scholarly journals Taxonomic signatures of cause-specific mortality risk in human gut microbiome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aaro Salosensaari ◽  
Ville Laitinen ◽  
Aki S. Havulinna ◽  
Guillaume Meric ◽  
Susan Cheng ◽  
...  
Keyword(s):  
Mortality Risk ◽  
Gut Microbiome ◽  
Human Gut ◽  
Cross Sectional ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Non Invasive ◽  
Sequencing Technologies

AbstractThe collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.

scholarly journals Taxonomic Signatures of Long-Term Mortality Risk in Human Gut Microbiota

2020 ◽  
Author(s):  
Aaro Salosensaari ◽  
Ville Laitinen ◽  
Aki Havulinna ◽  
Guillaume Meric ◽  
Susan Cheng ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Microbiome ◽  
Human Gut ◽  
Cross Sectional ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Sequencing Technologies ◽  
Microbiome Profiling

The collection of fecal material and developments in sequencing technologies have enabled cost-efficient, standardized, and non-invasive gut microbiome profiling. As a result, microbiome composition data from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases.1–5 In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterized due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data.6–8 Here, we analyse the long-term association between gut microbiome variation and mortality in a large, well-phenotyped, and representative population cohort (n = 7211, FINRISK 2002; Finland).9 We report specific taxonomic and functional signatures related to the Enterobacteriaceae family in the human gut microbiome that predict mortality during a 15-year follow-up. These associations can be observed both in the Eastern and Western Finns who have differing genetic backgrounds, lifestyles, and mortality rates.10,11 Our results supplement previously reported cross-sectional associations,1–4,12 and help to establish a methodological and conceptual basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status. These findings could serve as a solid framework for microbiome profiling in clinical risk prediction, paving the way towards clinical applications of human microbiome sequencing aimed at prediction, prevention, and treatment of disease.

scholarly journals Health and disease markers correlate with gut microbiome composition across thousands of people

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Ohad Manor ◽  
Chengzhen L. Dai ◽  
Sergey A. Kornilov ◽  
Brett Smith ◽  
Nathan D. Price ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Lifestyle Factors ◽  
Clinical Markers ◽  
Human Gut ◽  
Microbiome Composition ◽  
Targeted Interventions ◽  
Human Gut Microbiome ◽  
Host Diet ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Abstract Variation in the human gut microbiome can reflect host lifestyle and behaviors and influence disease biomarker levels in the blood. Understanding the relationships between gut microbes and host phenotypes are critical for understanding wellness and disease. Here, we examine associations between the gut microbiota and ~150 host phenotypic features across ~3,400 individuals. We identify major axes of taxonomic variance in the gut and a putative diversity maximum along the Firmicutes-to-Bacteroidetes axis. Our analyses reveal both known and unknown associations between microbiome composition and host clinical markers and lifestyle factors, including host-microbe associations that are composition-specific. These results suggest potential opportunities for targeted interventions that alter the composition of the microbiome to improve host health. By uncovering the interrelationships between host diet and lifestyle factors, clinical blood markers, and the human gut microbiome at the population-scale, our results serve as a roadmap for future studies on host-microbe interactions and interventions.

scholarly journals A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn’s Disease and Human Gut Microbiome Composition

2016 ◽  
Vol 151 (4) ◽  
pp. 724-732 ◽  
Author(s):  
Dalin Li ◽  
Jean-Paul Achkar ◽  
Talin Haritunians ◽  
Jonathan P. Jacobs ◽  
Ken Y. Hui ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Gut Microbiome ◽  
Missense Variant ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome

W1832 Diversity in Human Gut Microbiome Composition Assessed by Pyrosequencing: Comparison of Sampling Methods

2010 ◽  
Vol 138 (5) ◽  
pp. S-749
Author(s):  
James D. Lewis ◽  
Gary D. Wu ◽  
Ying-Yu Chen ◽  
Christian Hoffmann ◽  
Kyle Bittinger ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Sampling Methods ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome

scholarly journals Alterations in human gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME® technology

2021 ◽  
Author(s):  
Robin Mesnage ◽  
Marta Calatayud ◽  
Cindy Duysburgh ◽  
Massimo Marzorati ◽  
Michael Antoniou
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Large Scale ◽  
Epidemiological Studies ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Ammonium Production ◽  
Profiling Techniques ◽  
Microbial Environment

Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. As a step in addressing this knowledge gap, we describe for the first time the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology, which mimics the entire gastrointestinal tract. SHIME microbiota culture was undertaken in the presence of a concentration of 100 mg/L (corresponding to a dose of 1.6 mg/kg/day) glyphosate and the same glyphosate equivalent concentration of Roundup, which is in the range of the US chronic reference dose, and subjected to molecular profiling techniques to assess outcomes. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large scale disturbances in metabolite profiles, including an increased abundance of long chain polyunsaturated fatty acids (n3 and n6). Although changes in bacterial composition measured by qPCR and 16S rRNA sequencing were less clear, our results suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota at permitted regulatory levels of exposure, highlighting the need for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on human gut microbiome function.

scholarly journals Quantifying the impact of Human Leukocyte Antigen on the human gut microbiome

2020 ◽  
Author(s):  
Stijn P. Andeweg ◽  
Can Keşmir ◽  
Bas E. Dutilh
Keyword(s):  
Immune System ◽  
Gut Microbiome ◽  
Human Leukocyte ◽  
Human Gut ◽  
Microbiome Composition ◽  
Leukocyte Antigen ◽  
Human Gut Microbiome ◽  
Microbiome Diversity ◽  
Human Immune ◽  
Hla Molecules

AbstractObjectiveThe gut microbiome is affected by a number of factors, including the innate and adaptive immune system. The major histocompatibility complex (MHC), or the human leukocyte antigen (HLA) in humans, performs an essential role in vertebrate immunity, and is very polymorphic in different populations. HLA determines the specificity of T lymphocyte and natural killer (NK) cell responses, including against the commensal bacteria present in the human gut. Thus, it is likely that our HLA molecules and thereby the adaptive immune response, can shape the composition of our microbiome. Here, we investigated the effect of HLA haplotype on the microbiome composition.ResultsWe performed HLA typing and microbiota composition analyses on 3,002 public human gut microbiome datasets. We found that (i) individuals with functionally similar HLA molecules (i.e. presenting similar peptides) are also similar in their microbiota, and (ii) HLA homozygosity correlated with microbiome diversity, suggesting that diverse immune responses limit microbiome diversity.ConclusionOur results show a statistical association between host HLA haplotype and gut microbiome composition. Because the HLA haplotype is a readily measurable parameter of the human immune system, these results open the door to incorporating the immune system into predictive microbiome models.IMPORTANCEThe microorganisms that live in the digestive tracts of humans, known as the gut microbiome, are essential for hosts survival as they support crucial functions. For example, they support the host in facilitating the uptake of nutrients and give colonization resistance against pathogens. The composition of the gut microbiome varies among humans. Studies have proposed multiple factors driving the observed variation, including; diet, lifestyle, and health condition. Another major influence on the microbiome is the host’s genetic background. We hypothesized the immune system to be one of the most important genetic factors driving the differences observed between gut microbiomes. Therefore, we are interested in linking the polymorphic molecules that play a role in human immune responses to the composition of the microbiome. HLA molecules are the most polymorphic molecules in our genome and therefore makes an excellent candidate to test such an association/link. To our knowledge for the first time, our results indicate a significant impact of the HLA on the human gut microbiome composition.

scholarly journals Human gut microbiome composition and tryptophan metabolites were changed differently by fast food and Mediterranean diet in 4 days: a pilot study

2020 ◽  
Vol 77 ◽  
pp. 62-72 ◽  
Author(s):  
Chenghao Zhu ◽  
Lisa Sawrey-Kubicek ◽  
Elizabeth Beals ◽  
Chris H. Rhodes ◽  
Hannah Eve Houts ◽  
...  
Keyword(s):  
Pilot Study ◽  
Mediterranean Diet ◽  
Gut Microbiome ◽  
Fast Food ◽  
Human Gut ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Tryptophan Metabolites

scholarly journals Large-scale association analyses identify host factors influencing human gut microbiome composition

2021 ◽  
Vol 53 (2) ◽  
pp. 156-165
Author(s):  
Alexander Kurilshikov ◽  
Carolina Medina-Gomez ◽  
Rodrigo Bacigalupe ◽  
Djawad Radjabzadeh ◽  
Jun Wang ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Host Factors ◽  
Human Gut ◽  
Association Analyses ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Factors Influencing

scholarly journals Impact of Different Exercise Modalities on the Human Gut Microbiome

Sports ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 14
Author(s):  
Dierdra Bycura ◽  
Anthony C. Santos ◽  
Arron Shiffer ◽  
Shari Kyman ◽  
Kyle Winfree ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Sequence Data ◽  
Exercise Program ◽  
Rrna Gene ◽  
Human Gut ◽  
Post Intervention ◽  
Cross Sectional ◽  
Intervention Phase ◽  
Human Gut Microbiome

In this study we examined changes to the human gut microbiome resulting from an eight-week intervention of either cardiorespiratory exercise (CRE) or resistance training exercise (RTE). Twenty-eight subjects (21 F; aged 18–26) were recruited for our CRE study and 28 subjects (17 F; aged 18–33) were recruited for our RTE study. Fecal samples for gut microbiome profiling were collected twice weekly during the pre-intervention phase (three weeks), intervention phase (eight weeks), and post-intervention phase (three weeks). Pre/post VO2max, three repetition maximum (3RM), and body composition measurements were conducted. Heart rate ranges for CRE were determined by subjects’ initial VO2max test. RTE weight ranges were established by subjects’ initial 3RM testing for squat, bench press, and bent-over row. Gut microbiota were profiled using 16S rRNA gene sequencing. Microbiome sequence data were analyzed with QIIME 2. CRE resulted in initial changes to the gut microbiome which were not sustained through or after the intervention period, while RTE resulted in no detectable changes to the gut microbiota. For both CRE and RTE, we observe some evidence that the baseline microbiome composition may be predictive of exercise gains. This work suggests that the human gut microbiome can change in response to a new exercise program, but the type of exercise likely impacts whether a change occurs. The changes observed in our CRE intervention resemble a disturbance to the microbiome, where an initial shift is observed followed by a return to the baseline state. More work is needed to understand how sustained changes to the microbiome occur, resulting in differences that have been reported in cross sectional studies of athletes and non-athletes.

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