Gut microbiota from twins discordant for obesity modulate metabolism in mice

A physicians' wish list for the clinical application of intestinal metagenomics

Christoph Steininger and colleagues explore how multiple infectious, autoimmune, metabolic, and neoplastic diseases have been associated with changes in the intestinal microbiome, although a cause-effect relationship is often difficult to establish. Integration of metagenomics into clinical medicine is a challenge, and the authors highlight clinical approaches that are of high priority for the useful medical application of metagenomics. Please see later in the article for the Editors' Summary.

Glucagon-like peptide 1 analogue therapy directly modulates innate immune-mediated inflammation in individuals with type 2 diabetes mellitus

AIMS/HYPOTHESIS

Glucagon-like peptide 1 (GLP-1) is a gut hormone used in the treatment of type 2 diabetes mellitus. There is emerging evidence that GLP-1 has anti-inflammatory activity in humans, with murine studies suggesting an effect on macrophage polarisation. We hypothesised that GLP-1 analogue therapy in individuals with type 2 diabetes mellitus would affect the inflammatory macrophage molecule soluble CD163 (sCD163) and adipocytokine profile.

METHODS

We studied ten obese type 2 diabetes mellitus patients starting GLP-1 analogue therapy at a hospital-based diabetes service. We investigated levels of sCD163, TNF-α, IL-1β, IL-6, adiponectin and leptin by ELISA, before and after 8 weeks of GLP-1 analogue therapy.

RESULTS

GLP-1 analogue therapy reduced levels of the inflammatory macrophage activation molecule sCD163 (220 ng/ml vs 171 ng/ml, p < 0.001). This occurred independent of changes in body weight, fructosamine and HbA1c. GLP-1 analogue therapy was associated with a decrease in levels of the inflammatory cytokines TNF-α (264 vs 149 pg/ml, p < 0.05), IL-1β (2,919 vs 748 pg/ml, p < 0.05) and IL-6 (1,379 vs 461 pg/ml p < 0.05) and an increase in levels of the anti-inflammatory adipokine adiponectin (4,480 vs 6,290 pg/ml, p < 0.002).

CONCLUSIONS/INTERPRETATION

In individuals with type 2 diabetes mellitus, GLP-1 analogue therapy reduces the frequency of inflammatory macrophages. This effect is not dependent on the glycaemic or body weight effects of GLP-1.

Obesity and cancer pathogenesis

Overweight and obesity have reached pandemic levels on a worldwide basis and are associated with increased risk and worse prognosis for many but not all malignancies. Pathophysiologic processes that affect this association are reviewed, with a focus on the relationship between type 2 diabetes mellitus and cancer, lessons learned from the use of murine models to study the association, the impact of obesity on pancreatic cancer, the effects of dietary fats and cholesterol on cancer promotion, and the mechanisms by which the intestinal microbiome affects obesity and cancer.

Beneficial modulation of the gut microbiota

The human gut microbiota comprises approximately 100 trillion microbial cells and has a significant effect on many aspects of human physiology including metabolism, nutrient absorption and immune function. Disruption of this population has been implicated in many conditions and diseases, including examples such as obesity, inflammatory bowel disease and colorectal cancer that are highlighted in this review. A logical extension of these observations suggests that the manipulation of the gut microbiota can be employed to prevent or treat these conditions. Thus, here we highlight a variety of options, including the use of changes in diet (including the use of prebiotics), antimicrobial-based intervention, probiotics and faecal microbiota transplantation, and discuss their relative merits with respect to modulating the intestinal community in a beneficial way.

FXR is a molecular target for the effects of vertical sleeve gastrectomy

Bariatric surgical procedures, such as vertical sleeve gastrectomy (VSG), are currently the most effective therapy for the treatment of obesity, and are associated with substantial improvements in co-morbidities, including type-2 diabetes mellitus. The underlying molecular mechanisms contributing to these benefits remain largely undetermined, despite offering tremendous potential to reveal new targets for therapeutic intervention. The present study demonstrates that the therapeutic value of VSG does not result from mechanical restriction imposed by a smaller stomach. Rather, we report that VSG is associated with increased circulating bile acids, and associated changes to gut microbial communities. Moreover, in the absence of nuclear bile acid receptor FXR, the ability of VSG to reduce body weight and improve glucose tolerance is substantially reduced. These results point to bile acids and FXR signaling as an important molecular underpinning for the beneficial effects of this weight-loss surgery.

Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery

Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites. This review focuses on co-culture studies that aim to increase the diversity of metabolites obtained from microbes. The various strategies are summarized with a special emphasis on the multiple methods of performing co-culture experiments. The analytical approaches for studying these interaction phenomena are discussed, and the chemical diversity and biological activity observed among the induced metabolites are described.

Reprint of: Role of enteric neurotransmission in host defense and protection of the gastrointestinal tract

Host defense is a vital role played by the gastrointestinal tract. As host to an enormous and diverse microbiome, the gut has evolved an elaborate array of chemical and physicals barriers that allow the digestion and absorption of nutrients without compromising the mammalian host. The control of such barrier functions requires the integration of neural, humoral, paracrine and immune signaling, involving redundant and overlapping mechanisms to ensure, under most circumstances, the integrity of the gastrointestinal epithelial barrier. Here we focus on selected recent developments in the autonomic neural control of host defense functions used in the protection of the gut from luminal agents, and discuss how the microbiota may potentially play a role in enteric neurotransmission. Key recent findings include: the important role played by subepithelial enteric glia in modulating intestinal barrier function, identification of stress-induced mechanisms evoking barrier breakdown, neural regulation of epithelial cell proliferation, the role of afferent and efferent vagal pathways in regulating barrier function, direct evidence for bacterial communication to the enteric nervous system, and microbial sources of enteric neurotransmitters. We discuss these new and interesting developments in our understanding of the role of the autonomic nervous system in gastrointestinal host defense.

Glucose metabolism: focus on gut microbiota, the endocannabinoid system and beyond

The gut microbiota is now considered as a key factor in the regulation of numerous metabolic pathways. Growing evidence suggests that cross-talk between gut bacteria and host is achieved through specific metabolites (such as short-chain fatty acids) and molecular patterns of microbial membranes (lipopolysaccharides) that activate host cell receptors (such as toll-like receptors and G-protein-coupled receptors). The endocannabinoid (eCB) system is an important target in the context of obesity, type 2 diabetes (T2D) and inflammation. It has been demonstrated that eCB system activity is involved in the control of glucose and energy metabolism, and can be tuned up or down by specific gut microbes (for example, Akkermansia muciniphila). Numerous studies have also shown that the composition of the gut microbiota differs between obese and/or T2D individuals and those who are lean and non-diabetic. Although some shared taxa are often cited, there is still no clear consensus on the precise microbial composition that triggers metabolic disorders, and causality between specific microbes and the development of such diseases is yet to be proven in humans. Nevertheless, gastric bypass is most likely the most efficient procedure for reducing body weight and treating T2D. Interestingly, several reports have shown that the gut microbiota is profoundly affected by the procedure. It has been suggested that the consistent postoperative increase in certain bacterial groups such as Proteobacteria, Bacteroidetes and Verrucomicrobia (A. muciniphila) may explain its beneficial impact in gnotobiotic mice. Taken together, these data suggest that specific gut microbes modulate important host biological systems that contribute to the control of energy homoeostasis, glucose metabolism and inflammation in obesity and T2D.

The gut microbiota and the metabolic health of the host

PURPOSE OF REVIEW

It is clear that the metabolic activities of the gut microbiota significantly impact upon human health and disease.

RECENT FINDINGS

Recent analyses have correlated alterations in microbial community structure with the onset of diabetes, obesity and cardiovascular disease as well as inflammatory conditions of the intestine. This work has demonstrated the influence of diet upon the microbiota in disease states and has identified a number of microbial metabolites that orchestrate the crucial aspects of the host-microbe dialog. The microbial production of short-chain fatty acids, trimethylamine, acetaldehyde and inflammatory mediators has been shown to significantly impact upon the metabolic health of the host through pathways that influence satiety, gut permeability and immune function. In the small intestine, microbial metabolism alters the host bile acid profile affecting the interactions with dedicated bile acid receptors (including FXR and TGR5) to influence both local and systemic cellular responses. Recent findings have, therefore, identified specific microbiota profiles and metabolites as predictors of disease risk as well as determining the microbial species (such as Akkermansia muciniphila and Bilophila wadsworthia) which correlate with health and disease.

SUMMARY

This work identifies the microbiota as an important target for new diagnostic and therapeutic approaches in metabolic disease.

Role of the enteric microbiota in intestinal homeostasis and inflammation

The mammalian intestine encounters many more microorganisms than any other tissue in the body thus making it the largest and most complex component of the immune system. Indeed, there are greater than 100 trillion (10(14)) microbes within the healthy human intestine, and the total number of genes derived from this diverse microbiome exceeds that of the entire human genome by at least 100-fold. Our coexistence with the gut microbiota represents a dynamic and mutually beneficial relationship that is thought to be a major determinant of health and disease. Because of the potential for intestinal microorganisms to induce local and/or systemic inflammation, the intestinal immune system has developed a number of immune mechanisms to protect the host from pathogenic infections while limiting the inflammatory tissue injury that accompanies these immune responses. Failure to properly regulate intestinal mucosal immunity is thought to be responsible for the inflammatory tissue injury observed in the inflammatory bowel diseases (IBD; Crohn disease, ulcerative colitis). An accumulating body of experimental and clinical evidence strongly suggests that IBD results from a dysregulated immune response to components of the normal gut flora in genetically susceptible individuals. The objective of this review is to present our current understanding of the role that enteric microbiota play in intestinal homeostasis and pathogenesis of chronic intestinal inflammation.

Depression-related differences in lean body mass distribution from National Health and Nutrition Examination Survey 2005-2006

BACKGROUND

Although the association between depression and body composition has been widely discussed, the effects of depression on lean body mass (LBM) are unclear. The present study aimed to investigate the association of depression with LBM.

METHODS

The study included 2406 participants aged 18-69 years. The sex and body mass index (BMI) stratified analysis of covariance was performed to compare total LBM and percentage LBM (%LBM) in subjects with different depression score levels. Multiple linear regression analysis was conducted to estimate the association between depression score and serum albumin level.

RESULTS

An analysis of covariance stratified by sex showed that participants with moderate-to-severe depression had significantly decreased total LBM and total and regional %LBM in men, except for total LBM and percentage gynoid LBM, which was observed in women. In the BMI stratified analysis of covariance, depression was significantly associated with decreased total and regional %LBM and with increased total and regional percentage fat body mass. In people with BMI≥25kg/m(2), the associations between depression or depressive syndrome and LBM, and total and regional %LBM are stronger compared to those with BMI<25kg/m(2). Multiple linear regression analysis showed that depression score was significantly negatively associated with serum albumin level.

LIMITATIONS

This is a cross-sectional study based on a general population, some information about clinical diagnosis and medication use is not available.

CONCLUSIONS

Depression had a significant negative association with LBM and serum albumin level.

Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules

The human microbiome is a key contributor to health and development. Yet little is known about the ecological forces that are at play in defining the composition of such host-associated communities. Metagenomics-based studies have uncovered clear patterns of community structure but are often incapable of distinguishing alternative structuring paradigms. In a recent study, we integrated metagenomic analysis with a systems biology approach, using a reverse ecology framework to model numerous human microbiota species and to infer metabolic interactions between species. Comparing predicted interactions with species composition data revealed that the assembly of the human microbiome is dominated at the community level by habitat filtering. Furthermore, we demonstrated that this habitat filtering cannot be accounted for by known host phenotypes or by the metabolic versatility of the various species. Here we provide a summary of our findings and offer a brief perspective on related studies and on future approaches utilizing this metagenomic systems biology framework.

Genetics, genomics and metabolomics: new insights into maternal metabolism during pregnancy

Maternal glucose metabolism during pregnancy differs from the non-gravid state to allow the mother to meet her own and the growing fetus's energy needs. New insights into the mechanisms underlying maternal metabolism during pregnancy are being gained through the use of new 'omics' technologies. This review focuses on the application of genetics/genomics and metabolomics to the study of maternal metabolism during pregnancy. Following the identification of susceptibility genes for Type 2 diabetes through genome-wide association studies, association has been demonstrated of some Type 2 diabetes susceptibility genes with gestational diabetes mellitus, suggesting that the genetic architecture of Type 2 diabetes and gestational diabetes are, in part, similar. More recent genome-wide association studies examining maternal metabolism during pregnancy have demonstrated overlap of genes associated with metabolic traits in the gravid and non-gravid population, as well as genes that appear to be relatively unique to pregnancy. Metabolomics has also been used to profile the metabolic state of women during pregnancy through the multiplexed measurement of many low molecular weight metabolites. Measurement of amino acids and conventional metabolites have demonstrated changes in mothers with higher insulin resistance and glucose similar to changes in non-gravid, insulin-resistant populations, suggesting similarities in the metabolic profile characteristic of insulin resistance and hyperglycaemia in pregnant and non-pregnant populations. Metabolomics and genomics are but a few of the now available high-throughput 'omics' technologies. Future studies that integrate data from multiple technologies will allow an integrated systems biology approach to maternal metabolism during pregnancy.

Effect of diet on the intestinal microbiota and its activity

PURPOSE OF REVIEW

To summarize and discuss recent findings concerning diet-microbiota-health relations.

RECENT FINDINGS

Mouse and other model animal studies have provided detailed insight into host-microbiota interactions, but cannot be extrapolated easily to humans that have different dietary habits, intestinal architecture, and microbiota composition. In spite of the fact that all humans have a personalized microbiome, the discovery of the high-level clusters, such as enterotypes, offer great potential for stratifying individuals in intervention studies based on their intestinal microbiota. A highly diverse microbiota seems to be key to adult human health. Long-term dietary patterns have been found to be associated with specific microbiota compositions and in some cases enterotypes. Fecal transplantations indicate that homeostasis can be restored and indicate that diet-microbiota-induced disorders can be improved by therapeutic modification of the microbiota. The specificity of complex carbohydrate conversion is the driving ecological force in the colon, while competition for sugars with the host is the driver for the small intestinal ecosystem. At both locations, the microbial fermentation of dietary components occurs in trophic chains and insight into these multispecies conversions is essential to understand the impact of diet on health.

SUMMARY

There are clear associations between the microbiota, our diet and our health. However, as microbiota correlations with human health and diet are generally based on baseline comparisons between populations, there is a need for dedicated dietary intervention studies in humans to differentiate between correlation and causality.

Broad scope method for creating humanized animal models for animal health and disease research through antibiotic treatment and human fecal transfer

Traditionally, mouse humanization studies have used human fecal transfer to germ-free animals. This practice requires gnotobiotic facilities and is restricted to gnotobiotic mouse lines, which limits humanized mouse research. We have developed a generalizable method to humanize non germ-free mice using antibiotic treatment and human fecal transfer. The method involves depleting resident intestinal microbiota with broad-spectrum antibiotics, introducing human microbiota from frozen fecal samples by weekly gavage, and maintaining mice in HEPA-filtered microisolator cages. Pyrosequencing cecal microbiota 16S rRNA genes showed that recipient mice adopt a humanized microbiota profile analogous to their human donors, and distinct from mice treated with only antibiotics (no fecal transfer) or untreated control mice. In the humanized mice, 75% of the sequence mass was observed in their respective human donor and conversely, 68% of the donor sequence mass was recovered in the recipient mice. Principal component analyses of GC- and HPLC-separated cecal metabolites were performed to determine effects of transplanted microbiota on the metabolome. Cecal metabolite profiles of mice treated with only antibiotics (no fecal transfer) and control mice were dissimilar from each other and from humanized mice. Metabolite profiles for mice humanized from different donor samples clustered near each other, yet were sufficiently distinct that separate clusters were apparent for each donor. Also, cecal concentrations of 57 metabolites were significantly different between humanization treatments. These data demonstrate that our protocol can be used to humanize non germ-free mice and is sufficiently robust to generate metabolomic differences between mice humanized from different human donors.

Nutritional modulation of the metabonome: applications of metabolic phenotyping in translational nutritional research

PURPOSE OF REVIEW

Metabolic profiling technologies provide a global overview of complex dietary processes. Metabonomic analytical approaches have now been translated into multiple areas of clinical nutritional research based on the widespread adoption of high-throughput mass spectrometry and proton nuclear magnetic resonance spectroscopy. This has generated novel insights into the molecular mechanisms that shape the microbiome-dietary-chronic disease axis.

RECENT FINDINGS

Metabolome-wide association studies have created a new paradigm in nutritional molecular epidemiology and they have highlighted the importance of gut microbial cometabolic processes in the development of cardiovascular disease and diabetes. Targeted analyses are helping to explain the mechanisms by which high-risk diets (such as red meat) modulate disease risk and they are generating novel biomarkers that will serve to re-define how the efficacy of nutritional interventions is assessed. Nutritional metabonome-microbiome interactions have also been defined in extreme dietary states such as obesity and starvation, and they also serve as important models for understanding how the gut microbiome modifies disease risk. Finally, nutritional systems medicine approaches are creating novel insights into the functional components of our diet, and the mechanisms by which they cause disease.

SUMMARY

Diet is an important modulator of the human metabolic phenotype and the analysis of the nutritional metabolome will drive future development of personalized nutritional interventions.

Looking in the Porphyromonas gingivalis cabinet of curiosities: the microbium, the host and cancer association

The past decades of biomedical research have yielded massive evidence for the contribution of the microbiome in the development of a variety of chronic human diseases. There is emerging evidence that Porphyromonas gingivalis, a well-adapted opportunistic pathogen of the oral mucosa and prominent constituent of oral biofilms, best known for its involvement in periodontitis, may be an important mediator in the development of a number of multifactorial and seemingly unrelated chronic diseases, such as rheumatoid arthritis and orodigestive cancers. Orodigestive cancers represent a large proportion of the total malignancies worldwide, and include cancers of the oral cavity, gastrointestinal tract and pancreas. For prevention and/or enhanced prognosis of these diseases, a good understanding of the pathophysiological mechanisms and the interaction between P. gingivalis and host is much needed. With this review, we introduce the currently accumulated knowledge on P. gingivalis's plausible association with cancer as a risk modifier, and present the putative cancer-promoting cellular and molecular mechanisms that this organism may influence in the oral mucosa.

Mechanisms of obesity-induced gastrointestinal neoplasia

Obesity is among the fastest growing diseases worldwide; treatment is inadequate, and associated disorders, including gastrointestinal cancers, have high morbidity and mortality. An increased understanding of the mechanisms of obesity-induced carcinogenesis is required to develop methods to prevent or treat these cancers. In this report, we review the mechanisms of obesity-associated colorectal, esophageal, gastric, and pancreatic cancers and potential treatment strategies.

Metabolism in 2013: The gut microbiota manages host metabolism

In 2013, studies in rodents and humans have reaffirmed the essential role of the gut microbiota in host metabolism. More importantly, several converging results have increased our knowledge regarding the taxa and functions of the gut microbiota that contribute to the management of energy homeostasis, glucose metabolism and metabolic inflammation.

The human microbiome and bile acid metabolism: dysbiosis, dysmetabolism, disease and intervention

INTRODUCTION

Recent evidence indicates that the human gut microbiome plays a significant role in health and disease. Dysbiosis, defined as a pathological imbalance in a microbial community, is becoming increasingly appreciated as a 'central environmental factor' that is both associated with complex phenotypes and affected by host genetics, diet and antibiotic use. More recently, a link has been established between the dysmetabolism of bile acids (BAs) in the gut to dysbiosis.

AREAS COVERED

BAs, which are transformed by the gut microbiota, have been shown to regulate intestinal homeostasis and are recognized as signaling molecules in a wide range of metabolic processes. This review will examine the connection between BA metabolism as it relates to the gut microbiome and its implication in health and disease.

EXPERT OPINION

A disrupted gut microbiome, including a reduction of bile salt hydrolase (BSH)-active bacteria, can significantly impair the metabolism of BAs and may result in an inability to maintain glucose homeostasis as well as normal cholesterol breakdown and excretion. To better understand the link between dysbiosis, BA dysmetabolism and chronic degenerative disease, large-scale metagenomic sequencing studies, metatranscriptomics, metaproteomics and metabolomics should continue to catalog functional diversity in the gastrointestinal tract of both healthy and diseased populations. Further, BSH-active probiotics should continue to be explored as treatment options to help restore metabolic levels.

Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency

Ruminants are completely dependent on their microbiota for feed digestion and consequently, their viability. It is therefore tempting to hypothesize a connection between the composition and abundance of resident rumen bacterial taxa and the physiological parameters of the host. Using a pyrosequencing approach, we characterized the rumen bacterial community composition in 15 dairy cows and their physiological parameters. We analyzed the degree of divergence between the different animals and found that some physiological parameters, such as milk yield and composition, are highly correlated with the abundance of various bacterial members of the rumen microbiome. One apparent finding was a strong correlation between the ratio of the phyla Firmicutes to Bacteroidetes and milk-fat yield. These findings paralleled human studies showing similar trends of increased adiposity with an increase in Bacteroidetes. This correlation remained evident at the genus level, where several genera showed correlations with the animals' physiological parameters. This suggests that the bacterial community has a role in shaping host physiological parameters. A deeper understanding of this process may allow us to modulate the rumen microbiome for better agricultural yield through bacterial community design.

Hyperleucinemia causes hippocampal retromer deficiency linking diabetes to Alzheimer's disease

Type 2 diabetes (T2D) is a major risk factor for late-onset Alzheimer's disease (AD). A variety of metabolic changes related to T2D (e.g. hyperinsulinemia, hyperglycemia, and elevated branched-chain amino acids) have been proposed as mechanistic links, but the basis for this association remains unknown. Retromer-dependent trafficking is implicated in the pathogenesis of AD, and two key retromer proteins, VPS35 and VPS26, are deficient in the hippocampal formation of AD patients. We characterized VPS35 levels in five different mouse models of T2D/obesity to identify specific metabolic factors that could affect retromer in the brain. Mouse models in which hyperleucinemia was present displayed hippocampus-selective retromer deficiency. Wild-type lean mice fed a high leucine diet also developed hippocampal-selective retromer deficiency, and neuronal-like cells grown in high ambient leucine had reduced retromer complex proteins. Our results suggest that hyperleucinemia may account, in part, for the association of insulin resistance/T2D with AD.

Understanding the apothecaries within: the necessity of a systematic approach for defining the chemical output of the human microbiome

The human microbiome harbors a massive diversity of microbes that effectively form an "organ" that strongly influences metabolism and immune function and hence, human health. Although the growing interest in the microbiome has chiefly arisen due to its impact on human physiology, the probable rules of operation are embedded in the roots of microbiology where chemical communication (i.e., with metabolites) is a dominant feature of coexistence. Indeed, recent examples in microbiome research offer the impression that the collective microbiome operates as an "apothecary," creating chemical concoctions that influence health and alter drug response. Although these principles are not unappreciated, the majority of emphasis is on metagenomics and research efforts often omit systematic efforts to interrogate the chemical component of the complex equation between microbial community and host phenotype. One of the reasons for this omission may be due to the inaccessibility to high-breadth, high-throughput, and scalable technologies. Since these technologies are now available, we propose that a more systematic effort to survey the host-microbiota chemical output be embedded into microbiome research as there is strong likelihood, and growing precedence, that this component may often be integral to developing our understanding of these ultimate apothecaries and how they impact human health.

Advances in understanding of bile acid diarrhea

Bile acids (BA) are actively reabsorbed in the terminal ileum by the apical Na(+)-dependent bile salt transporter. This review addresses the epidemiology, pathophysiology, diagnosis and treatment of BA diarrhea (BAD). BAD is typically caused by ileal resection or disease; 25-33% of patients with chronic functional diarrhea or irritable bowel syndrome-diarrhea (IBS-D) have BAD, possibly from deficiency in the ileal hormone, FGF-19, which normally provides feedback inhibition of BA synthesis. Diagnosis of BAD is typically based on reduced BA retention of radiolabeled BA ((75)SeHCAT), increased BA synthesis (serum C4) or increased fecal BA loss. In clinical practice, diagnosis is often based on response to BA sequestrants (e.g., cholestyramine or colesevelam). Diagnostic tests for BA malabsorption (BAM) need to be used more extensively in clinical practice. In the future, farnesoid X receptor agonists that stimulate ileal production of FGF-19 may be alternative treatments of BAD.

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

BACKGROUND

Microbiome-wide gene expression profiling through high-throughput RNA sequencing ('metatranscriptomics') offers a powerful means to functionally interrogate complex microbial communities. Key to successful exploitation of these datasets is the ability to confidently match relatively short sequence reads to known bacterial transcripts. In the absence of reference genomes, such annotation efforts may be enhanced by assembling reads into longer contiguous sequences ('contigs'), prior to database search strategies. Since reads from homologous transcripts may derive from several species, represented at different abundance levels, it is not clear how well current assembly pipelines perform for metatranscriptomic datasets. Here we evaluate the performance of four currently employed assemblers including de novo transcriptome assemblers - Trinity and Oases; the metagenomic assembler - Metavelvet; and the recently developed metatranscriptomic assembler IDBA-MT.

RESULTS

We evaluated the performance of the assemblers on a previously published dataset of single-end RNA sequence reads derived from the large intestine of an inbred non-obese diabetic mouse model of type 1 diabetes. We found that Trinity performed best as judged by contigs assembled, reads assigned to contigs, and number of reads that could be annotated to a known bacterial transcript. Only 15.5% of RNA sequence reads could be annotated to a known transcript in contrast to 50.3% with Trinity assembly. Paired-end reads generated from the same mouse samples resulted in modest performance gains. A database search estimated that the assemblies are unlikely to erroneously merge multiple unrelated genes sharing a region of similarity (<2% of contigs). A simulated dataset based on ten species confirmed these findings. A more complex simulated dataset based on 72 species found that greater assembly errors were introduced than is expected by sequencing quality. Through the detailed evaluation of assembly performance, the insights provided by this study will help drive the design of future metatranscriptomic analyses.

CONCLUSION

Assembly of metatranscriptome datasets greatly improved read annotation. Of the four assemblers evaluated, Trinity provided the best performance. For more complex datasets, reads generated from transcripts sharing considerable sequence similarity can be a source of significant assembly error, suggesting a need to collate reads on the basis of common taxonomic origin prior to assembly.

Role of enteric neurotransmission in host defense and protection of the gastrointestinal tract

Host defense is a vital role played by the gastrointestinal tract. As host to an enormous and diverse microbiome, the gut has evolved an elaborate array of chemical and physicals barriers that allow the digestion and absorption of nutrients without compromising the mammalian host. The control of such barrier functions requires the integration of neural, humoral, paracrine and immune signaling, involving redundant and overlapping mechanisms to ensure, under most circumstances, the integrity of the gastrointestinal epithelial barrier. Here we focus on selected recent developments in the autonomic neural control of host defense functions used in the protection of the gut from luminal agents, and discuss how the microbiota may potentially play a role in enteric neurotransmission. Key recent findings include: the important role played by subepithelial enteric glia in modulating intestinal barrier function, identification of stress-induced mechanisms evoking barrier breakdown, neural regulation of epithelial cell proliferation, the role of afferent and efferent vagal pathways in regulating barrier function, direct evidence for bacterial communication to the enteric nervous system, and microbial sources of enteric neurotransmitters. We discuss these new and interesting developments in our understanding of the role of the autonomic nervous system in gastrointestinal host defense.

Obesity in the United States - dysbiosis from exposure to low-dose antibiotics?

The rapid increase in obesity prevalence in the United States in the last 20 years is unprecedented and not well explained. Here, we explore a hypothesis that the obesity epidemic may be driven by population-wide chronic exposures to low-residue antibiotics that have increasingly entered the American food chain over the same time period. We propose this hypothesis based on two recent bodies of published reports – (1) those that provide evidence for the spread of antibiotics into the American food chain, and (2) those that examine the relationship between the gut microbiota and body physiology. The livestock use of antimicrobial agents has sharply increased in the US over the same 20-year period of the obesity epidemic, especially with the expansion of intensified livestock production, such as the concentrated animal feeding operations. Observational and experimental studies support the idea that changes in the intestinal microbiota exert a profound effect on body physiology. We propose that chronic exposures to low-residue antimicrobial drugs in food could disrupt the equilibrium state of intestinal microbiota and cause dysbiosis that can contribute to changes in body physiology. The obesity epidemic in the United States may be partly driven by the mass exposure of Americans to food containing low-residue antimicrobial agents. While this hypothesis cannot discount the impact of diet and other factors associated with obesity, we believe studies are warranted to consider this possible driver of the epidemic.

Bespoke microbiome therapy to manage plant diseases

Information gathered with advanced nucleotide sequencing technologies, small molecule detection systems and computational biology is revealing that a community of microbes and their genes, now termed "the microbiome," located in gut and rhizosphere, is responsible for maintaining the health of human beings and plants, respectively. Within the complete microbiome a "core-microbiome" exists that plays the pivotal role in well being of humans and plants. Recent studies in medicine have shown that an artificial mixture of bacteria representing the core gut microbiome of healthy person when transferred into gut of diseased person results in re-establishment of normal microflora in the latter leading to alleviation from diseased condition. In agriculture, though not exactly in similar manner as in medicine, success in plant disease management has been achieved through transfer of microbiome by mixing disease suppressive soils with disease conducive soils. A study more similar to artificial gut microbiome transfer in medical field has been recently reported in agriculture, in which transfer of microbiome via soil solutions (filtered and unfiltered) has shown ability to alleviate drought stress in Arabidopsis thaliana. However, the exact practice of transferring artificially cultivated core-microbiome as in medicine has not thus far been attempted in plant disease management. Nonetheless, as the gut and rhizosphere microbiome are known to share many common traits, there exists a good scope for accomplishing similar studies in agriculture. Based upon the information drawn from all recent works in microbiome studies of gut and rhizosphere, we propose that tailor-made core-microbiome transfer therapy can be a success in agriculture too and it could become a viable strategy for management of plant diseases in future.

Emerging roles of the microbiome in cancer

Gene-environment interactions underlie cancer susceptibility and progression. Yet, we still have limited knowledge of which environmental factors are important and how they function during tumorigenesis. In this respect, the microbial communities that inhabit our gastrointestinal tract and other body sites have been unappreciated until recently. However, our microbiota are environmental factors that we are exposed to continuously, and human microbiome studies have revealed significant differences in the relative abundance of certain microbes in cancer cases compared with controls. To characterize the function of microbiota in carcinogenesis, mouse models of cancer have been treated with antibiotics. They have also been maintained in a germfree state or have been colonized with specific bacteria in specialized (gnotobiotic) facilities. These studies demonstrate that microbiota can increase or decrease cancer susceptibility and progression by diverse mechanisms such as by modulating inflammation, influencing the genomic stability of host cells and producing metabolites that function as histone deacetylase inhibitors to epigenetically regulate host gene expression. One might consider microbiota as tractable environmental factors because they are highly quantifiable and relatively stable within an individual compared with our exposures to external agents. At the same time, however, diet can modulate the composition of microbial communities within our gut, and this supports the idea that probiotics and prebiotics can be effective chemoprevention strategies. The trajectory of where the current work is headed suggests that microbiota will continue to provide insight into the basic mechanisms of carcinogenesis and that microbiota will also become targets for therapeutic intervention.

Genomic and epigenomic regulation of adipose tissue inflammation in obesity

Chronic inflammation of adipose tissue is viewed as a hallmark of obesity and contributes to the development of type 2 diabetes and cardiovascular disease. According to current models, nutrient excess causes metabolic and structural changes in adipocytes, which initiate transcriptional programs leading to the expression of inflammatory molecules and the subsequent recruitment of immune cells. Recent advances in deciphering the underlying mechanisms revealed that key regulatory events occur at the genomic and epigenomic levels. Here we review these advances because they offer a better understanding of the mechanisms behind the complex obesogenic program in adipose tissue, and because they may help in defining new therapeutic strategies that prevent, restrict, and resolve inflammation in the context of obesity.

Teaching about twins: college courses and public lectures

The present article describes teaching experiences and observations in college courses and public lectures on twins. It is concluded that much more information about twins, at both research and practical levels, requires general dissemination. This discussion is followed by reviews of recent twin research on the topics of obesity control, post-zygotic mutation, in vitro fertilization, and schisis-associated defects. Media reports of twins accused of rape, infant Chinese twins sold separately for profit, a twin CEO, and twins pursuing the same career are presented.

Ingestion of bacterial lipopolysaccharide inhibits peripheral taste responses to sucrose in mice

A fundamental role of the taste system is to discriminate between nutritive and toxic foods. However, it is unknown whether bacterial pathogens that might contaminate food and water modulate the transmission of taste input to the brain. We hypothesized that exogenous, bacterially-derived lipopolysaccharide (LPS), modulates neural responses to taste stimuli. Neurophysiological responses from the chorda tympani nerve, which innervates taste cells on the anterior tongue, were unchanged by acute exposure to LPS. Instead, neural responses to sucrose were selectively inhibited in mice that drank LPS during a single overnight period. Decreased sucrose sensitivity appeared 7days after LPS ingestion, in parallel with decreased lingual expression of Tas1r2 and Tas1r3 transcripts, which are translated to T1R2+T1R3 subunits forming the sweet taste receptor. Tas1r2 and Tas1r3 mRNA expression levels and neural responses to sucrose were restored by 14 days after LPS consumption. Ingestion of LPS, rather than contact with taste receptor cells, appears to be necessary to suppress sucrose responses. Furthermore, mice lacking the Toll-like receptor (TLR) 4 for LPS were resistant to neurophysiological changes following LPS consumption. These findings demonstrate that ingestion of LPS during a single period specifically and transiently inhibits neural responses to sucrose. We suggest that LPS drinking initiates TLR4-dependent hormonal signals that downregulate sweet taste receptor genes in taste buds. Delayed inhibition of sweet taste signaling may influence food selection and the complex interplay between gastrointestinal bacteria and obesity.

Frequent replenishment sustains the beneficial microbiome of Drosophila melanogaster

We report that establishment and maintenance of the Drosophila melanogaster microbiome depend on ingestion of bacteria. Frequent transfer of flies to sterile food prevented establishment of the microbiome in newly emerged flies and reduced the predominant members, Acetobacter and Lactobacillus spp., by 10- to 1,000-fold in older flies. Flies with a normal microbiome were less susceptible than germfree flies to infection by Serratia marcescens and Pseudomonas aeruginosa. Augmentation of the normal microbiome with higher populations of Lactobacillus plantarum, a Drosophila commensal and probiotic used in humans, further protected the fly from infection. Replenishment represents an unexplored strategy by which animals can sustain a gut microbial community. Moreover, the population behavior and health benefits of L. plantarum resemble features of certain probiotic bacteria administered to humans. As such, L. plantarum in the fly gut may serve as a simple model for dissecting the population dynamics and mode of action of probiotics in animal hosts.

Previous studies have defined the composition of the Drosophila melanogaster microbiome in laboratory and wild-caught flies. Our study advances current knowledge in this field by demonstrating that Drosophila must consume bacteria to establish and maintain its microbiome. This finding suggests that the dominant Drosophila symbionts remain associated with their host because of repeated reintroduction rather than internal growth. Furthermore, our study shows that one member of the microbiome, Lactobacillus plantarum, protects the fly from intestinal pathogens. These results suggest that, although not always present, the microbiota can promote salubrious effects for the host. In sum, our work provides a previously unexplored mechanism of microbiome maintenance and an in vivo model system for investigating the mechanisms of action of probiotic bacteria.