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Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Gut microbiome heritability is nearly universal but environmentally contingent. Science 2021; 373:181-186. [PMID: 34244407 PMCID: PMC8377764 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022]
Abstract
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
- Research Center, Montreal Heart Institute, Montréal, Quebec H1T 1C8, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Neil Gottel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jacob B Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
- The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Kenya
| | | | | | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
| | - Jack A Gilbert
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
- Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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Spradling KD, Glenn JP, Garcia R, Shade RE, Cox LA. The baboon kidney transcriptome: analysis of transcript sequence, splice variants, and abundance. PLoS One 2013; 8:e57563. [PMID: 23637735 PMCID: PMC3634053 DOI: 10.1371/journal.pone.0057563] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 01/24/2013] [Indexed: 12/25/2022] Open
Abstract
The baboon is an invaluable model for the study of human health and disease, including many complex diseases of the kidney. Although scientists have made great progress in developing this animal as a model for numerous areas of biomedical research, genomic resources for the baboon, such as a quality annotated genome, are still lacking. To this end, we characterized the baboon kidney transcriptome using high-throughput cDNA sequencing (RNA-Seq) to identify genes, gene variants, single nucleotide polymorphisms (SNPs), insertion-deletion polymorphisms (InDels), cellular functions, and key pathways in the baboon kidney to provide a genomic resource for the baboon. Analysis of our sequencing data revealed 45,499 high-confidence SNPs and 29,813 InDels comparing baboon cDNA sequences with the human hg18 reference assembly and identified 35,900 cDNAs in the baboon kidney, including 35,150 transcripts representing 15,369 genic genes that are novel for the baboon. Gene ontology analysis of our sequencing dataset also identified numerous biological functions and canonical pathways that were significant in the baboon kidney, including a large number of metabolic pathways that support known functions of the kidney. The results presented in this study catalogues the transcribed mRNAs, noncoding RNAs, and hypothetical proteins in the baboon kidney and establishes a genomic resource for scientists using the baboon as an experimental model.
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Affiliation(s)
- Kimberly D Spradling
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America.
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Kammerer CM, Cox LA, Mahaney MC, Rogers J, Shade RE. Sodium-lithium countertransport activity is linked to chromosome 5 in baboons. Hypertension 2001; 37:398-402. [PMID: 11230307 DOI: 10.1161/01.hyp.37.2.398] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genes involved in the regulation of cellular sodium transport characteristics, which are correlated with some forms of essential hypertension, have not yet been identified. We are studying the genes and environmental factors that affect red blood cell sodium-lithium countertransport (SLC) activity and intracellular sodium (ICNa) concentration in 634 baboons that comprise 11 pedigrees of 2 and 3 generations each. To detect and locate possible quantitative trait loci (QTLs) that affect SLC activity and ICNa concentration, we performed a genome screen by using a maximum likelihood-based variance-components linkage analysis program (SOLAR). SLC and ICNa phenotypes as well as genotypes on 281 microsatellite loci were available for all pedigreed animals. Both SLC and ICNa traits were highly heritable (residual heritability 0.593+/-0.083 [P<0.0001] and 0.739+/-0.082 [P<0.0001], respectively). We obtained evidence that a possible QTL for SLC activity is located on the baboon homologue of human chromosome 4 between D4S2456 and D4S2365 with a maximum multipoint lod score of 9.3 (P<10(-)(10)) near D4S1645. This QTL accounts for approximately two thirds of the total additive genetic variation in SLC activity in baboons. Although ICNa concentration was highly heritable, we found no evidence for linkage to a QTL with use of this methodology. Thus, we have evidence that a gene located on the baboon homologue of human chromosome 4 (baboon chromosome 5) affects cell sodium transport in baboons.
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Affiliation(s)
- C M Kammerer
- Southwest Foundation for Biomedical Research, San Antonio, Texas, USA
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Jaquish CE, Dyer T, Williams-Blangero S, Dyke B, Leland M, Blangero J. Genetics of adult body mass and maintenance of adult body mass in captive baboons (Papio hamadryas subspecies). Am J Primatol 2000; 42:281-8. [PMID: 9261509 DOI: 10.1002/(sici)1098-2345(1997)42:4<281::aid-ajp3>3.0.co;2-t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Adult body mass and changes in mass during an individual's life are important indicators of general health and reproductive fitness. Therefore, characterization of the factors that influence normal variation in body mass has important implications for colony management and husbandry. The main objective of this study was to quantify the genetic contribution to adult body mass and its maintenance in baboons. Intra-individual mean and variance in body mass were calculated from multiple weight measures available for each of 1,614 animals at least 10 years of age. Heritabilities were estimated using maximum likelihood methods. Mean adult body mass had a significant heritability (50%) as did variance in adult body mass (12%). The sexes differed in several respects: on average females were smaller than males and had greater variability in adult body mass; mean and variance in body mass increased with age in females only; and number of offspring showed a significant positive relationship with body mass in females only. There were significant differences between subspecies in body mass as well as ability to maintain body mass. These results indicate that there is a significant genetic influence on body mass and its maintenance, and suggest that different factors influence changes in body mass with age as well as body mass maintenance in male and female baboons.
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Affiliation(s)
- C E Jaquish
- Southwest Foundation for Biomedical Research, San Antonio, Texas, USA.
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Andersson L, Archibald A, Ashburner M, Audun S, Barendse W, Bitgood J, Bottema C, Broad T, Brown S, Burt D, Charlier C, Copeland N, Davis S, Davisson M, Edwards J, Eggen A, Elgar G, Eppig JT, Franklin I, Grewe P, Gill T, Graves JA, Hawken R, Hetzel J, Womack J. Comparative genome organization of vertebrates. The First International Workshop on Comparative Genome Organization. Mamm Genome 1996; 7:717-34. [PMID: 8854859 DOI: 10.1007/s003359900222] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- L Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Science, Uppsala, Sweden
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Newell-Morris L. Thoughts on gender-related research: Models, myths, and medicine. Am J Hum Biol 1995; 7:207-212. [PMID: 28557213 DOI: 10.1002/ajhb.1310070209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/1994] [Accepted: 10/19/1994] [Indexed: 11/10/2022] Open
Abstract
Gender-related research directed to hypertension and coronary artery disease (CAD) is discussed in terms of the one-sex and two-sex models. Gender "blind" research on the two conditions has resulted in questionable treatment regimes for women. In addition, the biomedical myth of CAD as a male disease has also perpetuated less-than-optimal treatment. Finally, the role of amount and distribution of body fat in the development of hypertension and CAD should be considered within an evolutionary framework. Body fatness in women has been of evolutionary survival value and current standards for ideal weight and risk for disease have to take this into account. © 1995 Wiley-Liss, Inc.
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Affiliation(s)
- Laura Newell-Morris
- Department of Anthropology DH-05, University of Washington, Seattle, Washington 98195
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