Zhernakova A.,University of Groningen |
Zhernakova A.,Top Institute Food and Nutrition |
Kurilshikov A.,Novosibirsk State University |
Bonder M.J.,University of Groningen |
And 47 more authors.
Science | Year: 2016
Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition.We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions. © 2016 by the American Association for the Advancement of Science; all rights reserved.
News Article | February 15, 2017
DayTwo Ltd. (http://www.daytwo.com), today announced a new collaboration with Janssen Research & Development, LLC (Janssen), one of the Janssen Pharmaceutical Companies of Johnson & Johnson, through its Janssen Human Microbiome Institute (JHMI), focused on DayTwo’s products and research conducted at the Weizmann Institute of Science, in Rehovot, Israel. The agreement was facilitated by Johnson & Johnson Innovation. DayTwo provides actionable health solutions based on gut microbiome, utilizing the DayTwo Microbiome Platform™. Its first product, the DayTwo Personalized Nutrition Platform, is based on groundbreaking research from the Weizmann Institute of Science led by Prof. Eran Segal and Dr. Eran Elinav (Cell, Nov15). The research showed that food that is healthy for one person may not be healthy for another, thus nutrition that lowers post meal sugar responses must be personally tailored. High blood sugar is linked to increased risk for diseases like obesity, diabetes, and hypertension, as well as to energy dips, excessive hunger and weight gain. The DayTwo algorithm accurately predicts individual blood sugar responses to different foods based on the unique microbiome and other personal parameters and provides users with tailored recommendations. The DayTwo Personalized Nutrition Platform is available in the US and is scheduled to begin shipping to consumers later this quarter. DayTwo and the Weizmann Institute scientists will work together with Janssen to evaluate DayTwo’s platform for the effective interception of gestational diabetes mellitus (GDM), type 2 diabetes mellitus (T2DM) and metabolic syndrome-associated disorders. This newest collaboration with Janssen is the latest in a series of high profile collaborations with leading health related organizations in the US, including the Mayo Clinic. “Working with the Janssen Human Microbiome Institute and its internal and external network is an exciting and beneficial opportunity for us,” said Lihi Segal, Co-founder and CEO of Daytwo. “This collaboration will create critical new insights to address metabolic disorders through microbiome-based diagnostics and therapeutics and we believe Janssen’s experience in developing diagnostic and therapeutic products will help us introduce new and groundbreaking innovations that promote individual health.” About DayTwo DayTwo (http://www.daytwo.com) is the world's first provider of health improvement and disease prevention solutions based on Gut Microbiome research. Its first product, based on groundbreaking research led by Prof. Eran Segal and Dr. Eran Elinav from the Weizmann Institute of Science in Israel, and exclusively licensed to DayTwo, is a personalized nutrition platform. It aims to normalize blood sugar levels and reduce risk for metabolic diseases like obesity, diabetes, and hypertension, leveraging the world's largest and most detailed microbiome database. DayTwo's product pipeline includes additional microbiome-based diagnostic and therapeutic solutions.
Yassour M.,Cambridge Broad Institute |
Yassour M.,Harvard University |
Vatanen T.,Cambridge Broad Institute |
Vatanen T.,Aalto University |
And 20 more authors.
Science Translational Medicine | Year: 2016
The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life. Longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed detection of strain-level variation as well as the abundance of antibiotic resistance genes. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. Our results highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the infant gut microbiome. © 2016, American Association for the Advancement of Science. All rights reserved.
Luo C.,The Broad Institute of MIT and Harvard |
Luo C.,Harvard University |
Knight R.,University of Colorado at Boulder |
Knight R.,Howard Hughes Medical Institute |
And 11 more authors.
Nature Biotechnology | Year: 2015
An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics. © 2015 Nature America, Inc. All rights reserved.
Blekhman R.,University of Minnesota |
Goodrich J.K.,Cornell University |
Huang K.,The Broad Institute of MIT and Harvard |
Sun Q.,Cornell University |
And 8 more authors.
Genome Biology | Year: 2015
Background: The composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale. Results: Here, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes. Conclusions: Our results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease. © 2015 Blekhman et al.
Yassour M.,Cambridge Broad Institute |
Yassour M.,Harvard University |
Lim M.Y.,Seoul National University |
Yun H.S.,Seoul National University |
And 21 more authors.
Genome Medicine | Year: 2016
Background: Obesity and type 2 diabetes (T2D) are linked both with host genetics and with environmental factors, including dysbioses of the gut microbiota. However, it is unclear whether these microbial changes precede disease onset. Twin cohorts present a unique genetically-controlled opportunity to study the relationships between lifestyle factors and the microbiome. In particular, we hypothesized that family-independent changes in microbial composition and metabolic function during the sub-clinical state of T2D could be either causal or early biomarkers of progression. Methods: We collected fecal samples and clinical metadata from 20 monozygotic Korean twins at up to two time points, resulting in 36 stool shotgun metagenomes. While the participants were neither obese nor diabetic, they spanned the entire range of healthy to near-clinical values and thus enabled the study of microbial associations during sub-clinical disease while accounting for genetic background. Results: We found changes both in composition and in function of the sub-clinical gut microbiome, including a decrease in Akkermansia muciniphila suggesting a role prior to the onset of disease, and functional changes reflecting a response to oxidative stress comparable to that previously observed in chronic T2D and inflammatory bowel diseases. Finally, our unique study design allowed us to examine the strain similarity between twins, and we found that twins demonstrate strain-level differences in composition despite species-level similarities. Conclusions: These changes in the microbiome might be used for the early diagnosis of an inflamed gut and T2D prior to clinical onset of the disease and will help to advance toward microbial interventions. © 2016 Yassour et al.