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Genetics

MaximilianKohler edited this page Jul 27, 2019 · 5 revisions

It is known that certain genes, which are shared by both Crohn’s disease (CD) and ulcerative colitis (UC) patients, may show a predisposition to the development of IBD. A new study reveals that the IBD disease risk previously related to genetics is partly mediated by the gut microbiome. (Mar 2019) https://www.gutmicrobiotaforhealth.com/en/new-research-sheds-light-on-the-effects-of-inflammatory-bowel-disease-risk-alleles-on-gut-bacterial-taxa/


Impact of genetics on the microbiome:

For:

Murine Genetic Background has a Stronger Impact on the Composition of the Gut Microbiota than Maternal Inoculation or Exposure to Unlike Exogenous Microbiota (July 2019) https://www.asm.org/Press-Releases/2019/July/Mouse-Genetics,-More-than-Environment,-Influences

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes (Apr 2019) https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(19)30113-1 "This study establishes AMY1-CN as a genetic factor associated with microbiome composition and function"

Species identity dominates over environment in shaping the microbiota of small mammals (Mar 2019): https://onlinelibrary.wiley.com/doi/pdf/10.1111/ele.13240

Diet matters less than evolutionary relationships in shaping gut microbiome. Study is the largest published comparative dataset of non-human primate gut microbiomes to date. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes (2018): https://www.nature.com/articles/s41396-018-0175-0 - https://www.eurekalert.org/pub_releases/2018-07/nu-dml073018.php

Fecal metabolome was found to be only modestly influenced by host genetics (heritability (H2)= 17.9%) (2018): https://www.nature.com/articles/s41588-018-0135-7

Host genetics strongly influences the composition of vaginal microbiota. Host obesity significantly increased the diversity of the vaginal microbiota in association with Prevotella. (2017): https://www.sciencedirect.com/science/article/pii/S1931312816304887

The effect of host genetics on the gut microbiome (2016): https://www.nature.com/articles/ng.3663

Genetic Association with Subgingival Bacterial Colonization in Chronic Periodontitis (2018): http://www.mdpi.com/2073-4425/9/6/271/htm "strong evidence supporting a direct connection between the host’s genetic profile and the occurrence of chronic periodontitis-associated bacteria"

Sea lion and dolphin bacterial communities were very different, despite originating from animals living in the same water and eating the same diet. Dolphin bacterial suites were a closer match to one another, regardless of location, than to those of sea lions. (2017): https://blogs.scientificamerican.com/guest-blog/the-secret-lives-of-marine-mammal-microbes/

Host species determined gut microbial assemblies, even if fed with the same food (fish vs mice, 2018): https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0471-y "The extensive divergences in gut microbiota between mice and fish strongly indicate that host species determines an essential role in microbial assemblages [6], consistent with observations from previous studies of different mammals [21] and other wild and domesticated animals [22, 23]."

Review, 2017: Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5481955/ - "Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity"

By distilling associations between ethnicity and gut microbiota variation in two American datasets including 1,673 individuals, we report 12 microbial genera and families that reproducibly vary by ethnicity. These results demonstrate recurrent associations between specific taxa in the gut microbiota and ethnicity, providing hypotheses for examining specific members of the gut microbiota as mediators of health disparities (2018): https://www.biorxiv.org/content/early/2018/06/08/342915

Host Genome Influence on Gut Microbial Composition and Microbial Prediction of Complex Traits in Pigs (2017): http://www.genetics.org/content/206/3/1637.long

The effect of heritability and host genetics on the gut microbiota and metabolic syndrome (2016): http://gut.bmj.com/content/66/6/1031.long

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients (2018): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199664

Neonatal selection by Toll-like receptor 5 influences long-term gut microbiota composition (2018): https://www.nature.com/articles/s41586-018-0395-5 | News article on this study: https://www.nature.com/articles/d41586-018-05861-z

Human genetics shape the gut microbiome (2014): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255478/

Association between the ABO blood group and the human intestinal microbiota composition (2016): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485159/ "ABO blood group is one of the genetically determined host factors modulating the composition of the human intestinal microbiota"

Host mitochondria influence gut microbiome diversity: A role for ROS (July 2019) https://stke.sciencemag.org/content/12/588/eaaw3159 "These data suggest that microbiome diversity is genetically encoded. That the mitochondrial genotype modulates both ROS production and the species diversity of the gut microbiome"

Diet during Pregnancy and Infancy and the Infant Intestinal Microbiome (2018): https://doi.org/10.1016/j.jpeds.2018.07.066 "The relationship between breastfeeding status and intestinal microbiome composition varies by child race/ethnicity. Although our findings suggest that race/ethnicity modifies the relationship between diet and the microbiome, this observation needs to be replicated. If confirmed, this relationship may suggest early genetic influences or other unmeasured factors in the response of the microbiome to the diet in different ethnic groups."

Early‐life exposure to gut microbiota from disease protected mice does not impact disease outcome in type 1 diabetes susceptible NOD mice (2018): https://doi.org/10.1111/imcb.12201

Deletion of poly(ADP‑ribose) polymerase-1 changes the composition of the microbiome in the gut (2018): http://dx.doi.org/10.3892/mmr.2018.9474

The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis (2018): https://doi.org/10.1016/j.chom.2018.08.009

IL23R-protective coding variant promotes beneficial bacteria and diversity in the ileal microbiome in healthy individuals without inflammatory bowel disease (2018): https://doi.org/10.1093/ecco-jcc/jjy188 "The observation of low diversity and low abundance of beneficial bacteria in healthy control subjects carrying the IL23R (rs11209026) wild-type GG genotype indicates that the gut microbiome is influenced by host genetics and is altered prior to disease diagnosis"

Against:

The Human Salivary Microbiome Is Shaped by Shared Environment Rather than Genetics: Evidence from a Large Family of Closely Related Individuals: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596345/ - https://www.sciencedaily.com/releases/2017/09/170912102810.htm

Weizmann researchers were surprised to discover that the host’s genetics play a very minor role in determining microbiome composition – only accounting for about 2% of the variation between populations (2018): https://www.technologynetworks.com/tn/news/study-casts-doubt-on-gut-microbiotas-genetic-influence-298078 - https://www.nature.com/articles/nature25973 - weak study too high up on the taxonomy.

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction (2018): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790872/

Structure similarity of gastric microbial community between co-twins did not increase compared to unrelated individuals. These results suggest that host genetic backgrounds had little effect in shaping the gastric microbiota. (2017): https://link.springer.com/article/10.1007%2Fs00284-016-1176-8

Social relationships, social isolation, and the human gut microbiota (2018): https://doi.org/10.1101/428938 "spouses have more similar microbiota and more bacterial taxa in common than siblings, with no observed differences between sibling and unrelated pairs. The differences between unrelated individuals and married couples was driven entirely by couples who reported close relationships"

Other:

Existing studies are underpowered to identify microbiome-associated genetic variants (2018): https://www.sciencedirect.com/science/article/pii/S1369527418300079

Oral microbiota of twins could be distinguished from each other despite the similarities in genetic make-up, living environment, and lifestyle (2018): https://www.nature.com/articles/s41598-018-25636-w

Gut and skin phage-bacteria network structures were person-specific and not conserved among cohabitating family members (2018): http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006099

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography [Aug 2018] https://www.nature.com/articles/s41591-018-0160-1 Ethnicity contributed to explain the interindividual dissimilarities in gut microbiota composition.

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