Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village

Preliminary profile of the gut microbiota from amerindians in the Brazilian amazon experiencing a process of transition to urbanization

The Yanomami are one of the oldest indigenous tribes in the Amazon and are direct descendants of the first people to colonize South America 12,000 years ago. They are located on the border between Venezuela and Brazil, with the Venezuelan side remaining uncontacted. While they maintain a hunter-gatherer society, they are currently experiencing contact with urbanized populations in Brazil. The human gut microbiota of traditional communities has become the subject of recent studies due to the Westernization of their diet and the introduction of antibiotics and other chemicals, which have affected microbial diversity in indigenous populations, thereby threatening their existence. In this study, we preliminarily characterized the diversity of the gut microbiota of the Yanomami, a hunter-gatherer society from the Amazon, experiencing contact with urbanized populations. Similarly, we compared their diversity with the population in Manaus, Amazonas. A metabarcoding approach of the 16 S rRNA gene was carried out on fecal samples. Differences were found between the two populations, particularly regarding the abundance of genera (e.g., Prevotella and Bacteroides) and the higher values of the phyla Bacteroidetes over Firmicutes, which were significant only in the Yanomami. Some bacteria were found exclusively in the Yanomami (Treponema and Succinivibrio). However, diversity was statistically equal between them. In conclusion, the composition of the Yanomami gut microbiota still maintains the profile characteristic of a community with a traditional lifestyle. However, our results suggest an underlying Westernization process of the Yanomami microbiota when compared with that of Manaus, which must be carefully monitored by authorities, as the loss of diversity can be a sign of growing danger to the health of the Yanomami.

Impact of evolution on lifestyle in microbiome

This chapter analyses the interaction between microbiota and humans from an evolutionary point of view. Long-term interactions between gut microbiota and host have been generated as a result of dietary choices through coevolutionary processes, where mutuality of advantage is essential. Likewise, the characteristics of the intestinal environment have made it possible to describe different intrahost evolutionary mechanisms affecting microbiota. For its part, the intestinal microbiota has been of great importance in the evolution of mammals, allowing the diversification of dietary niches, phenotypic plasticity and the selection of host phenotypes. Although the origin of the human intestinal microbial community is still not known with certainty, mother-offspring transmission plays a key role, and it seems that transmissibility between individuals in adulthood also has important implications. Finally, it should be noted that certain aspects inherent to modern lifestyle, including refined diets, antibiotic intake, exposure to air pollutants, microplastics, and stress, could negatively affect the diversity and composition of our gut microbiota. This chapter aims to combine current knowledge to provide a comprehensive view of the interaction between microbiota and humans throughout evolution.

Gut Microbiota and Microbial Metabolism in Early Risk of Cardiometabolic Disease

Cardiometabolic disease comprises cardiovascular and metabolic dysfunction and underlies the leading causes of morbidity and mortality, both within the United States and worldwide. Commensal microbiota are implicated in the development of cardiometabolic disease. Evidence suggests that the microbiome is relatively variable during infancy and early childhood, becoming more fixed in later childhood and adulthood. Effects of microbiota, both during early development, and in later life, may induce changes in host metabolism that modulate risk mechanisms and predispose toward the development of cardiometabolic disease. In this review, we summarize the factors that influence gut microbiome composition and function during early life and explore how changes in microbiota and microbial metabolism influence host metabolism and cardiometabolic risk throughout life. We highlight limitations in current methodology and approaches and outline state-of-the-art advances, which are improving research and building toward refined diagnosis and treatment options in microbiome-targeted therapies.

The Gut Microbiome of an Indigenous Agropastoralist Population in a Remote Area of Colombia with High Rates of Gastrointestinal Infections and Dysbiosis

An Indigenous agropastoralist population called the Wiwa from the Sierra Nevada de Santa Marta, in North-East Colombia, shows high rates of gastrointestinal infections. Chronic gut inflammatory processes and dysbiosis could be a reason, suggesting an influence or predisposing potential of the gut microbiome composition. The latter was analyzed by 16S rRNA gene amplicon next generation sequencing from stool samples. Results of the Wiwa population microbiomes were associated with available epidemiological and morphometric data and compared to control samples from a local urban population. Indeed, locational-, age-, and gender-specific differences in the Firmicutes/Bacteriodetes ratio, core microbiome, and overall genera-level microbiome composition were shown. Alpha- and ß-diversity separated the urban site from the Indigenous locations. Urban microbiomes were dominated by Bacteriodetes, whereas Indigenous samples revealed a four times higher abundance of Proteobacteria. Even differences among the two Indigenous villages were noted. PICRUSt analysis identified several enriched location-specific bacterial pathways. Moreover, on a general comparative scale and with a high predictive accuracy, we found Sutterella associated with the abundance of enterohemorrhagic Escherichia coli (EHEC), Faecalibacteria associated with enteropathogenic Escherichia coli (EPEC) and helminth species Hymenolepsis nana and Enterobius vermicularis. Parabacteroides, Prevotella, and Butyrivibrio are enriched in cases of salmonellosis, EPEC, and helminth infections. Presence of Dialister was associated with gastrointestinal symptoms, whereas Clostridia were exclusively found in children under the age of 5 years. Odoribacter and Parabacteroides were exclusively identified in the microbiomes of the urban population of Valledupar. In summary, dysbiotic alterations in the gut microbiome in the Indigenous population with frequent episodes of self-reported gastrointestinal infections were confirmed with epidemiological and pathogen-specific associations. Our data provide strong hints of microbiome alterations associated with the clinical conditions of the Indigenous population.

Greater alteration of gut microbiota occurs in childhood obesity than in adulthood obesity

The children's gut microbiota, associated with the development of obesity, is in maturation. The impact of obesity on the gut microbiota in childhood could have a more significant effect than on adulthood and eventually be lifelong lasting, but it has been rarely studied. Aimed to discover the difference in gut microbiota between children and adults with obesity, we collected published amplicon sequencing data from National Center for Biotechnology Information (NCBI) and re-analyzed them using a uniform bioinformatic pipeline, as well as predicted the obesity using gut microbiota based on the random forest model. Summarizing common points among these cohorts, we found that the gut microbiota had a significant difference between children with and without obesity, but this difference was not observed in adult cohorts. Based on the random forest model, it was more challenging to predict childhood obesity using gut microbiota than adulthood obesity. Our results suggest that gut microbiota in childhood is more easily affected than in adulthood. Early intervention for childhood obesity is essential to improve children's health and lifelong gut microbiota-related health.

The developing infant gut microbiome: A strain-level view

At birth, neonates provide a vast habitat awaiting microbial colonization. Microbiome assembly is a complex process involving microbial seeding and succession driven by ecological forces and subject to environmental conditions. These successional events not only significantly affect the ecology and function of the microbiome, but also impact host health. While the establishment of the infant microbiome has been a point of interest for decades, an integrated view focusing on strain level colonization has been lacking until recently. Technological and computational advancements enabling strain-level analyses of the infant microbiome have demonstrated the immense complexity of this system and allowed for an improved understanding of how strains of the same species spread, colonize, evolve, and affect the host. Here, we review the current knowledge of the establishment and maturation of the infant gut microbiome with particular emphasis on newer discoveries achieved through strain-centric analyses.

Human Gut Microbiome Across Different Lifestyles: From Hunter-Gatherers to Urban Populations

Human lifestyle and its relationship with the human microbiome has been a line of research widely studied. This is because, throughout human history, civilizations have experienced different environments and lifestyles that could have promoted changes in the human microbiome. The comparison between industrialized and non-industrialized human populations in several studies has allowed to observe variation in the microbiome structure due to the population lifestyle. Nevertheless, the lifestyle of human populations is a gradient where several subcategories can be described. Yet, it is not known how these different lifestyles of human populations affect the microbiome structure on a large scale. Therefore, the main goal of this work was the collection and comparison of 16S data from the gut microbiome of populations that have different lifestyles around the world. With the data obtained from 14 studies, it was possible to compare the gut microbiome of 568 individuals that represent populations of hunter-gatherers, agricultural, agropastoral, pastoral, and urban populations. Results showed that industrialized populations present less diversity than those from non-industrialized populations, as has been described before. However, by separating traditional populations into different categories, we were able to observe patterns that cannot be appreciated by encompassing the different traditional lifestyles in a single category. In this sense, we could confirm that different lifestyles exhibit distinct alpha and beta diversity. In particular, the gut microbiome of pastoral and agropastoral populations seems to be more similar to those of urban populations according to beta diversity analysis. Beyond that, beta diversity analyses revealed that bacterial composition reflects the different lifestyles, representing a transition from hunters-gatherers to industrialized populations. Also, we found that certain groups such as Bacteoidaceae, Lanchospiraceae, and Rickenellaceae have been favored in the transition to modern societies, being differentially abundant in urban populations. Thus, we could hypothesize that due to adaptive/ecological processes; multifunctional bacterial groups (e.g., Bacteroidaceae) could be replacing some functions lost in the transition to modern lifestyle.

Human gut-microbiome interplay: Analysis of clinical studies for the emerging roles of diagnostic microbiology in inflammation, oncogenesis and cancer management

Microorganisms have been known to coexist in various parts of human body including the gut. The interactions between microbes and the surrounding tissues of the host are critical for fine fettle of the gut. The incidence of such microorganisms tends to vary among specific type of cancer affected individuals. Such microbial communities of specific tumor sites in cancer affected individuals could plausibly be used as prognostic and/or diagnostic markers for tumors associated with that specific site. Microorganisms of intestinal and non-intestinal origins including Helicobacter pylori can target several organs, act as carcinogens and promote cancer. It is interesting to note that diets causing inflammation can also increase the cancer risk. Yet, dietary supplementation with prebiotics and probiotics can reduce the incidence of cancer. Therefore, both diet and microbial community of the gut have dual roles of prevention and oncogenesis. Hence, this review intends to summarize certain important details related to gut microbiome and cancer.

Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador

Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.

Predictive Metagenomic Analysis of Autoimmune Disease Identifies Robust Autoimmunity and Disease Specific Microbial Signatures

Within the last decade, numerous studies have demonstrated changes in the gut microbiome associated with specific autoimmune diseases. Due to differences in study design, data quality control, analysis and statistical methods, many results of these studies are inconsistent and incomparable. To better understand the relationship between the intestinal microbiome and autoimmunity, we have completed a comprehensive re-analysis of 42 studies focusing on the gut microbiome in 12 autoimmune diseases to identify a microbial signature predictive of multiple sclerosis (MS), inflammatory bowel disease (IBD), rheumatoid arthritis (RA) and general autoimmune disease using both 16S rRNA sequencing data and shotgun metagenomics data. To do this, we used four machine learning algorithms, random forest, eXtreme Gradient Boosting (XGBoost), ridge regression, and support vector machine with radial kernel and recursive feature elimination to rank disease predictive taxa comparing disease vs. healthy participants and pairwise comparisons of each disease. Comparing the performance of these models, we found the two tree-based methods, XGBoost and random forest, most capable of handling sparse multidimensional data, to consistently produce the best results. Through this modeling, we identified a number of taxa consistently identified as dysregulated in a general autoimmune disease model including Odoribacter, Lachnospiraceae Clostridium, and Mogibacteriaceae implicating all as potential factors connecting the gut microbiome to autoimmune response. Further, we computed pairwise comparison models to identify disease specific taxa signatures highlighting a role for Peptostreptococcaceae and Ruminococcaceae Gemmiger in IBD and Akkermansia, Butyricicoccus, and Mogibacteriaceae in MS. We then connected a subset of these taxa with potential metabolic alterations based on metagenomic/metabolomic correlation analysis, identifying 215 metabolites associated with autoimmunity-predictive taxa.

The Biodiversity Paradigm: Building Resilience for Human and Environmental Health

It is a well-established fact that biodiversity is pivotal to human and planetary health, completely entwining biodiverse natural systems into a continuum, through our food systems, into human health. This means there is an intimate connection between the biodiversity of the soil, the biodiversity and interrelationships of cultivated and wild plants and animals. This article looks through an ecological sciences perspective at the interconnections and interrelations between human health and Earth’s health. But regardless of the wide recognition of the benefits of biodiversity, we are seeing a political and economic landscape which actively runs contrary to and further erodes diversity in favor of the globalized industrial food system, seed uniformity and further centralization through false tech solutions. A food system which is responsible for both setting the preconditions for the severity of the global COVID-19 pandemic by weakening human and animal health through an explosion of non-communicable diseases. The way forward is instead shown by small farmers, local communities and gardeners who are already implementing biodiversity-based organic agroecology, which both preserves and rejuvenates the health continuum between the soil, plants, animals, food and humans. Acting as a holistic paradigm shift where diversity in all areas is cultivated for ecological resilience.

Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions

BACKGROUND

The development and maturation of rumen microbiota across the lifetime of grazing yaks remain unexplored due to the varied lifestyles and feed types of yaks as well as the challenges of obtaining samples. In addition, the interactions among four different rumen microbial groups (bacteria, archaea, fungi and protozoa) in the rumen of yak are not well defined. In this study, the rumen microbiota of full-grazing yaks aged 7 days to 12 years old was assessed to determine the maturation patterns of these four microbial groups and the dynamic interactions among them during different growth stages.

RESULTS

The rumen microbial groups (bacteria, archaea, protozoa and fungi) varied through the growth of yaks from neonatal (7 days) to adult (12 years), and the bacterial and archaeal groups were more sensitive to changes in growth stages compared to the two eukaryotic microbial groups. The age-discriminatory taxa within each microbial group were identified with the random forest model. Among them, Olsenella (bacteria), Group 10 sp., belonging to the family Methanomassiliicoccaceae (archaea), Orpinomyces (fungi), and Dasytricha (protozoa) contributed the most to discriminating the age of the rumen microbiota. Moreover, we found that the rumen archaea reached full maturation at 5 approximately years of age, and the other microbial groups matured between 5 and 8 years of age. The intra-interactions patterns and keystone species within each microbial group were identified by network analysis, and the inter-interactions among the four microbial groups changed with growth stage. Regarding the inter-interactions among the four microbial groups, taxa from bacteria and protozoa, including Christensenellaceae R-7 group, Prevotella 1, Trichostomatia, Ruminococcaceae UCG-014 and Lachnospiraceae, were the keystone species in the network based on betweenness centrality scores.

CONCLUSIONS

This study depicted a comprehensive view of rumen microbiota changes in different growth stages of grazing yaks. The results revealed the unique microbiota maturation trajectory and the intra- and inter-interactions among bacteria, archaea, fungi and protozoa in the rumen of grazing yaks across the lifetime of yaks. The information obtained in this study is vital for the future development of strategies to manipulate rumen microbiota in grazing yaks for better growth and performance in the harsh Qinghai-Tibetan Plateau ecosystem.

The Role of the Gut Microbiota in Dietary Interventions for Depression and Anxiety

There is emerging evidence that an unhealthy dietary pattern may increase the risk of developing depression or anxiety, whereas a healthy dietary pattern may decrease it. This nascent research suggests that dietary interventions could help prevent, or be an alternative or adjunct therapy for, depression and anxiety. The relation, however, is complex, affected by many confounding variables, and is also likely to be bidirectional, with dietary choices being affected by stress and depression. This complexity is reflected in the data, with sometimes conflicting results among studies. As the research evolves, all characteristics of the relation need to be considered to ensure that we obtain a full understanding, which can potentially be translated into clinical practice. A parallel and fast-growing body of research shows that the gut microbiota is linked with the brain in a bidirectional relation, commonly termed the microbiome-gut-brain axis. Preclinical evidence suggests that this axis plays a key role in the regulation of brain function and behavior. In this review we discuss possible reasons for the conflicting results in diet-mood research, and present examples of areas of the diet-mood relation in which the gut microbiota is likely to be involved, potentially explaining some of the conflicting results from diet and depression studies. We argue that because diet is one of the most significant factors that affects human gut microbiota structure and function, nutritional intervention studies need to consider the gut microbiota as an essential piece of the puzzle.

Recipe for a Healthy Gut: Intake of Unpasteurised Milk Is Associated with Increased Lactobacillus Abundance in the Human Gut Microbiome

INTRODUCTION

The gut microbiota plays a role in gut-brain communication and can influence psychological functioning. Diet is one of the major determinants of gut microbiota composition. The impact of unpasteurised dairy products on the microbiota is unknown. In this observational study, we investigated the effect of a dietary change involving intake of unpasteurised dairy on gut microbiome composition and psychological status in participants undertaking a residential 12-week cookery course on an organic farm.

METHODS

Twenty-four participants completed the study. The majority of food consumed during their stay originated from the organic farm itself and included unpasteurised milk and dairy products. At the beginning and end of the course, participants provided faecal samples and completed self-report questionnaires on a variety of parameters including mood, anxiety and sleep. Nutrient intake was monitored with a food frequency questionnaire. Gut microbiota analysis was performed with 16S rRNA gene sequencing. Additionally, faecal short chain fatty acids (SCFAs) were measured.

RESULTS

Relative abundance of the genus Lactobacillus increased significantly between pre- and post-course time points. This increase was associated with participants intake of unpasteurised milk and dairy products. An increase in the faecal SCFA, valerate, was observed along with an increase in the functional richness of the microbiome profile, as determined by measuring the predictive neuroactive potential using a gut-brain module approach.

CONCLUSIONS

While concerns in relation to safety need to be considered, intake of unpasteurised milk and dairy products appear to be associated with the growth of the probiotic bacterial genus, Lactobacillus, in the human gut. More research is needed on the effect of dietary changes on gut microbiome composition, in particular in relation to the promotion of bacterial genera, such as Lactobacillus, which are recognised as being beneficial for a range of physical and mental health outcomes.

Evolution of the gut microbiome in infancy within an ecological context

PURPOSE OF REVIEW

Humans and their commensal microbiota coexist in a complex ecosystem molded by evolutionary and ecological factors. Ecological opportunity is the prospective, lineage-specific characteristic of an environment that contains both niche availability leading to persistence coupled with niche discordance that drives selection within that lineage. The newborn gut ecosystem presents vast ecological opportunity. Herein, factors affecting perinatal infant microbiome composition are discussed.

RECENT FINDINGS

Establishing a healthy microbiota in early life is required for immunological programming and prevention of both short-term and long-term health outcomes. The holobiont theory infers that host genetics contributes to microbiome composition. However, in most human studies, environmental factors are predominantly responsible for microbiome composition and function. Key perinatal elements are route of delivery, diet and the environment in which that infant resides. Vaginal delivery seeds an initial microbiome, and breastfeeding refines the community by providing additional microbes, human milk oligosaccharides and immunological proteins.

SUMMARY

Early life represents an opportunity to implement clinical practices that promote the optimal seeding and feeding of the gut microbial ecosystem. These include reducing nonemergent cesarean deliveries, avoiding the use of antibiotics, and promoting exclusive breastfeeding.

An Integrative Approach to Assessing Diet-Cancer Relationships

The relationship between diet and cancer is often viewed with skepticism by the public and health professionals, despite a considerable body of evidence and general consistency in recommendations over the past decades. A systems biology approach which integrates 'omics' data including metabolomics, genetics, metagenomics, transcriptomics and proteomics holds promise for developing a better understanding of how diet affects cancer and for improving the assessment of diet through biomarker discovery thereby renewing confidence in diet-cancer links. This review discusses the application of multi-omics approaches to studies of diet and cancer. Considerations and challenges that need to be addressed to facilitate the investigation of diet-cancer relationships with multi-omic approaches are also discussed.

The Gut Microbiota and Its Implication in the Development of Atherosclerosis and Related Cardiovascular Diseases

The importance of gut microbiota in health and disease is being highlighted by numerous research groups worldwide. Atherosclerosis, the leading cause of heart disease and stroke, is responsible for about 50% of all cardiovascular deaths. Recently, gut dysbiosis has been identified as a remarkable factor to be considered in the pathogenesis of cardiovascular diseases (CVDs). In this review, we briefly discuss how external factors such as dietary and physical activity habits influence host-microbiota and atherogenesis, the potential mechanisms of the influence of gut microbiota in host blood pressure and the alterations in the prevalence of those bacterial genera affecting vascular tone and the development of hypertension. We will also be examining the microbiota as a therapeutic target in the prevention of CVDs and the beneficial mechanisms of probiotic administration related to cardiovascular risks. All these new insights might lead to novel analysis and CVD therapeutics based on the microbiota.

The Gut Microbiota in the First Decade of Life

Appreciation of the importance of the gut microbiome is growing, and it is becoming increasingly relevant to identify preventive or therapeutic solutions targeting it. The composition and function of the gut microbiota are relatively well described for infants (less than 3 years) and adults, but have been largely overlooked in pre-school (3-6 years) and primary school-age (6-12 years) children, as well as teenagers (12-18 years). Early reports suggested that the infant microbiota would attain an adult-like structure at the age of 3 years, but recent studies have suggested that microbiota development may take longer. This development time is of key importance because there is evidence to suggest that deviations in this development may have consequences in later life. In this review, we provide an overview of current knowledge concerning the gut microbiota, its evolution, variation, and response to dietary challenges during the first decade of life with a focus on healthy pre-school and primary school-age children (up to 12 years) from various populations around the globe. This knowledge should facilitate the identification of diet-based approaches targeting individuals of this age group, to promote the development of a healthy microbiota in later life.

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints

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. However, the comparative models used to date have mainly included a limited set of closely related primates. To further understand the forces that shape the primate gut microbiome, with reference to human populations, we expanded the comparative analysis of variation among gut microbiome compositions and their primate hosts, including 9 different primate species and 4 human groups characterized by a diverse set of subsistence patterns (n = 448 samples). The results show that the taxonomic composition of the human gut microbiome, at the genus level, exhibits increased compositional plasticity. Specifically, we show unexpected similarities between African Old World monkeys that rely on eclectic foraging and human populations engaging in nonindustrial subsistence patterns; these similarities transcend host phylogenetic constraints. Thus, instead of following evolutionary trends that would make their microbiomes more similar to that of conspecifics or more phylogenetically similar apes, gut microbiome composition in humans from nonindustrial populations resembles that of generalist cercopithecine monkeys. We also document that wild cercopithecine monkeys with eclectic diets and humans following nonindustrial subsistence patterns harbor high gut microbiome diversity that is not only higher than that seen in humans engaging in industrialized lifestyles but also higher compared to wild primates that typically consume fiber-rich diets.IMPORTANCE The results of this study indicate a discordance between gut microbiome composition and evolutionary history in primates, calling into question previous notions about host genetic control of the primate gut microbiome. Microbiome similarities between humans consuming nonindustrialized diets and monkeys characterized by subsisting on eclectic, omnivorous diets also raise questions about the ecological and nutritional drivers shaping the human gut microbiome. Moreover, a more detailed understanding of the factors associated with gut microbiome plasticity in primates offers a framework to understand why humans following industrialized lifestyles have deviated from states thought to reflect human evolutionary history. The results also provide perspectives for developing therapeutic dietary manipulations that can reset configurations of the gut microbiome to potentially improve human health.

Multi-Omic Analysis of the Microbiome and Metabolome in Healthy Subjects Reveals Microbiome-Dependent Relationships Between Diet and Metabolites

The human microbiome has been associated with health status, and risk of disease development. While the etiology of microbiome-mediated disease remains to be fully elucidated, one mechanism may be through microbial metabolism. Metabolites produced by commensal organisms, including in response to host diet, may affect host metabolic processes, with potentially protective or pathogenic consequences. We conducted multi-omic phenotyping of healthy subjects (N = 136), in order to investigate the interaction between diet, the microbiome, and the metabolome in a cross-sectional sample. We analyzed the nutrient composition of self-reported diet (3-day food records and food frequency questionnaires). We profiled the gut and oral microbiome (16S rRNA) from stool and saliva, and applied metabolomic profiling to plasma and stool samples in a subset of individuals (N = 75). We analyzed these multi-omic data to investigate the relationship between diet, the microbiome, and the gut and circulating metabolome. On a global level, we observed significant relationships, particularly between long-term diet, the gut microbiome and the metabolome. Intake of plant-derived nutrients as well as consumption of artificial sweeteners were associated with significant differences in circulating metabolites, particularly bile acids, which were dependent on gut enterotype, indicating that microbiome composition mediates the effect of diet on host physiology. Our analysis identifies dietary compounds and phytochemicals that may modulate bacterial abundance within the gut and interact with microbiome composition to alter host metabolism.

Comparative prevalence of Oxalobacter formigenes in three human populations

There has been increasing interest in the human anaerobic colonic bacterium Oxalobacter formigenes because of its ability to metabolize oxalate, and its potential contribution to protection from calcium oxalate kidney stones. Prior studies examining the prevalence of this organism have focused on subjects in developed countries and on adults. Now using O. formigenes-specific PCR, we have compared the prevalence of these organisms among subjects in two remote areas in which modern medical practices have hardly been present with a USA group of mothers and their infants for the first three years of life. Among the Amerindians of the Yanomami-Sanema and Yekwana ethnic groups in Venezuela and the Hadza in Tanzania, O. formigenes was detected in 60–80% of the adult subjects, higher than found in adults from USA in this and prior studies. In young children, the prevalence was much lower in USA than in either tribal village. These data extend our understanding of the epidemiology of O. formigenes carriage, and are consistent with the hypothesis that the rising incidence of kidney stones is associated with the progressive loss of O. formigenes colonization in populations that have been highly impacted by modern medical practices.

Development of the Gut Microbiome in Children, and Lifetime Implications for Obesity and Cardiometabolic Disease

Emerging evidence suggests that microbiome composition and function is associated with development of obesity and metabolic disease. Microbial colonization expands rapidly following birth, and microbiome composition is particularly variable during infancy. Factors that influence the formation of the gut microbiome during infancy and childhood may have a significant impact on development of obesity and metabolic dysfunction, with life-long consequences. In this review, we examine the determinants of gut microbiome composition during infancy and childhood, and evaluate the potential impact on obesity and cardiometabolic risk.