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
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 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*
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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
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
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 ...
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
The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters. Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven
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 ...
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 ...
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 ...
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? ...
Interrelationship between gut microbiota composition and host metabolic parameters significantly modified by arabinoxylan supplementation.Green connections indi
To characterize gene expression in the gut microbiome, we analyzed cDNA and DNA datasets obtained from sequencing total community cDNA and DNA prepared from the two fecal samples of TS28 and TS29. All sequencing reads were mapped against the database of 122 gut microbial genomes and the microbiome bins (Metatranscriptome analysis in SI Text). The results revealed marked differences in gene abundance and expression (Figs. S6 and S7). In all cases, technical replicates of each microbiome and metatranscriptome (n = 3-4) clustered together; this clustering was robust to subsampling by COG functional categories (Fig. S6). Microbiome profiles showed the highest average correlation between individuals (R2 = 0.37), relative to metatranscriptomes (R2 = 0.12) and the relative abundance of species-level phylotypes (R2 = 0.18). As with the microbiome, rarefaction analysis of the metatranscriptome revealed that the number of expressed genes and gene clusters continues to increase even after 500,000 mapped ...
A pleiotropic missense variant in SLC39A8 is associated with Crohns disease and human gut microbiome composition. Li D, Achkar JP, Haritunians T, Jacobs JP, Hui KY, DAmato M, Brand S, Radford-Smith G, Halfvarson J, Niess JH, Kugathasan S, Buning C, Schumm LP, Klei L, Ananthakrishnan A, Aumais G, Baidoo L, Dubinsky M, Fiocchi C, Glas J, Milgrom R, Proctor DD, Regueiro M, Simms LA, Stempak JM, Targan S, Torkvist L, Sharma Y, Devlin B, Borneman J, Hakonarson H, Xavier RJ, Daly M, Brant SR, Rioux JD, Silverberg MS, Cho JH, Braun J, McGovern DPB, Duerr RH. A pleiotropic missense variant in SLC39A8 is associated with Crohns disease and human gut microbiome composition. Gastroenterology 2016;151:724-732 ...
Taken together, the topological features that were found to vary with obesity and IBD suggest a characteristic mode of deviation from a normal microbiome organization that may be associated with a disease state. This suggests that in addition to, or potentially as a consequence of, alterations in the abundance of individual genes or functional classes, disease may be associated with higher order modes of deviation in the microbiome. Clearly, such associations alone cannot directly implicate a mechanism for disease; both obesity and IBD are poorly understood diseases and embody extremely complex phenotypes. Accordingly, the system-level observations reported in this study can have multiple alternative interpretations and stem from mechanisms that are yet unknown. These observations, however, allow us to posit intriguing hypotheses for further study.. Specifically, we find that enzymes typifying various host states tend to have low centrality and are found mostly in the periphery of the network. ...
To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human bodys greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites. The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral
2. The gut microbiome of the mother. As discussed by the authors, stool microbiome of the mother was unfortunately not investigated. During the first year, the gut microbiome of infants become increasingly similar to the gut microbiome of their mothers 4. It could be speculated that a significant proportion of the unknown source of the infants stool microbiome (,70%, Figure 4b) could be the mothers gut. Importantly, low diversity of gut microbiome has been reported in several HIV cohorts, in part associated with immune dysfunction and use of ART 5-9 . The authors discuss maternal ART as a contributing factor, and it is noteworthy that we reported decreased alpha diversity and reduction in Prevotella few months after ART initiation 7, the same findings as reported in HIV-exposed children in the present study ...
Neither ART nor immune reconstitution affect the vaginal microbiome of HIV-infected women, according to the results of an observational study published in Open Forum Infectious Diseases. “To our knowledge, this is the first study that examines the vaginal microbiome during ART initiation,” Cindy M. Liu, MD, PhD, MPH, associate professor of environmental and occupational health at
The symbiotic gut microbiota modulate health and disease of the host through a series of transgenomic metabolic and immune regulatory axes. We explore connections between microbiome composition and function related to individual metabolic phenotypes and consider these interactions as possible targets for developing new personalized therapies and clinical management strategies.. ...
To address these questions, the researchers used a high-throughput sequencing technology to characterize the gut microbiota associated with multiple members of the firebug family and its sister family, the bordered plant bugs or Largidae. They discovered that many different members of the firebug family share the same core microbiota. Interestingly, all the insect taxa that harbored the core microbiota were confined to a single clade within the Pyrrhocoridae, while the core microbes were completely absent from their sister family, the Largidae.. According to phylogenetic analyses, the association between firebugs and the core microbiota originated around 81 million years ago (in the late Cretaceous) which coincided with the emergence of their host plants, the Malvales. "The acquisition of the gut-associated core microbiota apparently enabled firebugs to successfully overcome the plants defenses and nutritional shortcomings and utilize the Malvales seeds as a food source," explains Sailendharan ...
Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacterial communities have the potential to elucidate global-scale patterns of microbial community structure and function. It is possible that host surface-associated (external) microbiomes respond more strongly to variations in environmental factors, whereas internal microbiomes are more tightly linked to host factors. Here, we use the dataset from the Earth Microbiome Project and accumulate data from 50 additional studies totaling 654 host species and over 15,000 samples to examine global-scale patterns of bacterial diversity and function. We analyze microbiomes from non-captive hosts sampled from natural habitats and find patterns with bioclimate and geophysical factors, as well as land use, host
Commensal microbes must control viral infection by facilitating web host immune system defenses often. germfree (GF) and injected intraperitoneally (we.p.) with an sent retrovirus, the pets became contaminated but didnt transmit infectious trojan with their offspring (6). As a result, very similar compared to that of reoviruses and picornaviruses, transmission of the milk-borne retrovirus in prone animals depends completely over the hosts microbiota. Unlike retrovirus-susceptible mice, retrovirus-resistant mice usually do not move infectious trojan also in the current presence of microbiota; these animals generate antivirus immune reactions capable of removing the disease (7, 8). With this current work, we set out to determine if production of protecting retrovirus-specific immune reactions in retrovirus-resistant mice requires the microbiota. GF mice show normal production of antigen-specific antibodies (Abs) in response to immunization. There have been conflicting reports concerning the ...
The impact of the gut microbiota on immune homeostasis within the gut and, importantly, also at systemic sites has gained tremendous research interest over the last few years. The intestinal microbiota is an integral component of a fascinating ecosystem that interacts with and benefits its host on several complex levels to achieve a mutualistic relationship. Host-microbial homeostasis involves appropriate immune regulation within the gut mucosa to maintain a healthy gut while preventing uncontrolled immune responses against the beneficial commensal microbiota potentially leading to chronic inflammatory bowel diseases (IBD). Furthermore, recent studies suggest that the microbiota composition might impact on the susceptibility to immune-mediated disorders such as autoimmunity and allergy. Understanding how the microbiota modulates susceptibility to these diseases is an important step toward better prevention or treatment options for such diseases.. ...
Abstract Colon Cancer is the most common cancer among Inflammatory Bowel Disease (IBD) patients and IBD is one of the three leading high-risk factors for Colon Cancer. In 2012 it was found, by using genetic sequencing of the gut microbiome, that Fusobacteria sequences were enriched in colorectal carcinomas (CRC). To explore this possible link between inflammation, gut microbes, and colon cancer I have turned my own body into a
Overview:. This project has two objectives: to understand the factors that shape symbiotic microbial. communities, and to understand how symbiotic microbial communities interact with invading. pathogens. Animals serve as habitats to complex symbiotic microbial communities (referred. to as the microbiome). The microbiome may interact with pathogens encountered by the host,. and this interaction can affect disease resistance and/or alter the species composition of. the microbiome. This project will examine microbiome assembly and microbiome-pathogen interactions. in a wildlife disease system consisting of a frog species, the symbiotic bacteria inhabiting. its skin, and a fungal pathogen. Molecular methods (16S amplicon sequencing and metagenomics. of bacterial communities; microsatellite analysis of host genotypes) will be combined with. field surveys and laboratory experiments to understand the relative influence of environment. and host on microbial community composition. Mathematical models ...
The human gut microbiome is a highly diverse microbial ecosystem of approximately 400 different species, with most of the species belonging to the phylum Bacteroidetes or Firmicutes. Each person has an unique composition of bacteria, and its also clear that subsets of the population have microbiomes that look more a like, as different diets promote the growth of certain species in the gut, and some health disorders are characterized by a specific microbial profile. By now its well established that obesity is associated with an "obese microbiota" that is quite different than the microbiota of a lean person (1,2).. The first studies looking into the microbiota in overweight and obesity found that obese individuals have a decreased Bacteroidetes/Firmicutes ratio, but recent findings show that this isnt always the case. Also, since both "good" and "bad" bugs belong to both of these major groups of bacteria, the ratio between Bacteroidetes and Firmicutes doesnt necessarily tell us much about the ...
TY - JOUR. T1 - Impact of the gut microbiome on the genome and epigenome of colon epithelial cells. T2 - Contributions to colorectal cancer development 11 Medical and Health Sciences 1112 Oncology and Carcinogenesis. AU - Allen, Jawara. AU - Sears, Cynthia Louise. PY - 2019/2/25. Y1 - 2019/2/25. N2 - In recent years, the number of studies investigating the impact of the gut microbiome in colorectal cancer (CRC) has risen sharply. As a result, we now know that various microbes (and microbial communities) are found more frequently in the stool and mucosa of individuals with CRC than healthy controls, including in the primary tumors themselves, and even in distant metastases. We also know that these microbes induce tumors in various mouse models, but we know little about how they impact colon epithelial cells (CECs) directly, or about how these interactions might lead to modifications at the genetic and epigenetic levels that trigger and propagate tumor growth. Rates of CRC are increasing in ...
If the human gut microbiome contains two times more gene power than that of our total human cells, then the microbiome has a total of 40,000 genes of protein producing ability. Our gastrointestinal tract is awash with a myriad of enzymes, messengers molecules, binding molecules, protein cascade molecules derived from both our human cells and our microbial communitys cells.. This is the arena that the National Institute of Healths Human Microbiome Project is now putting their full attention into understanding. Traditionally, microbiology has focused on the study of individual species as isolated units, making it difficult to develop and inventory all of the microbes in an area such as the human GI tract. However new technologies have emerged which enable scientists to quantify the different organisms present in the milieu of an ecosystem. Instead of isolating and culturing each microbe, all of the DNA within the collected samples will be sequenced and analzyed through PCR technology and ...