Heritable components of the human fecal microbiome are associated with visceral fat

Visceral adipose tissue predicts severity and prognosis of acute pancreatitis in obese patients

Acute pancreatitis is a common systemic inflammatory disease, manifested by a spectrum of severity, ranging from mild in the majority of patients to severe acute pancreatitis. Patients with severe acute pancreatitis suffer from severe local and systemic complications and organ failure, leading to a poor prognosis. The early recognition of the severe condition is important to improve prognosis. Obesity has risen in tandem with an increase in the severity of acute pancreatitis in recent years. Studies have revealed that adipose tissue, particularly visceral adipose tissue is associated with the prognosis of acute pancreatitis. This review discussed the role of visceral adipose tissue in obese patients with acute pancreatitis and explored the possible mechanism involved.

Impairment of oocyte quality caused by gut microbiota dysbiosis in obesity

Obesity poses risks to oocyte maturation and embryonic development in mice and humans, linked to gut microbiota dysbiosis and altered host metabolomes. However, it is unclear whether symbiotic gut microbes have a pivotal role in oocyte quality. In mouse models of fecal microbiota transplantation, we demonstrated aberrant meiotic apparatus and impaired maternal mRNA in oocytes, which is coincident with the poor developmental competence of embryos. Using metabolomics profiling, we discovered that the cytosine and cytidine metabolism was disturbed, which could account for the fertility defects observed in the high-fat diet (HFD) recipient mice. Additionally, cytosine and cytidine are closely related with gut microbiota dysbiosis, which is accompanied by a notable reduction of abundance of Christensenellaceae R-7 group in the HFD mice. In summary, our findings provided evidence that modifying the gut microbiota may be of value in the treatment of infertile female individuals with obesity.

Comprehensive Strategies for Metabolic Syndrome: How Nutrition, Dietary Polyphenols, Physical Activity, and Lifestyle Modifications Address Diabesity, Cardiovascular Diseases, and Neurodegenerative Conditions

Several hallmarks of metabolic syndrome, such as dysregulation in the glucose and lipid metabolism, endothelial dysfunction, insulin resistance, low-to-medium systemic inflammation, and intestinal microbiota dysbiosis, represent a pathological bridge between metabolic syndrome and diabesity, cardiovascular, and neurodegenerative disorders. This review aims to highlight some therapeutic strategies against metabolic syndrome involving integrative approaches to improve lifestyle and daily diet. The beneficial effects of foods containing antioxidant polyphenols, intestinal microbiota control, and physical activity were also considered. We comprehensively examined a large body of published articles involving basic, animal, and human studie, as well as recent guidelines. As a result, dietary polyphenols from natural plant-based antioxidants and adherence to the Mediterranean diet, along with physical exercise, are promising complementary therapies to delay or prevent the onset of metabolic syndrome and counteract diabesity and cardiovascular diseases, as well as to protect against neurodegenerative disorders and cognitive decline. Modulation of the intestinal microbiota reduces the risks associated with MS, improves diabetes and cardiovascular diseases (CVD), and exerts neuroprotective action. Despite several studies, the estimation of dietary polyphenol intake is inconclusive and requires further evidence. Lifestyle interventions involving physical activity and reduced calorie intake can improve metabolic outcomes.

Advances in the mechanism of metformin with wide-ranging effects on regulation of the intestinal microbiota

Metformin is of great focus because of its high safety, low side effects, and various effects other than lowering blood sugar, such as anti-inflammation, anti-tumor, and anti-aging. Studies have shown that metformin has a modulating effect on the composition and function of the intestinal microbiota other than acting on the liver. However, the composition of microbiota is complex and varies to some extent between species and individuals, and the experimental design of each study is also different. Multiple factors present a major obstacle to better comprehending the effects of metformin on the gut microbiota. This paper reviews the regulatory effects of metformin on the gut microbiota, such as increasing the abundance of genus Akkermansia, enriching short-chain fatty acids (SCFAs)-producing bacterial genus, and regulating gene expression of certain genera. The intestinal microbiota is a large and vital ecosystem in the human body and is considered to be the equivalent of an "organ" of the human body, which is highly relevant to human health and disease status. There are a lot of evidences that the gut microbiota is responsible for metformin's widespread effects. However, there are only a few systematic studies on this mechanism, and the specific mechanism is still unclear. This paper aims to summarize the possible mechanism of metformin in relation to gut microbiota.

Scrutinizing microbiome determinism: why deterministic hypotheses about the microbiome are conceptually ungrounded

This paper addresses the topic of determinism in contemporary microbiome research. I distinguish two types of deterministic claims about the microbiome, and I show evidence that both types of claims are present in the contemporary literature. First, the idea that the host genetics determines the composition of the microbiome which I call "host-microbiome determinism". Second, the idea that the genetics of the holobiont (the individual unit composed by a host plus its microbiome) determines the expression of certain phenotypic traits, which I call "microbiome-phenotype determinism". Drawing on the stability of traits conception of individuality (Suárez in Hist Philos Life Sci 42:11, 2020) I argue that none of these deterministic hypotheses is grounded on our current knowledge of how the holobiont is transgenerationally assembled, nor how it expresses its phenotypic traits.

Gut microbiome diversity, variability, and latent community types compared with shifts in body weight during the freshman year of college in dormitory-housed adolescents

Significant human gut microbiome changes during adolescence suggest that microbial community evolution occurs throughout important developmental periods including the transition to college, a typical life phase of weight gain. In this observational longitudinal study of 139 college freshmen living in on-campus dormitories, we tracked changes in the gut microbiome via 16S amplicon sequencing and body weight across a single academic year. Participants were grouped by weight change categories of gain (WG), loss (WL), and maintenance (WM). Upon assessment of the community structure, unweighted and weighted UniFrac metrics revealed significant shifts with substantial variation explained by individual effects within weight change categories. Genera that positively contributed to these associations with weight change included Bacteroides, Blautia, and Bifidobacterium in WG participants and Prevotella and Faecalibacterium in WL and WM participants. Moreover, the Prevotella/Bacteroides ratio was significantly different by weight change category, with WL participants displaying an increased ratio. Importantly, these genera did not display co-dominance nor ease of transition between Prevotella- and Bacteroides-dominated states. We further assessed the overall taxonomic variation, noting the increased stability of the WL compared to the WG microbiome. Finally, we found 30 latent community structures within the microbiome with significant associations with waist circumference, sleep, and dietary factors, with alcohol consumption chief among them. Our findings highlight the high level of individual variation and the importance of initial gut microbiome community structure in college students during a period of major lifestyle changes. Further work is needed to confirm these findings and explore mechanistic relationships between gut microbes and weight change in free-living individuals.

A Keystone Gut Bacterium Christensenella minuta-A Potential Biotherapeutic Agent for Obesity and Associated Metabolic Diseases

A new next-generation probiotic, Christensenella minuta was first discovered in 2012 from healthy human stool and described under the phylum Firmicutes. C. minuta is a subdominant commensal bacterium with highly heritable properties that exhibits mutual interactions with other heritable microbiomes, and its relative abundance is positively correlated with the lean host phenotype associated with a low BMI index. It has been the subject of numerous studies, owing to its potential health benefits. This article reviews the evidence from various studies of C. minuta interventions using animal models for managing metabolic diseases, such as obesity, inflammatory bowel disease, and type 2 diabetes, characterized by gut microbiota dysbiosis and disruption of host metabolism. Notably, more studies have presented the complex interaction between C. minuta and host metabolism when it comes to metabolic health. Therefore, C. minuta could be a potential candidate for innovative microbiome-based biotherapy via fecal microbiota transplantation or oral administration. However, the detailed underlying mechanism of action requires further investigation.

The gut microbiome and regional fat distribution: Findings from the Baltimore Longitudinal Study of Aging

OBJECTIVE

The aim of this study was to examine associations of gut microbiome diversity and composition with directly measured regional fat distribution, including central fat, in a large community-based cohort.

METHODS

A cross-sectional investigation was conducted in the Baltimore Longitudinal Study of Aging (N = 815, 55.2% female, 65.9% White). The fecal microbiome was assessed using whole-genome shotgun metagenomic sequencing, and trunk and leg fat was measured using dual x-ray absorptiometry. Multivariable-adjusted associations of regional fat measures, BMI, or waist circumference with microbiome alpha diversity metrics, microbiome beta diversity metrics, and species differential abundance (verified using two compositional statistical approaches) were examined.

RESULTS

Trunk fat, leg fat, BMI, and waist circumference all significantly explained similar amounts of variance in microbiome structure. Differential abundance testing identified 11 bacterial species significantly associated with at least one measure of body composition or anthropometry. Ruminococcus gnavus was strongly and consistently associated with trunk fat mass, which is congruent with prior literature.

CONCLUSIONS

Microbiome diversity and composition, in particular higher abundance of Ruminococcus gnavus, were associated with greater trunk fat, in addition to other measures of obesity. Longitudinal studies are needed to replicate these findings, and if replicated, randomized trials are needed to determine whether interventions targeting microbiome features such as abundance of Ruminococcus gnavus can lead to reductions in trunk fat and its metabolic sequelae.

Gut microbiome and atrial fibrillation-results from a large population-based study

BACKGROUND

Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with the risk of AF remains unknown.

METHODS

We examined the associations of prevalent and incident AF with gut microbiota in the FINRISK 2002 study, a random population sample of 6763 individuals. We replicated our findings in an independent case-control cohort of 138 individuals in Hamburg, Germany.

FINDINGS

Multivariable-adjusted regression models revealed that prevalent AF (N = 116) was associated with nine microbial genera. Incident AF (N = 539) over a median follow-up of 15 years was associated with eight microbial genera with false discovery rate (FDR)-corrected P < 0.05. Both prevalent and incident AF were associated with the genera Enorma and Bifidobacterium (FDR-corrected P < 0.001). AF was not significantly associated with bacterial diversity measures. Seventy-five percent of top genera (Enorma, Paraprevotella, Odoribacter, Collinsella, Barnesiella, Alistipes) in Cox regression analyses showed a consistent direction of shifted abundance in an independent AF case-control cohort that was used for replication.

INTERPRETATION

Our findings establish the basis for the use of microbiome profiles in AF risk prediction. However, extensive research is still warranted before microbiome sequencing can be used for prevention and targeted treatment of AF.

FUNDING

This study was funded by European Research Council, German Ministry of Research and Education, Academy of Finland, Finnish Medical Foundation, and the Finnish Foundation for Cardiovascular Research, the Emil Aaltonen Foundation, and the Paavo Nurmi Foundation.

Combing fecal microbial community data to identify consistent obesity-specific microbial signatures and shared metabolic pathways

Obesity is associated with altered gut microbiome composition but data across different populations remain inconsistent. We meta-analyzed publicly available 16S-rRNA sequence datasets from 18 different studies and identified differentially abundant taxa and functional pathways of the obese gut microbiome. Most differentially abundant genera (Odoribacter, Oscillospira, Akkermansia, Alistipes, and Bacteroides) were depleted in obesity, indicating a deficiency of commensal microbes in the obese gut microbiome. From microbiome functional pathways, elevated lipid biosynthesis and depleted carbohydrate and protein degradation suggested metabolic adaptation to high-fat, low-carbohydrate, and low-protein diets in obese individuals. Machine learning models trained on the 18 studies were modest in predicting obesity with a median AUC of 0.608 using 10-fold cross-validation. The median AUC increased to 0.771 when models were trained in eight studies designed for investigating obesity-microbiome association. By meta-analyzing obesity-associated microbiota signatures, we identified obesity-associated depleted taxa that may be exploited to mitigate obesity and related metabolic diseases.

Multi-dimensional investigation and distribution characteristics analysis of gut microbiota of different marine fish in Fujian Province of China

The gut microbiota plays an important role in animal health and behavior. In marine fish, the composition of the gut microbiota is affected by many complex factors, such as diet, species, and regional factors. Since more than one hundred fish species have been cultured in fish farms along with the 3,324 km coastline of Fujian Province in South China, we chose this region to study the gut microbiota composition of marine commercial fishes because sufficient different species, diets, and regional factors were observed. We investigated the distribution characteristics of the gut microbiota of seven cultured species (Epinephelus akaara, Epinephelus coioides, Epinephelus lanceolatus ♂ × Epinephelus fuscoguttatus ♀, Siganus fuscescens, Pagrus major, Lateolabrax japonicus, and Acanthopagrus schlegelii) living in the same aquatic region and one species (E. akaara) living separately in five regions separated by latitude. The impacts of diet, region, and species factors on fish gut microbiota were also evaluated. Diversity and multivariate analyses showed that the patterns of the microbiota were significantly different in different fish species within the same habitat and E. akaara with five latitude regions. Mantel analysis showed that AN, SiO₃^2–, DO, and NO₂^– were the principal factors affecting the microbial community of E. akaara in the five habitats. Additionally, similar distribution characteristics occurred in different gut parts of different fishes, with an increasing trend of Proteobacteria and Vibrionaceae abundance and a decreasing trend of Firmicutes and Bacillaceae abundance from the foregut to the hindgut. Vibrionaceae was the most abundant family in the content. This study highlights that a persistent core microbiota was established in marine commercial fishes spanning multiple scales. The factors with the greatest effect on fish gut microbiota may be (i) host genetics and (ii) geographic factors rather than the microbiota in the diet and water environment. These core microbes regularly colonized from the foregut to the hindgut, which was driven by their underlying functions, and they were well adapted to the gut environment. Moreover, the microbiota in the content may have contributed more to the gut microbial communities than previously reported. This study could complement basic data on the composition of marine commercial fishes and facilitate relatively complete investigations, which would be beneficial for the healthy and sustainable development of aquaculture.

Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota

Background

The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota.

Results

Analysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects.

Conclusions

This study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00738-2.

Dried chicory root improves bowel function, benefits intestinal microbial trophic chains and increases faecal and circulating short chain fatty acids in subjects at risk for type 2 diabetes

We investigated the impact of dried chicory root in a randomised, placebo-controlled trial with 55 subjects at risk for type 2 diabetes on bowel function, gut microbiota and its products, and glucose homeostasis. The treatment increased stool softness (+1.1 ± 0.3 units; p = 0.034) and frequency (+0.6 ± 0.2 defecations/day; p < 0.001), strongly modulated gut microbiota composition (7 % variation; p = 0.001), and dramatically increased relative levels (3-4-fold) of Anaerostipes and Bifidobacterium spp., in a dose-dependent, reversible manner. A synthetic community, including selected members of these genera and a Bacteroides strain, generated a butyrogenic trophic chain from the product. Faecal acetate, propionate and butyrate increased by 25.8 % (+13.0 ± 6.3 mmol/kg; p = 0.023) as did their fasting circulating levels by 15.7 % (+7.7 ± 3.9 μM; p = 0.057). In the treatment group the glycaemic coefficient of variation decreased from 21.3 ± 0.94 to 18.3 ± 0.84 % (p = 0.004), whereas fasting glucose and HOMA-ir decreased in subjects with low baseline Blautia levels (-0.3 ± 0.1 mmol/L fasting glucose; p = 0.0187; -0.14 ± 0.1 HOMA-ir; p = 0.045). Dried chicory root intake rapidly and reversibly affects bowel function, benefits butyrogenic trophic chains, and promotes glycaemic control.

Bifidobacterium Is Enriched in Gut Microbiome of Kashmiri Women with Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) is a very common endocrine condition in women in India. Gut microbiome alterations were shown to be involved in PCOS, yet it is remarkably understudied in Indian women who have a higher incidence of PCOS as compared to other ethnic populations. During the regional PCOS screening program among young women, we recruited 19 drug naive women with PCOS and 20 control women at the Sher-i-Kashmir Institute of Medical Sciences, Kashmir, North India. We profiled the gut microbiome in faecal samples by 16S rRNA sequencing and included 40/58 operational taxonomic units (OTUs) detected in at least 1/3 of the subjects with relative abundance (RA) ≥ 0.1%. We compared the RAs at a family/genus level in PCOS/non-PCOS groups and their correlation with 33 metabolic and hormonal factors, and corrected for multiple testing, while taking the variation in day of menstrual cycle at sample collection, age and BMI into account. Five genera were significantly enriched in PCOS cases: Sarcina, Megasphaera, and previously reported for PCOS Bifidobacterium, Collinsella and Paraprevotella confirmed by different statistical models. At the family level, the relative abundance of Bifidobacteriaceae was enriched, whereas Peptococcaceae was decreased among cases. We observed increased relative abundance of Collinsella and Paraprevotella with higher fasting blood glucose levels, and Paraprevotella and Alkalibacterium with larger hip, waist circumference, weight, and Peptococcaceae with lower prolactin levels. We also detected a novel association between Eubacterium and follicle-stimulating hormone levels and between Bifidobacterium and alkaline phosphatase, independently of the BMI of the participants. Our report supports that there is a relationship between gut microbiome composition and PCOS with links to specific reproductive health metabolic and hormonal predictors in Indian women.

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP-taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host-microbiota interactions and their association with disease.

Exploring the role of gut microbiota in host feeding behavior among breeds in swine

BACKGROUND

The interplay between the gut microbiota and feeding behavior has consequences for host metabolism and health. The present study aimed to explore gut microbiota overall influence on feeding behavior traits and to identify specific microbes associated with the traits in three commercial swine breeds at three growth stages. Feeding behavior measures were obtained from 651 pigs of three breeds (Duroc, Landrace, and Large White) from an average 73 to 163 days of age. Seven feeding behavior traits covered the information of feed intake, feeder occupation time, feeding rate, and the number of visits to the feeder. Rectal swabs were collected from each pig at 73 ± 3, 123 ± 4, and 158 ± 4 days of age. DNA was extracted and subjected to 16 S rRNA gene sequencing.

RESULTS

Differences in feeding behavior traits among breeds during each period were found. The proportion of phenotypic variances of feeding behavior explained by the gut microbial composition was small to moderate (ranged from 0.09 to 0.31). A total of 21, 10, and 35 amplicon sequence variants were found to be significantly (q-value < 0.05) associated with feeding behavior traits for Duroc, Landrace, and Large White across the three sampling time points. The identified amplicon sequence variants were annotated to five phyla, with Firmicutes being the most abundant. Those amplicon sequence variants were assigned to 28 genera, mainly including Christensenellaceae_R-7_group, Ruminococcaceae_UCG-004, Dorea, Ruminococcaceae_UCG-014, and Marvinbryantia.

CONCLUSIONS

This study demonstrated the importance of the gut microbial composition in interacting with the host feeding behavior and identified multiple archaea and bacteria associated with feeding behavior measures in pigs from either Duroc, Landrace, or Large White breeds at three growth stages. Our study provides insight into the interaction between gut microbiota and feeding behavior and highlights the genetic background and age effects in swine microbial studies.

Study on the differences of gut microbiota composition between phlegm-dampness syndrome and qi-yin deficiency syndrome in patients with metabolic syndrome

BACKGROUND

Metabolic syndrome (MS) is a group of complex medical conditions that can lead to serious cardiovascular and cerebrovascular diseases. According to the theory of traditional Chinese medicine (TCM), MS can be divided into two main subtypes termed 'phlegm-dampness syndrome' (TSZE) and 'qi-yin deficiency syndrome' (QYLX). At present, the research into intestinal microbiota of different TCM syndromes of MS and its association with clinical manifestation is lacking.

MATERIALS AND METHODS

Using 16S rRNA sequencing, we performed a cross-sectional analysis of human gut microbiota between two different TCM syndromes (QYLX and TSZE, n=60) of MS, and their differences with healthy participants (n=30).

RESULTS

We found that the QYLX and TSZE groups differ from the healthy control group in the overall gut microbiota composition, and some specific microbial taxa and functional pathways. Moreover, significantly differentially abundant taxa and distinct BMI-correlated taxa were observed between QYLX and TSZE groups, suggesting the potential contribution of gut microbiota to the distinction between the two TCM syndromes. The predicted functional profiles also showed considerable differences, especially pathways related to amino acid metabolism and lipopolysaccharide synthesis.

CONCLUSION

Our study highlights the gut microbiota's contribution to the differentiation between two TCM syndromes of MS and may provide the rationale for adopting different microbiota-directed treatment strategies for different TCM syndromes of MS in the future.

Gut microbiota: A new target for T2DM prevention and treatment

Type 2 diabetes mellitus (T2DM), one of the fastest growing metabolic diseases, has been characterized by metabolic disorders including hyperglycemia, hyperlipidemia and insulin resistance (IR). In recent years, T2DM has become the fastest growing metabolic disease in the world. Studies have indicated that patients with T2DM are often associated with intestinal flora disorders and dysfunction involving multiple organs. Metabolites of the intestinal flora, such as bile acids (BAs), short-chain fatty acids (SCFAs) and amino acids (AAs)may influence to some extent the decreased insulin sensitivity associated with T2DM dysfunction and regulate metabolic as well as immune homeostasis. In this paper, we review the changes in the gut flora in T2DM and the mechanisms by which the gut microbiota modulates metabolites affecting T2DM, which may provide a basis for the early identification of T2DM-susceptible individuals and guide targeted interventions. Finally, we also highlight gut microecological therapeutic strategies focused on shaping the gut flora to inform the improvement of T2DM progression.

Host genetic control of gut microbiome composition

The gut microbiome plays a significant role in health and disease, and there is mounting evidence indicating that the microbial composition is regulated in part by host genetics. Heritability estimates for microbial abundance in mice and humans range from (0.05-0.45), indicating that 5-45% of inter-individual variation can be explained by genetics. Through twin studies, genetic association studies, systems genetics, and genome-wide association studies (GWAS), hundreds of specific host genetic loci have been shown to associate with the abundance of discrete gut microbes. Using genetically engineered knock-out mice, at least 30 specific genes have now been validated as having specific effects on the microbiome. The relationships among of host genetics, microbiome composition, and abundance, and disease is now beginning to be unraveled through experiments designed to test causality. The genetic control of disease and its relationship to the microbiome can manifest in multiple ways. First, a genetic variant may directly cause the disease phenotype, resulting in an altered microbiome as a consequence of the disease phenotype. Second, a genetic variant may alter gene expression in the host, which in turn alters the microbiome, producing the disease phenotype. Finally, the genetic variant may alter the microbiome directly, which can result in the disease phenotype. In order to understand the processes that underlie the onset and progression of certain diseases, future research must take into account the relationship among host genetics, microbiome, and disease phenotype, and the resources needed to study these relationships.

Effect of High-Fat Diet on the Intestinal Flora in Letrozole-Induced Polycystic Ovary Syndrome Rats

Aim

The aim of this study was to explore whether letrozole and high-fat diets (HFD) can induce obese insulin-resistant polycystic ovary syndrome (PCOS) with intestinal flora dysbiosis in a rat model. We compared the changes in the intestinal flora of letrozole-induced rats fed with HFD or normal chow, to explore the effects of HFD and letrozole independently and synergistically on the intestinal flora.

Methods

Five-week-old female Sprague Dawley (SD) rats were divided into four groups: control (C) group fed with regular diet; L1 group administered with letrozole and fed with regular diet; L2 group received letrozole and fed with HFD; and HFD group fed with HFD. At the end of the experiment, ovarian morphology, hormones, metabolism, oxidative stress, and inflammatory status of all rats were studied. 16S rDNA high-throughput sequencing was used to profile microbial communities, and various multivariate analysis approaches were used to quantitate microbial composition, abundance, and diversity.

Results

Compared to the C group, the increased plasma fasting insulin and glucose, HOMA-IR, triglyceride, testosterone, and malondialdehyde were significantly higher in the L2 group, while high-density lipoprotein cholesterol was significantly lower in the L1 group and L2 group. The indices of Chao1 and the Abundance-based Coverage Estimator (ACE) (α-diversity) in the L2 and HFD groups were significantly lower than that in the C group. Bray–Curtis dissimilarity based principal coordinate analysis (PCoA) plots and analysis of similarities (ANOSIM) test showed obvious separations between the L2 group and C group, between the HFD group and C group, and between the L2 and HFD groups. At the phylum level, Firmicutes and ratio of Firmicutes and Bacteroidetes (F/B ratio) were increased in the L2 group; Bacteroidetes was decreased in the L2 and HFD groups. No significant differences in bacterial abundance between the C group and L1 group were observed at the phylum level. Based on linear discriminant analysis (LDA) effect size (LEfSe) analysis, the bacterial genera (the relative abundance > 0.1%, LDA > 3, p < 0.05) were selected as candidate bacterial signatures. They showed that the abundance of Vibrio was significantly increased in the L1 group; Bacteroides and Phascolarctobacterium were enriched in the HFD group, and Bacteroides, Phascolarctobacterium, Blautia, Parabacteroides, Akkermansia [Ruminococcus]_torques_group, and Anaerotruncus were enriched in the L2 group.

Conclusion

The effect of letrozole on intestinal flora was not significant as HFD. HFD could destroy the balance of intestinal flora and aggravate the intestinal flora dysbiosis in PCOS. Letrozole-induced rats fed with HFD have many characteristics like human PCOS, including some metabolic disorders and intestinal flora dysbiosis. The dysbiosis was characterized by an increased Firmicutes/Bacteroidetes ratio, an expansion of Firmicutes, a contraction of Bacteroidetes, and the decreased microbial richness. Beta-diversity also showed significant differences in intestinal microflora, compared with control rats.

Amino Acids Regulate Glycolipid Metabolism and Alter Intestinal Microbial Composition

Amino acids (AAs) and their metabolites regulate key metabolic pathways that are necessary for growth, reproduction, immunity and metabolism of the body. It has been convinced that metabolic diseases are closely related to disorders of glycolipid metabolism. A growing number of studies have shown that AAs are closely related to energy metabolism. This review focuses on the effects of amino acids (arginine, branched-chain amino acids, glutamine) and their metabolites (short chain fatty acids) on glycolipid metabolism by regulating PI3K/AKT/mTOR and AMPK signaling pathways and GPCRs receptors, reducing intestinal Firmicutes/Bacteroidetes ratio associated with obesity.

Regulation of Probiotics on Metabolism of Dietary Protein in Intestine

Proteins are indispensable components of living organisms, which are derived mainly from diet through metabolism. Dietary proteins are degraded by endogenous digestive enzymes to di- or tripeptides and free amino acids (AAs) in the small intestine lumen and then absorbed into blood and lymph through intestinal epithelial cells via diverse transporters. Microorganisms are involved not only in the proteins' catabolism, but also the AAs, especially essential AAs, anabolism. Probiotics regulate these processes by providing exogenous proteases and AAs and peptide transporters, and reducing hazardous substances in the food and feed. But the core mechanism is modulating of the composition of intestinal microorganisms through their colonization and exclusion of pathogens. The other effects of probiotics are associated with normal intestinal morphology, which implies that the enterocytes secrete more enzymes to decompose dietary proteins and absorb more nutrients.

Novel biotechnological approaches for monitoring and immunization against resistant to antibiotics Escherichia coli and other pathogenic bacteria

The application of next-generation molecular, biochemical and immunological methods for developing new vaccines, antimicrobial compounds, probiotics and prebiotics for zoonotic infection control has been fundamental to the understanding and preservation of the symbiotic relationship between animals and humans. With increasing rates of antibiotic use, resistant bacterial infections have become more difficult to diagnose, treat, and eradicate, thereby elevating the importance of surveillance and prevention programs. Effective surveillance relies on the availability of rapid, cost-effective methods to monitor pathogenic bacterial isolates. In this opinion article, we summarize the results of some research program initiatives for the improvement of live vaccines against avian enterotoxigenic Escherichia coli using virulence factor gene deletion and engineered vaccine vectors based on probiotics. We also describe methods for the detection of pathogenic bacterial strains in eco-environmental headspace and aerosols, as well as samples of animal and human breath, based on the composition of volatile organic compounds and fatty acid methyl esters. We explain how the introduction of these low-cost biotechnologies and protocols will provide the opportunity to enhance co-operation between networks of resistance surveillance programs and integrated routine workflows of veterinary and clinical public health microbiology laboratories.

Impact of host genetics on gut microbiome: Take-home lessons from human and mouse studies

The intestinal microbiome has emerged as an important component involved in various diseases. Therefore, the interest in understanding the factors shaping its composition is growing. The gut microbiome, often defined as a complex trait, contains diverse components and its properties are determined by a combination of external and internal effects. Although much effort has been invested so far, it is still difficult to evaluate the extent to which human genetics shape the composition of the gut microbiota. However, in mouse studies, where the environmental factors are better controlled, the effect of the genetic background was significant. The purpose of this paper is to provide a current assessment of the role of human host genetics in shaping the gut microbiome composition. Despite the inconsistency of the reported results, it can be estimated that the genetic factor affects a portion of the microbiome. However, this effect is currently lower than the initial estimates, and it is difficult to separate the genetic influence from the environmental effect. Additionally, despite the differences between the microbial composition of humans and mice, results from mouse models can strengthen our knowledge of host genetics underlying the human gut microbial variation.

Heritability and genome-wide association of swine gut microbiome features with growth and fatness parameters

Despite recent efforts to characterize longitudinal variation in the swine gut microbiome, the extent to which a host's genome impacts the composition of its gut microbiome is not yet well understood in pigs. The objectives of this study were: i) to identify pig gut microbiome features associated with growth and fatness, ii) to estimate the heritability of those features, and, iii) to conduct a genome-wide association study exploring the relationship between those features and single nucleotide polymorphisms (SNP) in the pig genome. A total of 1,028 pigs were characterized. Animals were genotyped with the Illumina PorcineSNP60 Beadchip. Microbiome samples from fecal swabs were obtained at weaning (Wean), at mid-test during the growth trial (MidTest), and at the end of the growth trial (OffTest). Average daily gain was calculated from birth to week 14 of the growth trial, from weaning to week 14, from week 14 to week 22, and from week 14 to harvest. Backfat and loin depth were also measured at weeks 14 and 22. Heritability estimates (±SE) of Operational Taxonomic Units ranged from 0.025 (±0.0002) to 0.139 (±0.003), from 0.029 (±0.003) to 0.289 (±0.004), and from 0.025 (±0.003) to 0.545 (±0.034) at Wean, MidTest, and OffTest, respectively. Several SNP were significantly associated with taxa at the three time points. These SNP were located in genomic regions containing a total of 68 genes. This study provides new evidence linking gut microbiome composition with growth and carcass traits in swine, while also identifying putative host genetic markers associated with significant differences in the abundance of several prevalent microbiome features.

Systems Genetics for Mechanistic Discovery in Heart Diseases

Cardiovascular diseases are the leading cause of death worldwide. Complex diseases with highly heterogenous disease progression among patient populations, cardiovascular diseases feature multifactorial contributions from both genetic and environmental stressors. Despite significant effort utilizing multiple approaches from molecular biology to genome-wide association studies, the genetic landscape of cardiovascular diseases, particularly for the nonfamilial forms of heart failure, is still poorly understood. In the past decade, systems-level approaches based on omics technologies have become an important approach for the study of complex traits in large populations. These advances create opportunities to integrate genetic variation with other biological layers to identify and prioritize candidate genes, understand pathogenic pathways, and elucidate gene-gene and gene-environment interactions. In this review, we will highlight some of the recent progress made using systems genetics approaches to uncover novel mechanisms and molecular bases of cardiovascular pathophysiological manifestations. The key technology and data analysis platforms necessary to implement systems genetics will be described, and the current major challenges and future directions will also be discussed. For complex cardiovascular diseases, such as heart failure, systems genetics represents a powerful strategy to obtain mechanistic insights and to develop individualized diagnostic and therapeutic regiments, paving the way for precision cardiovascular medicine.

Fermented barley β-glucan regulates fat deposition in Caenorhabditis elegans

BACKGROUND

Barley contains a relatively high concentration of the mixed-linkage (1 → 3) (1 → 4) β-glucan, which has been reported to be a functional food with prebiotic potential. In the current study we compared the properties of two neutral barley β-glucans, obtained from raw barley: raw barley β-glucan (RBG) and Lactobacillus plantarum dy-1-fermented barley (FBG).

RESULTS

Molecular characteristics revealed that the molecular weight of barley β-glucan decreased from 1.13 × 10⁵ D to 6.35 × 10⁴ D after fermentation. Fermentation also improved the water / oil holding capacity, solubility, and swelling capacity of barley β-glucan. Both RBG and FBG significantly improved the locomotive behavior of nematodes, thereby increasing their energy consumption and reducing fat deposition - the effect was more significant with FBG. These effects could potentially depend on nhr-49, TGF-daf-7 mediated pathways and so on, in which nhr-49 factor is particularly required.

CONCLUSION

These results suggested that fermentation may enhance in vitro physiological activities of barley β-glucan, thereby altering the effects on the lipid metabolism in vivo. © 2020 Society of Chemical Industry.

Contribution of macronutrients to obesity: implications for precision nutrition

The specific metabolic contribution of consuming different energy-yielding macronutrients (namely, carbohydrates, protein and lipids) to obesity is a matter of active debate. In this Review, we summarize the current research concerning associations between the intake of different macronutrients and weight gain and adiposity. We discuss insights into possible differential mechanistic pathways where macronutrients might act on either appetite or adipogenesis to cause weight gain. We also explore the role of dietary macronutrient distribution on thermogenesis or energy expenditure for weight loss and maintenance. On the basis of the data discussed, we describe a novel way to manage excessive body weight; namely, prescribing personalized diets with different macronutrient compositions according to the individual's genotype and/or enterotype. In this context, the interplay of macronutrient consumption with obesity incidence involves mechanisms that affect appetite, thermogenesis and metabolism, and the outcomes of these mechanisms are altered by an individual's genotype and microbiota. Indeed, the interactions of the genetic make-up and/or microbiota features of a person with specific macronutrient intakes or dietary pattern consumption help to explain individualized responses to macronutrients and food patterns, which might represent key factors for comprehensive precision nutrition recommendations and personalized obesity management.

Comparison Between the Gut Microbiota in Different Gastrointestinal Segments of Large-Tailed Han and Small-Tailed Han Sheep Breeds with High-Throughput Sequencing

Commensal microorganisms are essential to the normal development and function of many aspects of animal biology. However, the dynamic shift patterns of the microbiota of different gut segments in sheep and the correlation between fat type large-tailed phenotype and microbiota remain poorly unknown. This study therefore sought to assess the composition and distribution of the intestinal microbiome, and compared the difference of gut microbiota from different gastrointestinal segments within breeds and same intestinal sections between breeds. For these analyses, 16S rRNA V4 regions from 4 gut sections prepared from each of six individuals (3 from each breed) were sequenced to detect the microbiome composition in these samples. These analyses revealed the presence of 51,173 operational taxonomic units distributed across 24 phyla and 420 genera in these samples, with Firmicutes and Bacteroidetes being the most prevalent phyla of microbes present in these samples. Moreover, the bacterial composition showed distinct microbial communities in different gastrointestinal segments within breed, but showed similar and relative fixed bacterial abundance in the same intestinal segments from individuals of different breeds. We also found that only a few bacterial species (Lachnospiraceae, Akkermansia) were needed to distinguish between Small-tailed Han sheep (STH) and Large-tailed Han sheep (LTH) and their metabolic process maybe influence the fat type large-tailed phenotype formation in sheep. The functional profile analysis revealed that the environment information processing, genetic information processing, and metabolic pathways were enriched in all samples. The main functional roles of the gut microbiota were amino acid metabolism, replication and repair, carbohydrate metabolism, and membrane transport. Finally, our findings suggested that distinguished gut species between STH and LTH have relative fixed and the potential correlation is existing between the intestinal microorganisms and the large-tailed phenotype trait formation of sheep, which may offer clues for further investigation to detect the roles of intestinal microbiota in the metabolism and fat deposition in the tail of sheep.

Phenotypes of Sarcopenic Obesity: Exploring the Effects on Peri-Muscular Fat, the Obesity Paradox, Hormone-Related Responses and the Clinical Implications

Sarcopenic obesity combines the words sarcopenia and obesity. This definition of obesity should be better differentiated between visceral and subcutaneous fat phenotypes. For this reason, this review lays the foundation for defining the subcutaneous and the visceral fat into the context of sarcopenia. Thus, the review aims to explore the missing links on pathogenesis of visceral fat and its relationship on age: defining the peri-muscular fat as a new entity and the subcutaneous fat as a first factor that leads to the obesity paradox. Last but not least, this review underlines and motivates the mechanisms of the hormonal responses and anti-inflammatory adipokines responsible for the clinical implications of sarcopenic visceral obesity, describing factor by factor the multiple axis between the visceral fat-sarcopenia and all mortality outcomes linked to cancer, diabetes, cardiovascular diseases, cirrhosis, polycystic ovary, disability and postoperative complications.

Effect of Short-Term Dietary Intervention and Probiotic Mix Supplementation on the Gut Microbiota of Elderly Obese Women

Accumulating literature is providing evidence that the gut microbiota is involved in metabolic disorders, but the question of how to effectively modulate it to restore homeostasis, especially in the elderly, is still under debate. In this study, we profiled the intestinal microbiota of 20 elderly obese women (EO) at the baseline (T0), after 15 days of hypocaloric Mediterranean diet administered as part of a nutritional-metabolic rehabilitation program for obesity (T1), and after a further 15 days of the same diet supplemented with a probiotic mix (T2). Fecal samples were characterized by Illumina MiSeq sequencing of the 16S rRNA gene. The EO microbiota showed the typical alterations found in obesity, namely, an increase in potential pro-inflammatory components (i.e., Collinsella) and a decrease in health-promoting, short-chain fatty acid producers (i.e., Lachnospiraceae and Ruminococcaceae members), with a tendency to reduced biodiversity. After 15 days of the rehabilitation program, weight decreased by (2.7 ± 1.5)% and the gut microbiota dysbiosis was partially reversed, with a decline of Collinsella and an increase in leanness-related taxa. During the next 15 days of diet and probiotics, weight dropped further by (1.2 ± 1.1)%, markers of oxidative stress improved, and Akkermansia, a mucin degrader with beneficial effects on host metabolism, increased significantly. These findings support the relevant role of a correct dietetic approach, even in the short term, to modulate the EO gut microbiota towards a metabolic health-related configuration, counteracting the increased risk of morbidity in these patients.

Childhood obesity: an overview of laboratory medicine, exercise and microbiome

In the last few years, a significant increase of childhood obesity incidence unequally distributed within countries and population groups has been observed, thus representing an important public health problem associated with several health and social consequences. Obese children have more than a 50% probability of becoming obese adults, and to develop pathologies typical of obese adults, that include type 2-diabetes, dyslipidemia and hypertension. Also environmental factors, such as reduced physical activity and increased sedentary activities, may also result in increased caloric intake and/or decreased caloric expenditure. In the present review, we aimed to identify and describe a specific panel of parameters in order to evaluate and characterize the childhood obesity status useful in setting up a preventive diagnostic approach directed at improving health-related behaviors and identifying predisposing risk factors. An early identification of risk factors for childhood obesity could definitely help in setting up adequate and specific clinical treatments.

Neighborhoods to Nucleotides - Advances and gaps for an obesity disparities systems epidemiology model

Purpose of Review

Disparities in obesity rates in the US continue to increase. Here we review progress and highlight gaps in understanding disparities in obesity with a focus on the Hispanic/Latino population from a systems epidemiology framework. We review seven domains: environment, behavior, biomarkers, nutrition, microbiome, genomics, and epigenomics/transcriptomics. We focus on recent advances that include at least two or more of these domains, and then provide a real world example of data collection efforts that reflect these domains.

Recent Findings

Research into DNA methylation related to discrimination and microbiome relating to eating behaviors and food content is furthering understanding of why disparities in obesity persist. Environmental and neighborhood level research is uncovering the importance of exposures such as air and noise pollution and systematic or structural racism for obesity and related outcomes through behaviors such as sleep.

Sick Individuals and Sick (Microbial) Populations: Challenges in Epidemiology and the Microbiome

The human microbiome represents a new frontier in understanding the biology of human health. While epidemiology in this area is still in its infancy, its scope will likely expand dramatically over the coming years. To rise to the challenge, we argue that epidemiology should capitalize on its population perspective as a critical complement to molecular microbiome research, allowing for the illumination of contextual mechanisms that may vary more across populations rather than among individuals. We first briefly review current research on social context and the gut microbiome, focusing specifically on socioeconomic status (SES) and race/ethnicity. Next, we reflect on the current state of microbiome epidemiology through the lens of one specific area, the association of the gut microbiome and metabolic disorders. We identify key methodological shortcomings of current epidemiological research in this area, including extensive selection bias, the use of noncompositionally robust measures, and a lack of attention to social factors as confounders or effect modifiers.

Blautia genus associated with visceral fat accumulation in adults 20-76 years of age

The gut microbiota is reported to be related to obesity, and visceral fat is reported to be strongly associated with cardiovascular disease and overall mortality. However, the association between the gut microbiota and obesity has mainly been studied using body mass index (BMI) as a proxy for obesity. We investigated the relationship of both visceral fat and BMI with the gut microbiota stratified by sex in a population-based cross-sectional study of Japanese men and women 20-76 years of age (n = 1001). Women with a higher visceral fat area (VFA) harboured a higher relative abundance of the Firmicutes phylum (P for trend <0.001) and a lower relative abundance of the Bacteroidetes phylum (P for trend 0.030), whereas men with higher VFA harboured a lower relative abundance of the Firmicutes phylum (P for trend 0.076) and a higher relative abundance of the Bacteroidetes phylum (P for trend 0.013). Similar results were obtained using BMI as an index, but the differences were not significant in men. At the genus level, Blautia was the only gut microbe significantly and inversely associated with VFA regardless of sex. In conclusion, at the genus level we found that Blautia was the only gut microbe significantly and inversely associated with VFA, regardless of sex.

TwinsUK: The UK Adult Twin Registry Update

TwinsUK is the largest cohort of community-dwelling adult twins in the UK. The registry comprises over 14,000 volunteer twins (14,838 including mixed, single and triplets); it is predominantly female (82%) and middle-aged (mean age 59). In addition, over 1800 parents and siblings of twins are registered volunteers. During the last 27 years, TwinsUK has collected numerous questionnaire responses, physical/cognitive measures and biological measures on over 8500 subjects. Data were collected alongside four comprehensive phenotyping clinical visits to the Department of Twin Research and Genetic Epidemiology, King’s College London. Such collection methods have resulted in very detailed longitudinal clinical, biochemical, behavioral, dietary and socioeconomic cohort characterization; it provides a multidisciplinary platform for the study of complex disease during the adult life course, including the process of healthy aging. The major strength of TwinsUK is the availability of several ‘omic’ technologies for a range of sample types from participants, which includes genomewide scans of single-nucleotide variants, next-generation sequencing, metabolomic profiles, microbiomics, exome sequencing, epigenetic markers, gene expression arrays, RNA sequencing and telomere length measures. TwinsUK facilitates and actively encourages sharing the ‘TwinsUK’ resource with the scientific community — interested researchers may request data via the TwinsUK website (http://twinsuk.ac.uk/resources-for-researchers/access-our-data/) for their own use or future collaboration with the study team. In addition, further cohort data collection is planned via the Wellcome Open Research gateway (https://wellcomeopenresearch.org/gateways). The current article presents an up-to-date report on the application of technological advances, new study procedures in the cohort and future direction of TwinsUK.

Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition

Obesity and type 2 diabetes (T2D) are metabolic disorders that are linked to microbiome alterations. However, their co-occurrence poses challenges in disentangling microbial features unique to each condition. We analyzed gut microbiomes of lean non-diabetic (n = 633), obese non-diabetic (n = 494), and obese individuals with T2D (n = 153) from German population and metabolic disease cohorts. Microbial taxonomic and functional profiles were analyzed along with medical histories, serum metabolomics, biometrics, and dietary data. Obesity was associated with alterations in microbiome composition, individual taxa, and functions with notable changes in Akkermansia, Faecalibacterium, Oscillibacter, and Alistipes, as well as in serum metabolites that correlated with gut microbial patterns. However, microbiome associations were modest for T2D, with nominal increases in Escherichia/Shigella. Medications, including antihypertensives and antidiabetics, along with dietary supplements including iron, were significantly associated with microbiome variation. These results differentiate microbial components of these interrelated metabolic diseases and identify dietary and medication exposures to consider in future studies.

Dissecting the role of the gut microbiota and diet on visceral fat mass accumulation

Both gut microbiota and diet have been shown to impact visceral fat mass (VFM), a major risk factor for cardiometabolic disease, but their relative contribution has not been well characterised. We aimed to estimate and separate the effect of gut microbiota composition from that of nutrient intake on VFM in 1760 older female twins. Through pairwise association analyses, we identified 93 operational taxonomic units (OTUs) and 10 nutrients independently linked to VFM (FDR < 5%). Conditional analyses revealed that the majority (87%) of the 93 VFM-associated OTUs remained significantly associated with VFM irrespective of nutrient intake correction. In contrast, we observed that the effect of fibre, magnesium, biotin and vitamin E on VFM was partially mediated by OTUs. Moreover, we estimated that OTUs were more accurate predictors of VFM than nutrients and accounted for a larger percentage of its variance. Our results suggest that while the role of certain nutrients on VFM appears to depend on gut microbiota composition, specific gut microbes may affect host adiposity regardless of dietary intake. The findings imply that the gut microbiota may have a greater contribution towards shaping host VFM than diet alone. Thus, microbial-based therapy should be prioritised for VFM reduction in overweight and obese subjects.

Integrating tumor genomics into studies of the microbiome in colorectal cancer

Although the gut microbiome has been linked to colorectal cancer (CRC) development, associations of microbial taxa with CRC status are often inconsistent across studies. We have recently shown that tumor genomics, a factor that is rarely incorporated in analyses of the CRC microbiome, has a strong effect on the composition of the microbiota. Here, we discuss these results in the wider context of studies characterizing interaction between host genetics and the microbiome, and describe the implications of our findings for understanding the role of the microbiome in CRC.

Gut Microbiota and Their Neuroinflammatory Implications in Alzheimer's Disease

The bidirectional communication between the central nervous system (CNS) and the gut microbiota plays a pivotal role in human health. Increasing numbers of studies suggest that the gut microbiota can influence the brain and behavior of patients. Various metabolites secreted by the gut microbiota can affect the cognitive ability of patients diagnosed with neurodegenerative diseases. Nearly one in every ten Korean senior citizens suffers from Alzheimer’s disease (AD), the most common form of dementia. This review highlights the impact of metabolites from the gut microbiota on communication pathways between the brain and gut, as well as the neuroinflammatory roles they may have in AD patients. The objectives of this review are as follows: (1) to examine the role of the intestinal microbiota in homeostatic communication between the gut microbiota and the brain, termed the microbiota–gut–brain (MGB) axis; (2) to determine the underlying mechanisms of signal dysfunction; and (3) to assess the impact of signal dysfunction induced by the microbiota on AD. This review will aid in understanding the microbiota of elderly people and the neuroinflammatory roles they may have in AD.

Using the natural variation of mouse populations to understand host-gut microbiome interactions

One approach to understanding gut microbiome-host interactions, described in this review, is to examine how natural variation in a model organism, where environmental factors can be controlled, affects the microbiome and, in turn, how the microbiome is associated with physiological or clinical traits. A variation of this approach, termed "systems genetics" is to characterize both the microbiome and the host using various high throughput technologies, such as metabolomics or gene expression of the microbiome and the host. By relating variation in the microbiome and host functions to such "molecular phenotypes", hypotheses can be generated and then experimentally tested. To model human gut microbiome-host interactions in this way, the mouse is particularly useful given the extensive body of genetic resources and experimental tools that are available.