Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Antibiotic use in neonates can have detrimental effects on the developing gut microbiome, increasing the risk of morbidity. A likely mechanism is that of changing gene regulation in interfacing host epithelial cells. Nov 06, 2014 wikimedia commons, twinsuk previous research suggested host genetic variation can influence microbial phenotype, but an analysis of data from a large twin study published in cell today november 6 solidifies the connection between human genotype and the composition of the gut microbiome. Host genetic effects upon the early gut microbiota in a bovine model. There also have been studies of previously isolated human populations and. Human genetic variation and the gut microbiome in disease. For example, strong and sustained dietary changes have been shown to shape the abundance of different species in both mice and humans 2,3. Thus, the extent to which human genetics shape microbiome composition remains unclear.
Crossspecies comparisons of host genetic associations. Interplay of host genetics and gut microbiota underlying. Genetic differences in the immune system shape the microbiome. This study is part of an expanding effort to comprehensively profile the interactions. Its composition varies substantially between individuals and populations due to local, personal, and stochastic factors. In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. The microbiome has received increasing attention over the last 15 years. Obesity also is influenced by many human genes, and the gut microbiome clearly is influenced by the environment. Recent investigations of the human microbiome have revealed that it plays diverse roles in health and disease, and gut microbiome composition has been. Microbiome profiling of drinking water in relation to incidence of inflammatory bowel disease.
Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. In israeli and dutch human cohorts, the gut microbiome and host genetics have been shown to be largely independent and a combination of both factors has a higher power to predict host phenotypes. Human genetics shape the gut microbiome europe pmc. Genetic factors and the intestinal microbiome guide.
The gut microbiota has a variety of functions within the host, such as metabolism of certain. Metaanalysis of human genomemicrobiome association studies. Host genes and their effect on the intestinal microbiome. The composition of the human gut microbiome is now well established as a factor important to human health conditions, including metabolic, pathogen, and immunerelated diseases. In this context, only a relatively small number of opportunistic pathogens are considered to be members of the gut microbiota, residing unperturbed within the enteric host. Host and microbiome genomewide association studies. Our growing understanding of the role of the microbiome in complex diseases naturally leads us to examine the concept of the microbiome as a complex trait, and hence to measure genetic versus environmental control of microbiome composition. Nov 26, 2014 an explosion of evidence in the past 5 years links the microbial composition of the gut to obesity in humans. Diet shapes the gut microbiome of pigs during nursing and. Walter and ley, 2011, therefore it may function as an environmental factor that interacts with host genetics to shape phenotype, as well as a genetically determined attribute that is shaped by, and interacts with, the host bevins and salzman, 2011. Microbiome refers to the collective genomes of the microorganisms in a particular environment, and microbiota is the community of microorganisms themselves. Host genetic variation impacts microbiome composition. Variation in gut microbiome is associated with wellness and disease in humans, and yet the molecular mechanisms by which this variation affects the host are not well understood.
The long list of microbiome related health disorders raises the question of what in fact determines microbiome composition. Investigators in this study were interested in how seasonality affects the gut microbiome among canadian inuit people, assuming that variations in food sources available during different seasons would contribute to large shifts in. Summaryhost genetics and the gut microbiome can both influence metabolic phenotypes. Environment dominates over host genetics in shaping human. Various cohort studies of the human gut microbiome based on a metagenomic approach using nextgeneration sequencing ngs have been reported. However, whether host genetic variation shapes the. Host genetics and the gut microbiome can both influence metabolic phenotypes. The long list of microbiomerelated health disorders raises the question of what in fact determines microbiome composition. Evidence has already shown that the gut microbiome can be shaped by host genetics.
Here, we treated colonic epithelial cells with live microbiota from five healthy individuals and quantified induced changes. Two recent studies help to disentangle this interaction and show that genetic loci across the human genome shape the gut microbiome. In addition to the twin studies in human, benson et al. Jun 26, 2018 the human microbiota consists of a wide variety of bacteria, viruses, fungi, and other singlecelled animals that live in the body. Identifying the mechanisms of these interactions has remained challenging. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. Role of the gut microbiota in nutrition and health the bmj. However, the comparative models used to date have mainly included a limited set of closely related primates. A majority of preterm neonates receive antibiotics after birth without clear evidence to guide this practice. A a principal coordinates plot of unweighted unifrac distances computed using the earth microbiome project emp data set 24 and the fecal samples from the american gut project agp data set.
Here we examine genotype and microbiome data from 1,046 healthy. Request pdf human genetics shape the gut microbiome host genetics and the gut microbiome can both influence metabolic phenotypes. Genetics shape microbiota and metabolism host genetic variation effects on human gut microbiome and associated metabolites lb thingholm, mc ruhlemann, a franke, institut fur klinische molekularbiologie, ukshchristianalbrechtsuniversitat zu kiel in short identify associations of human genetic variants with gut microbial community. Microbial genes significantly influence how the body operates and even outnumber human genes by a ratio of 100. Goodrich jk, waters jl, poole ac, sutter jl, koren o, blekhman r, et al. Certain host genetic variants predispose an individual towards. Introduction the human gut microbiome has been linked to metabolic disease and obesity karlsson et al. Current understanding of the gut microbiota shaping mechanisms. However, whether host genetic variationshapes thegut microbiome and interacts with it to affect host phenotype is unclear. Our unique microbial identity genome biology full text. Several preliminary genomewide association studies gwas have been completed, but. University of groningen the interplay between genetics, the.
Wikimedia commons, twinsuk previous research suggested host genetic variation can influence microbial phenotype, but an analysis of data from a large twin study published in cell today november 6 solidifies the connection between human genotype and the composition of the gut microbiome. To further understand the forces that shape the primate gut microbiome, with. As early as the 1980s, the gut microbiota has been associated with obesity in human 19 and rats 20 by utilizing culturedependent methods, which only sees pieces of microbes in the gut. Influence of diet on the gut microbiome and implications for human health 18. Human gut microbiome composition is shaped by multiple host intrinsic and extrinsic factors, but the relative contribution of host genetic. The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. The gut microbiome of primates, including humans, is reported to closely follow host evolutionary history, with gut microbiome composition being specific to the genetic background of its primate host. Gut microbiome heritability the scientist magazine. The interplay between host genetics and the gut microbiome.
Host genes and their effect on the intestinal microbiome garden. Here, we compared microbiotas across 1,000 fecal samples obtained from the twinsuk population, including 416 twin pairs. Environmental factors dominate over host genetics in shaping. However, whether host genetic variation shapes the gut microbiome and interacts. The connection between gut microbiome health and human health is. Coproid predicts the source of coprolites and paleofeces. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention beyond classical infectious diseases. Aug 30, 2016 the human gut microbiome has a considerable impact on host health. The human gut microbiome has been linked to metabolic disease and obesity. The gut microbiome is environmentally acquired from birth costello et al. The microbiome is the name given to all of the genes inside. Approximately 100 trillion microorganisms most of them bacteria, but also viruses, fungi, and protozoa exist in the human gastrointestinal tract1 2the microbiome is now best thought of as a virtual organ of the body. We are only beginning to understand the relationship between host genetics and the gut microbiome.
However, whether host genetic variation shapes the gut microbiome and inter acts with it to affect host phenotype is unclear. Systems genetics in laboratory mice mus musculus enables datadriven discovery of biological network components and mechanisms of hostmicrobial interactions. The intestinal microbiota is a dynamic community of bacteria, fungi, and viruses that mediates mucosal homeostasis and physiology. The human gut microbiota is composed of autochthonous, also known as indigenous, microorganisms and allochthonous or transient microorganisms 6. Variability in gut microbiota composition is related to many factors, including medication, diet, and genetics 4 16. This is a pdf file of an unedited manuscript that has. The gut microbiome in young pigs is dramatically shaped by the composition of dietary glycans, reflected by the different functional capacities of the microbiome before and after weaning. May 14, 2015 additionally, host genetics can shape individual microbiomes. This opens the possibility that an unexpected number of genetic factors act directly on microbial composition and function to modulate immune pathways and. Mar 01, 2020 the microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment.
The composition of the gut microbiota is modulated by multiple factors, including the age, sex and diet of the host. We performed a microbiome genomewide association study to identify host genetic variants associated. An operational taxonomic unitotu is a definition used to classify groups of closely related individuals. A considerable impact of other factors, such as diet, may outweigh the. Studying more than 1,000 fecal samples from 416 monozygotic and dizygotic twin pairs. Correlations of host genetics and gut microbiome composition. This study is part of an expanding effort to comprehensively profile the interactions between. Host genetic variation and its microbiome interactions. Human genetics shape the gut microbiome sciencedirect. The effect of heritability and host genetics on the gut. Human genetics shape the gut microbiome request pdf.
Host genetics shape the composition of the gut microbiome in concert with environmental factors such as diet and lifestyle. While host genetics and lifestyle influence the gut microbiome, we know that diet is the major factor shaping it. Use of the microbiome in the practice of epidemiology. They showed how migration from a nonwestern country to the usa is associated with immediate loss of gut microbiome diversity and function. The gut microbiome is affected by multiple factors, including genetics. Host genetic architecture and the landscape of microbiome. Increasing evidence suggests associations between earlylife antibiotic use, intestinal dysbiosis, and morbidity that challenge the efficacy of this common. Genetic and environmental factors converge in many different ways and bring about remarkable diversity in complex traits. Metaanalysis of human genomemicrobiome association. Several of the cohorts were set up to investigate certain phenotypes andor diseases, for in. As we have multiple phenotypes in addition to microbiome and host genotypes available, we can assess the putative effect of the gut microbiome on human health. Metataxonomic analysis of individuals at bmi extremes and. However, whether host genetic variation shapes the gut.
However, whether host genetic variation shapes the gut microbiome and interacts with it to affect host phenotype is unclear. Jan 22, 2019 the involvement of the microbiome in health and disease is well established. Dec 17, 2014 we are only beginning to understand the relationship between host genetics and the gut microbiome. Examples of how metagenomic data from the hmp have been used include characterizing mobile gene content in the microbiome, identifying the prevalence of specific enzymes in human microbiome samples 7, 8, dissecting factors that shape skin microbial communities, contrasting ancient and modern oral microbiomes, and studying the gut. Finally, the gut microbiome is a dynamic ecosystem, and as such is undergoing successional ecology. For example, numerous studies have reported changes in the gut microbiota during not only obesity, diabetes, and liver.
The microbial community in the human digestive tract, the gut microbiota, is highly complex and also displays strong variation across individuals 1 3. Environment dominates over host genetics in shaping human gut. The newborn mammal is rapidly colonized by a complex microbial community, whose importance for host health is becoming increasingly clear. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly. Thus, the extent to which human genetics shape microbiome composition remainsunclear. Aug 21, 2017 host genetics shape the composition of the gut microbiome in concert with environmental factors such as diet and lifestyle. To distinguish the effect of gut bacteria from genetic modification, turnbaugh et al. The human gut microbiota has been demonstrated to be associated with a number of host phenotypes, including obesity and a number of obesityassociated phenotypes. Systems genetics in laboratory mice mus musculus enables datadriven discovery of biological network components and mechanisms of hostmicrobial interactions underlying disease phenotypes.
Host genetic variation impacts microbiome composition across. Hopes, threats and promises article pdf available in gut 679. Dec 22, 2016 the collection of microbes that live in and on the human body is known as the microbiota. Diet and feeding pattern affect the diurnal dynamics of the gut microbiome 16. The emergence of this relatively new field has been facilitated by the advent of next generation sequencing technologies that enable the investigation of the complex interaction. Antibiotics may influence gut microbiome signaling to the. The impact of diet and lifestyle on gut microbiota and human health 17.
In a mediator model, the gut microbiome mediates the effects of genetic and environmental factors on complex diseases fig. Apoe genotype influences the gut microbiome structure and. There is increasing interest about the interplay between host genetics and gut microbiome on human complex diseases, with prior evidence mainly derived from animal models. Genetics maximiliankohlerhumanmicrobiome wiki github. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. This opens the possibility that an unexpected number of genetic factors act directly on microbial composition and function to modulate immune pathways and metabolic.
Here we studied microbialgenetic associations using. In addition, the shared and distinct microbiome features among human complex diseases remain largely unclear. In the 1990s, the application of cultureindependent molecular techniques based on 16s ribosomal rna rrna genes e. The gut microbiome, located in the distal colon and primarily studied through the analysis of feces, is the largest and arguably most influential microbial community within the body the human microbiome project consortium, 2012. The human gut bacteria christensenellaceae are widespread. This study is aimed at further understanding and describing the relationship between the gut microbiota and obesityassociated measurements obtained from human participants. In line with these observations, altering the gut microbiome in humans and mice has shown. Human genetics shape the gut microbiome europe pmc article. Apolipoprotein e apoe genotype is the strongest prevalent risk factor for neuropathology and ad 9 11.
Imbalances in the microbiome and aberrant immune responses to gut bacteria can disrupt homeostasis and are associated with inflammatory bowel diseases ibds in humans and colitis in mice. Pdf human genetics shape the gut microbiome omry koren. The human gut microbiome has a considerable impact on host health. Microbiome genomewide association studies mgwas are used to elucidate the interaction of host genetic variation with the microbiome. A multicenter team asked whether human genes might influence composition of the gut microbiome. Frontiers correlations of host genetics and gut microbiome.
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