and compared this in newborn mice of dams housed under the same conditions. A distinct bacteria profile rich in staphylococci was found at postnatal days (PND) 1-4 in NOD mice. Furthermore, a distinct splenic cell profile high in a granulocytic phenotype was evident in the neonatal NOD mice whereas neonatal C57BL/6 mice showed a profile rich in monocytes. Neonatal expression of Reg3g and Muc2 in the gut was deviating in NOD mice and coincided with fewer bacteria attaching to the Mucosal surface in NOD compared to C57BL/6 mice.

The influence of the young microbiome on inflammatory diseases--Lessons from animal studies

Chronic inflammatory diseases are on the rise in the Westernized world. This rise has been correlated to a range of environmental factors, such as birth mode, rural versus urban living conditions, and use of antibiotics. Such environmental factors also influence early life gut microbiota (GM) colonization and maturation--and there is growing evidence that the negative effects of these factors on human health are mediated via GM alterations. Colonization of the gut initiates priming of the immune system from birth, driving tolerance towards non-harmful microorganisms and dietary antigens and proper reactions towards invading pathogens. This early colonization is crucial for the establishment of a healthy GM, and throughout life the balanced interaction of GM and immune system is a key element in maintaining health. An immune system out of balance increases the risk for later life inflammatory diseases. Animal models are indispensable in the studies of GM influence on disease mechanisms and progression, and focus points include studies of GM modification during pregnancy and perinatal life. Here, we present an overview of animal studies which have contributed to our understanding of GM functions in early life and how alterations affect risk and expression of certain inflammatory diseases with juvenile onset, including interventions, such as birth mode, antibiotics, and probiotics.

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

BACKGROUND

The human gut is densely populated with archaea, eukaryotes, bacteria, and their viruses, such as bacteriophages. Advances in high-throughput sequencing (HTS) as well as bioinformatics have opened new opportunities for characterizing the viral communities harbored in our gut. However, limited attention has been given to the efficiency of protocols dealing with extraction of phages from fecal communities prior to HTS and their impact on the metagenomic dataset.

RESULTS

We describe two optimized methods for extraction of phages from fecal samples based on tangential-flow filtration (TFF) and polyethylene glycol precipitation (PEG) approaches using an adapted method from a published protocol as control (literature-adapted protocol (LIT)). To quantify phage recovery, samples were spiked with low numbers of c2, ϕ29, and T4 phages (representatives of the Siphoviridae, Podoviridae, and Myoviridae families, respectively) and their concentration (plaque-forming units) followed at every step during the extraction procedure. Compared with LIT, TFF and PEG had higher recovery of all spiked phages, yielding up to 16 times more phage particles (PPs) and up to 68 times more phage DNA per volume, increasing thus the chances of extracting low abundant phages. TFF- and PEG-derived metaviromes showed 10% increase in relative abundance of Caudovirales and unclassified phages infecting gut-associated bacteria (>92% for TFF and PEG, 82.4% for LIT). Our methods obtained lower relative abundance of the Myoviridae family (<16%) as compared to the reference protocol (22%). This decline, however, was not considered a true loss of Myoviridae phages but rather a greater level of extraction of Siphoviridae phages (TFF and PEG >32.5%, LIT 22.6%), which was achieved with the enhanced conditions of our procedures (e.g., reduced filter clogging). A high degree of phage diversity in samples extracted using TFF and PEG was documented by transmission electron microscopy.

CONCLUSIONS

Two procedures (TFF and PEG) for extraction of bacteriophages from fecal samples were optimized using a set of spiked bacteriophages as process control. These protocols are highly efficient tools for extraction and purification of PPs prior to HTS in phage-metavirome studies. Our methods can be easily modified, being thus applicable and adjustable for in principle any solid environmental material in dissolution.

Prediction and prevention of type 1 diabetes: update on success of prediction and struggles at prevention

Type 1 diabetes mellitus (T1DM) is the archetypal example of a T cell-mediated autoimmune disease characterized by selective destruction of pancreatic β cells. The pathogenic equation for T1DM presents a complex interrelation of genetic and environmental factors, most of which have yet to be identified. On the basis of observed familial aggregation of T1DM, it is certain that there is a decided heritable genetic susceptibility for developing T1DM. The well-known association of T1DM with certain human histocompatibility leukocyte antigen (HLA) alleles of the major histocompatibility complex (MHC) was a major step toward understanding the role of inheritance in T1DM. Type 1 diabetes is a polygenic disease with a small number of genes having large effects (e.g., HLA) and a large number of genes having small effects. Risk of T1DM progression is conferred by specific HLA DR/DQ alleles [e.g., DRB1*03-DQB1*0201 (DR3/DQ2) or DRB1*04-DQB1*0302 (DR4/DQ8)]. In addition, the HLA allele DQB1*0602 is associated with dominant protection from T1DM in multiple populations. A concordance rate lower than 100% between monozygotic twins indicates a potential involvement of environmental factors on disease development. The detection of at least two islet autoantibodies in the blood is virtually pre-diagnostic for T1DM. The majority of children who carry these biomarkers, regardless of whether they have an a priori family history of the disease, will develop insulin-requiring diabetes. Facilitating pre-diagnosis is the timing of seroconversion which is most pronounced in the first 2 yr of life. Unfortunately the significant progress in improving prediction of T1DM has not yet been paralleled by safe and efficacious intervention strategies aimed at preventing the disease. Herein we summarize the chequered history of prediction and prevention of T1DM, describing successes and failures alike, and thereafter examine future trends in the exciting, partially explored field of T1DM prevention.

Diabetes-related dysfunction of the small intestine and the colon: focus on motility

In contrast to gastric dysfunction, diabetes-related functional impairments of the small and large intestine have been studied less intensively. The gastrointestinal tract accomplishes several functions, such as mixing and propulsion of luminal content, absorption and secretion of ions, water, and nutrients, defense against pathogens, and elimination of waste products. Diverse functions of the gut are regulated by complex interactions among its functional elements, including gut microbiota. The network-forming tissues, the enteric nervous system) and the interstitial cells of Cajal, are definitely impaired in diabetic patients, and their loss of function is closely related to the symptoms in diabetes, but changes of other elements could also play a role in the development of diabetes mellitus-related motility disorders. The development of our understanding over the recent years of the diabetes-induced dysfunctions in the small and large intestine are reviewed in this article.

Infant Feeding and Timing of Complementary Foods in the Development of Type 1 Diabetes

Type 1 diabetes (T1D) is an autoimmune disease that results from the destruction of the β cells of the pancreas in genetically at-risk individuals. The autoimmune process that precedes the development of T1D is believed to be triggered by environmental factors, including nutrition. Early introduction of complementary foods has been implicated in the etiology of T1D as a possible explanation of the increasing incidence of the disease, particularly in children younger than 5 years of age. Infant feeding recommendations have been designed to promote adequate growth, provide essential nutrients, and reduce the risk of developing chronic illnesses. The World Health Organization and the American Academy of Pediatrics recommend exclusive breastfeeding to 6 months of age followed by continued breastfeeding as complementary foods are introduced. A lack of compliance with these recommendations has been observed in the general population as well as in infants at high risk for T1D. Dietary factors such as the provision of breast milk and duration of breastfeeding, the age at introduction of cow's milk and gluten-containing foods, as well as other complementary feeding have been investigated. However, the evidence that early infant feeding patterns are linked with T1D currently remains inconclusive.

Dietary intake of soluble fiber and risk of islet autoimmunity by 5 y of age: results from the TEDDY study

BACKGROUND

Deficient soluble fiber intake has been suggested to dysregulate the immune response either directly or through alterations of the microbial composition in the gut.

OBJECTIVE

We hypothesized that a high intake of dietary soluble fiber in early childhood decreases the risk of type 1 diabetes (T1D)-associated islet autoimmunity.

DESIGN

We analyzed 17,620 food records collected between age 9 and 48 mo from 3358 children from the United States and Germany prospectively followed in the TEDDY (The Environmental Determinants of Diabetes in the Young) study. HRs for the development of any/multiple islet autoantibodies (242 and 151 events, respectively) and T1D (71 events) by soluble fiber intake were calculated in Cox regression models and adjusted for potential confounders.

RESULTS

There were no statistically significantly protective associations observed between a high intake of soluble fiber and islet autoimmunity or T1D. For example, the adjusted HRs (95% CIs) for high intake (highest compared with lowest quintile) at age 12 mo were 0.90 (0.55, 1.45) for any islet autoantibody, 1.20 (0.69, 2.11) for multiple islet autoantibodies, and 1.24 (0.57, 2.70) for T1D. In analyzing soluble fiber intake as a time-varying covariate, there were also no short-term associations between soluble fiber intake and islet autoimmunity development, with adjusted HRs of 0.85 (0.51, 1.42) for high intake and development of any islet autoantibody, for example.

CONCLUSION

These results indicate that the intake level of dietary soluble fiber is not associated with islet autoimmunity or T1D in early life.

The microbiome at the pulmonary alveolar niche and its role in Mycobacterium tuberculosis infection

Advances in next generation sequencing (NGS) technology have provided the tools to comprehensively and accurately characterize the microbial community in the respiratory tract in health and disease. The presence of commensal and pathogenic bacteria has been found to have important effects on the lung immune system. Until relatively recently, the lung has received less attention compared to other body sites in terms of microbiome characterization, and its study carries special technological difficulties related to obtaining reliable samples as compared to other body niches. Additionally, the complexity of the alveolar immune system, and its interactions with the lung microbiome, are only just beginning to be understood. Amidst this complexity sits Mycobacterium tuberculosis (Mtb), one of humanity's oldest nemeses and a significant public health concern, with millions of individuals infected with Mtb worldwide. The intricate interactions between Mtb, the lung microbiome, and the alveolar immune system are beginning to be understood, and it is increasingly apparent that improved treatment of Mtb will only come through deep understanding of the interplay between these three forces. In this review, we summarize our current understanding of the lung microbiome, alveolar immunity, and the interaction of each with Mtb.

Sex, body mass index, and dietary fiber intake influence the human gut microbiome

Increasing evidence suggests that the composition of the human gut microbiome is important in the etiology of human diseases; however, the personal factors that influence the gut microbiome composition are poorly characterized. Animal models point to sex hormone-related differentials in microbiome composition. In this study, we investigated the relationship of sex, body mass index (BMI) and dietary fiber intake with the gut microbiome in 82 humans. We sequenced fecal 16S rRNA genes by 454 FLX technology, then clustered and classified the reads to microbial genomes using the QIIME pipeline. Relationships of sex, BMI, and fiber intake with overall gut microbiome composition and specific taxon abundances were assessed by permutational MANOVA and multivariate logistic regression, respectively. We found that sex was associated with the gut microbiome composition overall (p=0.001). The gut microbiome in women was characterized by a lower abundance of Bacteroidetes (p=0.03). BMI (>25 kg/m2 vs. <25 kg/m2) was associated with the gut microbiome composition overall (p=0.05), and this relationship was strong in women (p=0.03) but not in men (p=0.29). Fiber from beans and from fruits and vegetables were associated, respectively, with greater abundance of Actinobacteria (p=0.006 and false discovery rate adjusted q=0.05) and Clostridia (p=0.009 and false discovery rate adjusted q=0.09). Our findings suggest that sex, BMI, and dietary fiber contribute to shaping the gut microbiome in humans. Better understanding of these relationships may have significant implications for gastrointestinal health and disease prevention.

Immunogenetics of type 1 diabetes mellitus

Type 1 diabetes mellitus (T1DM) is an autoimmune disease arising through a complex interaction of both genetic and immunologic factors. Similar to the majority of autoimmune diseases, T1DM usually has a relapsing remitting disease course with autoantibody and T cellular responses to islet autoantigens, which precede the clinical onset of the disease process. The immunological diagnosis of autoimmune diseases relies primarily on the detection of autoantibodies in the serum of T1DM patients. Although their pathogenic significance remains uncertain, they have the practical advantage of serving as surrogate biomarkers for predicting the clinical onset of T1DM. Type 1 diabetes is a polygenic disease with a small number of genes having large effects (i.e. HLA), and a large number of genes having small effects. Risk of T1DM progression is conferred by specific HLA DR/DQ alleles [e.g., DRB1*03-DQB1*0201 (DR3) or DRB1*04-DQB1*0302 (DR4)]. In addition, HLA alleles such as DQB1*0602 are associated with dominant protection from T1DM in multiple populations. A discordance rate of greater than 50% between monozygotic twins indicates a potential involvement of environmental factors on disease development. Viral infections may play a role in the chain of events leading to disease, albeit conclusive evidence linking infections with T1DM remains to be firmly established. Two syndromes have been described in which an immune-mediated form of diabetes occurs as the result of a single gene defect. These syndromes are termed autoimmune polyglandular syndrome type I (APS-I) or autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), and X-linked poyendocrinopathy, immune dysfunction and diarrhea (XPID). These two syndromes are unique models to understand the mechanisms involved in the loss of tolerance to self-antigens in autoimmune diabetes and its associated organ-specific autoimmune disorders. A growing number of animal models of these diseases have greatly helped elucidate the immunologic mechanisms leading to autoimmune diabetes.

Gut immune deficits in LEW.1AR1-iddm rats partially overcome by feeding a diabetes-protective diet

The gut immune system and its modification by diet have been implicated in the pathogenesis of type 1 diabetes (T1D). Therefore, we investigated gut immune status in non-diabetes-prone LEW.1AR1 and diabetes-prone LEW.1AR1-iddm rats and evaluated the effect of a low antigen, hydrolysed casein (HC)-based diet on gut immunity and T1D. Rats were weaned onto a cereal-based or HC-based diet and monitored for T1D. Strain and dietary effects on immune homeostasis were assessed in non-diabetic rats (50-60 days old) and rats with recent-onset diabetes using flow cytometry and immunohistochemistry. Immune gene expression was analysed in mesenteric lymph nodes (MLN) and jejunum using quantitative RT-PCR and PCR arrays. T1D was prevented in LEW.1AR1-iddm rats by feeding an HC diet. Diabetic LEW.1AR1-iddm rats had fewer lymphoid tissue T cells compared with LEW.1AR1 rats. The percentage of CD4(+)  Foxp3(+) regulatory T (Treg) cells was decreased in pancreatic lymph nodes (PLN) of diabetic rats. The jejunum of 50-day LEW.1AR1-iddm rats contained fewer CD3(+) T cells, CD163(+) M2 macrophages and Foxp3(+) Treg cells. Ifng expression was increased in MLN and Foxp3 expression was decreased in the jejunum of LEW.1AR1-iddm rats; Ifng/Il4 was decreased in jejunum of LEW.1AR1-iddm rats fed HC. PCR arrays revealed decreased expression of M2-associated macrophage factors in 50-day LEW.1AR1-iddm rats. Wheat peptides stimulated T-cell proliferation and activation in MLN and PLN cells from diabetic LEW.1AR1-iddm rats. LEW.1AR1-iddm rats displayed gut immune cell deficits and decreased immunoregulatory capacity, which were partially corrected in animals fed a low antigen, protective HC diet consistent with other models of T1D.

The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity

Diabetes is a group of metabolic disorders characterized by persistent hyperglycemia and has become a major public health concern. Autoimmune type 1 diabetes (T1D) and insulin resistant type 2 diabetes (T2D) are the two main types. A combination of genetic and environmental factors contributes to the development of these diseases. Gut microbiota have emerged recently as an essential player in the development of T1D, T2D and obesity. Altered gut microbiota have been strongly linked to disease in both rodent models and humans. Both classic 16S rRNA sequencing and shot-gun metagenomic pyrosequencing analysis have been successfully applied to explore the gut microbiota composition and functionality. This review focuses on the association between gut microbiota and diabetes and discusses the potential mechanisms by which gut microbiota regulate disease development in T1D, T2D and obesity.

Does the microbiota play a role in the pathogenesis of autoimmune diseases?

The microbiota of the human metaorganism is not a mere bystander. These microbes have coevolved with us and are pivotal to normal development and homoeostasis. Dysbiosis of the GI microbiota is associated with many disease susceptibilities, including obesity, malignancy, liver disease and GI pathology such as IBD. It is clear that there is direct and indirect crosstalk between this microbial community and host immune response. However, the precise mechanism of this microbial influence in disease pathogenesis remains elusive and is now a major research focus. There is emerging literature on the role of the microbiota in the pathogenesis of autoimmune disease, with clear and increasing evidence that changes in the microbiota are associated with some of these diseases. Examples include type 1 diabetes, coeliac disease and rheumatoid arthritis, and these contribute significantly to global morbidity and mortality. Understanding the role of the microbiota in autoimmune diseases may offer novel insight into factors that initiate and drive disease progression, stratify patient risk for complications and ultimately deliver new therapeutic strategies. This review summarises the current status on the role of the microbiota in autoimmune diseases.

Diet and host-microbial crosstalk in postnatal intestinal immune homeostasis

Neonates face unique challenges in the period following birth. The postnatal immune system is in the early stages of development and has a range of functional capabilities that are distinct from the mature adult immune system. Bidirectional immune-microbial interactions regulate the development of mucosal immunity and alter the composition of the microbiota, which contributes to overall host well-being. In the past few years, nutrition has been highlighted as a third element in this interaction that governs host health by modulating microbial composition and the function of the immune system. Dietary changes and imbalances can disturb the immune-microbiota homeostasis, which might alter susceptibility to several autoimmune and metabolic diseases. Major changes in cultural traditions, socioeconomic status and agriculture are affecting the nutritional status of humans worldwide, which is altering core intestinal microbial communities. This phenomenon is especially relevant to the neonatal and paediatric populations, in which the microbiota and immune system are extremely sensitive to dietary influences. In this Review, we discuss the current state of knowledge regarding early-life nutrition, its effects on the microbiota and the consequences of diet-induced perturbation of the structure of the microbial community on mucosal immunity and disease susceptibility.