Murine gut microbiota and transcriptome are diet dependent

A GLM-based zero-inflated generalized Poisson factor model for analyzing microbiome data

Motivation

High-throughput sequencing technology facilitates the quantitative analysis of microbial communities, improving the capacity to investigate the associations between the human microbiome and diseases. Our primary motivating application is to explore the association between gut microbes and obesity. The complex characteristics of microbiome data, including high dimensionality, zero inflation, and over-dispersion, pose new statistical challenges for downstream analysis.

Results

We propose a GLM-based zero-inflated generalized Poisson factor analysis (GZIGPFA) model to analyze microbiome data with complex characteristics. The GZIGPFA model is based on a zero-inflated generalized Poisson (ZIGP) distribution for modeling microbiome count data. A link function between the generalized Poisson rate and the probability of excess zeros is established within the generalized linear model (GLM) framework. The latent parameters of the GZIGPFA model constitute a low-rank matrix comprising a low-dimensional score matrix and a loading matrix. An alternating maximum likelihood algorithm is employed to estimate the unknown parameters, and cross-validation is utilized to determine the rank of the model in this study. The proposed GZIGPFA model demonstrates superior performance and advantages through comprehensive simulation studies and real data applications.

Breastfeeding is associated with enhanced intestinal gluconeogenesis in infants

BACKGROUND

Breastfeeding (BF) confers metabolic benefits to infants, including reducing risks of metabolic syndrome such as obesity and diabetes later in life. However, the underlying mechanism is not yet fully understood. Hence, we aim to investigate the impacts of BF on the metabolic organs of infants.

METHODS

Previous literatures directly studying the influences of BF on offspring's metabolic organs in both animal models and humans were comprehensively reviewed. A microarray dataset of intestinal gene expression comparing infants fed on breastmilk versus formula milk was analyzed.

RESULTS

Reanalysis of microarray data showed that BF is associated with enhanced intestinal gluconeogenesis in infants. This resembles observations in other mammalian species showing that BF was also linked to increased gluconeogenesis.

CONCLUSIONS

BF is associated with enhanced intestinal gluconeogenesis in infants, which may underpin its metabolic advantages through finetuning metabolic homeostasis. This observation seems to be conserved across species, hinting its biological significance.

Impact of Maternal Mediterranean-Type Diet Adherence on Microbiota Composition and Epigenetic Programming of Offspring

Understanding how maternal diet affects in utero neonatal gut microbiota and epigenetic regulation may provide insight into disease origins and long-term health. The impact of Mediterranean diet pattern adherence (MDA) on fetal gut microbiome and epigenetic regulation was assessed in 33 pregnant women. Participants completed a validated food frequency questionnaire in each trimester of pregnancy; the alternate Mediterranean diet (aMED) score was applied. Umbilical cord blood, placental tissue, and neonatal meconium were collected from offspring. DNA methylation patterns were probed using the Illumnia EPICarray Methylation Chip in parturients with high versus low MDA. Meconium microbial abundance in the first 24 h after birth was identified using 16s rRNA sequencing and compared among neonates born to mothers with high and low aMED scores. Twenty-one mothers were classified as low MDA and 12 as high MDA. Pasteurellaceae and Bacteroidaceae trended towards greater abundance in the high-MDA group, as well as other short-chain fatty acid-producing species. Several differentially methylated regions varied between groups and overlapped gene regions including NCK2, SNED1, MTERF4, TNXB, HLA-DPB, BAG6, and LMO3. We identified a beneficial effect of adherence to a Mediterranean diet on fetal in utero development. This highlights the importance of dietary counseling for mothers and can be used as a guide for future studies of meconium and immuno-epigenetic modulation.

Biomarkers of necrotizing enterocolitis in the era of machine learning and omics

Necrotizing enterocolitis (NEC) continues to be a major cause of morbidity and mortality in preterm infants. Despite decades of research in NEC, no reliable biomarkers can accurately diagnose NEC or predict patient prognosis. The recent emergence of multi-omics could potentially shift NEC biomarker discovery, particularly when evaluated using systems biology techniques. Furthermore, the use of machine learning and artificial intelligence in analyzing this 'big data' could enable novel interpretations of NEC subtypes, disease progression, and potential therapeutic targets, allowing for integration with personalized medicine approaches. In this review, we evaluate studies using omics technologies and machine learning in the diagnosis of NEC. Future implications and challenges inherent to the field are also discussed.

A Single Strain of Lactobacillus (CGMCC 21661) Exhibits Stable Glucose- and Lipid-Lowering Effects by Regulating Gut Microbiota

Type 2 diabetes (T2D) is usually accompanied by obesity and nonalcoholic fatty-liver-related insulin resistance. The link between T2D and dysbiosis has been receiving increasing attention. Probiotics can improve insulin sensitivity by regulating imbalances in microbiota, but efficacy varies based on the probiotic used. This study screened the main strain in the feces of healthy adult mice and found it to be a new Lactobacillus (abbreviated as Lb., named as CGMCC No. 21661) after genetic testing. We designed the most common Bifidobacterium longum subsp. longum (CGMCC1.2186, abbreviated as B. longum. subsp.), fecal microbiota transplantation (FMT), and Lb. CGMCC No. 21661 protocols to explore the best way for modulating dysbiosis to improve T2D. After 6 weeks of gavage in T2D mice, it was found that all three protocols had a therapeutic alleviating effect. Among them, compared with the B. longum. subsp. and FMT, the Lb. CGMCC No. 21661 showed a 1- to 2-fold decrease in blood glucose (11.84 ± 1.29 mmol/L, p < 0.05), the lowest HOMA-IR (p < 0.05), a 1 fold increase in serum glucagon-like peptide-1 (5.84 ± 1.1 pmol/L, p < 0.05), and lowest blood lipids (total cholesterol, 2.21 ± 0.68 mmol/L, p < 0.01; triglycerides, 0.4 ± 0.15 mmol/L, p < 0.01; Low-density lipoprotein cholesterol, 0.53 ± 0.16 mmol/L, p < 0.01). In addition, tissue staining in the Lb. CGMCC No. 21661 showed a 2- to 3-fold reduction in T2D-induced fatty liver (p < 0.0001), a 1- to 2-fold decrease in pancreatic apoptotic cells (p < 0.05), and a significant increase in colonic mucus layer thickness (p < 0.05) compared with the B. longum. subsp. and FMT. The glucose and lipid lowering effects of this Lb. CGMCC No. 21661 indicate that it may provide new ideas for the treatment of diabetes.

Intestinal Epithelial Barrier Function and Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is a major cause of morbidity and mortality in premature infants. NEC is characterized by intestinal tissue inflammation and necrosis. The intestinal barrier is altered in NEC, which potentially contributes to its pathogenesis by promoting intestinal bacterial translocation and stimulating the inflammatory response. In premature infants, many components of the intestinal barrier are immature. This article reviews the different components of the intestinal barrier and how their immaturity contributes to intestinal barrier dysfunction and NEC.

Epigallocatechin Gallate (EGCG) Promotes the Immune Function of Ileum in High Fat Diet Fed Mice by Regulating Gut Microbiome Profiling and Immunoglobulin Production

This study aimed to investigate the regulatory effect of epigallocatechin gallate (EGCG) on the composition of the gut microbiome, the transcriptomic profiling of ileum, and their interplay in high fat diet (HFD) induced obese mice. Intragastric administration of EGCG to C57BL/6J mice for 14 consecutive weeks remarkably decreased HFD induced excessive fat deposition (p < 0.001), and the increment of serum TG, TC, HDL-C (p < 0.05), as well as improved glucose tolerance (p < 0.001). EGCG shifted the gut microbiota mainly by elevating the relative abundance of Parasutterrlla, Bacteroides, and Akkermansia (p < 0.01), decreasing that of norank_f_Erysipelotrichaceae, unclassified_f_Ruminococcaceae, Anaerotruncus, Roseburia, norank_Lachnospiraceae, and Lachnospiraceae_UCG_006 (p < 0.01) at the genus level. In addition, EGCG affected the transcriptomic profiling of ileum, and the differentially expressed (DE) genes after HFD or/and EGCG treatment were mostly enriched in the immune reaction of ileum, such as the GO term of “immune effector process” and “phagocytosis, recognition.” Furthermore, the KEGG category of “immune diseases,” “immune system,” and “infection diseases: bacterial” were commonly enriched by the DE genes of the two treatments. Among those DE genes, 16 immunoglobulins heavy chain variable region encoded genes (Ighvs) and other immunity-related genes, such as complement component 2 (C2), interferon-induced transmembrane protein 1 (Iftm1), polymeric immunoglobulin receptor (pigR), and alanyl aminopeptidase (Anpep), were highly correlated with the shifted microbes in the gut (p < 0.05, absolute r > 0.5). Overall, the results suggested that EGCG ameliorated the HFD induced metabolic disorder mainly by regulating gut microbiome profiling and the immunoglobulin production of ileum, while the genes expressed in the ileum, especially Ighvs, C2, Iftm1, pigR, and Anpep, might play important roles in coordinating the immunity of mice regarding the gut microbes and the host interactions.

Soil exposure accelerates recovery of the gut microbiota in antibiotic-treated mice

Environmental exposure to low cleanliness prevents the occurrence of allergic diseases and increases the richness and diversity of the intestinal microbiota. Antibiotics are widely used in clinical infection therapy but destroy the balance of the gut microbiota. In this study, the effects of cleanliness of the living environment on the gut microbiota are evaluated after administration of antibiotics. The patterns of gut microbiota are compared before and after antibiotic treatment in mice living in a higher standard clean environment with those of mice living in an unclean environment. The results show that dust exposure prevents the reduction in gut microbiota diversity following antibiotic treatment in mice and impaired structural changes in the gut microbiota. Additionally, dust exposure accelerates the recovery of the gut microbiota, regardless of consumption of a high-fat or normal diet. An unsanitary environment can reduce the effects of antibiotics on intestinal microecology in mice. These findings provide insights into approaches for regulating antibiotic-induced symbiosis of the gut microbiota and preventing diseases.

Chronic Critical Illness and PICS Nutritional Strategies

The nutritional hallmark of chronic critical illness (CCI) after sepsis is persistent inflammation, immunosuppression, and catabolism syndrome (PICS), which results in global resistance to the anabolic effect of nutritional supplements. This ultimately leaves these patients in a downward phenotypic spiral characterized by cachexia with profound weakness, decreased capacity for rehabilitation, and immunosuppression with the propensity for sepsis recidivism. The persistent catabolism is driven by a pathologic low-grade inflammation with the inability to return to homeostasis and by ongoing increased energy expenditure. Better critical care support systems and advances in technology have led to increased intensive care unit (ICU) survival, but CCI due to PICS with poor long-term outcomes has emerged as a frequent phenotype among ICU sepsis survivors. Unfortunately, therapies to mitigate or reverse PICS-CCI are limited, and recent evidence supports that these patients fail to respond to early ICU evidence-based nutrition protocols. A lack of randomized controlled trials has limited strong recommendations for nutrition adjuncts in these patients. However, based on experience in other conditions characterized by a similar phenotype, immunonutrients aimed at counteracting inflammation, immunosuppression, and catabolism may be important for improving outcomes in PICS-CCI patients. This manuscript intends to review several immunonutrients as adjunctive therapies in treating PICS-CCI.

Maternal Intake of Dietary Fat Pre-Programs Offspring's Gut Ecosystem Altering Colonization Resistance and Immunity to Infectious Colitis in Mice

SCOPE

The transgenerational impact of dietary fat remains unclear. Here, the role of maternal fat consumption as a modulator of gut microbial communities and infectious disease outcomes in their offspring is explored.

METHODS AND RESULTS

C57BL/6 mice are fed isocaloric high-fat diets throughout breeding, gestation and lactation. Diets contained either milk fat (MF), olive oil (OO) or corn oil (CO), with or without fish oil. The pups born to maternally exposed mice are weaned on to chow and raised into adulthood. At 8 weeks, the offsprings are either euthanized for colonic 16S rRNA analysis or challenged with the enteric pathogen, Citrobacter rodentium. Maternal CO exposure resulted in unique clustering of bacterial communities in offspring compared with MF and OO. Diets rich in CO reduced survival in offspring challenged with C. rodentium. The addition of fish oil did not improve mortality caused by CO and worsened disease outcomes when combined with OO. Unlike the unsaturated diets, MF is protective with and without fish oil.

CONCLUSIONS

Overall, these data reveal that maternal intake of fatty acids do have transgenerational impacts on their offspring's bacteriome and enteric infection risk. Based on this study, saturated fats should be included in maternal diets.

Metatranscriptomic analyses of the oral microbiome

Although the composition of the oral human microbiome is now well studied, regulation of genes within oral microbial communities remains mostly uncharacterized. Current concepts of periodontal disease and caries highlight the importance of oral biofilms and their role as etiological agents of those diseases. Currently, there is increased interest in exploring and characterizing changes in the composition and gene-expression profiles of oral microbial communities. These efforts aim to identify changes in functional activities that could explain the transition from health to disease and the reason for the chronicity of those infections. It is now clear that the functions of distinct species within the subgingival microbiota are intimately intertwined with the rest of the microbial community. This point highlights the relevance of examining the expression profile of specific species within the subgingival microbiota in the case of periodontal disease or caries lesions, in the context of the other members of the biofilm in vivo. Metatranscriptomic analysis of the oral community is the starting point for identifying environmental signals that modulate the shift in metabolism of the community from commensal to dysbiotic. These studies give a snapshot of the expression patterns of microbial communities and also allow us to determine triggers to diseases. For example, in the case of caries, studies have unveiled a potential new pathway of sugar metabolism, namely the use of sorbitol as an additional source of carbon by Streptococcus mutans; and in the case of periodontal disease, high levels of extracellular potassium could be a signal of disease. Longitudinal studies are needed to identify the real markers of the initial stages of caries and periodontal disease. More information on the gene-expression profiles of the host, along with the patterns from the microbiome, will lead to a clearer understanding of the modulation of health and disease. This review presents a summary of these initial studies, which have opened the door to a new understanding of the dynamics of the oral community during the dysbiotic process in the oral cavity.

A Microbe Associated with Sleep Revealed by a Novel Systems Genetic Analysis of the Microbiome in Collaborative Cross Mice

The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host-microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7m +/+ Leprdb/J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms.

DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq

Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.

Dietary Fatty Acids and Host-Microbial Crosstalk in Neonatal Enteric Infection

Human milk is the best nutritional choice for infants. However, in instances where breastfeeding is not possible, infant formulas are used as alternatives. While formula manufacturers attempt to mimic the performance of human breast milk, formula-fed babies consistently have higher incidences of infection from diarrheal diseases than those breastfed. Differences in disease susceptibility, progression and severity can be attributed, in part, to nutritional fatty acid differences between breast milk and formula. Despite advances in our understanding of breast milk properties, formulas still present major differences in their fatty acid composition when compared to human breast milk. In this review, we highlight the role of distinct types of dietary fatty acids in modulating host inflammation, both directly and through the microbiome-immune nexus. We present evidence that dietary fatty acids influence enteric disease susceptibility and therefore, altering the fatty acid composition in formula may be a potential strategy to improve infectious outcomes in formula-fed infants.

Feeding Pasteurized Waste Milk to Preweaned Dairy Calves Changes Fecal and Upper Respiratory Tract Microbiota

In the present study bacterial communities from both, the gastrointestinal and respiratory tract of pre-weaned dairy calves fed two different milk-feeding programs were characterized using 16S rRNA gene sequencing. Twenty female Holstein calves (38.8 ± 1.40 kg of BW) were fed pasteurized waste milk (pWM) containing residues of various antimicrobials. Twenty additional calves (38.1 ± 1.19 kg of BW) were fed milk replacer (MR) with similar nutrient composition (27.5% crude protein, 32.1% fat) compared to waste milk (28.6% crude protein, 30.0% fat) from day 1 to weaning at day 49 of study. Fecal samples and nasal swabs were collected on day 42 only from calves that were not treated with therapeutic antibiotics throughout the study, which were 8 MR and 10 pWM calves. To assess the impact of the two feeding regimes on the fecal and nasal microbiota, α and β-diversity measures were calculated, and the relative abundance of operational taxonomic units (OTUs) at different taxonomic levels was determined for each sample. In general, Chao1, PD Whole Tree, and Shannon diversity indices were similar for the fecal and nasal bacterial communities of calves regardless of the feeding regime. However, principal coordinate analysis based on unweighted Unifrac distances indicated differences in the structure of bacterial communities of calves fed milk replacer compared with those from calves fed pasteurized waste milk. The relative abundance of the Streptococcaceae family and the genus Histophilus was greater (P < 0.05) in the nasal microbiota of calves fed milk replacer than in those fed pasteurized waste milk. However, the genus Prevotella tended (P = 0.06) to be more relatively abundant in the respiratory tract of calves fed pasteurized waste milk than in those fed milk replacer. Differences in relative abundances of bacterial taxa in gut microbiota were only observed at the phylum level, suggesting that antimicrobial residues present in waste milk have a non-specific influence at a lower taxonomical level.

Pathophysiology of Necrotizing Enterocolitis: An Update

NEC is a devastating disease that, once present, is very difficult to treat. In the absence of an etiologic treatment, preventive measures are required. Advances in decoding the pathophysiology of NEC are being made but a more comprehensive understanding is needed for the targeting of preventative strategies. A better definition of the disease as well as diagnostic criteria are needed to be able to specifically label a disease as NEC. Multiple environmental factors combined with host susceptibility appear to contribute to enhanced risks for developing this disease. Several different proximal pathways are involved, all leading to a common undesired outcome: Intestinal necrosis. The most common form of this disease appears to involve inflammatory pathways that are closely meshed with the intestinal microbiota, where a dysbiosis may result in dysregulated inflammation. The organisms present in the intestinal tract prior to the onset of NEC along with their diversity and functional capabilities are just beginning to be understood. Fulfillment of postulates that support causality for particular microorganisms is needed if bacteriotherapies are to be intelligently applied for the prevention of NEC. Identification of molecular effector pathways that propagate inflammation, understanding of, even incipient role of genetic predisposition and of miRNAs may help solve the puzzle of this disease and may bring the researchers closer to finding a treatment. Despite recent progress, multiple limitations of the current animal models, difficulties related to studies in humans, along with the lack of a "clear" definition will continue to make it a very challenging disease to decipher.

Rumen bacterial communities can be acclimated faster to high concentrate diets than currently implemented feedlot programs

Aims

Recent studies have demonstrated RAMP^®, a complete starter feed, to have beneficial effects for animal performance. However, how RAMP may elicit such responses is unknown. To understand if RAMP adaptation results in changes in the rumen bacterial community that can potentially affect animal performance, we investigated the dynamics of rumen bacterial community composition in corn‐adapted and RAMP‐adapted cattle.

Methods and Results

During gradual acclimation of the rumen bacterial communities, we compared the bacterial community dynamics in corn and RAMP‐adapted using 16S rRNA gene amplicon sequencing. Significant shifts in bacterial populations across diets were identified. The shift in corn‐adapted animals occurred between adaptation step3 and step4, whereas in RAMP‐adapted cattle, the shift occurred between step2 and step3. As the adaptation program progressed, the abundance of OTUs associated with family Prevotellaceae and S24‐7 changed in corn‐adapted animals. In RAMP‐adapted animals, OTUs belonging to family Ruminococcaceae and Lachnospiraceae changed in abundance.

Conclusions

Rumen bacteria can be acclimated faster to high concentrate diets, such as RAMP, than traditional adaptation programs and the speed of bacterial community acclimation depends on substrate composition.

Significance and Impact of the Study

These findings may have implications for beef producers to reduce feedlot costs, as less time adapting animals would result in lower feed costs. However, animal feeding behavior patterns and other factors must be considered.

Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design

Targeted manipulation of the gut flora is increasingly being recognized as a means to improve human health. Yet, the temporal dynamics and intra- and interindividual heterogeneity of the microbiome represent experimental limitations, especially in human cross-sectional studies. Therefore, rodent models represent an invaluable tool to study the host–microbiota interface. Progress in technical and computational tools to investigate the composition and function of the microbiome has opened a new era of research and we gradually begin to understand the parameters that influence variation of host-associated microbial communities. To isolate true effects from confounding factors, it is essential to include such parameters in model intervention studies. Also, explicit journal instructions to include essential information on animal experiments are mandatory. The purpose of this review is to summarize the factors that influence microbiota composition in mice and to provide guidelines to improve the reproducibility of animal experiments.

Given the unmet need for standardizing the experimental work flow related to gut microbial research in animals, guidelines are required to isolate true effects from confounding factors.

Environmental-mediated intestinal homeostasis in neonatal mice

BACKGROUND

Immunoglobulin A (IgA) plays a key role in coating luminal antigens and preventing translocation of harmful bacteria. The aryl hydrocarbon receptor (AhR) is a basic helix-loop-helix transcription factor that when stimulated activates factors important for barrier function and intestinal homeostasis. We hypothesize that AhR signaling is critical for establishment of intestinal homeostasis in neonates.

MATERIAL AND METHODS

Mice: C57BL/6 (B6) AhR+/+ wild type (WT), B6.AhR-/- Aryl-hydrocarbon receptor knockout (KO), and B6.AhR+/+ raised on an AhR ligand-free diet (AhR LF). Enzyme-linked immunosorbent assay was used to measure fecal and serum IgA levels. Bacterial translocation was measured by culturing the mesenteric lymph nodes.

RESULTS

Two week old KO mice had significantly less fecal IgA compared with WT (and AhR LF, P value = 0.0393. The amount of IgA from the gastric contents of 2-wk-old mice was not significantly different. At age 8 wk, AhR LF mice had significantly less fecal IgA than WT and KO P value = 0.0077. At 2 wk, KO mice had significantly higher levels of bacterial translocation and at 8 wk AhR LF had significantly higher levels of bacterial translocation compared with WT.

CONCLUSIONS

In neonatal mice, the lack of AhR signaling is associated with loss of intestinal homeostasis, evidenced by decreased levels of IgA and increased bacterial translocation. In adult mice, exogenous AhR ligand and not receptor signaling is necessary for maintenance of intestinal integrity.

Sexually dimorphic characteristics of the small intestine and colon of prepubescent C57BL/6 mice

BACKGROUND

There is increasing appreciation for sexually dimorphic effects, but the molecular mechanisms underlying these effects are only partially understood. In the present study, we explored transcriptomics and epigenetic differences in the small intestine and colon of prepubescent male and female mice. In addition, the microbiota composition of the colonic luminal content has been examined.

METHODS

At postnatal day 14, male and female C57BL/6 mice were sacrificed and the small intestine, colon and content of luminal colon were isolated. Gene expression of both segments of the intestine was analysed by microarray analysis. DNA methylation of the promoter regions of selected sexually dimorphic genes was examined by pyrosequencing. Composition of the microbiota was explored by deep sequencing.

RESULTS

Sexually dimorphic genes were observed in both segments of the intestine of 2-week-old mouse pups, with a stronger effect in the small intestine. Amongst the total of 349 genes displaying a sexually dimorphic effect in the small intestine and/or colon, several candidates exhibited a previously established function in the intestine (i.e. Nts, Nucb2, Alox5ap and Retnlγ). In addition, differential expression of genes linked to intestinal bowel disease (i.e. Ccr3, Ccl11 and Tnfr) and colorectal cancer development (i.e. Wt1 and Mmp25) was observed between males and females. Amongst the genes displaying significant sexually dimorphic expression, nine genes were histone-modifying enzymes, suggesting that epigenetic mechanisms might be a potential underlying regulatory mechanism. However, our results reveal no significant changes in DNA methylation of analysed CpGs within the selected differentially expressed genes. With respect to the bacterial community composition in the colon, a dominant effect of litter origin was found but no significant sex effect was detected. However, a sex effect on the dominance of specific taxa was observed.

CONCLUSIONS

This study reveals molecular dissimilarities between males and females in the small intestine and colon of prepubescent mice, which might underlie differences in physiological functioning and in disease predisposition in the two sexes.

Systematic analysis of the association between gut flora and obesity through high-throughput sequencing and bioinformatics approaches

Eighty-one stool samples from Taiwanese were collected for analysis of the association between the gut flora and obesity. The supervised analysis showed that the most, abundant genera of bacteria in normal samples (from people with a body mass index (BMI) ≤ 24) were Bacteroides (27.7%), Prevotella (19.4%), Escherichia (12%), Phascolarctobacterium (3.9%), and Eubacterium (3.5%). The most abundant genera of bacteria in case samples (with a BMI ≥ 27) were Bacteroides (29%), Prevotella (21%), Escherichia (7.4%), Megamonas (5.1%), and Phascolarctobacterium (3.8%). A principal coordinate analysis (PCoA) demonstrated that normal samples were clustered more compactly than case samples. An unsupervised analysis demonstrated that bacterial communities in the gut were clustered into two main groups: N-like and OB-like groups. Remarkably, most normal samples (78%) were clustered in the N-like group, and most case samples (81%) were clustered in the OB-like group (Fisher's P  value = 1.61E − 07). The results showed that bacterial communities in the gut were highly associated with obesity. This is the first study in Taiwan to investigate the association between human gut flora and obesity, and the results provide new insights into the correlation of bacteria with the rising trend in obesity.

Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome

We sought to determine whether a low fermentable substrate diet (LFSD) decreases abdominal pain frequency in children with irritable bowel syndrome (IBS) and to identify potential microbial factors related to diet efficacy. Pain symptoms, stooling characteristics, breath hydrogen and methane, whole intestinal transit time, stool microbiome, and metabolite composition were collected and/or documented in eight children with IBS at baseline and during one week of an LFSD intervention. Pain frequency (P<0.05), pain severity (P<0.05), and pain-related interference with activities (P<0.05) decreased in the subjects while on the LFSD. Responders vs. non-responders: four children (50%) were identified as responders (> 50% decrease in abdominal pain frequency while on the LFSD). There were no differences between responders and non-responders with respect to hydrogen production, methane production, stooling characteristics, or gut transit time. Responders were characterized by increased pre-LFSD abundance of bacterial taxa belonging to the genera Sporobacter (P<0.05) and Subdoligranulum (P<0.02) and decreased abundance of taxa belonging to Bacteroides (P<0.05) relative to non-responders. In parallel, stool metabolites differed between responders and non-responders and were associated with differences in microbiome composition. These pilot study results suggest that an LFSD may be effective in decreasing GI symptoms in children with IBS. Microbial factors such as gut microbiome composition and stool metabolites while on the diet may relate to LFSD efficacy.

Excess body weight during pregnancy and offspring obesity: potential mechanisms

The rates of child and adult obesity have increased in most developed countries over the past several decades. The health consequences of obesity affect both physical and mental health, and the excess body weight can be linked to an elevated risk for developing type 2 diabetes, cardiovascular problems, and depression. Among the factors that can influence the development of obesity are higher infant weights and increased weight gain, which are associated with higher risk for excess body weight later in life. In turn, mother's excess body weight during and after pregnancy can be linked to the risk for offspring overweight and obesity through dietary habits, mode of delivery and feeding, breast milk composition, and through the influence on infant gut microbiota. This review considers current knowledge of these potential mechanisms that threaten to create an intergenerational cycle of obesity.

Proteobacteria-specific IgA regulates maturation of the intestinal microbiota

The intestinal microbiota changes dynamically from birth to adulthood. In this study we identified γ-Proteobacteria as a dominant phylum present in newborn mice that is suppressed in normal adult microbiota. The transition from a neonatal to a mature microbiota was in part regulated by induction of a γ-Proteobacteria-specific IgA response. Neocolonization experiments in germ-free mice further revealed a dominant Proteobacteria-specific IgA response triggered by the immature microbiota. Finally, a role for B cells in the regulation of microbiota maturation was confirmed in IgA-deficient mice. Mice lacking IgA had persistent intestinal colonization with γ-Proteobacteria that resulted in sustained intestinal inflammation and increased susceptibility to neonatal and adult models of intestinal injury. Collectively, these results identify an IgA-dependent mechanism responsible for the maturation of the intestinal microbiota.

The colon: from banal to brilliant

The colon serves as the habitat for trillions of microbes, which it must maintain, regulate, and sequester. This is managed by what is termed the mucosal barrier. The mucosal barrier separates the gut flora from the host tissues; regulates the absorption of water, electrolytes, minerals, and vitamins; and facilitates host-flora interactions. Colonic homeostasis depends on a complex interaction between the microflora and the mucosal epithelium, immune system, vasculature, stroma, and nervous system. Disruptions in the colonic microenvironment such as changes in microbial composition, epithelial cell function/proliferation/differentiation, mucus production/makeup, immune function, diet, motility, or blood flow may have substantial local and systemic consequences. Understanding the complex activities of the colon in health and disease is important in drug development, as xenobiotics can impact all segments of the colon. Direct and indirect effects of pharmaceuticals on intestinal function can produce adverse findings in laboratory animals and humans and can negatively impact drug development. This review will discuss normal colon homeostasis with examples, where applicable, of xenobiotics that disrupt normal function.

Nutrition, microbiomes, and intestinal inflammation

PURPOSE OF REVIEW

To present and evaluate the recent findings that contribute to our understanding of the functional impact of diet on the enteric microbiome and outcomes of disease.

RECENT FINDINGS

Nutrients in excess and in deficiency have significant impact on gut microbial communities in both rodents and humans, acting directly on the microbiota or indirectly via altering host physiology. Furthermore, the effects of diet on the microbiome in determining health or disease can differ substantially depending on the age and environment of the individual.

SUMMARY

Dietary compounds can have profound short-term and long-term effects on the assemblage of the gut microbiome, which in turn affects the host-microbe interactions critically important for intestinal, metabolic, and immune homeostasis. Until recently, the mechanisms underlying these effects were poorly understood. However, new insights have now been gained, made possible through the application of advanced technologies and bioinformatics, novel experimental models, and human research. As a result, our conceptual framework for understanding the impact of diet on the gut microbiome, health, and disease has advanced considerably, bringing the promise of better tools of risk assessment, diagnostics, and therapeutic intervention in an age of personalized medicine.

Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data

MOTIVATION

Gut microbiota can be classified at multiple taxonomy levels. Strategies to use changes in microbiota composition to effect health improvements require knowing at which taxonomy level interventions should be aimed. Identifying these important levels is difficult, however, because most statistical methods only consider when the microbiota are classified at one taxonomy level, not multiple.

RESULTS

Using L1 and L2 regularizations, we developed a new variable selection method that identifies important features at multiple taxonomy levels. The regularization parameters are chosen by a new, data-adaptive, repeated cross-validation approach, which performed well. In simulation studies, our method outperformed competing methods: it more often selected significant variables, and had small false discovery rates and acceptable false-positive rates. Applying our method to gut microbiota data, we found which taxonomic levels were most altered by specific interventions or physiological status.

AVAILABILITY

The new approach is implemented in an R package, which is freely available from the corresponding author.

CONTACT

tpgarcia@srph.tamhsc.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.