The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, and discoveries that link interactions between humans and their microbiomes to health-related outcomes. The recently completed second phase, the Integrative Human Microbiome Project, comprised studies of dynamic changes in the microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and stressors that affect individuals with prediabetes. The associated research begins to elucidate mechanisms of host-microbiome interactions under these conditions, provides unique data resources (at the HMP Data Coordination Center), and represents a paradigm for future multi-omic studies of the human microbiome. Over ten years, the Human Microbiome Project has provided resources for studying the microbiome and its relationship to disease; this Perspective summarizes the key achievements and findings of the project and its relationship to the broader field.

The human gut microbiome has a considerable impact on host health. The long list of microbiome-related health disorders raises the question of what in fact determines microbiome composition. In this review we sought to understand how the host itself impacts the structure of the gut microbiota population, specifically by correlations of host genetics and gut microbiome composition.Host genetic profile has been linked to differences in microbiome composition, thus suggesting that host genetics can shape the gut microbiome of the host. However, cause-consequence mechanisms behind these links are still unclear. A survey of the possible mechanisms allowing host genetics to shape microbiota composition in the gut demonstrated the major role of metabolic functions and the immune system. A considerable impact of other factors, such as diet, may outweigh the effects of host genetic background. More studies are necessary for good understanding of the relations between the host genetic profile, gut microbiome

Background There has been much interest in the relationship between the types of gut microbiota and the development of obesity in recent years. It has been reported that the proportions of Firmicutes and Bacteroidetes differ between obese and normal weight human subjects. Human intestinal microbiota compositions have been found to be associated with long-term dietary habits and lifestyle. However, an increasing number of researches show that intestinal microbiota composition may be affected after short-term diet intervention. Importantly, obesity and metabolic problems play important roles in morbidity and mortality of schizophrenia patients. Human intestinal microbiota compositions related with obesity may impact the heath of this population. Therefore, we searched current advances about the connection of obesity, intestinal microbiota compositions, and diet in schizophrenia to conduct a clinical research focus on the effect of high fiber diet on the intestinal microbiota of schizophrenia ...

TY - JOUR. T1 - Liver Injury, Endotoxemia, and Their Relationship to Intestinal Microbiota Composition in Alcohol-Preferring Rats. AU - Posteraro, Brunella. AU - Paroni Sterbini, Francesco. AU - Petito, Valentina. AU - Rocca, Stefano. AU - Cubeddu, Tiziana. AU - Graziani, Cristina. AU - Arena, Vincenzo. AU - Vassallo, Gabriele A.. AU - Mosoni, Carolina. AU - Lopetuso, Loris. AU - Lorrai, Irene. AU - Maccioni, Paola. AU - Masucci, Luca. AU - Martini, Cecilia. AU - Gasbarrini, Antonio. AU - Sanguinetti, Maurizio. AU - Colombo, Giancarlo. AU - Addolorato, Giovanni. PY - 2018/12/1. Y1 - 2018/12/1. N2 - Background: There is strong evidence that alcoholism leads to dysbiosis in both humans and animals. However, it is unclear how changes in the intestinal microbiota (IM) relate to ethanol (EtOH)-induced disruption of gut-liver homeostasis. We investigated this issue using selectively bred Sardinian alcohol-preferring (sP) rats, a validated animal model of excessive EtOH consumption. Methods: ...

The goal of the Human Microbiome Project is to characterize the human microbiome and analyze its role in human health and disease.

In this study, we aimed to investigate the characteristics of the duodenal mucosal microbiota of patients with intestinal metaplasia (IM) and compare it with those of the gastric mucosal microbiota. We collected the duodenal and gastric mucosal samples from 10 adult patients with IM and 10 healthy controls (HC). The V3-V4 region of the bacterial 16S rRNA gene was examined by high throughput sequencing method. The diversity of the HC duodenal microbiota was higher than that of IM patient based on the Shannon and Simpson index while the Chao indices of IM duodenal mucosal microbiota was significantly higher than that of gastric mucosal microbiota of patients with IM. There was a marked difference in the duodenal microbiota structure between patients with IM and HC (ANOSIM, R = 1, P = 0.001). We also found that the Helicobacter pylori infection in gastric mucosa did not influence the structure of duodenal mucosal microbiota. The gastric mucosal microbiota structure significantly differed between patients

Gut Microbiota Composition Reflects Disease Severity and Dysfunctional Immune Responses in Patients with COVID-19. Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus…. What are the new findings?. Composition of the gut microbiota in patients with COVID-19 is concordant with disease severity and magnitude of plasma concentrations of several inflammatory cytokines, chemokines and blood markers of tissue damage.. Patients with COVID-19 were depleted in gut bacteria with known immunomodulatory potential, such as Faecalibacterium prausnitzii, Eubacterium rectale and several bifidobacterial species.. The dysbiotic gut microbiota composition in patients with COVID-19 persists after clearance of the ...

The human microbiome includes bacteria, viruses, and small eukaryotes, such as fungi, and this chapter focuses on the bacterial members of the microbiome. The Human Microbiome Project (HMP) aims at developing tools and resources for characterization of the human microbiota and to relate this microbiota to human health and disease. The goals of the jumpstart phase have been to sequence 900 reference genomes to provide a catalog of genomes for metagenomic studies, to sample at least 300 healthy adults between 18 and 40 years of age at five body sites, and to develop sequencing and analysis protocols for the samples derived from human subjects. The second phase of the HMP includes human microbiome studies that target particular disease states. In a recent study, four phyla comprised 92.3% of bacterial DNA sequences analyzed from multiple human sources, including hair, oral cavity, skin, genitourinary, and gastrointestinal tract. A study by Pei et al. showed that the distal esophageal microbiomes of four

The human microbiome is the community of microorganisms that reside in different body habitats. Host-microbiome interactions play an important but poorly-characterized role in health. Advances in high-throughput technologies including next-generation sequencing and mass spectroscopy allow us to query the population of micro-organisms and observe the interactions in greater detail. The effect of choices in measurement protocols, the multivariate longitudinal nature of data, and combining measurements on different scales pose difficulties in discovering and confirming significant relationships in the human microbiome.. The aim of this workshop was to create a forum for ideas for overcoming current and future challenges in the analysis of human microbiome data. In this workshop, participants learned how metagenomic (sequence-based) and metabolomic (mass spectroscopy-based) data are generated and the implications for analysis. Gaps in the current state-of-the-art methods were highlighted, ...

Omega-3 fatty acids may influence human physiological parameters in part by affecting the gut microbiome. The aim of this study was to investigate the links between omega-3 fatty acids, gut microbiome diversity and composition and faecal metabolomic profiles in middle aged and elderly women. We analysed data from 876 twins with 16S microbiome data and DHA, total omega-3, and other circulating fatty acids. Estimated food intake of omega-3 fatty acids were obtained from food frequency questionnaires. Both total omega-3and DHA serum levels were significantly correlated with microbiome alpha diversity (Shannon index) after adjusting for confounders (DHA Beta(SE) = 0.13(0.04), P = 0.0006 total omega-3: 0.13(0.04), P = 0.001). These associations remained significant after adjusting for dietary fibre intake. We found even stronger associations between DHA and 38 operational taxonomic units (OTUs), the strongest ones being with OTUs from the Lachnospiraceae family (Beta(SE) = 0.13(0.03), P = 8 × 10−7). Some

The one consistent finding among viral metagenomics studies has been the high proportion of sequences having no significant homology to a known sequence within one of the large sequence databases (e.g., GenBank, UniRef etc.). Those viral metagenome libraries having the highest frequency of hits to known sequences typically come from marine environments where the hit frequency for longer Sanger reads is around 30% (at a BLAST e-score of ≤0.001) [12]. Sanger libraries from soils show even lower hit rates at ~20%. The lack of homology to known sequences is only exacerbated by the shorter read lengths of next-generation sequencing technology [33] where libraries sequenced using the longest average read length next generation sequencing technology (i.e., 450 bp for the 454 pyrosequencing Ti FLX chemistry) yield hit rates to known sequence databases of less than 20%. In contrast, microbial shotgun metagenome libraries analyzed using the same databases and approaches will yield hit frequencies of ca. ...

via +Humberto González-Díaz *NIH Human Microbiome Project*Data Portalhttp://bit.ly/LhsWi2 | Complex Insight - Understanding our world

The very low birth weight (VLBW) infant is at great risk for marked dysbiosis of the gut microbiome due to multiple factors, including physiological immaturity and prenatal/postnatal influences that disrupt the development of a normal gut flora. However, little is known about the developmental succession of the microbiota in preterm infants as they grow and mature. This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant. The role of human milk in normal gut microbial development is emphasized, along with the role of the gut microbiome in immune development and gastroenteric health. Current research provides evidence that the gut microbiome interacts extensively with many physiological systems and metabolic processes in the developing infant. However, to the best of our knowledge, there are currently no studies prospectively mapping the gut microbiome of VLBW infants through early

Multiple sclerosis is a chronic inflammatory disease of the central nervous system (CNS). It is widely accepted that autoimmune response against the antigens of the CNS is the essential pathogenic force in the disease. It has recently become increasingly appreciated that activated encephalitogenic cells tend to migrate toward gut associated lymphoid tissues (GALTs) and that interrupted balance between regulatory and inflammatory immunity within the GALT might have decisive role in the initiation and propagation of the CNS autoimmunity. Gut microbiota composition and function has the major impact on the balance in the GALT. Thus, our aim was to perform analyses of gut microbiota in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. Albino Oxford (AO) rats that are highly resistant to EAE induction and Dark Agouti (DA) rats that develop EAE after mild immunization were compared for gut microbiota composition in different phases after EAE induction. Microbial analyses

The 6th Congress of the International Human Microbiome Consortium took place on November 9-11, 2016 in Houston, TX. This first IHMC congress to be held in the USA attracted a wide international audience with attendees from Africa, Asia, Latin America, Australia, Europe, and the United States. This unique community of scientists came together to discuss a wide range of topics in the field of human microbiome science, including crosstalk of environmental microbes with the human microbiome, the importance of microbial communities outside the gut, the role of maternal-infant interactions in the early establishment of the microbiome, and the importance of microbiome science in global health. In this post, we highlight a few key topics that generated significant discussion at the conference.. Sequencing the microbiome: 16S or WGS - or both? On the first day of the conference, an important question was posed to the audience which generated significant debate thereafter: as the field of microbiome ...

The human gut microbiome is a diverse community of microbial eukaryotes, viruses, archaea, and mostly bacteria [1-3], many of which play important roles in immunity, metabolism and nutrition [4-6]. The community structure of the microbiome is determined by many factors, including geography, sex, host genetics, and age [7-11].. Microbiome composition and structure may also vary within individuals over time, although most individuals have a relatively stable microbiome [12, 13]. Individuals with highly diverse microbiomes tend to be more stable through time [12]. Other studies have shown that individuality is preserved through time, underlying an overall stable and personalized microbiome [14]. On time scales of days to weeks, diet is the main factor driving composition and structure of the gut microbiome [13]. For example, some types of dietary fiber transits through the digestive tract without being assimilated by the human body, providing a food source for fermentative bacteria [15]. High fiber ...

RAPD Primer Design from Metagenomes RPDM scans metagenome sequences identifying and determining relative frequency of candidate primers for Random Amplification of Polymorphic DNA RAPD assays

A major role played by the intestinal microbiota is to aid in the harvest of nutrients from the diet (1). Dietary components that are not readily absorbed in the small intestine serve as growth substrates for members of the gut microbiota, which in turn can modify the bioavailability and nutritional properties of those same dietary components (1). For example, many of the beneficial effects associated with consumption of whole grains, vegetables, and fruits are at least in part mediated by end products of microbial metabolism, including short-chain fatty acids (e.g., butyrate) and phenolic acids (e.g., protocatechuic acid) (2-6). Likewise, gut microbes can also convert otherwise beneficial dietary compounds, such as choline, into metabolites that are detrimental to human health (7-10).. Choline is required for a wide range of biological activities, including maintaining the structural integrity of cell membranes, supporting cholinergic neurotransmission, and donating methyl groups in a number of ...

Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates viral dissemination, facilitates microbial translocation, and fosters establishment of one of the largest HIV reservoirs. Here we test the prediction that HIV infection modifies the composition and function of the mucosal commensal microbiota. Rectal mucosal microbiota were collected from human subjects using a sponge-based sampling methodology. Samples were collected from 20 HIV-positive men not receiving combination anti-retroviral therapy (cART), 20 HIV-positive men on cART and 20 healthy, HIV-negative men. Microbial composition of samples was analyzed using barcoded 16S Illumina deep sequencing (85,900 reads per sample after processing). Microbial metagenomic information for the samples was imputed using the bioinformatic tools PICRUST and HUMAnN. Microbial composition and imputed function in

16S rRNA sequencing data on human skin microbiome samples collected before and after swimming in the ocean. This dataset contains raw sequencing data contained in fasta and qual files produced from an Ion Torrent PGM sequencer. There were 2 sampling occurrences (041218 and 092718) and each occurrence has an associated fasta and qual file. This dataset contains the 092718 sampling data only due to storage restrictions. The other dataset is published separately. Our research has shown that the human skin microbiome is altered after swimming in the ocean. Normal commensals were washed off and simultaneously, exogenous bacteria were deposited on the skin. QIIME was used for initial analysis and indicated that the abundance and diversity of microbial communities on the skin increased after swimming and these changes persisted for more than 24 hours. Downstream analysis using PICRUSt to predict functional metagenomics indicated that there was an increase in antibiotic resistance genes, antibiotic biosynthesis

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human ...

Interest toward the human microbiome, particularly gut microbiome has flourished in recent decades owing to the rapidly advancing sequence-based screening and humanized gnotobiotic model in interrogating the dynamic operations of commensal microbiota. Available data indicates multiple factors have contributed to discrepancies between studies. The study of the human microbiome is important, and it gives an in-depth understanding of the interplay between humans and its indigenous microbiota. Using stool samples (n = 298; aged 1-11 months) from a US birth cohort and 16S rRNA sequencing, neonates (median age, 35 d) were divisible into three microbiota composition states (NGM1-3). The authors declare no conflicts of interest. Due to the coevolution of the human microbiota and the immune system, a balanced and systematic interaction occurs over time. It is important to note that the continuous use of broad-spectrum antibiotics may disrupt the human microbiota. Genome Medicine is pleased to present a ...

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitats signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of ...

The latest revelation in human gut microbiome research is the gut bacterial profiles of fifteen tribal populations representing four geographic regions (Assam, Telangana, Manipur and Sikkim) from India. The study by Dehingia, et al. (2015), Gut bacterial diversity of the tribes of India and comparison with the worldwide data (see References), is a good addition to the knowledge base of gut microbiome profiles across various human populations (Dehingia et al., 2015).. Why is this study relevant and important? Because most of the tribes around the world represent a gut microbiome profile of human ancestral lifestyle, one that was unaffected by junk food and was more physically active. Several lifestyle-associated disorders/diseases like type 2 diabetes, metabolic syndrome, and obesity have been linked to variations in human gut microbiome composition and function. Thus, having the knowledge of our ancestral gut microbiome is a good starting point to identify what changes have occurred since the ...

The theme for the meeting was frontiers of microbiome science and metagenomic medicine. This meant that there was a heavy focus on microbiome studies that utilized metagenomic shotgun sequencing to understand the human microbiome. I honestly felt throughout the meeting that this choice might have been a little too restrictive and had the focus too much on the method and not enough on the actual biology and medicine. There was certainly some excellent science, but it would have been nice to have the focus more on how we can use tools to answer important questions instead of looking for questions we can answer with a tool. But I could do a whole post on this so for now I am going to leave it at that. In the end, I think that the next meeting could really benefit from a broader theme that focuses less on a specific method. For example, I preferred the broad theme last year: future directions for human microbiome research in health and disease ...

Evaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearsons correlation coefficients were obtained between ...

Gut bacteria are an important component of the microbiota ecosystem in humans and other animals, and they play important roles in human health. The aim of this study was to investigate the relationship between gut microbiota and multiple demographical-, behavioral-, or biochemical-related factors in subjects with chronic disease. Subjects with a very wide age range who participated in community-based chronic disease prevention and screening programs in China were enrolled. We analyzed the intestinal microbiota composition using 16S rRNA-based high-throughput sequencing of fecal samples, analyzed the association between gut microbiota structure and multiple demographical, behavioral, and biochemical factors, and compared the differences in microbiota composition in age-stratified groups with different blood glucose levels. Our results showed that both age and blood glucose levels had a significant impact on the gut microbiota structure. We also identified several taxa showed distinct abundance in groups

Obesity is an important and intractable public health problem. In addition to the well-known risk factors of behavior, diet, and genetics, gut microbial communities were recently identified as another possible source of risk and a potential therapeutic target. However, human and animal-model studies have yielded conflicting results about the precise nature of associations between microbiome composition and obesity. In this paper, we use publicly available data from the Human Microbiome Project (HMP) and MetaHIT, both surveys of healthy adults that include obese individuals, plus two smaller studies that specifically examined lean versus obese adults. We find that inter-study variability in the taxonomic composition of stool microbiomes far exceeds differences between lean and obese individuals within studies. Our analyses further reveal a high degree of variability in stool microbiome composition and diversity across individuals. While we confirm the previously published small, but statistically

Microbiome studies of respiratory secretions have provided exciting new observations regarding the bacterial causation of exacerbations of COPD, and the impact of treatment of the exacerbation on the airway microbiome. Bacterial exacerbations likely represent abrupt major changes in the microbiome with resultant large increases in airway and systemic inflammation. Microbiome studies could lead to discovery of new pathogens that have been difficult to obtain with standard culture techniques.. The Vicious Circle Hypothesis embodies the likely contribution of an altered microbiome to COPD progression, with an unhealthy microbiome driving the inflammatory process in stable COPD. While studies with conventional microbiology found potential pathogenic bacteria to be virtually absent in bronchoscopic samples in healthy controls, smoking and development of COPD was associated with 35-50% incidence of isolation of pathogenic bacteria. In contrast, recent microbiome studies have found no or minor ...

A distinct bacterial signature of the placenta was reported, providing evidence that the fetus does not develop in a sterile environment. The oral microbiome was suggested as a possible source of the bacterial DNA present in the placenta based on similarities to the oral non-pregnant microbiome. Here, the possible origin of the placental microbiome was assessed, examining the gut, oral and placental microbiomes from the same pregnant women. Microbiome profiles from 37 overweight and obese pregnant women were examined by 16SrRNA sequencing. Fecal and oral contributions to the establishment of the placental microbiome were evaluated. Core phylotypes between body sites and metagenome predictive functionality were determined. The placental microbiome showed a higher resemblance and phylogenetic proximity with the pregnant oral microbiome. However, similarity decreased at lower taxonomic levels and microbiomes clustered based on tissue origin. Core genera: Prevotella, Streptococcus and Veillonella ...

The gut microbiome is a highly complex microbial community that strongly impacts human health and disease. The two dominant phyla in healthy humans are Bacteroidetes and Firmicutes, with minor phyla such as Proteobacteria having elevated abundances in various disease states. While the gut microbiome has been widely studied, relatively little is known about the role of interspecies interactions in promoting microbiome stability and function. We developed a biofilm metabolic model of a very simple gut microbiome community consisting of a representative bacteroidete (Bacteroides thetaiotaomicron), firmicute (Faecalibacterium prausnitzii) and proteobacterium (Escherichia coli) to investigate the putative role of metabolic byproduct cross feeding between species on community stability, robustness and flexibility. The model predicted coexistence of the three species only if four essential cross-feeding relationships were present. We found that cross feeding allowed coexistence to be robustly maintained for

Abstract: We propose to investigate the hypothesis that consistent changes in the human gut microbiome are associated with Crohns disease, a form of inflammatory bowel disease, and that altered microbiota contributes to pathogenesis. Analysis of this problem is greatly complicated by the fact that multiple factors influence the composition of the gut microbiota, including diet, host genotype, and disease state. For example, data from others and us document a drastic impact of diet on the composition of the gut microbiome. No amount of sequencing will yield a useful picture of the role of the microbiota in disease if samples are confounded with uncontrolled variables. Our proposed project will take advantage of our experience with deep sequencing to characterize the composition of the gut microbiome, but also control diet, host genotype, and disease state. Diet will be controlled by analyzing children treated for Crohns disease by placing them on a standardized elemental diet, and by testing ...

PMID: Expert Rev Gastroenterol Hepatol. 2018 Oct ;12(10):985-996. Epub 2018 Sep 3. PMID: 30146910 Abstract Title: Microbial modulation of the gut microbiome for treating autoimmune diseases. Abstract: Many studies have shown the relationship between autoimmune diseases and the gut microbiome in humans: those with autoimmune conditions display gut microbiome dysbiosis. The big question that needs to be addressed is if restoring eubiosis of the gut microbiota can help suppress the autoimmune condition by activating various immune regulatory mechanisms. Inducing these self-healing mechanisms should prolong good health in affected individuals. Area covered: Here, we review the available clinical and preclinical studies that have used selective bacteria for modulating gut microbiota for treating autoimmune diseases. The potential bacterial candidates and their mechanism of action in treating autoimmune diseases will be discussed. We searched for genetically modified and potential probiotics for ...

Diet and nutritional status are among the most important modifiable determinants of human health. The nutritional value of food is influenced in part by a persons gut microbial community (microbiota) and its component genes (microbiome). Unraveling the interrelations among diet, the structure and operations of the gut microbiota, and nutrient and energy harvest is confounded by variations in human environmental exposures, microbial ecology, and genotype. To help overcome these problems, we created a well-defined, representative animal model of the human gut ecosystem by transplanting fresh or frozen adult human fecal microbial communities into germ-free C57BL/6J mice. Culture-independent metagenomic analysis of the temporal, spatial, and intergenerational patterns of bacterial colonization showed that these humanized mice were stably and heritably colonized and reproduced much of the bacterial diversity of the donors microbiota. Switching from a low-fat, plant polysaccharide-rich diet to a ...

In an effort to reduce Lyme transmission in Dutchess county, the Carry Institute of Ecosystem Studies is evaluating various vector management strategies for their safety and efficacy. One strategy under consideration is treatment of voluntarily enrolled residential areas with Met52, a biopesticide which kills Ixodes scapularis, a principle Lyme vector. The goal of this Senior Project is to evaluate how application of Metarhizium anisopliae F52, commonly known as Met52, changes the soil bacterial microbiome of plots representative of residential areas. We analyzed the microbiomes of 55 samples using the QIIME pipeline. We found that the edge effect was not detectable at distances of 1 m. This allowed us to pool inner and edge samples for comparisons of how lawn and forest microbiomes responded to Met52. We found that despite greater macro scale diversity, the lawn microbiome actually harbored a more diverse soil microbiome. Surprisingly, this complexity was not correlated with greater microbiome

Microscopic study of the healthy human body has demonstrated that microbial cells outnumber human cells by about ten to one. Prior to the start of the HMP, this abundant community of human-associated microbes remained largely unstudied, leaving their influence upon human development, physiology, immunity, and nutrition almost entirely unknown. The HMP was established with the mission of generating research resources, which were rapidly and broadly shared, enabling comprehensive characterization of the human microbiota and their metabolic capabilities and analysis of their role in human health and disease. The information generated by HMP is now available worldwide for use by investigators and others in efforts to understand and improve human health.. The first phase of HMP was focused on the development of DNA sequence datasets and computational tools for characterizing the microbiome in healthy adults and in people with specific microbiome-associated diseases. An Ethical, Legal and Societal ...

Taken together, the bacteria, viruses, fungi and other microbes that live in our intestines form the gut microbiome, which plays a key role in the health of people and animals. In new research from the University of Minnesota, University of Notre Dame and Duke University, scientists found that genetics nearly always plays a role in the composition of the gut microbiome of wild baboons.. In humans, research has shown that family members share a significant portion of microbes in their gut, but its hard to answer if our microbiome is shaped more by nature, such as those we inherit from our family, or nurture, such as the similar diets, environments and behaviors families share, said lead author Laura Grieneisen, a postdoctoral fellow in the College of Biological Sciences. Many human diseases and other markers of health have a genetic component. The number and types of bacteria in the gut are no different. By understanding the heritability of the gut microbiome will help us better link genes, ...

The researchers compared the microbiome composition of four groups of participants: Hmong and Karen people living in Thailand, Hmong and Karen people who immigrated to the U.S., U.S.-born children of Hmong immigrants, and U.S. Americans with European ancestry. The team also measured participants body mass index and asked them to report what they had eaten in the past 24 hours. In a subset of participants, they tracked changes in microbiome composition, diet, and weight at several time points before and after the people arrived in the U.S.. ...

In 2012, we began working on a new project at the University of Chicagos new hospital facility: the Center for Care and Discovery. The Hospital Microbiome Project was designed to collect microbial samples from surfaces, air, staff, and patients from the University of Chicagos new hospital pavilion in order to better understand the factors that influence bacterial population development in healthcare environments. Of particular importance and interest are the microbes and viruses that may influence the spread of hospital acquired infections.. We were involved on this project as a subcontract to the University of Chicago to collect data for a number of building environmental and operational parameters - collectively called building science measurements or built environment data that may influence microbial communities in the hospital. The PI on the project is Dr. Jack Gilbert, who is dually appointed in the Department of Ecology & Evolution at U of C and as an Environmental Microbiologist at ...

Perturbations in intestinal microbiota composition have been associated with a variety of gastrointestinal tract-related diseases. The alleviation of symptoms has been achieved using treatments that alter the gastrointestinal tract microbiota toward that of healthy individuals. Identifying

In short, the paper goes over the history of skin microbial community studies, an overview of how the skin microbiome has been implicated in contributing to health and disease, and some ways our understanding of the skin microbiome has contributed to therapeutic interventions. We focused primarily on the bacterial, fungal, and viral communities associated with the skin, and how they contribute to health and disease. We go over potential roles of microbes in diseases including atopic dermatitis, psoriasis, acne, dandruff, and skin cancer. So go ahead and check it out ...

The microbiome is a community of microbes that inhabit various surfaces of different hosts, including mammals. Recent developments in genomics and the human microbiome project have fostered the awareness that microbes are key organisms despite their minute size. A balanced microbiome plays a major role in digesting the diet but also in keeping pathogens at bay, controlling metabolism, shaping the immune system and promoting mental health. In accord, changes in the human microbiome have been linked to a variety of diseases. Understanding the microbiome and its crosstalk with the diet and host systems is undoubtedly crucial to maintain host health and prevent disease ...

In the study, Jennifer Fouquier and colleagues compared fecal samples from individuals with ASD and controls in Arizona and Colorado, using standardized DNA extraction and sequencing methods. The Arizona participants included 36 children with ASD and 38 age-matched neurotypical controls who did not have first-degree relatives with autism. The Colorado participants included 13 children with ASD and 16 matched neurotypical controls; five of the controls had siblings with ASD.. The researchers found that gut microbiomes differed between individuals in Arizona and those in Colorado. Moreover, in Arizona but not Colorado, gastrointestinal symptoms were higher in individuals with ASD than in controls. Gut microbiome composition was significantly associated with ASD when the researchers controlled for study site location but not when they controlled for gastrointestinal symptoms.. Taken together, the researchers say, these results suggest that geographical differences in gut microbiome composition ...

Researchers demonstrate for the first time that the immune system influences the skin microbiome. A new study found that the skin microbiome a collection of microorganisms inhabiting the human body is governed, at least in part, by an ancient branch of the immune system called complement.http://feeds.feedburner.com/~r/sciencedaily/health_medicine/~4/VKXbSZandvU More...

The human microbiome is dynamic and unique to each individual, and its role is being increasingly recognized in healthy physiology and in disease, including gastrointestinal and neuropsychiatric disorders. Therefore, characterizing the human microbiome and the factors that shape its bacterial population, how they are related to host-specific attributes, and understanding the ways in which it can be manipulated and the phenotypic consequences of such manipulations are of great importance. Characterization of the microbiome so far has been mostly based on compositional studies alone, where relative abundances of different species are compared in different conditions, such as health and disease. However, inter-relationships among the bacterial species, such as competition and cooperation over metabolic resources, may be an important factor that affects the structure and function of the microbiome. Here we review the network-based approaches in answering such questions and explore the first attempts that

Gelatin tannate ameliorates acute colitis in mice by reinforcing mucus layer and modulating gut microbiota composition: Emerging role for gut barrier protectors in IBD? ...

Fingerprint Dive into the research topics of Fermented green tea extract alleviates obesity and related complications and alters gut microbiota composition in diet-induced obese mice. Together they form a unique fingerprint. ...

Our gut microbiota can crucially influence our behavior and neurodevelopment. New research from the Ethology Department at the Faculty of Science at Eötvös Loránd University indicates that dogs aging mechanism and memory performance are also linked to their gut microbiome composition. According to the study, dogs and humans may have similar mechanisms in cognitive aging.

In the present study, we found that AAU patients had a characteristic fecal metabolite profile, irrespective of the presence of AS or their HLA-B27 status. Although the alpha analysis or abundance of gut microbiota between patients and controls failed to show any significant differences, we revealed significant alterations in microbiota composition in AAU patients compared with healthy controls following analysis of PCoA plots of unweighted UniFrac distances. Our findings are, by and large, in agreement with recent observations showing that the development of ocular inflammation during experimental autoimmune uveitis in mice is dependent on the presence of certain bacteria in the gut of these animals.14 To our knowledge this is the first report concerning the analysis of gut microbiota composition and fecal metabolite profile in clinical AAU, although we are aware of the fact that due to the various limitations of our study, one should see this report as a preliminary observation in an important ...

Davenport, C. F. and Tümmler, B. (2013), Advances in computational analysis of metagenome sequences. Environmental Microbiology, 15: 1-5. doi: 10.1111/j.1462-2920.2012.02843.x ...

宮崎大学ハイステップ研究者 表彰者リスト（2014.10.27） 代表者氏名 林 哲也 所 属 論文タイトル 受賞者名 NATURE 473 2011 An extensive repertoire of type III secretion effectors in PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 2006 1494114946 林 哲也 DNA RESEARCH 14 2007 169-181 林 哲也 小椋義俊 Vol.59 No.SP1 2007 S1-S7 フロンティア科学実験総 Escherichia coli O157 and the role of lambdoid phages in 合センター長 Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes 情報統括機構情報基盤 The X-Ray Observatory Suzaku センター長 The COMPASS experiment at CERN 松田 達郎 Vol. 発刊年 ページ番号 Enterotypes of the human gut microbiome their dissemination 廿日出 勇 ジャーナル名 工学教育研究部工学基 Evidence for the Theta(+) in the gamma d -, K(+)K(-)pn 礎教育センター教授 reaction by detecting K+K- pairs Publications of ...

In this study, C57BL/6J mice were fed diets supplemented with different proportions of lactulose (0%, 5%, and 15%) for 2 weeks to study its effects on the luminal and mucosal microbiota. The luminal and mucosal samples of cecum and colon were investigated. After high-lactulose treatment (15%), pH of …

Microbes inhabit just about every part of the human body outnumbering human cells by 10 to 1. The 10-year, National Institutes of Health Common Fund Human Microbiome Project was established to understand how microbial communities impact human...

The role of the intestinal microbiota as a regulator of autoimmune diabetes in animal models is well-established, but data on human type 1 diabetes are tentative and based on studies including only a few study subjects. To exclude secondary effects of diabetes and HLA risk genotype on gut microbiota, we compared the intestinal microbiota composition in children with at least two diabetes-associated autoantibodies (n = 18) with autoantibody-negative children matched for age, sex, early feeding history, and HLA risk genotype using pyrosequencing. Principal component analysis indicated that a low abundance of lactate-producing and butyrate-producing species was associated with β-cell autoimmunity. In addition, a dearth of the two most dominant Bifidobacterium species, Bifidobacterium adolescentis and Bifidobacterium pseudocatenulatum, and an increased abundance of the Bacteroides genus were observed in the children with β-cell autoimmunity. We did not find increased fecal calprotectin or IgA as ...

Next-generation sequencing has allowed us to characterize cetacean gut microbial communities and discover surprising similarities to the microbiomes of terrestrial herbivores and carnivores.. I am thrilled to announce the publication of our paper on the whale gut microbiome in Nature Communications.. By sequencing the bacterial genomes contained in whale fecal samples, we explore the gut community of baleen whales and its functional potential. We find a remarkable fusion microbiome that, while highly diverged overall from that of terrestrial mammals, contains functional elements characteristic of both terrestrial carnivore and terrestrial herbivore gut microbiomes. We find evidence to support the hypothesis that whales (which are descended from herbivorous terrestrial mammals, but are carnivores, eating small crustaceans and small fish) may use foregut fermentation to break down their food, much as ruminants do. In particular, the need to break down recalcitrant chitin in the exoskeletons of ...

It has been proposed that the gut microbiome may be related to obesity, and diet-induced obesity may induce changes in the gut microbiota composition. Our previous studies suggested that persimmon tannin (PT), which is highly polymerized and non-absorbable in the intestine, showed anti-hyperlipidemic and cholestero

TY - JOUR. T1 - Circadian disruption changes gut microbiome taxa and functional gene composition. AU - Deaver, Jessica A.. AU - Eum, Sung Y.. AU - Toborek, Michal. N1 - Funding Information: We would like to acknowledge the assistance of Second Genome (San Francisco, CA, United States) in metatranscriptome analyses. The current study was supported in part by grants from the National Institutes of Health (CA133257) and Alltech Nutrigenomics. Publisher Copyright: © 2018 Deaver, Eum and Toborek.. PY - 2018/4/13. Y1 - 2018/4/13. N2 - Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light-dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool ...

The gut microbiota has the capability to generate a series of metabolites and thereby regulate homeostasis of the host metabolism (1). Antibiotic treatment, as an important therapeutic approach in clinical practice, can adversely affect the gut microbiota, inevitably giving rise to metabolic disorders (19). However, whether antibiotics have sex-dependent effects on the gut microbiota and host metabolism is unknown.. In the present study, at first we found that the gut microbiome and metabolome are influenced by gender. Results showed that male mice had higher abundances of Adlercreutzia, AF12, Anaeroplasma, Bacteroides, Dehalobacterium, Dorea, Mucispirillum, Roseburia, and Ruminococcus as well as lower levels of Lactobacillus, Prevotella, and Sutterella than female mice. In fact, sex-dependent differences in the gut microbiota have been reported due to hormonal effects (20), but many other factors may also affect microbial composition changes, such as genotype (21), age (22), body weight (23), ...

What is Vaginal Microbiome Dysbiosis? Does it matter, Yes…The vaginal microbiome is a symbiotic relationship between good & bad bacteria.

While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were

Ritter Pharmaceuticals, Inc. Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published In PNAS - read this article along with other careers information, tips and advice on BioSpace

The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this

Karlsson and colleagues draw a parallel between intestinal microbiota becoming pro-inflammatory resulting in increased mucosal permeability and the oxidative stress-induced subclinical inflammation that leads to chronic inflammation within arteries as seen in atherosclerosis.[83] Although difficult to prove, ongoing research suggests increased translocation of intestinal microbiota into the bloodstream through disruption of epithelial tight junctions. Karlsson performed a randomized controlled trial with 16 male patients diagnosed with carotid wall atherosclerotic plaques. Nine patients were given a 4-week trial of a L. plantarum-fermented oat drink and seven patients were in the placebo arm (unfermented oat drink without L. plantarum). Study patients demonstrated increased intestinal microbiome diversity and lower concentrations of fecal carboxylic acids, specifically isovaleric (p = 0.006) and valeric (p = 0.029) acid, surrogate markers for inflammatory disease. There were no significant ...

Aims/hypothesis: Individuals with type 2 diabetes have aberrant intestinal microbiota. However, recent studies suggest that metformin alters the composition and functional potential of gut microbiota, thereby interfering with the diabetes-related microbial signatures. We tested whether specific gut microbiota profiles are associated with prediabetes (defined as fasting plasma glucose of 6.1-7.0 mmol/l or HbA1c of 42-48 mmol/mol [6.0-6.5%]) and a range of clinical biomarkers of poor metabolic health. Methods: In the present case-control study, we analysed the gut microbiota of 134 Danish adults with prediabetes, overweight, insulin resistance, dyslipidaemia and low-grade inflammation and 134 age- and sex-matched individuals with normal glucose regulation. Results: We found that five bacterial genera and 36 operational taxonomic units (OTUs) were differentially abundant between individuals with prediabetes and those with normal glucose regulation. At the genus level, the abundance of Clostridium ...

Intestinal failure (IF) is the reduction of gut function or mass below a minimum needed to absorb nutrients and fluids, such that patients are dependent on parenteral nutrition (PN). Patients with IF have an altered gut microbiome. Our aim was to review and evaluate the current evidence on gut microbiome and its metabolic activity, as well as its association with disease characteristics in adults and children with IF. We performed a PubMed literature search for articles published after 2000 using the following terms: intestinal, microbiome, microbiota, short‐chain fatty acids, short bowel syndrome, and PN. Literature search was restricted to human studies only. The gut microbiome diversity is remarkably reduced, and community structure is altered with a noticeable overabundance of Proteobacteria, especially the Enterobacteriaceae family. A substantial increase in Lactobacillus level is often reported in patients with IF. Gut microbiome characteristics have been associated with poor growth, ...

HUDSON, NY--(Marketwired - May 8, 2014) - Today, Taconic announced the launch of the Translational Microbiome Research Forum website, which provides an opportunity for investigators worldwide to access and exchange information in the emerging field of microbiome research. The Translational Microbiome Research Forum website provides up-to-date news, publications, events, and...

The human microbiome (or human microbiota) is the collection of microorganisms which live on us. They live on the skin, in the saliva and mouth, in the eyes, and in the gut and the rest of the gastrointestinal tract. They include bacteria, archaea, fungi and single-celled eukaryotes (protozoa).[1] Everyone carries around far more of these microbes than the number of human cells in the body. The human body has about 100 trillion cells, and carries about ten times as many microorganisms in the intestines alone.[2][3][4][5] The microbiome is the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space.[6][7] The term was originally coined by Joshua Lederberg. He thought the microorganisms living in the human body in health and disease were important. Many scientific articles distinguish microbiome and microbiota to describe either the collective genomes of the microorganisms that live in an environmental niche or the microorganisms ...

To address how the microbiome might modify the interaction between diet and cardiometabolic health, we analyzed longitudinal microbiome data from 307 male participants in the Health Professionals Follow-Up Study, together with long-term dietary information and measurements of biomarkers of glucose homeostasis, lipid metabolism and inflammation from blood samples. Here, we demonstrate that a healthy Mediterranean-style dietary pattern is associated with specific functional and taxonomic components of the gut microbiome, and that its protective associations with cardiometabolic health vary depending on microbial composition. In particular, the protective association between adherence to the Mediterranean diet and cardiometabolic disease risk was significantly stronger among participants with decreased abundance of Prevotella copri. Our findings advance the concept of precision nutrition and have the potential to inform more effective and precise dietary approaches for the prevention of ...

Obesity has been linked to the human gut microbiota; however, the contribution of gut bacterial species to the obese phenotype remains controversial because of conflicting results from studies in different populations. To explore the possible dysbiosis of gut microbiota in obesity and its metabolic complications, we studied men and women over a range of body mass indices from the Old Order Amish sect, a culturally homogeneous Caucasian population of Central European ancestry. We characterized the gut microbiota in 310 subjects by deep pyrosequencing of bar-coded PCR amplicons from the V1-V3 region of the 16S rRNA gene. Three communities of interacting bacteria were identified in the gut microbiota, analogous to previously identified gut enterotypes. Neither BMI nor any metabolic syndrome trait was associated with a particular gut community. Network analysis identified twenty-two bacterial species and four OTUs that were either positively or inversely correlated with metabolic syndrome traits, suggesting

Background: The human microbiota is postulated to affect cancer risk, but collecting microbiota specimens with prospective follow-up for diseases will take time. Buccal cell samples have been obtained from mouthwash for the study of human genomic DNA in many cohort studies. Here, we evaluate the feasibility of using buccal cell samples to examine associations of human microbiota and disease risk.. Methods: We obtained buccal cells from mouthwash in 41 healthy participants using a protocol that is widely employed to obtain buccal cells for the study of human DNA. We compared oral microbiota from buccal cells with that from eight other oral sample types collected by following the protocols of the Human Microbiome Project. Microbiota profiles were determined by sequencing 16S rRNA gene V3-V4 region.. Results: Compared with each of the eight other oral samples, the buccal cell samples had significantly more observed species (P , 0.002) and higher alpha diversity (Shannon index, P , 0.02). The ...

The UMass Center for Microbiome Research was created to accelerate our understanding of how the microbes that live in and on us influence our lives, our health and our environment. Our missions are to: • Educate and inform Research generates the discoveries that change our lives. We want to communicate these discoveries to you. Human microbiome research is creating new therapies and new approaches to understanding disease. We want to make our research accessible so everyone can share our excitement.

ASM had organized lots of interesting presentations and the size of the venue was such that it took more than 15 minutes to walk from one side to the other side of the conference. Due to the time overlap of presentations and posters and the huge size of the venue, I was only able to attend a certain number of oral presentations. One of the best parts of the ASM conference was that I was able to see the trend of current research. To me, working on the human microbiome study, it was quite impressive because the number of talks and posters on human microbiome was significantly increased compared with my previous ASM meeting in San Francisco 2 years back. The microbiome studies was not limited to understanding microbial communities by 16S rRNA gene sequencing any more, but expanded their scope at the functional level with more mechanistical and practical approaches. One interesting session, for example, was on fecal microbiota transplantation. The talks were about successful trials on Clostridium ...

In this study we followed the temporal development of the intestinal microbiota from birth onward in infants with and without colic by using the HITChip, a phylogenetic microarray that allows a highly reproducible and comprehensive analysis of the known intestinal microbiota.18 Colic was determined at 6 weeks of age with a cry diary. The infants with colic were characterized by a microbiota that developed slower than that of the control infants and that also showed a reduced temporal stability. Infants with colic also showed a significantly reduced microbiota diversity at 14 and 28 days of life. In addition, already in the first 2 weeks of life, specific significant differences between both groups were found; proteobacteria were increased in infants with colic, with a more than doubled relative abundance, whereas bifidobacteria and lactobacilli were increased in control infants. Moreover, samples from infants with colic were found to contain fewer bacteria related to butyrate-producing ...

The majority of human gut microbiome is comprised of obligate anaerobic bacteria that exert essential metabolic functions in the human colon. These anaerobic gut bacteria constantly crosstalk with the colonic epithelium in a mucosal anoxic-oxic interface (AOI). However, in vitro recreation of the metabolically mismatched colonic AOI has been technically challenging. Furthermore, stable co-culture of the obligate anaerobic commensal microbiome and epithelial cells in a mechanically dynamic condition is essential for demonstrating the host-gut microbiome crosstalk. Here, we developed an anoxic-oxic interface-on-a-chip (AOI Chip) by leveraging amodified human gut-on-a-chip to demonstrate a controlled oxygen gradient in the lumen-capillary transepithelial interface by flowing anoxic and oxic culture medium at various physiological milieus. Computational simulation and experimental results revealed that the presence of the epithelial cell layer and the flow-dependent conditioning in the lumen ...

Esberg A, Haworth S, Hasslöf P, Lif Holgerson P, Johansson I Nutrients 12 (3) - [2020-03-03; online 2020-03-03] Oral microbiota ecology is influenced by environmental and host conditions, but few studies have evaluated associations between untargeted measures of the entire oral microbiome and potentially relevant environmental and host factors. This study aimed to identify salivary microbiota cluster groups using hierarchical cluster analyses (Wards method) based on 16S rRNA gene amplicon sequencing, and identify lifestyle and host factors which were associated with these groups. Group members ( n = 175) were distinctly separated by microbiota profiles and differed in reported sucrose intake and allelic variation in the taste-preference-associated genes TAS1R1 (rs731024) and GNAT3 (rs2074673). Groups with higher sucrose intake were either characterized by a wide panel of species or phylotypes with fewer aciduric species, or by a narrower profile that included documented aciduric- and ...

Objective This study aimed at establishing bacterial flagellin-recognizing toll-like receptor 5 (TLR5) as a novel link between gut microbiota composition, adipose tissue inflammation, and obesity. Methods An adipose tissue microarray database was used to compare women having the highest (n = 4, H-TLR) and lowest (n = 4, L-TLR) expression levels of TLR5-signaling pathway genes. Gut microbiota composition was profiled using flow cytometry and FISH. Standard laboratory techniques were used to determine anthropometric and clinical variables. In vivo results were verified using cultured human adipocytes. Results The H-TLR group had higher flagellated Clostridium cluster XIV abundance and Firmicutes-to-Bacteroides ratio. H-TLR subjects had obese phenotype characterized by greater waist circumference, fat %, and blood pressure (P , 0.05 for all). They also had higher leptin and lower adiponectin levels (P , 0.05 for both). Six hundred and sixty-eight metabolism-and inflammation-related adipose tissue ...

The microbiota profile assessed from urine EVs might reflect a large part of the gut microbiota. Nonetheless, we do believe that the microbiota profile assessed from urine EVs is not likely a simple alternative for microbiota profile assessed from stool. Possible sources for metagenome analysis of bodily microbiota may include stool bacteria, stool EVs, gut (ex, stomach and/or specific regions of the small and large intestines) bacteria, respiratory exhale EVs, oral/nasal bacteria and EVs, urinary system bacteria and EVs, and blood EVs. Generally speaking, microbiota in stool represents the intestinal compartment, whereas microbiota in urine or blood reflects the whole body including the intestinal compartments, oral system, respiratory system, and urinary system. Nonetheless, among the body parts, the gut is the major source of bodily microbiota. It was reported that the metabolites of intestinal microbiota activities, including phenyllactate, p-cresol sulfate, concentrations, and serotonin in ...

In this issue of Immunity, Zelante et al. (2013) and Qiu et al. (2013) provide mechanistic insights into functional interactions between commensal microbes and innate lymphoid cells via the aryl hydrocarbon receptor.

The gut microbiota is a complex ecosystem that wields great influence over the health of its host.32 Conversely, mammalian hosts use a broad array of mechanisms to shape the microbiota in a way that maximises its benefit and minimises its potential to harm.33 That, at least among healthy persons, intraindividual variance in microbiota composition (ie, repeat sampling of individual subjects) is much smaller than that seen when comparing different individuals33-35 indicates that the ability of host and microbiota to influence each other typically results in a relatively stable equilibrium within specific hosts. Yet, some exogenous factors, for example, pathogens or antibiotics, can dramatically and lastingly disturb this equilibrium in a manner that promotes persistent disease.36 Moreover, even factors that cause relatively modest disturbances of the host-microbiota relationship have been associated with chronic low-grade inflammatory diseases, including metabolic syndrome.36 The genetics of the ...

Ayurveda has a rich history and its significance woven deeply in the Indian culture. The concept of prakriti (a persons nature or constitutional type determined by the proportion of three doshas, namely - vata, pitta and kapha) in Ayurveda is deeply rooted in personalized health management. While the attributes of prakriti has been established to have a genomic basis, there is dearth of elaborate evidences linking prakriti with manifestation of diseases. Next generation sequencing studies have provided a causal link between variation in the gut microbiome and its effect on an individuals fitness. Separately, reports have identified gut microbial patterns associated with several host variables such as geography, age, diet and extreme prakriti phenotypes. Recently, few reports have identified a core gut microbiome consisting of Bacteroides, Faecalibacterium, Prevotella and Ruminococcus prevalent across the Indian population; however, a few bacterial genera were specifically enriched in ...

PMID: J Neuroendocrinol. 2019 May ;31(5):e12684. Epub 2019 Feb 1. PMID: 30614568 Abstract Title: The role of the gut microbiota in development, function and disorders of the central nervous system and the enteric nervous system. Abstract: The gut microbiota has emerged as an environmental factor that modulates the development of the central nervous system (CNS) and the enteric nervous system (ENS). Before obtaining its own microbiota, eutherian foetuses are exposed to products and metabolites from the maternal microbiota. At birth, the infants are colonised by microorganisms. The microbial composition in early life is strongly influenced by the mode of delivery, the feeding method, the use of antibiotics and the maternal microbial composition. Microbial products and microbially produced metabolites act as signalling molecules that have direct or indirect effects on the CNS and the ENS. An increasing number of studies show that the gut microbiota can modulate important processes during ...

A new study in mice unveils the role of vitamin A in immune system regulation, a finding that could assist in developing treatments for autoimmune and inflammatory diseases as well as vitamin A deficiency.. PROVIDENCE, R.I. [Brown University] - Scientists have long known that bacteria in the intestines, also known as the microbiome, perform a variety of useful functions for their hosts, such as breaking down dietary fiber in the digestive process and making vitamins K and B7.. Yet a new study unveils another useful role the microbiome plays. A team of researchers from Brown University found that in mice, the gut microbiome regulates the hosts immune system - so that rather than the hosts defense system attacking these helpful bacteria, the bacteria can coexist peacefully with the immune system.. Whats the trick to the microbiomes work with the immune system? Vitamin A - the bacteria moderate active vitamin A levels in the intestine, protecting the microbiome from an overactive immune ...

The human infant gut is relatively sterile up until birth, where it takes up bacteria from its surrounding environment and its mother.[13] The microbiota that makes up the infant gut differs from the adult gut. An infant reaches the adult stage of their microbiome at around 3 years of age, when their microbiome diversity increases, stabilizes, and the infant switches over to solid foods. When breast-fed, infants are colonized earlier by Bifidobacterium when compared to babies that are primarily formula-fed.[14] Bifidobacterium is the most common bacteria in the infant gut microbiome.[15] There is more variability in genotypes over time in infants, making them less stable compared to the adult Bifidobacterium. Infants and children under 3 years old show low diversity in microbiome bacteria, but more diversity between individuals when compared to adults.[16] Reduction of Bifidobacterium and increase in diversity of the infant gut microbiome occurs with less breast-milk intake and increase of solid ...

TY - JOUR. T1 - Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response. AU - Sethi, Vrishketan. AU - Kurtom, Saba. AU - Tarique, Mohammad. AU - Lavania, Shweta. AU - Malchiodi, Zoe. AU - Hellmund, Leonor. AU - Zhang, Li. AU - Sharma, Umakant. AU - Giri, Bhuwan. AU - Garg, Bharti. AU - Ferrantella, Anthony. AU - Vickers, Selwyn M.. AU - Banerjee, Sulagna. AU - Dawra, Rajinder. AU - Roy, Sabita. AU - Ramakrishnan, Sundaram. AU - Saluja, Ashok. AU - Dudeja, Vikas. N1 - Publisher Copyright: © 2018 AGA Institute. PY - 2018/7. Y1 - 2018/7. N2 - We studied the effects of gut microbiome depletion by oral antibiotics on tumor growth in subcutaneous and liver metastases models of pancreatic cancer, colon cancer, and melanoma. Gut microbiome depletion significantly reduced tumor burden in all the models tested. However, depletion of gut microbiome did not reduce tumor growth in Rag1-knockout mice, which lack mature T and B cells. Flow cytometry analyses demonstrated that gut microbiome ...

3-Deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHPS) is a key rate-limiting enzyme in aromatic amino acid anabolism. A new Iβ-type DAHPS gene (aro1A) was identified in a metagenomic library from subtropical marine mangrove sediment. The gene encoded a polypeptide composed of 272 amino acids and had a maximum similarity of 52.4% to a known DAHPS at the amino acid level. Multiple sequence alignment, homologous modeling, and molecular docking showed that Aro1A had the typical (β/α)8 barrel-shaped catalytic structural domain of DAHPS. The motifs and amino acid residues involved in the combination of substrates and metal ligand were highly conservative with the known DAHPS. The putative DAHPS gene was subcloned into a pET-30a(+) vector and was overexpressed in Escherichia coli Rosetta (DE3) cells. The recombinant protein was purified to homogeneity. The maximum activity for the recombinant Aro1A protein occurred at pH 8.0 and 40 °C. Ba2+ and Ca2+ stimulated the activity of Aro1A protein. The