Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits

Microbiota, natural products, and human health: exploring interactions for therapeutic insights

The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.

Comparative Study of Bacterial Microbiota Differences in the Rumen and Feces of Xinjiang Brown and Holstein Cattle

Xinjiang Brown cattle are a unique and widely distributed breed of dual-purpose cattle in the Xinjiang area of China, whose milk production performance differs from Holstein cattle. It has been known that variations in bacterial species of the gastrointestinal tract influence milk protein, fat, and lactose synthesis. However, the microbiota differences between Xinjiang Brown and Holstein cattle are less known. This study aims to compare the bacterial community composition of the rumen and feces of these two cattle breeds under the same dietary and management conditions. The 16s rRNA sequencing data and milk production of 18 Xinjiang Brown cows and 20 Holstein cows on the same farm were obtained for analysis. The results confirmed differences in milk production between Xinjiang Brown and Holstein cattle. Microbiota with different relative abundance between these two cattle breeds were identified, and their biological functions might be related to milk synthesis. This study increases the understanding of the differences in microbiota between Xinjiang Brown and Holstein cattle and might provide helpful information for microbiota composition optimization of these dairy cattle.

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.

Multi-omics data elucidate parasite-host-microbiota interactions and resistance to Haemonchus contortus in sheep

BACKGROUND

The integration of molecular data from hosts, parasites, and microbiota can enhance our understanding of the complex biological interactions underlying the resistance of hosts to parasites. Haemonchus contortus, the predominant sheep gastrointestinal parasite species in the tropics, causes significant production and economic losses, which are further compounded by the diminishing efficiency of chemical control owing to anthelmintic resistance. Knowledge of how the host responds to infection and how the parasite, in combination with microbiota, modulates host immunity can guide selection decisions to breed animals with improved parasite resistance. This understanding will help refine management practices and advance the development of new therapeutics for long-term helminth control.

METHODS

Eggs per gram (EPG) of feces were obtained from Morada Nova sheep subjected to two artificial infections with H. contortus and used as a proxy to select animals with high resistance or susceptibility for transcriptome sequencing (RNA-seq) of the abomasum and 50 K single-nucleotide genotyping. Additionally, RNA-seq data for H. contortus were generated, and amplicon sequence variants (ASV) were obtained using polymerase chain reaction amplification and sequencing of bacterial and archaeal 16S ribosomal RNA genes from sheep feces and rumen content.

RESULTS

The heritability estimate for EPG was 0.12. GAST, GNLY, IL13, MGRN1, FGF14, and RORC genes and transcripts were differentially expressed between resistant and susceptible animals. A genome-wide association study identified regions on chromosomes 2 and 11 that harbor candidate genes for resistance, immune response, body weight, and adaptation. Trans-expression quantitative trait loci were found between significant variants and differentially expressed transcripts. Functional co-expression modules based on sheep genes and ASVs correlated with resistance to H. contortus, showing enrichment in pathways of response to bacteria, immune and inflammatory responses, and hub features of the Christensenellaceae, Bacteroides, and Methanobrevibacter genera; Prevotellaceae family; and Verrucomicrobiota phylum. In H. contortus, some mitochondrial, collagen-, and cuticle-related genes were expressed only in parasites isolated from susceptible sheep.

CONCLUSIONS

The present study identified chromosome regions, genes, transcripts, and pathways involved in the elaborate interactions between the sheep host, its gastrointestinal microbiota, and the H. contortus parasite. These findings will assist in the development of animal selection strategies for parasite resistance and interdisciplinary approaches to control H. contortus infection in sheep.

Male and female variability in response to chronic stress and morphine in C57BL/6J, DBA/2J, and their BXD progeny

Drug addiction is a multifactorial syndrome in which genetic predispositions and exposure to environmental stressors constitute major risk factors for the early onset, escalation, and relapse of addictive behaviors. While it is well known that stress plays a key role in drug addiction, the genetic factors that make certain individuals particularly sensitive to stress and thereby more vulnerable to becoming addicted are unknown. In an effort to test a complex set of gene x environment interactions-specifically gene x chronic stress -here we leveraged a systems genetics resource: BXD recombinant inbred mice (BXD5, BXD8, BXD14, BXD22, BXD29, and BXD32) and their parental mouse lines, C57BL/6J and DBA/2J. Utilizing the chronic social defeat stress (CSDS) and chronic variable stress (CVS) paradigms, we first showed sexual dimorphism in the behavioral stress response between the mouse strains. Further, we observed an interaction between genetic background and vulnerability to prolonged exposure to non-social stressors. Finally, we found that DBA/2J and C57BL/6J mice pre-exposed to stress displayed differences in morphine sensitivity. Our results support the hypothesis that genetic variation in predisposition to stress responses influences morphine sensitivity and is likely to modulate the development of drug addiction.

Opioid trail: Tracking contributions to opioid use disorder from host genetics to the gut microbiome

Opioid use disorder (OUD) is a worldwide public health crisis with few effective treatment options. Traditional genetics and neuroscience approaches have provided knowledge about biological mechanisms that contribute to OUD-related phenotypes, but the complexity and magnitude of effects in the brain and body remain poorly understood. The gut-brain axis has emerged as a promising target for future therapeutics for several psychiatric conditions, so characterizing the relationship between host genetics and the gut microbiome in the context of OUD will be essential for development of novel treatments. In this review, we describe evidence that interactions between host genetics, the gut microbiome, and immune signaling likely play a key role in mediating opioid-related phenotypes. Studies in humans and model organisms consistently demonstrated that genetic background is a major determinant of gut microbiome composition. Furthermore, the gut microbiome is susceptible to environmental influences such as opioid exposure. Additional work focused on gene by microbiome interactions will be necessary to gain improved understanding of their effects on OUD-related behaviors.

Mechanism of action of gut microbiota and probiotic Lactobacillus rhamnosus GG on skeletal remodeling in mice

INTRODUCTION

Gut microbiota (GM) is the collection of small organisms such as bacteria, fungi, bacteriophages and protozoans living in the intestine in symbiotics relation within their host. GM regulates host metabolism by various mechanisms.

METHODS

This review aims to consolidate current information for physicians on the effect of GM on bone health. For this, an online search of the literature was conducted using the keywords gut microbiota, bone mass, osteoporosis, Lactobacillus and sex steroid.

RESULTS AND CONCLUSIONS

There is a considerable degree of variation in bone mineral density (BMD) within populations, and it is estimated that a significant component of BMD variability is due to genetics. However, the remaining causes of bone mass variance within populations remain largely unknown. A well-recognized cause of phenotypic variation in bone mass is the composition of the microbiome. Studies have shown that germ-free (GF) mice have higher bone mass compared to conventionally raised (CR) mice. Furthermore, GM dysbiosis, also called dysbacteriosis, is defined as any alteration in the composition of the microbial community that has been colonized in the host intestine and associated with the development of bone diseases. For instance, postmenopausal osteoporosis (PMO) and diabetes. GM can be modulated by several factors such as genetics, age, drugs, food habits and probiotics. Probiotics are defined as viable bacteria that confer health benefits by modulating GM when administered in adequate quantity. Lactobacillus rhamnosus GG (LGG) is a great example of such a probiotic. LGG has been shown to regulate bone mass in healthy mice as well as ovariectomized (OVX) mice via two different mechanisms. This review will focus on the literature regarding the mechanism by which GM and probiotic LGG regulate bone mass in healthy mice as well as in OVX mice, a model of PMO.

Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools

Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.

Effects of melatonin on rumen microorganisms and methane production in dairy cow: results from in vitro and in vivo studies

BACKGROUND

Methane (CH4) is a major greenhouse gas, and ruminants are one of the sources of CH4 which is produced by the rumen microbiota. Modification of the rumen microbiota compositions will impact the CH4 production. In this study, the effects of melatonin on methane production in cows were investigated both in the in vitro and in vivo studies.

RESULTS

Melatonin treatment significantly reduced methane production in both studies. The cows treated with melatonin reduced methane emission from their respiration by approximately 50%. The potential mechanisms are multiple. First, melatonin lowers the volatile fatty acids (VFAs) production in rumen and reduces the raw material for CH4 synthesis. Second, melatonin not only reduces the abundance of Methanobacterium which are responsible for generating methane but also inhibits the populations of protozoa to break the symbiotic relationship between Methanobacterium and protozoa in rumen to further lowers the CH4 production. The reduced VFA production is not associated with food intake, and it seems also not to jeopardize the nutritional status of the cows. This was reflected by the increased milk lipid and protein contents in melatonin treated compared to the control cows. It is likely that the energy used to synthesize methane is saved to compensate the reduced VFA production.

CONCLUSION

This study enlightens the potential mechanisms by which melatonin reduces rumen methane production in dairy cows. Considering the greenhouse effects of methane on global warming, these findings provide valuable information using different approaches to achieve low carbon dairy farming to reduce the methane emission. Video Abstract.

Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata

A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.

Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome

BACKGROUND

The human gut microbiota is a complex community comprised of trillions of bacteria and is critical for the digestion and absorption of nutrients. Bacterial communities of the intestinal microbiota influence the development of several conditions and diseases. We studied the effect of host genetics on gut microbial composition using Collaborative Cross (CC) mice. CC mice are a panel of mice that are genetically diverse across strains, but genetically identical within a given strain allowing repetition and deeper analysis than is possible with other collections of genetically diverse mice.

RESULTS

16S rRNA from the feces of 167 mice from 28 different CC strains was sequenced and analyzed using the Qiime2 pipeline. We observed a large variance in the bacterial composition across CC strains starting at the phylum level. Using bacterial composition data, we identified 17 significant Quantitative Trait Loci (QTL) linked to 14 genera on 9 different mouse chromosomes. Genes within these intervals were analyzed for significant association with pathways and the previously known human GWAS database using Enrichr analysis and Genecards database. Multiple host genes involved in obesity, glucose homeostasis, immunity, neurological diseases, and many other protein-coding genes located in these regions may play roles in determining the composition of the gut microbiota. A subset of these CC mice was infected with Salmonella Typhimurium. Using infection outcome data, an increase in abundance of genus Lachnospiraceae and decrease in genus Parasutterella correlated with positive health outcomes after infection. Machine learning classifiers accurately predicted the CC strain and the infection outcome using pre-infection bacterial composition data from the feces.

CONCLUSION

Our study supports the hypothesis that multiple host genes influence the gut microbiome composition and homeostasis, and that certain organisms may influence health outcomes after S. Typhimurium infection. Video Abstract.

Comparison of the gut microbiota and metabolites between Diannan small ear pigs and Diqing Tibetan pigs

Objective

Host genetics and environment participate in the shaping of gut microbiota. Diannan small ear pigs and Diqing Tibetan pigs are excellent native pig breeds in China and live in different environments. However, the gut microbiota of Diannan small ear pigs and Diqing Tibetan pigs were still rarely understood. Therefore, this study aimed to analyze the composition characteristics of gut microbiota and metabolites in Diannan small ear pigs and Diqing Tibetan pigs.

Methods

Fresh feces of 6 pigs were randomly collected from 20 4-month-old Diannan small ear pigs (DA group) and 20 4-month-old Diqing Tibetan pigs (TA group) for high-throughput 16S rRNA sequencing and liquid chromatography-mass spectrometry (LC-MS) non-targeted metabolome analysis.

Results

The results revealed that Firmicutes and Bacteroidetes were the dominant phyla in the two groups. Chao1 and ACE indices differed substantially between DA and TA groups. Compared with the DA group, the relative abundance of Prevotellaceae, and Ruminococcus was significantly enriched in the TA group, while the relative abundance of Lachnospiraceae, Actinomyces, and Butyricicoccus was significantly reduced. Cholecalciferol, 5-dehydroepisterol, stigmasterol, adrenic acid, and docosahexaenoic acid were significantly enriched in DA group, which was involved in the steroid biosynthesis and biosynthesis of unsaturated fatty acids. 3-phenylpropanoic acid, L-tyrosine, phedrine, rhizoctin B, and rhizoctin D were significantly enriched in TA group, which was involved in the phenylalanine metabolism and phosphonate and phosphinate metabolism.

Conclusion

We found that significant differences in gut microbiota composition and metabolite between Diannan small ear pigs and Diqing Tibetan pigs, which provide a theoretical basis for exploring the relationship between gut microbiota and pig breeds.

Human gut microbiome: A primer for the clinician

The human host gets tremendously influenced by a genetically and phenotypically distinct and heterogeneous constellation of microbial species-the human microbiome-the gut being one of the most densely populated and characterized site for these organisms. Microbiome science has advanced rapidly, technically with respect to the analytical methods and biologically with respect to its mechanistic influence in health and disease states. A clinician conducting a microbiome study should be aware of the nuances related to microbiome research, especially with respect to the technical and biological factors that can influence the interpretation of research outcomes. Hence, this review is an attempt to detail these aspects of the human gut microbiome, with emphasis on its determinants in a healthy state.

Human Genes Involved in the Interaction between Host and Gut Microbiome: Regulation and Pathogenic Mechanisms

Introduction: The umbrella term “human gut microbiota” describes the complex ecosystem harboring our gut. It includes bacteria, viruses, protozoa, archaea, fungi, and yeasts. This taxonomic classification does not describe its functions, which encompass nutrients digestion and absorption, immune system regulation, and host metabolism. “Gut microbiome” indicates instead the genome belonging to these “microbes” actively involved in these functions. However, the interaction between the host genome and the microbial ones determines the fine functioning of our organism. Methods: We reviewed the data available in the scientific literature on the definition of gut microbiota, gut microbiome, and the data on human genes involved in the interaction with the latter. We consulted the main medical databases using the following keywords, acronyms, and their associations: gut microbiota, gut microbiome, human genes, immune function, and metabolism. Results: Candidate human genes encoding enzymes, inflammatory cytokines, and proteins show similarity with those included in the gut microbiome. These findings have become available through newer artificial intelligence (AI) algorithms allowing big data analysis. From an evolutionary point of view, these pieces of evidence explain the strict and sophisticated interaction at the basis of human metabolism and immunity regulation in humans. They unravel more and more physiopathologic pathways included in human health and disease. Discussion: Several lines of evidence also obtained through big data analysis support the bi-directional role of gut microbiome and human genome in host metabolism and immune system regulation.

Impact of diet and host genetics on the murine intestinal mycobiome

The mammalian gut is home to a diverse microbial ecosystem, whose composition affects various physiological traits of the host. Next-generation sequencing-based metagenomic approaches demonstrated how the interplay of host genetics, bacteria, and environmental factors shape complex traits and clinical outcomes. However, the role of fungi in these complex interactions remains understudied. Here, using 228 males and 363 females from an advanced-intercross mouse line, we provide evidence that fungi are regulated by host genetics. In addition, we map quantitative trait loci associated with various fungal species to single genes in mice using whole genome sequencing and genotyping. Moreover, we show that diet and its' interaction with host genetics alter the composition of fungi in outbred mice, and identify fungal indicator species associated with different dietary regimes. Collectively, in this work, we uncover an association of the intestinal fungal community with host genetics and a regulatory role of diet in this ecological niche.

Post-weaning diarrhea in pigs from a single Danish production herd was not associated with the pre-weaning fecal microbiota composition and diversity

Introduction

The association between the porcine pre-weaning gut microbiota composition and diversity, and subsequent post-weaning diarrhea (PWD) susceptibility is currently being studied. In this longitudinal study, we examined the association between pre-weaning fecal microbiome composition and diversity, and PWD development in a Danish sow herd.

Methods

Forty-five pigs were followed from birth until 7 days after weaning (post-natal day (PND) 33). At PND 33, the pigs were categorized as PWD cases or healthy controls based on fecal consistency. We compared their fecal microbiomes at PND 8, late lactation (PND 27) and 7 days post weaning (PND 33) using 16S rRNA V3 region high-throughput sequencing. At PND 27 and 33, we also weighed the pigs, assessed fecal shedding of hemolytic Escherichia coli by culture and characterized hemolytic isolates by ETEC virulence factors with PCR and by whole genome sequencing.

Results

A total of 25 out of 45 pigs developed PWD and one Enterotoxigenic E. coli strain with F18:LT:EAST1 virotype was isolated from most pigs. At PND 33, we found differences in beta diversity between PWD and healthy pigs (R² = 0.027, p = 0.009) and that body weight was associated with both alpha and beta diversity. Pre-weaning fecal microbiome diversity did not differ between PWD and healthy pigs and we found no significant, differentially abundant bacteria between them.

Conclusion

In the production herd under study, pre-weaning fecal microbiome diversity and composition were not useful indicators of PWD susceptibility.

Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals

BACKGROUND

Animals form complex symbiotic associations with their gut microbes, whose evolution is determined by an intricate network of host and environmental factors. In many insects, such as Drosophila melanogaster, the microbiome is flexible, environmentally determined, and less diverse than in mammals. In contrast, mammals maintain complex multispecies consortia that are able to colonize and persist in the gastrointestinal tract. Understanding the evolutionary and ecological dynamics of gut microbes in different hosts is challenging. This requires disentangling the ecological factors of selection, determining the timescales over which evolution occurs, and elucidating the architecture of such evolutionary patterns.

RESULTS

We employ experimental evolution to track the pace of the evolution of a common gut commensal, Lactiplantibacillus plantarum, within invertebrate (Drosophila melanogaster) and vertebrate (Mus musculus) hosts and their respective diets. We show that in Drosophila, the nutritional environment dictates microbial evolution, while the host benefits L. plantarum growth only over short ecological timescales. By contrast, in a mammalian animal model, L. plantarum evolution results to be divergent between the host intestine and its diet, both phenotypically (i.e., host-evolved populations show higher adaptation to the host intestinal environment) and genomically. Here, both the emergence of hypermutators and the high persistence of mutated genes within the host's environment strongly differed from the low variation observed in the host's nutritional environment alone.

CONCLUSIONS

Our results demonstrate that L. plantarum evolution diverges between insects and mammals. While the symbiosis between Drosophila and L. plantarum is mainly determined by the host diet, in mammals, the host and its intrinsic factors play a critical role in selection and influence both the phenotypic and genomic evolution of its gut microbes, as well as the outcome of their symbiosis.

Genetic diversity of honeybee colonies predicts gut bacterial diversity of individual colony members

The gut microbiota of social bees is relatively simple and dominated by a set of core taxa found consistently in individuals around the world. Yet, variation remains and can affect host health. We characterized individual- and regional-scale variation in honeybee (Apis mellifera) gut microbiota from 64 colonies in North-West England by sequencing the V4 region of the 16S rRNA gene and asked whether microbiota were influenced by host genotype and landscape composition. We also characterized the genotypes of individual bees and the land cover surrounding each colony. The literature-defined core taxa dominated across the region despite the varied environments. However, there was variation in the relative abundance of core taxa, and colony membership explained much of this variation. Individuals from more genetically diverse colonies had more diverse microbiotas, but individual genetic diversity did not influence gut microbial diversity. There were weak trends for colonies in more similar landscapes to have more similar microbiota, and for bees from more urban landscapes to have less diverse microbiota. To our knowledge, this is the first report for any species that the gut bacterial communities of individuals are influenced by the genotypes of others in the population.

Insight into role of short chain fatty acids in regulating intestinal mucosal barrier and alleviating inflammatory bowel disease

In recent years, the importance of intestinal microbiota and its metabolites in maintaining the human intestinal environment has been gradually revealed. Therefore, short chain fatty acids (SCFAs), as the metabolites produced by the intestinal microbiota, play a momentous part in regulating the balance between the function and morphology of the mucosal barrier, regulating the proliferation and differentiation of mucosal cells, protecting the integrity and permeability of the mucosal barrier, and maintainingthe stability of tight junctions. Inflammatory bowel disease (IBD) is a chronic, inflammatory condition of the gastrointestinal tract, associated with a disturbance of intestinal barrier function and dysregulation of the intestinal immune responses, the etiology and pathogenesis of which, however, are not yet fully uncovered. Animal models and human studies have corroborated the contribution of SCFAs in enhancing the barrier function through protective effects. This review will summarize the potential role of SCFAs in IBD with regard to regulating intestinal function, hoping to provide a new target for clinical treatment of IBD.

The road not taken: host genetics in shaping intergenerational microbiomes

The early-life gut microbiome is linked to human phenotypes as an imbalanced microbiome of this period is implicated in diseases throughout life. Several determinants of early-life gut microbiome are explored, however, mechanisms of acquisition, colonization, and stability of early-life gut microbiome and their interindividual variability remain elusive. Host genetics play a vital role to shape the gut microbiome and interact with it to modulate individual phenotypes in human studies and animal models. Given the microbial linkage between host generations, we discuss the current state of roles of host genetics in forming intergenerational microbiomes associated with mothers, offspring, and those vertically transmitted, providing a basis for taking into account host genetics in future early-life microbiome research. We further expand our discussion to the bidirectional interactions between host gene expression and microbiome in human health.

Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice

Determining the forces that shape diversity in host-associated bacterial communities is critical to understanding the evolution and maintenance of metaorganisms. To gain deeper understanding of the role of host genetics in shaping gut microbial traits, we employed a powerful genetic mapping approach using inbred lines derived from the hybrid zone of two incipient house mouse species. Furthermore, we uniquely performed our analysis on microbial traits measured at the gut mucosal interface, which is in more direct contact with host cells and the immune system. Several mucosa-associated bacterial taxa have high heritability estimates, and interestingly, 16S rRNA transcript-based heritability estimates are positively correlated with cospeciation rate estimates. Genome-wide association mapping identifies 428 loci influencing 120 taxa, with narrow genomic intervals pinpointing promising candidate genes and pathways. Importantly, we identified an enrichment of candidate genes associated with several human diseases, including inflammatory bowel disease, and functional categories including innate immunity and G-protein-coupled receptors. These results highlight key features of the genetic architecture of mammalian host-microbe interactions and how they diverge as new species form.

The digestive system, particularly the large intestine, hosts many types of bacteria which together form the gut microbiome. The exact makeup of different bacterial species is specific to an individual, but microbiomes are often more similar between related individuals, and more generally, across related species. Whether this is because individuals share similar environments or similar genetic backgrounds remains unclear. These two factors can be disentangled by breeding different animal lineages – which have different genetic backgrounds while belonging to the same species – and then raising the progeny in the same environment.

To investigate this question, Doms et al. studied the genes and microbiomes of mice resulting from breeding strains from multiple locations in a natural hybrid zone between different subspecies. The experiments showed that 428 genetic regions affected the makeup of the microbiome, many of which were known to be associated with human diseases. Further analysis revealed 79 genes that were particularly interesting, as they were involved in recognition and communication with bacteria. These results show how the influence of the host genome on microbiome composition becomes more specialized as animals evolve.

Overall, the work by Doms et al. helps to pinpoint the genes that impact the microbiome; this knowledge could be helpful to examine how these interactions contribute to the emergence of conditions such as diabetes or inflammatory bowel disease, which are linked to perturbations in gut bacteria.

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

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

Butyrate supplementation to pregnant mice elicits cytoprotection against colonic injury in the offspring

BACKGROUND

Maternal diet during pregnancy can impact progeny health and disease by influencing the offspring's gut microbiome and immune development. Gut microbial metabolism generates butyrate, a short-chain fatty acid that benefits intestinal health. Here we assess the effects of antenatal butyrate on the offspring's gastrointestinal health. We hypothesized that antenatal butyrate supplementation will induce protection against colitis in the offspring.

METHODS

C57BL/6 mice received butyrate during pregnancy and a series of experiments were performed on their offspring. RNA sequencing was performed on colonic tissue of 3-week-old offspring. Six-8-week-old offspring were subjected to dextran sulfate sodium-induced colitis. Fecal microbiome analysis was performed on the 6-8-week-old offspring.

RESULTS

Antenatal butyrate supplementation dampened transcript enrichment of inflammation-associated colonic genes and prevented colonic injury in the offspring. Antenatal butyrate increased the offspring's stool microbiome diversity and expanded the prevalence of specific gut microbes.

CONCLUSIONS

Antenatal butyrate supplementation resulted in downregulation of genes in the offspring's colon that function in inflammatory signaling. In addition, antenatal butyrate supplementation was associated with protection against colitis and an expanded fecal microbiome taxonomic diversity in the offspring.

IMPACT

Dietary butyrate supplementation to pregnant mice led to downregulation of colonic genes involved in inflammatory signaling and cholesterol synthesis, changes in the fecal microbiome composition of the offspring, and protection against experimentally induced colitis in the offspring. These data support the mounting evidence that the maternal diet during pregnancy has enduring effects on the offspring's long-term health and disease risk. Although further investigations are needed to identify the mechanism of butyrate's effects on fetal gut development, the current study substantiates the approach of dietary intervention during pregnancy to optimize the long-term gastrointestinal health of the offspring.

New Insights on Gene by Environmental Effects of Drugs of Abuse in Animal Models Using GeneNetwork

Gene-by-environment interactions are important for all facets of biology, especially behaviour. Families of isogenic strains of mice, such as the BXD strains, are excellently placed to study these interactions, as the same genome can be tested in multiple environments. BXD strains are recombinant inbred mouse strains derived from crossing two inbred strains—C57BL/6J and DBA/2J mice. Many reproducible genometypes can be leveraged, and old data can be reanalysed with new tools to produce novel insights. We obtained drug and behavioural phenotypes from Philip et al. Genes, Brain and Behaviour 2010, and reanalysed their data with new genotypes from sequencing, as well as new models (Genome-wide Efficient Mixed Model Association (GEMMA) and R/qtl2). We discovered QTLs on chromosomes 3, 5, 9, 11, and 14, not found in the original study. We reduced the candidate genes based on their ability to alter gene expression or protein function. Candidate genes included Slitrk6 and Cdk14. Slitrk6, in a Chromosome14 QTL for locomotion, was found to be part of a co-expression network involved in voluntary movement and associated with neuropsychiatric phenotypes. Cdk14, one of only three genes in a Chromosome5 QTL, is associated with handling induced convulsions after ethanol treatment, that is regulated by the anticonvulsant drug valproic acid. By using families of isogenic strains, we can reanalyse data to discover novel candidate genes involved in response to drugs of abuse.

Determining the Composition of Resident and Transient Members of the Oyster Microbiome

To better understand how complex microbial communities become assembled on eukaryotic hosts, it is essential to disentangle the balance between stochastic and deterministic processes that drive their assembly. Deterministic processes can create consistent patterns of microbiome membership that result in persistent resident communities, while stochastic processes can result in random fluctuation of microbiome members that are transient with regard to their association to the host. We sampled oyster reefs from six different populations across the east coast of the United States. At each site we collected gill tissues for microbial community analysis and additionally collected and shipped live oysters to Northeastern University where they were held in a common garden experiment. We then examined the microbiome shifts in gill tissues weekly for 6 weeks using 16S rRNA gene amplicon sequencing. We found a strong population-specific signal in the microbial community composition of field-sampled oysters. Surprisingly, the oysters sampled during the common garden experiment maintained compositionally distinct gill-associated microbial communities that reflected their wild population of origin, even after rearing them in a common garden for several weeks. This indicates that oyster gill-associated microbiota are predominantly composed of resident microbes specific to host population, rather than being a reflection of their immediate biotic and abiotic surroundings. However, certain bacterial taxa tended to appear more frequently on individuals from different populations than on individuals from the same population, indicating that there is a small portion of the gill microbiome that is transient and is readily exchanged with the environmental pool of microbes. Regardless, the majority of gill-associated microbes were resident members that were specific to each oyster population, suggesting that there are strong deterministic factors that govern a large portion of the gill microbiome. A small portion of the microbial communities, however, was transient and moved among oyster populations, indicating that stochastic assembly also contributes to the oyster gill microbiome. Our results are relevant to the oyster aquaculture industry and oyster conservation efforts because resident members of the oyster microbiome may represent microbes that are important to oyster health and some of these key members vary depending on oyster population.

Role of Dietary Supplements and Probiotics in Modulating Microbiota and Bone Health: The Gut-Bone Axis

Osteoporosis is characterized by an alteration of bone microstructure with a decreased bone mineral density, leading to the incidence of fragility fractures. Around 200 million people are affected by osteoporosis, representing a major health burden worldwide. Several factors are involved in the pathogenesis of osteoporosis. Today, altered intestinal homeostasis is being investigated as a potential additional risk factor for reduced bone health and, therefore, as a novel potential therapeutic target. The intestinal microflora influences osteoclasts’ activity by regulating the serum levels of IGF-1, while also acting on the intestinal absorption of calcium. It is therefore not surprising that gut dysbiosis impacts bone health. Microbiota alterations affect the OPG/RANKL pathway in osteoclasts, and are correlated with reduced bone strength and quality. In this context, it has been hypothesized that dietary supplements, prebiotics, and probiotics contribute to the intestinal microecological balance that is important for bone health. The aim of the present comprehensive review is to describe the state of the art on the role of dietary supplements and probiotics as therapeutic agents for bone health regulation and osteoporosis, through gut microbiota modulation.

Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle

Animals harbor diverse communities of microbes within their gastrointestinal tracts. Phylogenetic relationship, diet, gut morphology, host physiology, and ecology all influence microbiome composition within and between animal clades. Emerging evidence points to host genetics as also playing a role in determining gut microbial composition within species. Here, we discuss recent advances in the study of microbiome heritability across a variety of animal species. Candidate gene and discovery-based studies in humans, mice, Drosophila, Caenorhabditis elegans, cattle, swine, poultry, and baboons reveal trends in the types of microbes that are heritable and the host genes and pathways involved in shaping the microbiome. Heritable gut microbes within a host species tend to be phylogenetically restricted. Host genetic variation in immune- and growth-related genes drives the abundances of these heritable bacteria within the gut. With only a small slice of the metazoan branch of the tree of life explored to date, this is an area rife with opportunities to shed light into the mechanisms governing host-microbe relationships.

Habitats Show More Impacts Than Host Species in Shaping Gut Microbiota of Sympatric Rodent Species in a Fragmented Forest

Gut microbiota play a significant role for animals to adapt to the changing environment. Host species and habitats are key drivers in shaping the diversity and composition of the microbiota, but the determinants of composition of the sympatric host gut microbiome remain poorly understood within an ecosystem. In this study, we examined the effects of habitats of different succession stages and host species on the diversity and composition of fecal gut microbiota in four sympatric rodent species (Apodemus draco, Leopoldamys edwardsi, Niviventer confucianus, and Niviventer fulvescens) in a subtropical forest. We found, as compared to the differences between species, habitat types showed a much larger effect on the gut microbiota of rodents. Alpha diversity of the microbial community of A. draco, N. fulvescens, and N. confucianus was highest in farmland, followed by primary forest and shrubland, and lowest in secondary forest. Beta diversity of the three rodent species showed significant different among habitats. The alpha diversity of gut microbiota of L. edwardsi was significantly higher than those of A. draco and N. confucianus, and its beta diversity showed significant difference from A. draco. Our results suggested that gut microbiota were important for animals in responding to diet changes in different habitats under human disturbances.

How microbiomes can help inform conservation: landscape characterisation of gut microbiota helps shed light on additional population structure in a specialist folivore

BACKGROUND

The koala (Phascolarctos cinereus), an iconic yet endangered specialised folivore experiencing widespread decline across Australia, is the focus of many conservation programs. Whilst animal translocation and progressive conservation strategies such as faecal inoculations may be required to bring this species back from the brink of extinction, insight into the variation of host-associated gut microbiota and the factors that shape this variation are fundamental for their success. Despite this, very little is known about the landscape variability and factors affecting koala gut microbial community dynamics. We used large scale field surveys to evaluate the variation and diversity of koala gut microbiotas and compared these diversity patterns to those detected using a population genetics approach. Scat samples were collected from five locations across South East Queensland with microbiota analysed using 16S rRNA gene amplicon sequencing.

RESULTS

Across the landscape koala gut microbial profiles showed large variability, with location having a large effect on bacterial community composition and bacterial diversity. Certain bacteria were found to be significantly differentially abundant amongst locations; koalas from Noosa showed a depletion in two bacterial orders (Gastranaerophilales and Bacteroidales) which have been shown to provide beneficial properties to their host. Koala gut microbial patterns were also not found to mirror population genetic patterns, a molecular tool often used to design conservation initiatives.

CONCLUSIONS

Our data shows that koala gut microbiotas are extremely variable across the landscape, displaying complex micro- and macro- spatial variation. By detecting locations which lack certain bacteria we identified koala populations that may be under threat from future microbial imbalance or dysbiosis. Additionally, the mismatching of gut microbiota and host population genetic patterns exposed important population structure that has previously gone undetected across South East Queensland. Overall, this baseline data highlights the importance of integrating microbiota research into conservation biology in order to guide successful conservation programs such as species translocation and the implementation of faecal inoculations.

Integrative Analysis of LGR5/6 Gene Variants, Gut Microbiota Composition and Osteoporosis Risk in Elderly Population

Objective: This study aimed to explore the relationships between the common variants of R-spondin/Wnt signaling genes, gut microbiota composition, and osteoporosis (OP) risk in elderly Chinese Han population.

Design: Dual-energy X-ray absorptiometry was used to obtain the OP-associated measurements at multiple skeleton sites among all 1,168 participants. Genotyping data was obtained by using the next-generation sequencing in the discovery stage (n = 400, 228 OP patients) and SNPscan technology in the replication stage (n = 768, 356 OP patients). Bioinformatic analysis was performed to provide more evidence for the genotype-OP associations. The 16S ribosomal RNA gene high-throughput sequencing technology was adopted to explore OP-associated gut microbiota variations.

Results: The genetic variants of rs10920362 in the LGR6 gene (P-FDR = 1.19 × 10^–6) and rs11178860 in the LGR5 gene (P-FDR = 1.51 × 10^–4) were found to associate with OP risk significantly. Several microbial taxa were associated with the BMDs and T-scores at multiple skeleton sites. The associations between rs10920362 and BMD-associated microbiota maintained significance after adjusting confounders. The rs10920362 CT/TT genotype associated with a decreased relative abundance of Actinobacteria (β = −1.32, P < 0.001), Bifidobacteriaceae (β = −1.70, P < 0.001), and Bifidobacterium (β = −1.70, P < 0.001) compared to the CC genotype.

Conclusion: Our findings suggested that the variants loci of LGR6 may be associate with OP pathogenesis via gut microbiota modifications. The relationship between host genetics and gut microbiome provides new perspectives about OP prevention and treatment.

Ace2 and Tmprss2 Expressions Are Regulated by Dhx32 and Influence the Gastrointestinal Symptoms Caused by SARS-CoV-2

Studies showed that the gastrointestinal (GI) tract is one of the most important pathways for SARS-CoV-2 infection and coronavirus disease 2019 (COVID-19). As SARS-CoV-2 cellular entry depends on the ACE2 receptor and TMPRSS2 priming of the spike protein, it is important to understand the molecular mechanisms through which these two proteins and their cognate transcripts interact and influence the pathogenesis of COVID-19. In this study, we quantified the expression, associations, genetic modulators, and molecular pathways for Tmprss2 and Ace2 mRNA expressions in GI tissues using a systems genetics approach and the expanded family of highly diverse BXD mouse strains. The results showed that both Tmprss2 and Ace2 are highly expressed in GI tissues with significant covariation. We identified a significant expression quantitative trait locus on chromosome 7 that controls the expression of both Tmprss2 and Ace2. Dhx32 was found to be the strongest candidate in this interval. Co-expression network analysis demonstrated that both Tmprss2 and Ace2 were located at the same module that is significantly associated with other GI-related traits. Protein-protein interaction analysis indicated that hub genes in this module are linked to circadian rhythms. Collectively, our data suggested that genes with circadian rhythms of expression may have an impact on COVID-19 disease, with implications related to the timing and treatment of COVID-19.

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.

Family SES Is Associated with the Gut Microbiome in Infants and Children

BACKGROUND

While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic factors and microbiome composition. This study expands on this prior work by examining the association between family socioeconomic status (SES) and host genetics with microbiome composition in infants and children.

METHODS

Family SES was used to predict a latent variable representing six genera abundances generated from whole-genome shotgun sequencing. A polygenic score derived from a microbiome genome-wide association study was included to control for potential genetic associations. Associations between family SES and microbiome diversity were assessed.

RESULTS

Anaerostipes, Bacteroides, Eubacterium, Faecalibacterium, and Lachnospiraceae spp. significantly loaded onto a latent factor, which was significantly predicted by SES (p < 0.05) but not the polygenic score (p > 0.05). Our results indicate that SES did not predict alpha diversity but did predict beta diversity (p < 0.001).

CONCLUSIONS

Our results demonstrate that modifiable environmental factors influence gut microbiome composition at an early age. These results are important as our understanding of gut microbiome influences on health continue to expand.

Do Primocolonizing Bacteria Enable Bacteroides thetaiotaomicron Intestinal Colonization Independently of the Capacity To Consume Oxygen?

Aerobic bacteria are frequent primocolonizers of the human naive intestine. Their generally accepted role is to eliminate oxygen, which would allow colonization by anaerobes that subsequently dominate bacterial gut populations.

Aerobic bacteria are frequent primocolonizers of the human naive intestine. Their generally accepted role is to eliminate oxygen, which would allow colonization by anaerobes that subsequently dominate bacterial gut populations. In this hypothesis-based study, we revisited this dogma experimentally in a germfree mouse model as a mimic of the germfree newborn. We varied conditions leading to the establishment of the dominant intestinal anaerobe Bacteroides thetaiotaomicron. Two variables were introduced: Bacteroides inoculum size and preestablishment by bacteria capable or not of consuming oxygen. High Bacteroides inoculum size enabled its primocolonization. At low inocula, we show that bacterial preestablishment was decisive for subsequent Bacteroides colonization. However, even non-oxygen-respiring bacteria, a hemAEscherichia coli mutant and the intestinal obligate anaerobe Clostridium scindens, facilitated Bacteroides establishment. These findings, which are supported by recent reports, revise the long-held assumption that oxygen scavenging is the main role for aerobic primocolonizing bacteria. Instead, we suggest that better survival of aerobic bacteria ex vivo during vectorization between hosts could be a reason for their frequent primocolonization.

Domestication Shapes the Community Structure and Functional Metagenomic Content of the Yak Fecal Microbiota

Domestication is a key factor of genetic variation; however, the mechanism by which domestication alters gut microbiota is poorly understood. Here, to explore the variation in the structure, function, rapidly evolved genes (REGs), and enzyme profiles of cellulase and hemicellulose in fecal microbiota, we studied the fecal microbiota in wild, half-blood, and domestic yaks based on 16S rDNA sequencing, shotgun-metagenomic sequencing, and the measurement of short-chain-fatty-acids (SCFAs) concentration. Results indicated that wild and half-blood yaks harbored an increased abundance of the phylum Firmicutes and reduced abundance of the genus Akkermansia, which are both associated with efficient energy harvesting. The gut microbial diversity decreased in domestic yaks. The results of the shotgun-metagenomic sequencing showed that the wild yak harbored an increased abundance of microbial pathways that play crucial roles in digestion and growth of the host, whereas the domestic yak harbored an increased abundance of methane-metabolism-related pathways. Wild yaks had enriched amounts of REGs in energy and carbohydrate metabolism pathways, and possessed a significantly increased abundance of cellulases and endohemicellulases in the glycoside hydrolase family compared to domestic yaks. The concentrations of acetic, propionic, n-butyric, i-butyric, n-valeric, and i-valeric acid were highest in wild yaks. Our study displayed the domestic effect on the phenotype of composition, function in gut microbiota, and SCFAs associated with gut microbiota, which had a closely association with the growth performance of the livestock. These findings may enlighten the researchers to construct more links between economic characteristics and gut microbiota, and develop new commercial strains in livestock based on the biotechnology of gut microbiota.

Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes

Effects of metformin, the first-line drug for type 2 diabetes therapy, on gut microbiome composition in type 2 diabetes have been described in various studies both in human subjects and animals. However, the details of the molecular mechanisms of metformin action have not been fully understood. Moreover, there is a significant lack of information on how metformin affects gut microbiome composition in female mouse models, depending on sex and metabolic status in well controlled experimental setting. Our study aimed to examine metformin-induced alterations in gut microbiome diversity, composition, and functional implications of high-fat diet-induced type 2 diabetes mouse model, using, for the first time in mice study, the shotgun metagenomic sequencing that allows estimation of microorganisms at species level. We also employed a randomized block, factorial study design, and including 24 experimental units allocated to 8 treatment groups to systematically evaluate the effect of sex and metabolic status on metformin interaction with microbiome. We used DNA obtained from fecal samples representing gut microbiome before and after ten weeks-long metformin treatment. We identified 100 metformin-related differentially abundant species in high-fat diet-fed mice before and after the treatment, with most of the species relative abundances increased. In contrast, no significant changes were observed in control diet-fed mice. Functional analysis targeted to carbohydrate, lipid, and amino acid metabolism pathways revealed 14 significantly altered hierarchies. We also observed sex-specific differences in response to metformin treatment. Males experienced more pronounced changes in metabolic markers, while in females the extent of changes in gut microbiome representatives was more marked, indicated by 53 differentially abundant species with more remarkable Log fold changes compared to the combined-sex analysis. The same pattern manifested regarding the functional analysis, where we discovered 5 significantly affected hierarchies in female groups but not in males. Our results suggest that both sexes of animals should be included in future studies focusing on metformin effects on the gut microbiome.

A platform for experimental precision medicine: The extended BXD mouse family

The challenge of precision medicine is to model complex interactions among DNA variants, phenotypes, development, environments, and treatments. We address this challenge by expanding the BXD family of mice to 140 fully isogenic strains, creating a uniquely powerful model for precision medicine. This family segregates for 6 million common DNA variants-a level that exceeds many human populations. Because each member can be replicated, heritable traits can be mapped with high power and precision. Current BXD phenomes are unsurpassed in coverage and include much omics data and thousands of quantitative traits. BXDs can be extended by a single-generation cross to as many as 19,460 isogenic F1 progeny, and this extended BXD family is an effective platform for testing causal modeling and for predictive validation. BXDs are a unique core resource for the field of experimental precision medicine.

Akkermansia, a Possible Microbial Marker for Poor Glycemic Control in Qataris Children Consuming Arabic Diet-A Pilot Study on Pediatric T1DM in Qatar

In Qatar, Type 1 Diabetes mellitus (T1DM) is one of the most prevalent disorders. This study aimed to explore the gut microbiome's relation to the continuous subcutaneous insulin infusion (CSII) therapy, dietary habits, and the HbA1c level in the pediatric T1DM subjects in Qatar. We recruited 28 T1DM subjects with an average age of 10.5 ± 3.53 years. The stool sample was used to measure microbial composition by 16s rDNA sequencing method. The results have revealed that the subjects who had undergone CSII therapy had increased microbial diversity and genus Akkermansia was significantly enriched in the subjects without CSII therapy. Moreover, genus Akkermansia was higher in the subjects with poor glycemic control (HbA1c > 7.5%). When we classified the subjects based on dietary patterns and nationality, Akkermansia was significantly enriched in Qataris subjects without the CSII therapy consuming Arabic diet than expatriates living in Qatar and eating a Western/mixed diet. Thus, this pilot study showed that abundance of Akkermansia is dependent on the Arabic diet only in poorly controlled Qataris T1DM patients, opening new routes to personalized treatment for T1DM in Qataris pediatric subjects. Further comprehensive studies on the relation between the Arabic diet, ethnicity, and Akkermansia are warranted to confirm this preliminary finding.

The gut microbiota is a transmissible determinant of skeletal maturation

Genetic factors account for the majority of the variance of human bone mass, but the contribution of non-genetic factors remains largely unknown. By utilizing maternal/offspring transmission, cohabitation, or fecal material transplantation (FMT) studies, we investigated the influence of the gut microbiome on skeletal maturation. We show that the gut microbiome is a communicable regulator of bone structure and turnover in mice. In addition, we found that the acquisition of a specific bacterial strain, segmented filamentous bacteria (SFB), a gut microbe that induces intestinal Th17 cell expansion, was sufficient to negatively impact skeletal maturation. These findings have significant translational implications, as the identification of methods or timing of microbiome transfer may lead to the development of bacteriotherapeutic interventions to optimize skeletal maturation in humans. Moreover, the transfer of SFB-like microbes capable of triggering the expansion of human Th17 cells during therapeutic FMT procedures could lead to significant bone loss in fecal material recipients.

Inbreeding Alters the Gut Microbiota of the Banna Minipig

Simple Summary

The mammalian gut microbiota is an indispensable part of host health. The gut microbiota plays a crucial role in nutrient digestibility, preventing colonization of pathogens and maintaining the host immune system. Host genetics has been conclusively shown to closely related to gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity, however, remarkably little is understood about the gut microbiota of pigs during inbreeding. The Banna minipig inbred is the world’s first successful large mammalian experimental animal inbred line since 1980 from full and half-siblings of the Diannan small-ear pig. Now, Banna minipig inbred has been inbred for over 37 generations, and the inbreeding coefficient is more than 99%. This study is the first to characterize and compare the composition and function of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to better understand the influence of inbreeding on the gut microbiota.

Abstract

The gut microbiota coevolve with the host and can be stably transmitted to the offspring. Host genetics plays a crucial role in the composition and abundance of gut microbiota. Inbreeding can cause a decrease of the host’s genetic diversity and the heterozygosity. In this study, we used 16S rRNA gene sequencing to compare the differences of gut microbiota between the Diannan small-ear pig and Banna minipig inbred, aiming to understand the impact of inbreeding on the gut microbiota. Three dominant bacteria (Stenotrophlomonas, Streptococcus, and Lactobacillus) were steadily enriched in both the Diannan small-ear pig and Banna minipig inbred. After inbreeding, the gut microbiota alpha diversity and some potential probiotics (Bifidobacterium, Tricibacter, Ruminocaccae, Christensenellaceae, etc.) were significantly decreased, while the pathogenic Klebsiella bacteria was significantly increased. In addition, the predicted metagenomic analysis (PICRUSt2) indicated that several amino acid metabolisms (‘‘Valine, leucine, and isoleucine metabolism’’, ‘‘Phenylalanine, tyrosine, and tryptophan biosynthesis’’, ‘‘Histidine metabolism’’) were also markedly decreased after the inbreeding. Altogether our data reveal that host inbreeding altered the composition and the predicted function of the gut microbiome, which provides some data for the gut microbiota during inbreeding.

Gut Microbiota between Environment and Genetic Background in Familial Mediterranean Fever (FMF)

The gastrointestinal tract hosts the natural reservoir of microbiota since birth. The microbiota includes various bacteria that establish a progressively mutual relationship with the host. Of note, the composition of gut microbiota is rather individual-specific and, normally, depends on both the host genotype and environmental factors. The study of the bacterial profile in the gut demonstrates that dominant and minor phyla are present in the gastrointestinal tract with bacterial density gradually increasing in oro-aboral direction. The cross-talk between bacteria and host within the gut strongly contributes to the host metabolism, to structural and protective functions. Dysbiosis can develop following aging, diseases, inflammatory status, and antibiotic therapy. Growing evidences show a possible link between the microbiota and Familial Mediterranean Fever (FMF), through a shift of the relative abundance in microbial species. To which extent such perturbations of the microbiota are relevant in driving the phenotypic manifestations of FMF with respect to genetic background, remains to be further investigated.

Gut microbiota in a host-brood parasite system: insights from common cuckoos raised by two warbler species

An animal's gut microbiota (GM) is shaped by a range of environmental factors affecting the bacterial sources invading the host. At the same time, animal hosts are equipped with intrinsic mechanisms enabling regulation of GM. However, there is limited knowledge on the relative importance of these forces. To assess the significance of host-intrinsic vs environmental factors, we studied GM in nestlings of an obligate brood parasite, the common cuckoo (Cuculus canorus), raised by two foster species, great reed warblers (Acrocephalus arundinaceus) and Eurasian reed warblers (A. scirpaceus), and compared these with GM of the fosterers' own nestlings. We show that fecal GM varied between cuckoo and warbler nestlings when accounting for the effect of foster/parent species, highlighting the importance of host-intrinsic regulatory mechanisms. In addition to feces, cuckoos also expel a deterrent secretion, which provides protection against olfactory predators. We observed an increased abundance of bacterial genera capable of producing repulsive volatile molecules in the deterrent secretion. Consequently, our results support the hypothesis that microbiota play a role in this antipredator mechanism. Interestingly, fosterer/parent identity affected only cuckoo deterrent secretion and warbler feces microbiota, but not that of cuckoo feces, suggesting a strong selection of bacterial strains in the GM by cuckoo nestlings.

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses

Recent population-based1-4 and clinical studies5 have identified a range of factors associated with human gut microbiome variation. Murine quantitative trait loci6, human twin studies7 and microbiome genome-wide association studies1,3,8-12 have provided evidence for genetic contributions to microbiome composition. Despite this, there is still poor overlap in genetic association across human studies. Using appropriate taxon-specific models, along with support from independent cohorts, we show an association between human host genotype and gut microbiome variation. We also suggest that interpretation of applied analyses using genetic associations is complicated by the probable overlap between genetic contributions and heritable components of host environment. Using faecal 16S ribosomal RNA gene sequences and host genotype data from the Flemish Gut Flora Project (n = 2,223) and two German cohorts (FoCus, n = 950; PopGen, n = 717), we identify genetic associations involving multiple microbial traits. Two of these associations achieved a study-level threshold of P = 1.57 × 10-10; an association between Ruminococcus and rs150018970 near RAPGEF1 on chromosome 9, and between Coprococcus and rs561177583 within LINC01787 on chromosome 1. Exploratory analyses were undertaken using 11 other genome-wide associations with strong evidence for association (P < 2.5 × 10-8) and a previously reported signal of association between rs4988235 (MCM6/LCT) and Bifidobacterium. Across these 14 single-nucleotide polymorphisms there was evidence of signal overlap with other genome-wide association studies, including those for age at menarche and cardiometabolic traits. Mendelian randomization analysis was able to estimate associations between microbial traits and disease (including Bifidobacterium and body composition); however, in the absence of clear microbiome-driven effects, caution is needed in interpretation. Overall, this work marks a growing catalogue of genetic associations that will provide insight into the contribution of host genotype to gut microbiome. Despite this, the uncertain origin of association signals will likely complicate future work looking to dissect function or use associations for causal inference analysis.

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.

Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle Change

Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.

Unveiling the presence of epigenetic mark by Lactobacillus supplementation in high-fat diet-induced metabolic disorder in Sprague-Dawley rats

Gut dysbiosis, particularly bacteria from Firmicutes and Bacteroidetes phyla, plays a fundamental role in the progression of metabolic disorders. Probiotics have shown to restore the gut microbiota composition in metabolic disorders with subsequent beneficial effects. Recent studies have reported that several species of Lactobacillus as probiotic supplementation improve insulin sensitivity and glucose metabolism. Nonetheless, whether Lactobacillus could influence the epigenetic modifications that underlie insulin-resistant conditions is still unexplored. Therefore, the current study examined the therapeutic effects and underlying epigenetic mechanisms of three different species of Lactobacillus in the high-fat diet (HFD)-induced insulin-resistant rats. Three different species of Lactobacillus; Lactobacillus casei, Lactobacillus gasseri, and Lactobacillus rhamnosus were individually supplemented orally (10⁹ CFU/mL) to insulin-resistant SD rats for 12 weeks. Lactobacillus supplementation led to a significant reduction in the hyperglycemia, hyperinsulinemia, and hyperlipidemia associated with HFD-induced insulin resistance. Histopathological examination also indicated the protective effects of Lactobacillus supplementation against the hepatic and intestinal damage caused by the high-fat diet. Lactobacillus supplementation also down-regulated the expression of FOXO1, a major transcription factor of insulin signaling. In addition, at the epigenetic level, Lactobacillus supplementation predominantly prevented methylation and demethylation of H3K79me2 and H3K27me3, respectively. Chromatin Immunoprecipitation (ChIP) coupled with quantitative PCR (ChIP-qPCR) assay revealed the presence of cross-talk between these two histone modifications at the promoter region of FOXO1. Taken together, this is the first report to observe that the effects of Lactobacillus supplementation involve alteration in FOXO1 expression via cross-talking between H3K79me2 and H3K27me3 histone modifications.

Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis)

The gut microbiome, or the community of microorganisms inhabiting the digestive tract, is often unique to its symbiont and, in many animal taxa, is highly influenced by host phylogeny and diet. In this study, we characterized the gut microbiome of the African savanna elephant (Loxodonta africana) and the African forest elephant (Loxodonta cyclotis), sister taxa separated by 2.6-5.6 million years of independent evolution. We examined the effect of host phylogeny on microbiome composition. Additionally, we examined the influence of habitat types (forest versus savanna) and diet types (crop-raiding versus noncrop-raiding) on the microbiome within L. africana. We found 58 bacterial orders, representing 16 phyla, across all African elephant samples. The most common phyla were Firmicutes, Proteobacteria, and Bacteroidetes. The microbiome of L. africana was dominated by Firmicutes, similar to other hindgut fermenters, while the microbiome of L. cyclotis was dominated by Proteobacteria, similar to more frugivorous species. Alpha diversity did not differ across species, habitat type, or diet, but beta diversity indicated that microbial communities differed significantly among species, diet types, and habitat types. Based on predicted KEGG metabolic pathways, we also found significant differences between species, but not habitat or diet, in amino acid metabolism, energy metabolism, and metabolism of terpenoids and polyketides. Understanding the digestive capabilities of these elephant species could aid in their captive management and ultimately their conservation.

A combination of genetics and microbiota influences the severity of the obesity phenotype in diet-induced obesity

Obesity has emerged as a major global health problem and is associated with various diseases, such as metabolic syndrome, type 2 diabetes mellitus, and cardiovascular diseases. The inbred C57BL/6 mouse strain is often used for various experimental investigations, such as metabolic research. However, over time, genetically distinguishable C57BL/6 substrains have evolved. The manifestation of genetic alterations has resulted in behavioral and metabolic differences. In this study, a comparison of diet-induced obesity in C57BL/6JHanZtm, C57BL/6NCrl and C57BL/6 J mice revealed several metabolic and immunological differences such as blood glucose level and cytokine expression, respectively, among these C57BL/6 substrains. For example, C57BL/6NCrl mice developed the most pronounced adiposity, whereas C57BL/6 J mice showed the highest impairment in glucose tolerance. Moreover, our results indicated that the immunological phenotype depends on the intestinal microbiota, as the cell subset composition of the colon was similar in obese ex-GF B6NRj^B6JHanZtm and obese B6JHanZtm mice. Phenotypic differences between C57BL/6 substrains are caused by a complex combination of genetic and microbial alterations. Therefore, in performing metabolic research, considering substrain-specific characteristics, which can influence the course of study, is important. Moreover, for unbiased comparison of data, the entire strain name should be shared with the scientific community.