1
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Allert M, Ferretti P, Johnson KE, Heisel T, Gonia S, Knights D, Fields DA, Albert FW, Demerath EW, Gale CA, Blekhman R. Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother's milk. bioRxiv 2024:2024.01.28.577594. [PMID: 38328166 PMCID: PMC10849666 DOI: 10.1101/2024.01.28.577594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as the sole source of nutrition for the human infant, little is known about how variation in milk composition, and especially the milk microbiome, shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiome using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. We found that the microbial taxonomic overlap between milk and the infant gut was driven by bifidobacteria, in particular by B. longum. Infant stool samples dominated by B. longum also showed higher temporal stability compared to samples dominated by other species. We identified two instances of strain sharing between maternal milk and the infant gut, one involving a commensal (B. longum) and one a pathobiont (K. pneumoniae). In addition, strain sharing between unrelated infants was higher among infants born at the same hospital compared to infants born in different hospitals, suggesting a potential role of the hospital environment in shaping the infant gut microbiome composition. The infant gut microbiome at one month compared to six months of age was enriched in metabolic pathways associated with de-novo molecule biosynthesis, suggesting that early colonisers might be more versatile and metabolically independent compared to later colonizers. Lastly, we found a significant overlap in antimicrobial resistance genes carriage between the mother's milk and their infant's gut microbiome. Taken together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.
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Affiliation(s)
- Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Pamela Ferretti
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Timothy Heisel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Sara Gonia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ellen W Demerath
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Cheryl A Gale
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
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2
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Chetty A, Blekhman R. Multi-omic approaches for host-microbiome data integration. Gut Microbes 2024; 16:2297860. [PMID: 38166610 PMCID: PMC10766395 DOI: 10.1080/19490976.2023.2297860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
The gut microbiome interacts with the host through complex networks that affect physiology and health outcomes. It is becoming clear that these interactions can be measured across many different omics layers, including the genome, transcriptome, epigenome, metabolome, and proteome, among others. Multi-omic studies of the microbiome can provide insight into the mechanisms underlying host-microbe interactions. As more omics layers are considered, increasingly sophisticated statistical methods are required to integrate them. In this review, we provide an overview of approaches currently used to characterize multi-omic interactions between host and microbiome data. While a large number of studies have generated a deeper understanding of host-microbiome interactions, there is still a need for standardization across approaches. Furthermore, microbiome studies would also benefit from the collection and curation of large, publicly available multi-omics datasets.
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Affiliation(s)
- Ashwin Chetty
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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3
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Abdill RJ, Graham SP, Rubinetti V, Albert FW, Greene CS, Davis S, Blekhman R. Integration of 168,000 samples reveals global patterns of the human gut microbiome. bioRxiv 2023:2023.10.11.560955. [PMID: 37873416 PMCID: PMC10592789 DOI: 10.1101/2023.10.11.560955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Understanding the factors that shape variation in the human microbiome is a major goal of research in biology. While other genomics fields have used large, pre-compiled compendia to extract systematic insights requiring otherwise impractical sample sizes, there has been no comparable resource for the 16S rRNA sequencing data commonly used to quantify microbiome composition. To help close this gap, we have assembled a set of 168,484 publicly available human gut microbiome samples, processed with a single pipeline and combined into the largest unified microbiome dataset to date. We use this resource, which is freely available at microbiomap.org, to shed light on global variation in the human gut microbiome. We find that Firmicutes, particularly Bacilli and Clostridia, are almost universally present in the human gut. At the same time, the relative abundance of the 65 most common microbial genera differ between at least two world regions. We also show that gut microbiomes in undersampled world regions, such as Central and Southern Asia, differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America. Moreover, humans in these overlooked regions likely harbor hundreds of taxa that have not yet been discovered due to this undersampling, highlighting the need for diversity in microbiome studies. We anticipate that this new compendium can serve the community and enable advanced applied and methodological research.
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Affiliation(s)
- Richard J. Abdill
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Samantha P. Graham
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vincent Rubinetti
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Frank W. Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Casey S. Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Sean Davis
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
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4
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Johnson KE, Heisel T, Fields DA, Isganaitis E, Jacobs KM, Knights D, Lock EF, Rudolph MC, Gale CA, Schleiss MR, Albert FW, Demerath EW, Blekhman R. Human Cytomegalovirus in breast milk is associated with milk composition, the infant gut microbiome, and infant growth. bioRxiv 2023:2023.07.19.549370. [PMID: 37503212 PMCID: PMC10370112 DOI: 10.1101/2023.07.19.549370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Human cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3- dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate a complex relationship between milk CMV, milk kynurenine, and infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full term infant development.
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Affiliation(s)
- Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Timothy Heisel
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, Diabetes-Endocrinology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Elvira Isganaitis
- Pediatric, Adolescent and Young Adult Unit, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Katherine M Jacobs
- Department of Obstetrics, Gynecology and Women's Health, Division of Maternal-Fetal Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Michael C Rudolph
- Harold Hamm Diabetes Center, Department of Physiology, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Cheryl A Gale
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark R Schleiss
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Division of Biological Sciences, University of Chicago, Chicago, IL, USA
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5
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Veseli I, Chen YT, Schechter MS, Vanni C, Fogarty EC, Watson AR, Jabri B, Blekhman R, Willis AD, Yu MK, Fernàndez-Guerra A, Füssel J, Eren AM. Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. bioRxiv 2023:2023.05.10.540289. [PMID: 37293035 PMCID: PMC10245760 DOI: 10.1101/2023.05.10.540289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health versus IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.
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Affiliation(s)
- Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Yiqun T. Chen
- Data Science Institute and Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Matthew S. Schechter
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Chiara Vanni
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Emily C. Fogarty
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Andrea R. Watson
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Ran Blekhman
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Amy D. Willis
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Michael K. Yu
- Toyota Technological Institute at Chicago, Chicago, IL 60605, USA
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jessika Füssel
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - A. Murat Eren
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Marine ‘Omics Bridging Group, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany
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6
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Roche KE, Bjork JR, Dasari MR, Grieneisen L, Jansen D, Gould TJ, Gesquiere LR, Barreiro LB, Alberts SC, Blekhman R, Gilbert JA, Tung J, Mukherjee S, Archie EA. Universal gut microbial relationships in the gut microbiome of wild baboons. eLife 2023; 12:e83152. [PMID: 37158607 PMCID: PMC10292843 DOI: 10.7554/elife.83152] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/08/2023] [Indexed: 05/10/2023] Open
Abstract
Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships is essential to learn how ecology scales up to affect microbiome assembly, dynamics, and host health. However, whether bacterial relationships are generalizable across hosts or personalized to individual hosts is debated. Here, we apply a robust, multinomial logistic-normal modeling framework to extensive time series data (5534 samples from 56 baboon hosts over 13 years) to infer thousands of correlations in bacterial abundance in individual baboons and test the degree to which bacterial abundance correlations are 'universal'. We also compare these patterns to two human data sets. We find that, most bacterial correlations are weak, negative, and universal across hosts, such that shared correlation patterns dominate over host-specific correlations by almost twofold. Further, taxon pairs that had inconsistent correlation signs (either positive or negative) in different hosts always had weak correlations within hosts. From the host perspective, host pairs with the most similar bacterial correlation patterns also had similar microbiome taxonomic compositions and tended to be genetic relatives. Compared to humans, universality in baboons was similar to that in human infants, and stronger than one data set from human adults. Bacterial families that showed universal correlations in human infants were often universal in baboons. Together, our work contributes new tools for analyzing the universality of bacterial associations across hosts, with implications for microbiome personalization, community assembly, and stability, and for designing microbiome interventions to improve host health.
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Affiliation(s)
- Kimberly E Roche
- Program in Computational Biology and Bioinformatics, Duke UniversityDurhamUnited States
| | - Johannes R Bjork
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and HepatologyGroningenNetherlands
- University of Groningen and University Medical Center Groningen, Department of GeneticsGroningenNetherlands
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Mauna R Dasari
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan CampusKelownaCanada
| | - David Jansen
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Trevor J Gould
- Department of Ecology, Evolution, and Behavior, University of MinnesotaMinneapolisUnited States
| | | | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of ChicagoChicagoUnited States
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
- Committee on Immunology, University of ChicagoChicagoUnited States
| | - Susan C Alberts
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke University Population Research Institute, Duke UniversityDurhamUnited States
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
| | - Jack A Gilbert
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San DiegoSan DiegoUnited States
| | - Jenny Tung
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke University Population Research Institute, Duke UniversityDurhamUnited States
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke UniversityDurhamUnited States
- Departments of Statistical Science, Mathematics, Computer Science, and Bioinformatics & Biostatistics, Duke UniversityDurhamUnited States
- Center for Scalable Data Analytics and Artificial Intelligence, University of LeipzigLeipzigGermany
- Max Plank Institute for Mathematics in the Natural SciencesLeipzigGermany
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
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7
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Johnson KE, Heisel T, Allert M, Fürst A, Yerabandi N, Knights D, Jacobs KM, Lock EF, Bode L, Fields DA, Rudolph MC, Gale CA, Albert FW, Demerath EW, Blekhman R. Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome. bioRxiv 2023:2023.01.24.525211. [PMID: 36747843 PMCID: PMC9900818 DOI: 10.1101/2023.01.24.525211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Human milk is a complex mix of nutritional and bioactive components that provide complete nutrition for the infant. However, we lack a systematic knowledge of the factors shaping milk composition and how milk variation influences infant health. Here, we used multi-omic profiling to characterize interactions between maternal genetics, milk gene expression, milk composition, and the infant fecal microbiome in 242 exclusively breastfeeding mother-infant pairs. We identified 487 genetic loci associated with milk gene expression unique to the lactating mammary gland, including loci that impacted breast cancer risk and human milk oligosaccharide concentration. Integrative analyses uncovered connections between milk gene expression and infant gut microbiome, including an association between the expression of inflammation-related genes with IL-6 concentration in milk and the abundance of Bifidobacteria in the infant gut. Our results show how an improved understanding of the genetics and genomics of human milk connects lactation biology with maternal and infant health.
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Affiliation(s)
- Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Timothy Heisel
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Annalee Fürst
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nikhila Yerabandi
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Katherine M Jacobs
- Department of Obstetrics, Gynecology and Women's Health, Division of Maternal-Fetal Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Human Milk Institute (HMI) and Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA, USA
| | - David A Fields
- Department of Pediatrics, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael C Rudolph
- Harold Hamm Diabetes Center, Department of Physiology, the University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Cheryl A Gale
- Division of Neonatology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Division of Biological Sciences, University of Chicago, Chicago, IL, USA
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8
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Grieneisen L, Blekhman R, Archie E. How longitudinal data can contribute to our understanding of host genetic effects on the gut microbiome. Gut Microbes 2023; 15:2178797. [PMID: 36794811 PMCID: PMC9980606 DOI: 10.1080/19490976.2023.2178797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
A key component of microbiome research is understanding the role of host genetic influence on gut microbial composition. However, it can be difficult to link host genetics with gut microbial composition because host genetic similarity and environmental similarity are often correlated. Longitudinal microbiome data can supplement our understanding of the relative role of genetic processes in the microbiome. These data can reveal environmentally contingent host genetic effects, both in terms of controlling for environmental differences and in comparing how genetic effects differ by environment. Here, we explore four research areas where longitudinal data could lend new insights into host genetic effects on the microbiome: microbial heritability, microbial plasticity, microbial stability, and host and microbiome population genetics. We conclude with a discussion of methodological considerations for future studies.
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Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Elizabeth Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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9
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Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE, Ngwese MM, Grießhammer A, Pfleiderer A, Adegbite BR, Zinsou JF, Esen M, Velavan TP, Adegnika AA, Song LH, Spector TD, Muehlbauer AL, Marchi N, Kang H, Maier L, Blekhman R, Ségurel L, Ko G, Youngblut ND, Kremsner P, Ley RE. Codiversification of gut microbiota with humans. Science 2022; 377:1328-1332. [PMID: 36108023 PMCID: PMC10777373 DOI: 10.1126/science.abm7759] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.
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Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - J. Liam Fitzstevens
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Victor T. Schmidt
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Kelsey E. Huus
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Mirabeau Mbong Ngwese
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Anne Grießhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Pfleiderer
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Bayode R. Adegbite
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Jeannot F. Zinsou
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Meral Esen
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Thirumalaisamy P. Velavan
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Vietnamese German Center for Medical Research, Hanoi, Vietnam
| | - Ayola A. Adegnika
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research, Tübingen, Germany
- Fondation pour la Recherche Scientifique, Cotonou, Bénin
| | - Le Huu Song
- Vietnamese German Center for Medical Research, Hanoi, Vietnam
- 108 Military Central Hospital, Hanoi, Vietnam
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Nina Marchi
- Eco-anthropologie, Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Hyena Kang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Laure Ségurel
- Eco-anthropologie, Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Paris, France
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, Villeurbanne, France
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Peter Kremsner
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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10
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Priya S, Burns MB, Ward T, Mars RAT, Adamowicz B, Lock EF, Kashyap PC, Knights D, Blekhman R. Identification of shared and disease-specific host gene-microbiome associations across human diseases using multi-omic integration. Nat Microbiol 2022; 7:780-795. [PMID: 35577971 PMCID: PMC9159953 DOI: 10.1038/s41564-022-01121-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/06/2022] [Indexed: 12/19/2022]
Abstract
While gut microbiome and host gene regulation independently contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here we developed a machine learning-based framework to jointly analyse paired host transcriptomic (n = 208) and gut microbiome (n = 208) profiles from colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease and irritable bowel syndrome. We identified associations between gut microbes and host genes that depict shared as well as disease-specific patterns. We found that a common set of host genes and pathways implicated in gastrointestinal inflammation, gut barrier protection and energy metabolism are associated with disease-specific gut microbes. Additionally, we also found that mucosal gut microbes that have been implicated in all three diseases, such as Streptococcus, are associated with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes. Our framework can be applied to other diseases for the identification of host gene-microbiome associations that may influence disease outcomes.
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Affiliation(s)
- Sambhawa Priya
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
| | - Michael B Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Beth Adamowicz
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA.
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11
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Abstract
The importance of sampling from globally representative populations has been well established in human genomics. In human microbiome research, however, we lack a full understanding of the global distribution of sampling in research studies. This information is crucial to better understand global patterns of microbiome-associated diseases and to extend the health benefits of this research to all populations. Here, we analyze the country of origin of all 444,829 human microbiome samples that are available from the world’s 3 largest genomic data repositories, including the Sequence Read Archive (SRA). The samples are from 2,592 studies of 19 body sites, including 220,017 samples of the gut microbiome. We show that more than 71% of samples with a known origin come from Europe, the United States, and Canada, including 46.8% from the US alone, despite the country representing only 4.3% of the global population. We also find that central and southern Asia is the most underrepresented region: Countries such as India, Pakistan, and Bangladesh account for more than a quarter of the world population but make up only 1.8% of human microbiome samples. These results demonstrate a critical need to ensure more global representation of participants in microbiome studies. The importance of sampling from globally representative populations has been well established in human genomics, but what about the microbiome? This study shows that metadata from almost half a million samples reveals worldwide human microbiome research is skewed heavily in favor of Europe and North America and excludes large but less developed nations in Asia and Africa.
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Affiliation(s)
- Richard J. Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Elizabeth M. Adamowicz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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12
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Muehlbauer AL, Richards AL, Alazizi A, Burns MB, Gomez A, Clayton JB, Petrzelkova K, Cascardo C, Resztak J, Wen X, Pique-Regi R, Luca F, Blekhman R. Interspecies variation in hominid gut microbiota controls host gene regulation. Cell Rep 2021; 37:110057. [PMID: 34818542 PMCID: PMC8647622 DOI: 10.1016/j.celrep.2021.110057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 07/22/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome exhibits extreme compositional variation between hominid hosts. However, it is unclear how this variation impacts host physiology across species and whether this effect can be mediated through microbial regulation of host gene expression in interacting epithelial cells. Here, we characterize the transcriptional response of human colonic epithelial cells in vitro to live microbial communities extracted from humans, chimpanzees, gorillas, and orangutans. We find that most host genes exhibit a conserved response, whereby they respond similarly to the four hominid microbiomes. However, hundreds of host genes exhibit a divergent response, whereby they respond only to microbiomes from specific host species. Such genes are associated with intestinal diseases in humans, including inflammatory bowel disease and Crohn’s disease. Last, we find that inflammation-associated microbial species regulate the expression of host genes previously associated with inflammatory bowel disease, suggesting health-related consequences for species-specific host-microbiome interactions across hominids. Muehlbauer et al. investigate how variation between different hominid microbiomes drives host gene expression in colonic epithelial cell cultures. They find that host genes that respond only to microbiomes from a specific hominid species are linked to gastrointestinal diseases, suggesting implications for understanding how the microbiome can impact human health.
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Affiliation(s)
- Amanda L Muehlbauer
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Allison L Richards
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Michael B Burns
- Department of Biology, Loyola University, Chicago, IL 60660, USA
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, Saint Paul, MN, USA
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, NB, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NB, USA
| | - Klara Petrzelkova
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic; Liberec Zoo, Liberec, Czech Republic; The Czech Academy of Sciences, Institute of Parasitology, Ceske Budejovice, Czech Republic
| | - Camilla Cascardo
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Justyna Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA; Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA; Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN, USA.
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13
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Mihindukulasuriya KA, Mars RAT, Johnson AJ, Ward T, Priya S, Lekatz HR, Kalari KR, Droit L, Zheng T, Blekhman R, D'Amato M, Farrugia G, Knights D, Handley SA, Kashyap PC. Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome. Gastroenterology 2021; 161:1194-1207.e8. [PMID: 34245762 PMCID: PMC8463486 DOI: 10.1053/j.gastro.2021.06.077] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/21/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS. METHODS We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets. RESULTS We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses). CONCLUSIONS We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.
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Affiliation(s)
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Abigail J Johnson
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Lindsay Droit
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Mauro D'Amato
- Gastrointestinal Genetics Laboratory, CIC bioGUNE, Basque Research and Technology Alliance, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Dan Knights
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota.
| | - Scott A Handley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; Department of Medicine and Physiology, Mayo Clinic, Rochester, Minnesota.
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14
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Bramble MS, Vashist N, Ko A, Priya S, Musasa C, Mathieu A, Spencer DA, Lupamba Kasendue M, Mamona Dilufwasayo P, Karume K, Nsibu J, Manya H, Uy MNA, Colwell B, Boivin M, Mayambu JPB, Okitundu D, Droit A, Mumba Ngoyi D, Blekhman R, Tshala-Katumbay D, Vilain E. The gut microbiome in konzo. Nat Commun 2021; 12:5371. [PMID: 34508085 PMCID: PMC8433213 DOI: 10.1038/s41467-021-25694-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Konzo, a distinct upper motor neuron disease associated with a cyanogenic diet and chronic malnutrition, predominately affects children and women of childbearing age in sub-Saharan Africa. While the exact biological mechanisms that cause this disease have largely remained elusive, host-genetics and environmental components such as the gut microbiome have been implicated. Using a large study population of 180 individuals from the Democratic Republic of the Congo, where konzo is most frequent, we investigate how the structure of the gut microbiome varied across geographical contexts, as well as provide the first insight into the gut flora of children affected with this debilitating disease using shotgun metagenomic sequencing. Our findings indicate that the gut microbiome structure is highly variable depending on region of sampling, but most interestingly, we identify unique enrichments of bacterial species and functional pathways that potentially modulate the susceptibility of konzo in prone regions of the Congo.
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Affiliation(s)
- Matthew S Bramble
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
| | - Neerja Vashist
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Arthur Ko
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sambhawa Priya
- Departments of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Céleste Musasa
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
| | - Alban Mathieu
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - D' Andre Spencer
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
| | | | - Patrick Mamona Dilufwasayo
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
| | - Kevin Karume
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
| | - Joanna Nsibu
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
| | - Hans Manya
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
| | - Mary N A Uy
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA
- College of Medicine, University of the Philippines, Manila, Manila, Philippines
| | - Brian Colwell
- School of Public Health, Texas A&M University, College Station, TX, USA
| | - Michael Boivin
- Department of Psychiatry and Neurology & Ophthalmology, Michigan State University, East Lansing, MI, USA
| | - J P Banae Mayambu
- Ministry of Health National Program on Nutrition (PRONANUT), Kinshasa, DR, Congo
| | - Daniel Okitundu
- Centre Neuro-Psychopathologique (CNPP), University of Kinshasa, Kinshasa, Congo
| | - Arnaud Droit
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Dieudonné Mumba Ngoyi
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo
- Department of Tropical Medicine, University of Kinshasa, Kinshasa, DR, Congo
| | - Ran Blekhman
- Departments of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Desire Tshala-Katumbay
- Institut National de Recherche Biomédicale (INRB), Kinshasa, DR, Congo.
- Department of Neurology and School of Public Health, Oregon Health & Science University, Portland, OR, USA.
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's Research Institute, Children's National Hospital, Washington, DC, USA.
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
- International Research Laboratory of Epigenetics, Data, Politics, Centre National de la Recherche Scientifique, Washington, DC, USA.
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15
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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 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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16
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Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021; 184:3376-3393.e17. [PMID: 34043940 PMCID: PMC8238498 DOI: 10.1016/j.cell.2021.05.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023]
Abstract
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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Affiliation(s)
- David Danko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Evan E Afshin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Chandrima Bhattacharya
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniel J Butler
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Kern Rei Chng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Daisy Donnellan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Katelyn Jackson
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Katerina Kuchin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Mikhail Karasikov
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail Lyons
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Lauren Mak
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dmitry Meleshko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Harun Mustafa
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Beth Mutai
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya
| | - Russell Y Neches
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Ng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | | | | | - Eileen Png
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Krista A Ryon
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jorge L Sanchez
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Heba Shaaban
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Maria A Sierra
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dominique Thomas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Ben Young
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Omar O Abudayyeh
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Josue Alicea
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | | | - Eduardo Castro-Nallar
- Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Ana M Cañas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Aspassia D Chatziefthimiou
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Youping Deng
- University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Christelle Desnues
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Emmanuel Dias-Neto
- Medical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil
| | - Marius Dybwad
- Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Dennis Gankin
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | | | - David C Green
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Iman Hajirasouliha
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jaden J A Hastings
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago, Chile; Wellcome Sanger Institute, Hinxton, UK
| | | | - Andre Kahles
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; Kyiv Academic University, Kyiv, Ukraine; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Frank J Kelly
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Kaymisha Knights
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paweł P Łabaj
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Boku University Viennna, Vienna, Austria
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Ken McGrath
- Microba, 388 Queen St, Brisbane City, QLD 4000, Australia
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | | | - Houtan Noushmehr
- University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto - SP, Brazil
| | - Manuela Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
| | - Orhan Özcan
- Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicolás Rascovan
- Microbial Paleogenomics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - Hugues Richard
- Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France; Robert Koch Institute, Berlin, Germany
| | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Rania Siam
- University of Medicine and Health Sciences, St. Kitts, West Indies and American University in Cairo, Cairo, Egypt
| | - Le Huu Song
- 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | | | - Denise Syndercombe Court
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | | | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Klas I Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; SciLife EVP, Department of Aquatic Sciences Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Brandon Valentine
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dimitar I Vassilev
- Faculty of Mathematics and Informatics, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Elena M Vayndorf
- Institute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, AK, USA
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Univeristätsklinikum Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam
| | - Jun Wu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Jifeng Zhu
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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17
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Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell 2020; 183:1137-1140. [PMID: 33186523 DOI: 10.1016/j.cell.2020.10.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Grieneisen L, Muehlbauer AL, Blekhman R. Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190598. [PMID: 32772669 PMCID: PMC7435160 DOI: 10.1098/rstb.2019.0598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2020] [Indexed: 12/23/2022] Open
Abstract
Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, MN 55455, 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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19
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Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell 2020; 182:1460-1473.e17. [PMID: 32916129 DOI: 10.1016/j.cell.2020.08.007] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/25/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. VIDEO ABSTRACT.
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Affiliation(s)
- Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yi Yang
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mo Houtti
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Heather R Lekatz
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Tal Korem
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; CIFAR Azrieli Global Scholars program, CIFAR, Toronto, ON M5G 1M1, Canada
| | - Yogesh Bhattarai
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, 3800 VIC, Australia
| | - Noam Bar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gary Frost
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK
| | - Abigail J Johnson
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Will van Treuren
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Shuo Han
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Madhusudan Grover
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Center for Human Microbiome Studies, Stanford University, Stanford, CA 94305, USA
| | - Mauro D'Amato
- School of Biological Sciences, Monash University, Clayton, 3800 VIC, Australia
| | - Michael Camilleri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel; Division of Cancer-Microbiome Research, DKFZ, 69120 Heidelberg, Germany
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gianrico Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Jonathan R Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College, London SW7 2AZ, UK; School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.
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20
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Abstract
Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors. Here, based on an analysis of 67,885 preprints posted on bioRxiv, we find that some countries, notably the United States and the United Kingdom, are overrepresented on bioRxiv relative to their overall scientific output, while other countries (including China, Russia, and Turkey) show lower levels of bioRxiv adoption. We also describe a set of 'contributor countries' (including Uganda, Croatia and Thailand): researchers from these countries appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the US.
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Affiliation(s)
- Richard J Abdill
- Department of Genetics, Cell Biology, and Development, University of MinnesotaMinneapolisUnited States
| | - Elizabeth M Adamowicz
- Department of Genetics, Cell Biology, and Development, University of MinnesotaMinneapolisUnited States
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of MinnesotaMinneapolisUnited States
- Department of Ecology, Evolution and Behavior, University of MinnesotaMinneapolisUnited States
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21
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Grieneisen LE, Charpentier MJE, Alberts SC, Blekhman R, Bradburd G, Tung J, Archie EA. Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proc Biol Sci 2020; 286:20190431. [PMID: 31014219 DOI: 10.1098/rspb.2019.0431] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host-population FST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.
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Affiliation(s)
- Laura E Grieneisen
- 1 Department of Genetics, Cell Biology, and Development, University of Minnesota , Minneapolis, MN 55455 , USA.,2 Department of Biology, University of Notre Dame , Notre Dame, IN 46556 , USA
| | - Marie J E Charpentier
- 3 Institut des Sciences de l'Evolution de Montpellier, Université Montpellier, CNRS, IRD, EPHE , Montpellier , France
| | - Susan C Alberts
- 4 Department of Biology, Duke University , Durham, NC 27708 , USA.,5 Department of Evolutionary Anthropology, Duke University , Durham, NC 27708 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
| | - Ran Blekhman
- 1 Department of Genetics, Cell Biology, and Development, University of Minnesota , Minneapolis, MN 55455 , USA.,7 Department of Ecology, Evolution, and Behavior, University of Minnesota , Minneapolis, MN 55455 , USA
| | - Gideon Bradburd
- 8 Department of Integrative Biology, Michigan State University , East Lansing, MI 48824 , USA
| | - Jenny Tung
- 4 Department of Biology, Duke University , Durham, NC 27708 , USA.,5 Department of Evolutionary Anthropology, Duke University , Durham, NC 27708 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
| | - Elizabeth A Archie
- 2 Department of Biology, University of Notre Dame , Notre Dame, IN 46556 , USA.,6 Institute for Primate Research, National Museums of Kenya , Nairobi 00502 , Kenya
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22
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Dayama G, Priya S, Niccum DE, Khoruts A, Blekhman R. Interactions between the gut microbiome and host gene regulation in cystic fibrosis. Genome Med 2020; 12:12. [PMID: 31992345 PMCID: PMC6988342 DOI: 10.1186/s13073-020-0710-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cystic fibrosis is the most common autosomal recessive genetic disease in Caucasians. It is caused by mutations in the CFTR gene, leading to poor hydration of mucus and impairment of the respiratory, digestive, and reproductive organ functions. Advancements in medical care have led to markedly increased longevity of patients with cystic fibrosis, but new complications have emerged, such as early onset of colorectal cancer. Although the pathogenesis of colorectal cancer in cystic fibrosis remains unclear, altered host-microbe interactions might play a critical role. To investigate this, we characterized changes in the microbiome and host gene expression in the colonic mucosa of cystic fibrosis patients relative to healthy controls, and identified host gene-microbiome interactions in the colon of cystic fibrosis patients. METHODS We performed RNA-seq on colonic mucosa samples from cystic fibrosis patients and healthy controls to determine differentially expressed host genes. We also performed 16S rRNA sequencing to characterize the colonic mucosal microbiome and identify gut microbes that are differentially abundant between patients and healthy controls. Lastly, we modeled associations between relative abundances of specific bacterial taxa in the gut mucosa and host gene expression. RESULTS We find that 1543 genes, including CFTR, show differential expression in the colon of cystic fibrosis patients compared to healthy controls. These genes are enriched with functions related to gastrointestinal and colorectal cancer, such as metastasis of colorectal cancer, tumor suppression, p53, and mTOR signaling pathways. In addition, patients with cystic fibrosis show decreased gut microbial diversity, decreased abundance of butyrate producing bacteria, such as Ruminococcaceae and Butyricimonas, and increased abundance of other taxa, such as Actinobacteria and Clostridium. An integrative analysis identified colorectal cancer-related genes, including LCN2 and DUOX2, for which gene expression is correlated with the abundance of colorectal cancer-associated bacteria, such as Ruminococcaceae and Veillonella. CONCLUSIONS In addition to characterizing host gene expression and mucosal microbiome in cystic fibrosis patients, our study explored the potential role of host-microbe interactions in the etiology of colorectal cancer in cystic fibrosis. Our results provide biomarkers that may potentially serve as targets for stratifying risk of colorectal cancer in patients with cystic fibrosis.
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Affiliation(s)
- Gargi Dayama
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Sambhawa Priya
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - David E Niccum
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Khoruts
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
- Center for Immunology, BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA.
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23
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Abstract
Characterization of the temporal dynamics of the human gut microbiome is crucial for understanding its role in modulating host health. Two recent studies explored the genetic diversity of gut microbes and unraveled extensive longitudinal dynamics within the host that is driven by natural selection.
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Affiliation(s)
- Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA.
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24
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Gomez A, Sharma AK, Mallott EK, Petrzelkova KJ, Jost Robinson CA, Yeoman CJ, Carbonero F, Pafco B, Rothman JM, Ulanov A, Vlckova K, Amato KR, Schnorr SL, Dominy NJ, Modry D, Todd A, Torralba M, Nelson KE, Burns MB, Blekhman R, Remis M, Stumpf RM, Wilson BA, Gaskins HR, Garber PA, White BA, Leigh SR. Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints. mSphere 2019; 4:e00271-19. [PMID: 31366708 PMCID: PMC6669335 DOI: 10.1128/msphere.00271-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/01/2019] [Indexed: 01/11/2023] Open
Abstract
The gut microbiome of primates, including humans, is reported to closely follow host evolutionary history, with gut microbiome composition being specific to the genetic background of its primate host. However, the comparative models used to date have mainly included a limited set of closely related primates. To further understand the forces that shape the primate gut microbiome, with reference to human populations, we expanded the comparative analysis of variation among gut microbiome compositions and their primate hosts, including 9 different primate species and 4 human groups characterized by a diverse set of subsistence patterns (n = 448 samples). The results show that the taxonomic composition of the human gut microbiome, at the genus level, exhibits increased compositional plasticity. Specifically, we show unexpected similarities between African Old World monkeys that rely on eclectic foraging and human populations engaging in nonindustrial subsistence patterns; these similarities transcend host phylogenetic constraints. Thus, instead of following evolutionary trends that would make their microbiomes more similar to that of conspecifics or more phylogenetically similar apes, gut microbiome composition in humans from nonindustrial populations resembles that of generalist cercopithecine monkeys. We also document that wild cercopithecine monkeys with eclectic diets and humans following nonindustrial subsistence patterns harbor high gut microbiome diversity that is not only higher than that seen in humans engaging in industrialized lifestyles but also higher compared to wild primates that typically consume fiber-rich diets.IMPORTANCE The results of this study indicate a discordance between gut microbiome composition and evolutionary history in primates, calling into question previous notions about host genetic control of the primate gut microbiome. Microbiome similarities between humans consuming nonindustrialized diets and monkeys characterized by subsisting on eclectic, omnivorous diets also raise questions about the ecological and nutritional drivers shaping the human gut microbiome. Moreover, a more detailed understanding of the factors associated with gut microbiome plasticity in primates offers a framework to understand why humans following industrialized lifestyles have deviated from states thought to reflect human evolutionary history. The results also provide perspectives for developing therapeutic dietary manipulations that can reset configurations of the gut microbiome to potentially improve human health.
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Affiliation(s)
- Andres Gomez
- Department of Animal Science, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Ashok Kumar Sharma
- Department of Animal Science, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Liberec Zoo, Liberec, Czech Republic
| | | | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, USA
| | - Franck Carbonero
- Department of Nutrition & Exercise Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington, USA
| | - Barbora Pafco
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of CUNY and New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Alexander Ulanov
- Metabolomics Center, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Klara Vlckova
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Stephanie L Schnorr
- Department of Anthropology, University of Nevada, Las Vegas, Nevada, USA
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, Hanover, New Hampshire, USA
| | - David Modry
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
- Central European Institute for Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Angelique Todd
- World Wildlife Fund, Dzanga-Sangha Protected Areas, Bayanga, Central African Republic
| | | | | | - Michael B Burns
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Melissa Remis
- Department of Anthropology, Purdue University, West Lafayette, Indiana, USA
| | - Rebecca M Stumpf
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Brenda A Wilson
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - H Rex Gaskins
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Paul A Garber
- Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Bryan A White
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, Colorado, USA
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25
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Sharma AK, Pafčo B, Vlčková K, Červená B, Kreisinger J, Davison S, Beeri K, Fuh T, Leigh SR, Burns MB, Blekhman R, Petrželková KJ, Gomez A. Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq. BMC Genomics 2019; 20:493. [PMID: 31200636 PMCID: PMC6567582 DOI: 10.1186/s12864-019-5813-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/20/2019] [Indexed: 12/30/2022] Open
Abstract
Background Limited accessibility to intestinal epithelial tissue in wild animals and humans makes it challenging to study patterns of intestinal gene regulation, and hence to monitor physiological status and health in field conditions. To explore solutions to this limitation, we have used a noninvasive approach via fecal RNA-seq, for the quantification of gene expression markers in gastrointestinal cells of free-range primates and a forager human population. Thus, a combination of poly(A) mRNA enrichment and rRNA depletion methods was used in tandem with RNA-seq to quantify and compare gastrointestinal gene expression patterns in fecal samples of wild Gorilla gorilla gorilla (n = 9) and BaAka hunter-gatherers (n = 10) from The Dzanga Sangha Protected Areas, Central African Republic. Results Although only a small fraction (< 4.9%) of intestinal mRNA signals was recovered, the data was sufficient to detect significant functional differences between gorillas and humans, at the gene and pathway levels. These intestinal gene expression differences were specifically associated with metabolic and immune functions. Additionally, non-host RNA-seq reads were used to gain preliminary insights on the subjects’ dietary habits, intestinal microbiomes, and infection prevalence, via identification of fungi, nematode, arthropod and plant RNA. Conclusions Overall, the results suggest that fecal RNA-seq, targeting gastrointestinal epithelial cells can be used to evaluate primate intestinal physiology and gut gene regulation, in samples obtained in challenging conditions in situ. The approach used herein may be useful to obtain information on primate intestinal health, while revealing preliminary insights into foraging ecology, microbiome, and diet. Electronic supplementary material The online version of this article (10.1186/s12864-019-5813-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Barbora Pafčo
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic.,Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Klára Vlčková
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic.,Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Barbora Červená
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic.,Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Jakub Kreisinger
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Praha, Czech Republic
| | - Samuel Davison
- Department of Animal Science, University of Minnesota, Twin Cities, USA
| | - Karen Beeri
- Vanderbilt University medical center Technologies for Advanced Genomics, Vanderbilt University medical center, Nashville, TN, USA
| | - Terence Fuh
- WWF Central African Republic, Bangui, Central African Republic
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - Michael B Burns
- Loyola University Chicago, Quinlan Life Sciences Building, Chicago, IL, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN, USA.,Department of Ecology, Evolution and Behavior, University of Minnesota, Twin Cities, MN, USA
| | - Klára J Petrželková
- The Czech Academy of Sciences, Institute of Vertebrate Biology, Květná 8, 603 65, Brno, Czech Republic. .,The Czech Academy of Sciences, Biology Centre, Institute of Parasitology, Branišovská 31, 370 05, České Budějovice, Czech Republic. .,Liberec Zoo, Lidové sady 425/1, 460 01, Liberec, Czech Republic.
| | - Andres Gomez
- Department of Animal Science, University of Minnesota, Twin Cities, USA.
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26
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Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AKM, Dayama G, Grieneisen L, Martin LS, Flint J, Eskin E, Blekhman R. Challenges and recommendations to improve the installability and archival stability of omics computational tools. PLoS Biol 2019; 17:e3000333. [PMID: 31220077 PMCID: PMC6605654 DOI: 10.1371/journal.pbio.3000333] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/02/2019] [Indexed: 01/07/2023] Open
Abstract
Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed "easy to install," and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.
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Affiliation(s)
- Serghei Mangul
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America
| | - Thiago Mosqueiro
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America
| | - Richard J. Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dat Duong
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Keith Mitchell
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Varuni Sarwal
- Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Brian Hill
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jaqueline Brito
- Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil
| | - Russell Jared Littman
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Benjamin Statz
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Angela Ka-Mei Lam
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Gargi Dayama
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lana S. Martin
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minnesota, United States of America
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27
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Abernathy B, Blekhman R, Schoenfuss T, Gallaher D. Changes in the Gut Microbiome Contribute to Changes in Tissue Gene Expression in Rats Fed Prebiotic Dietary Fibers (P15-022-19). Curr Dev Nutr 2019. [DOI: 10.1093/cdn/nzz037.p15-022-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objectives
We investigated the intersection between the gut microbiome and gene expression of colon and liver tissues in rats, using prebiotic dietary fibers to modulate the gut microbiome and elicit health benefits to the host.
Methods
Male Wistar rats were fed normal fat (NF) or high fat (HF, 51% fat by kcal) diets containing various fibers (6% fiber + 3% cellulose, by weight); including cellulose (NFC and HFC, non-fermentable), polylactose (HFPL, a novel prebiotic), and polydextrose (HFPD, an established prebiotic). After 10 weeks, tissues were harvested. Transcriptome analysis was performed by RNA sequencing of colon and liver tissues, and cecal contents were utilized for 16S microbiome sequencing. Analyses were conducted in R using DESeq2, DADA2, and phyloseq.
Results
Analysis of the gut microbiome revealed an increased abundance of probiotic genera, Bifidobacterium and Lactobacillus, in HFPL fed animals when compared to all other groups. These species are galactose fermenters which synthesize short chain fatty acids (SCFAs). This increased taxonomical abundance correlated with an increased FFar3 (SCFA receptor) expression in the colon. This suggests increased FFar3 signaling, leading to increased energy expenditure and GLP-1 and PYY secretion. Additionally, HFPL and HFPD groups had a decreased Firmicutes: Bacteroidetes ratio, which is associated with reduced adiposity due to the Bacteroidetes phylum being poor carbohydrate metabolizers, resulting in reduced energy uptake, yet increased SCFA synthesis.
Bacteriodetes are also able to survive in SCFA and bile acid rich environments and are involved in the recycling of bile acids which negatively regulates cholesterol synthesis. This corresponds to reduced liver cholesterol and cholesterol synthesis pathway expression in the HFPL group. Further, liver gene expression revealed reduced lipid synthesis and increased lipid oxidation pathway gene expression in the HFPL group, corresponding to the reduction in fatty liver found in this group.
Conclusions
Prebiotic dietary fibers elicit changes in the gut microbiome and gene expression in liver and colon. Changes in gene expression correlated with the abundance of beneficial gut bacteria, providing a connection between the gut microbiome and health benefits to the host.
Funding Sources
Midwest Dairy Association.
Supporting Tables, Images and/or Graphs
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28
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Abstract
Preprints have arrived. In increasing numbers, researchers across the life sciences are embracing the once-niche practice, shaking off decades of reluctance and posting hundreds of papers per week to preprint servers, sharing their findings with the community before embarking on the weary march through peer review. However, there are limited methods for individuals sifting through this avalanche of research to identify the preprints that are most relevant to their interests. Here, we describe Rxivist.org, a website that indexes all preprints posted to bioRxiv.org, the largest preprint server in the life sciences, and allows users to filter and sort papers based on download metrics and Twitter activity over a variety of categories and time periods. In this work, we hope to make it easier for readers to find relevant research on bioRxiv and to improve the visibility of preprints currently being read and discussed online. This Community Page article describes Rxivist.org, a new website that indexes all preprints posted to bioRxiv.org and allows users to filter and sort papers based on download metrics and Twitter activity over a variety of categories and time periods.
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Affiliation(s)
- Richard J. Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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29
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Abstract
The growth of preprints in the life sciences has been reported widely and is driving policy changes for journals and funders, but little quantitative information has been published about preprint usage. Here, we report how we collected and analyzed data on all 37,648 preprints uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. The rate of preprint uploads to bioRxiv continues to grow (exceeding 2,100 in October 2018), as does the number of downloads (1.1 million in October 2018). We also find that two-thirds of preprints posted before 2017 were later published in peer-reviewed journals, and find a relationship between the number of downloads a preprint has received and the impact factor of the journal in which it is published. We also describe Rxivist.org, a web application that provides multiple ways to interact with preprint metadata.
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Affiliation(s)
- Richard J Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, United States
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30
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Abstract
Implementation of bioinformatics software involves numerous unique challenges; a rigorous standardized approach is needed to examine software tools prior to their publication.
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Affiliation(s)
- Serghei Mangul
- Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA, 90095, USA. .,Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
| | - Lana S Martin
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California Los Angeles, 580 Portola Plaza, Los Angeles, CA, 90095, USA.,Department of Human Genetics, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St SE, Minneapolis, MN, 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Cir, Falcon Heights, MN, 55108, USA
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31
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Abstract
Although the gut microbiome has been linked to colorectal cancer (CRC) development, associations of microbial taxa with CRC status are often inconsistent across studies. We have recently shown that tumor genomics, a factor that is rarely incorporated in analyses of the CRC microbiome, has a strong effect on the composition of the microbiota. Here, we discuss these results in the wider context of studies characterizing interaction between host genetics and the microbiome, and describe the implications of our findings for understanding the role of the microbiome in CRC.
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Affiliation(s)
- Michael B. Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA,CONTACT Ran Blekhman Department of Genetics, Cell Biology, and Development, University of Minnesota, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
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32
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Abstract
Composed of hundreds of microbial species, the composition of the human gut microbiota can vary with chronic diseases underlying health disparities that disproportionally affect ethnic minorities. However, the influence of ethnicity on the gut microbiota remains largely unexplored and lacks reproducible generalizations across studies. By distilling associations between ethnicity and differences in two US-based 16S gut microbiota data sets including 1,673 individuals, we report 12 microbial genera and families that reproducibly vary by ethnicity. Interestingly, a majority of these microbial taxa, including the most heritable bacterial family, Christensenellaceae, overlap with genetically associated taxa and form co-occurring clusters linked by similar fermentative and methanogenic metabolic processes. 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.
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Affiliation(s)
- Andrew W. Brooks
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, United States of America
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Seth R. Bordenstein
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University, Nashville, Tennessee, United States of America
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33
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Lynch J, Tang K, Priya S, Sands J, Sands M, Tang E, Mukherjee S, Knights D, Blekhman R. HOMINID: a framework for identifying associations between host genetic variation and microbiome composition. Gigascience 2018; 6:1-7. [PMID: 29126115 PMCID: PMC5740987 DOI: 10.1093/gigascience/gix107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 10/31/2017] [Indexed: 02/02/2023] Open
Abstract
Recent studies have uncovered a strong effect of host genetic variation on the composition of host-associated microbiota. Here, we present HOMINID, a computational approach based on Lasso linear regression, that given host genetic variation and microbiome taxonomic composition data, identifies host single nucleotide polymorphisms (SNPs) that are correlated with microbial taxa abundances. Using simulated data, we show that HOMINID has accuracy in identifying associated SNPs and performs better compared with existing methods. We also show that HOMINID can accurately identify the microbial taxa that are correlated with associated SNPs. Lastly, by using HOMINID on real data of human genetic variation and microbiome composition, we identified 13 human SNPs in which genetic variation is correlated with microbiome taxonomic composition across body sites. In conclusion, HOMINID is a powerful method to detect host genetic variants linked to microbiome composition and can facilitate discovery of mechanisms controlling host-microbiome interactions.
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Affiliation(s)
- Joshua Lynch
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Karen Tang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Joanna Sands
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Margaret Sands
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Evan Tang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Sayan Mukherjee
- Departments of Statistical Science, Mathematics, and Computer Science, Duke University, 112 Old Chemistry, Box 90251, Durham NC 27708, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, 200 Union St SE, 4-192 Keller Hall, Minneapolis MN 55455, USA.,Biotechnology Institute, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St SE, 6-160 Jackson Hall, Minneapolis MN 55455, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, 1479 Gortner Ave, 140 Gortner Lab, Saint Paul MN 55108, USA
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34
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Hale VL, Jeraldo P, Chen J, Mundy M, Yao J, Priya S, Keeney G, Lyke K, Ridlon J, White BA, French AJ, Thibodeau SN, Diener C, Resendis-Antonio O, Gransee J, Dutta T, Petterson XM, Sung J, Blekhman R, Boardman L, Larson D, Nelson H, Chia N. Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers. Genome Med 2018; 10:78. [PMID: 30376889 PMCID: PMC6208080 DOI: 10.1186/s13073-018-0586-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/08/2018] [Indexed: 01/14/2023] Open
Abstract
Background Links between colorectal cancer (CRC) and the gut microbiome have been established, but the specific microbial species and their role in carcinogenesis remain an active area of inquiry. Our understanding would be enhanced by better accounting for tumor subtype, microbial community interactions, metabolism, and ecology. Methods We collected paired colon tumor and normal-adjacent tissue and mucosa samples from 83 individuals who underwent partial or total colectomies for CRC. Mismatch repair (MMR) status was determined in each tumor sample and classified as either deficient MMR (dMMR) or proficient MMR (pMMR) tumor subtypes. Samples underwent 16S rRNA gene sequencing and a subset of samples from 50 individuals were submitted for targeted metabolomic analysis to quantify amino acids and short-chain fatty acids. A PERMANOVA was used to identify the biological variables that explained variance within the microbial communities. dMMR and pMMR microbial communities were then analyzed separately using a generalized linear mixed effects model that accounted for MMR status, sample location, intra-subject variability, and read depth. Genome-scale metabolic models were then used to generate microbial interaction networks for dMMR and pMMR microbial communities. We assessed global network properties as well as the metabolic influence of each microbe within the dMMR and pMMR networks. Results We demonstrate distinct roles for microbes in dMMR and pMMR CRC. Bacteroides fragilis and sulfidogenic Fusobacterium nucleatum were significantly enriched in dMMR CRC, but not pMMR CRC. These findings were further supported by metabolic modeling and metabolomics indicating suppression of B. fragilis in pMMR CRC and increased production of amino acid proxies for hydrogen sulfide in dMMR CRC. Conclusions Integrating tumor biology and microbial ecology highlighted distinct microbial, metabolic, and ecological properties unique to dMMR and pMMR CRC. This approach could critically improve our ability to define, predict, prevent, and treat colorectal cancers. Electronic supplementary material The online version of this article (10.1186/s13073-018-0586-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vanessa L Hale
- Department of Veterinary Preventive Medicine, The Ohio State University College of Veterinary Medicine, Columbus, OH, USA.,Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Patricio Jeraldo
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Jun Chen
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Janet Yao
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Gary Keeney
- Division of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kelly Lyke
- Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Jason Ridlon
- Carl R. Woese Institute for Genomic Biology, Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - Bryan A White
- Carl R. Woese Institute for Genomic Biology, Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - Amy J French
- Division of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Stephen N Thibodeau
- Division of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Christian Diener
- Human Systems Biology Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico.,Coordinación de la Investigación Científica, Red de Apoyo a la Investigación, UNAM, Mexico City, Mexico
| | - Jaime Gransee
- Mayo Clinic Metabolomics Core Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Tumpa Dutta
- Mayo Clinic Metabolomics Core Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Xuan-Mai Petterson
- Mayo Clinic Metabolomics Core Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Jaeyun Sung
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Lisa Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - David Larson
- Division of Colon and Rectal Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Heidi Nelson
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Colon and Rectal Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA. .,Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, MN, USA.
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35
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Burns MB, Montassier E, Abrahante J, Priya S, Niccum DE, Khoruts A, Starr TK, Knights D, Blekhman R. Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PLoS Genet 2018; 14:e1007376. [PMID: 29924794 PMCID: PMC6028121 DOI: 10.1371/journal.pgen.1007376] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/02/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023] Open
Abstract
Variation in the gut microbiome has been linked to colorectal cancer (CRC), as well as to host genetic variation. However, we do not know whether, in addition to baseline host genetics, somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome, and if so, whether these changes can be used to understand microbe-host interactions with potential functional biological relevance. Here, we characterized the association between CRC microbial communities and tumor mutations using microbiome profiling and whole-exome sequencing in 44 pairs of tumors and matched normal tissues. We found statistically significant associations between loss-of-function mutations in tumor genes and shifts in the abundances of specific sets of bacterial taxa, suggestive of potential functional interaction. This correlation allows us to statistically predict interactions between loss-of-function tumor mutations in cancer-related genes and pathways, including MAPK and Wnt signaling, solely based on the composition of the microbiome. In conclusion, our study shows that CRC microbiomes are correlated with tumor mutational profiles, pointing towards possible mechanisms of molecular interaction.
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Affiliation(s)
- Michael B. Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- Department of Biology, Loyola University Chicago, Chicago, Illinois, United States of America
- * E-mail: (MBB); (RB)
| | - Emmanuel Montassier
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- MiHAR lab, Université de Nantes, 44000 Nantes, France
| | - Juan Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Sambhawa Priya
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - David E. Niccum
- Department of Medicine, Division of Gastroenterology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alexander Khoruts
- Department of Medicine, Division of Gastroenterology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Timothy K. Starr
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail: (MBB); (RB)
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36
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Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE, Cabana F, Johnson TJ. The gut microbiome of nonhuman primates: Lessons in ecology and evolution. Am J Primatol 2018; 80:e22867. [PMID: 29862519 DOI: 10.1002/ajp.22867] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 03/23/2018] [Accepted: 04/20/2018] [Indexed: 02/06/2023]
Abstract
The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa. Finally, we highlight how studying the gut microbiome offers new insights into primate nutrition, physiology, and immune system function, as well as enhances our understanding of primate ecology and evolution. Microbiome approaches are useful tools for studying relevant issues in primate ecology. Further study of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health.
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Affiliation(s)
- Jonathan B Clayton
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota.,GreenViet Biodiversity Conservation Center, Son Tra District, Danang, Vietnam.,Primate Microbiome Project, Minneapolis, Minnesota
| | - Andres Gomez
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Animal Science, University of Minnesota, St Paul, Minnesota
| | - Katherine Amato
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Anthropology, Northwestern University, Evanston, Illinois
| | - Dan Knights
- Primate Microbiome Project, Minneapolis, Minnesota.,Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Dominic A Travis
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Ran Blekhman
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Falcon Heights, Minnesota
| | - Rob Knight
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Computer Science & Engineering, UC San Diego, La Jolla, California.,Department of Pediatrics, UC San Diego, La Jolla, California.,Center for Microbiome Innovation, UC San Diego, La Jolla, California
| | - Steven Leigh
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Anthropology, University of Colorado Boulder, Boulder, Colorado.,C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois
| | - Rebecca Stumpf
- Primate Microbiome Project, Minneapolis, Minnesota.,C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois.,Department of Anthropology, University of Illinois, Urbana, Illinois
| | - Tiffany Wolf
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Kenneth E Glander
- Primate Microbiome Project, Minneapolis, Minnesota.,Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Francis Cabana
- Primate Microbiome Project, Minneapolis, Minnesota.,Wildlife Nutrition Centre, Wildlife Reserves Singapore, Singapore
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota.,Primate Microbiome Project, Minneapolis, Minnesota.,University of Minnesota, Mid-Central Research and Outreach Center, Willmar, Minnesota
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37
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Gomez A, Torralba M, Nelson KE, Stumpf R, Blekhman R, Petrzelkova K. Host microbe interactions in the primate gut: Implications for human origins. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.101.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Andres Gomez
- Department of Animal ScienceUniversity of MinnesotaSt PaulMN
| | - Manlito Torralba
- Human Biology, Genomic MedicineJ. Craig Venter InstituteLa JollaCA
| | - Karen E. Nelson
- Human Biology, Genomic MedicineJ. Craig Venter InstituteLa JollaCA
| | - Rebecca Stumpf
- Department of AnthropologyCarl R. Woese Institute for Genomic BiologyUniversity of IllinoisUrbanaIL
| | - Ran Blekhman
- Molecular and Cell BiologyUniversity of MinnesotaMinneapolisMN
| | - Klara Petrzelkova
- Institute of Vertebrate BiologyCzech Academy of SciencesBrnoCzech Republic
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38
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Affiliation(s)
- Andres Gomez
- Department of Animal Science, University of Minnesota, St Paul, MN
| | - Manlito Torralba
- Human Biology, Genomic Medicine, J. Craig Venter Institute, La Jolla, CA
| | - Karen E. Nelson
- Human Biology, Genomic Medicine, J. Craig Venter Institute, La Jolla, CA
| | - Rebecca Stumpf
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL
| | - Ran Blekhman
- Molecular and Cell Biology, University of Minnesota, Minneapolis, MN
| | - Klara Petrzelkova
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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39
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Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Mol Biol Evol 2017; 34:2704-2715. [PMID: 28957509 PMCID: PMC5850612 DOI: 10.1093/molbev/msx206] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
One of the most abundant proteins in human saliva, mucin-7, is encoded by the MUC7 gene, which harbors copy number variable subexonic repeats (PTS-repeats) that affect the size and glycosylation potential of this protein. We recently documented the adaptive evolution of MUC7 subexonic copy number variation among primates. Yet, the evolution of MUC7 genetic variation in humans remained unexplored. Here, we found that PTS-repeat copy number variation has evolved recurrently in the human lineage, thereby generating multiple haplotypic backgrounds carrying five or six PTS-repeat copy number alleles. Contrary to previous studies, we found no associations between the copy number of PTS-repeats and protection against asthma. Instead, we revealed a significant association of MUC7 haplotypic variation with the composition of the oral microbiome. Furthermore, based on in-depth simulations, we conclude that a divergent MUC7 haplotype likely originated in an unknown African hominin population and introgressed into ancestors of modern Africans.
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Affiliation(s)
- Duo Xu
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Pavlos Pavlidis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
| | - Recep Ozgur Taskent
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Nikolaos Alachiotis
- Institute of Computer Science (ICS), Foundation for Research and Technology - Hellas, Heraklion, Crete, Greece
| | - Colin Flanagan
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
| | - Michael DeGiorgio
- Department of Biology and the Institute for CyberScience, Pennsylvania State University, University Park, PA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY
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40
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Eaaswarkhanth M, Xu D, Flanagan C, Rzhetskaya M, Hayes MG, Blekhman R, Jablonski NG, Gokcumen O. Atopic Dermatitis Susceptibility Variants in Filaggrin Hitchhike Hornerin Selective Sweep. Genome Biol Evol 2016; 8:3240-3255. [PMID: 27678121 PMCID: PMC5174745 DOI: 10.1093/gbe/evw242] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human skin has evolved rapidly, leaving evolutionary signatures in the genome. The filaggrin (FLG) gene is widely studied for its skin-barrier function in humans. The extensive genetic variation in this gene, especially common loss-of-function (LoF) mutations, has been established as primary risk factors for atopic dermatitis. To investigate the evolution of this gene, we analyzed 2,504 human genomes and genotyped the copy number variation of filaggrin repeats within FLG in 126 individuals from diverse ancestral backgrounds. We were unable to replicate a recent study claiming that LoF of FLG is adaptive in northern latitudes with lower ultraviolet light exposure. Instead, we present multiple lines of evidence suggesting that FLG genetic variation, including LoF variants, have little or no effect on fitness in modern humans. Haplotype-level scrutinization of the locus revealed signatures of a recent selective sweep in Asia, which increased the allele frequency of a haplotype group (Huxian haplogroup) in Asian populations. Functionally, we found that the Huxian haplogroup carries dozens of functional variants in FLG and hornerin (HRNR) genes, including those that are associated with atopic dermatitis susceptibility, HRNR expression levels and microbiome diversity on the skin. Our results suggest that the target of the adaptive sweep is HRNR gene function, and the functional FLG variants that involve susceptibility to atopic dermatitis, seem to hitchhike the selective sweep on HRNR. Our study presents a novel case of a locus that harbors clinically relevant common genetic variation with complex evolutionary trajectories.
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Affiliation(s)
- Muthukrishnan Eaaswarkhanth
- Department of Biological Sciences, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY
| | - Duo Xu
- Department of Biological Sciences, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY
| | - Colin Flanagan
- Department of Biological Sciences, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY
| | - Margarita Rzhetskaya
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN
| | - Nina G Jablonski
- Department of Anthropology, Pennsylvania State University, University Park, PA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York at Buffalo, Buffalo, NY
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41
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Xu D, Pavlidis P, Thamadilok S, Redwood E, Fox S, Blekhman R, Ruhl S, Gokcumen O. Recent evolution of the salivary mucin MUC7. Sci Rep 2016; 6:31791. [PMID: 27558399 PMCID: PMC4997351 DOI: 10.1038/srep31791] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/26/2016] [Indexed: 11/23/2022] Open
Abstract
Genomic structural variants constitute the majority of variable base pairs in primate genomes and affect gene function in multiple ways. While whole gene duplications and deletions are relatively well-studied, the biology of subexonic (i.e., within coding exon sequences), copy number variation remains elusive. The salivary MUC7 gene provides an opportunity for studying such variation, as it harbors copy number variable subexonic repeat sequences that encode for densely O-glycosylated domains (PTS-repeats) with microbe-binding properties. To understand the evolution of this gene, we analyzed mammalian and primate genomes within a comparative framework. Our analyses revealed that (i) MUC7 has emerged in the placental mammal ancestor and rapidly gained multiple sites for O-glycosylation; (ii) MUC7 has retained its extracellular activity in saliva in placental mammals; (iii) the anti-fungal domain of the protein was remodified under positive selection in the primate lineage; and (iv) MUC7 PTS-repeats have evolved recurrently and under adaptive constraints. Our results establish MUC7 as a major player in salivary adaptation, likely as a response to diverse pathogenic exposure in primates. On a broader scale, our study highlights variable subexonic repeats as a primary source for modular evolutionary innovation that lead to rapid functional adaptation.
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Affiliation(s)
- Duo Xu
- Department of Biological Sciences, State University of New York at Buffalo, New York 14260, USA
| | - Pavlos Pavlidis
- Institute of Computer Science (ICS), Foundation of Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Supaporn Thamadilok
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, New York 14214, USA
| | - Emilie Redwood
- Department of Biological Sciences, State University of New York at Buffalo, New York 14260, USA
| | - Sara Fox
- Department of Biological Sciences, State University of New York at Buffalo, New York 14260, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minnesota 55455, USA
| | - Stefan Ruhl
- Department of Oral Biology, School of Dental Medicine, State University of New York at Buffalo, New York 14214, USA
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, New York 14260, USA
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42
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Blekhman R, Tang K, Archie EA, Barreiro LB, Johnson ZP, Wilson ME, Kohn J, Yuan ML, Gesquiere L, Grieneisen LE, Tung J. Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Sci Rep 2016; 6:31519. [PMID: 27528013 PMCID: PMC4985740 DOI: 10.1038/srep31519] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/20/2016] [Indexed: 02/01/2023] Open
Abstract
Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples—unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.
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Affiliation(s)
- Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55108, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55108, USA
| | - Karen Tang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55108, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55108, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 45665, USA.,Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya
| | - Luis B Barreiro
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Quebec, H3T 1C5 Canada
| | - Zachary P Johnson
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Mark E Wilson
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Jordan Kohn
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Michael L Yuan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | | | - Laura E Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 45665, USA
| | - Jenny Tung
- Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Department of Biology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham NC 27708, USA
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43
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Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umaña JD, Carbonero F, Gaskins HR, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R. Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns. Cell Rep 2016; 14:2142-2153. [PMID: 26923597 DOI: 10.1016/j.celrep.2016.02.013] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 12/07/2015] [Accepted: 01/28/2016] [Indexed: 12/20/2022] Open
Abstract
To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.
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Affiliation(s)
- Andres Gomez
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno 603 65, Czech Republic; Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Liberec Zoo, Liberec 460 01, Czech Republic
| | - Michael B Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | - Klara Vlckova
- Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
| | - David Modry
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic; CEITEC, Central European Institute for Technology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
| | - Angelique Todd
- Dzanga-Sangha Protected Areas, World Wildlife Fund, Bayanga, Central African Republic
| | | | - Melissa J Remis
- Department of Anthropology, Purdue University, West Lafayette, IN 47907, USA
| | | | - Elise Morton
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA
| | - Juan D Umaña
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AK 72704, USA
| | - H Rex Gaskins
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Brenda A Wilson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rebecca M Stumpf
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bryan A White
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steven R Leigh
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Colorado, Boulder, CO 80309, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
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Gomez A, Rothman JM, Petrzelkova K, Yeoman CJ, Vlckova K, Umaña JD, Carr M, Modry D, Todd A, Torralba M, Nelson KE, Stumpf RM, Wilson BA, Blekhman R, White BA, Leigh SR. Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp. ISME J 2016; 10:514-26. [PMID: 26315972 PMCID: PMC4737941 DOI: 10.1038/ismej.2015.146] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 07/07/2015] [Accepted: 07/14/2015] [Indexed: 11/09/2022]
Abstract
Although the critical role that our gastrointestinal microbes play in host physiology is now well established, we know little about the factors that influenced the evolution of primate gut microbiomes. To further understand current gut microbiome configurations and diet-microbe co-metabolic fingerprints in primates, from an evolutionary perspective, we characterized fecal bacterial communities and metabolomic profiles in 228 fecal samples of lowland and mountain gorillas (G. g. gorilla and G. b. beringei, respectively), our closest evolutionary relatives after chimpanzees. Our results demonstrate that the gut microbiomes and metabolomes of these two species exhibit significantly different patterns. This is supported by increased abundance of metabolites and bacterial taxa associated with fiber metabolism in mountain gorillas, and enrichment of markers associated with simple sugar, lipid and sterol turnover in the lowland species. However, longitudinal sampling shows that both species' microbiomes and metabolomes converge when hosts face similar dietary constraints, associated with low fruit availability in their habitats. By showing differences and convergence of diet-microbe co-metabolic fingerprints in two geographically isolated primate species, under specific dietary stimuli, we suggest that dietary constraints triggered during their adaptive radiation were potential factors behind the species-specific microbiome patterns observed in primates today.
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Affiliation(s)
- Andres Gomez
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of CUNY, New York, NY, USA
- New York Consortium in Evolutionary Primatology (NYCEP), New York, NY, USA
| | - Klara Petrzelkova
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Biology Centre, Institute of Parasitology, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic
- Liberec Zoo, Liberec, Czech Republic
| | - Carl J Yeoman
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, USA
| | - Klara Vlckova
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic
| | - Juan D Umaña
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - Monica Carr
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - David Modry
- Biology Centre, Institute of Parasitology, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Czech Republic
- CEITEC, Central European Institute for Technology, Brno, Czech Republic
| | - Angelique Todd
- World Wildlife Fund, Dzanga-Sangha Protected Areas, Bayanga, Central African Republic
| | | | | | - Rebecca M Stumpf
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
- Department of Anthropology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - Brenda A Wilson
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
- Department of Microbiology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota Twin Cities, St Paul, MN, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota Twin Cities, St Paul, MN, USA
| | - Bryan A White
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Champaign, IL, USA
| | - Steven R Leigh
- Department of Animal Sciences, Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
- Department of Anthropology, University of Illinois at Urbana–Champaign, Champaign, IL, USA
- Department of Anthropology, University of Colorado, Boulder, CO, USA
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Morton ER, Lynch J, Froment A, Lafosse S, Heyer E, Przeworski M, Blekhman R, Ségurel L. Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence. PLoS Genet 2015; 11:e1005658. [PMID: 26619199 PMCID: PMC4664238 DOI: 10.1371/journal.pgen.1005658] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/19/2015] [Indexed: 12/18/2022] Open
Abstract
The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite Entamoeba is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing Entamoeba absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.
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Affiliation(s)
- Elise R. Morton
- Department of Genetics, Cell Biology, and Development, Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Joshua Lynch
- Department of Genetics, Cell Biology, and Development, Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alain Froment
- Eco-anthropology and Ethnobiology, Museum national d'Histoire naturelle, Centre national de la recherche scientifique, University Denis Diderot, Paris, France
| | - Sophie Lafosse
- Eco-anthropology and Ethnobiology, Museum national d'Histoire naturelle, Centre national de la recherche scientifique, University Denis Diderot, Paris, France
| | - Evelyne Heyer
- Eco-anthropology and Ethnobiology, Museum national d'Histoire naturelle, Centre national de la recherche scientifique, University Denis Diderot, Paris, France
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Laure Ségurel
- Eco-anthropology and Ethnobiology, Museum national d'Histoire naturelle, Centre national de la recherche scientifique, University Denis Diderot, Paris, France
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Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG. Host genetic variation impacts microbiome composition across human body sites. Genome Biol 2015; 16:191. [PMID: 26374288 PMCID: PMC4570153 DOI: 10.1186/s13059-015-0759-1] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/24/2015] [Indexed: 12/21/2022] Open
Abstract
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.
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Affiliation(s)
- 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, St. Paul, MN, 55108, USA.
| | - Julia K Goodrich
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Katherine Huang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Robert Bukowski
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College, London, UK
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College, London, UK
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Current address: Janssen Human Microbiome Institute, Janssen Research and Development, Cambridge, MA, 02142, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
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Abstract
Background The human gut microbiome is associated with the development of colon cancer, and recent studies have found changes in the microbiome in cancer patients compared to healthy controls. Studying the microbial communities in the tumor microenvironment may shed light on the role of host–bacteria interactions in colorectal cancer. Here, we highlight the major shifts in the colorectal tumor microbiome relative to that of matched normal colon tissue from the same individual, allowing us to survey the microbial communities in the tumor microenvironment and providing intrinsic control for environmental and host genetic effects on the microbiome. Methods We sequenced the microbiome in 44 primary tumor and 44 patient-matched normal colon tissue samples to determine differentially abundant microbial taxa These data were also used to functionally characterize the microbiome of the cancer and normal sample pairs and identify functional pathways enriched in the tumor-associated microbiota. Results We find that tumors harbor distinct microbial communities compared to nearby healthy tissue. Our results show increased microbial diversity in the tumor microenvironment, with changes in the abundances of commensal and pathogenic bacterial taxa, including Fusobacterium and Providencia. While Fusobacterium has previously been implicated in colorectal cancer, Providencia is a novel tumor-associated agent which has not been identified in previous studies. Additionally, we identified a clear, significant enrichment of predicted virulence-associated genes in the colorectal cancer microenvironment, likely dependent upon the genomes of Fusobacterium and Providencia. Conclusions This work identifies bacterial taxa significantly correlated with colorectal cancer, including a novel finding of an elevated abundance of Providencia in the tumor microenvironment. We also describe the predicted metabolic pathways and enzymes differentially present in the tumor-associated microbiome, and show an enrichment of virulence-associated bacterial genes in the tumor microenvironment. This predicted virulence enrichment supports the hypothesis that the microbiome plays an active role in colorectal cancer development and/or progression. Our results provide a starting point for future prognostic and therapeutic research with the potential to improve patient outcomes. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0177-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael B Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
| | - Joshua Lynch
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
| | - Timothy K Starr
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA ; Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN USA ; Biotechnology Institute, University of Minnesota, Minneapolis, MN USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN USA ; Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN USA
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48
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Yu F, Lu J, Liu X, Gazave E, Chang D, Raj S, Hunter-Zinck H, Blekhman R, Arbiza L, Van Hout C, Morrison A, Johnson AD, Bis J, Cupples LA, Psaty BM, Muzny D, Yu J, Gibbs RA, Keinan A, Clark AG, Boerwinkle E. Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions. PLoS One 2015; 10:e0121644. [PMID: 25807536 PMCID: PMC4373932 DOI: 10.1371/journal.pone.0121644] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/14/2014] [Indexed: 12/13/2022] Open
Abstract
Whole genome analysis in large samples from a single population is needed to provide adequate power to assess relative strengths of natural selection across different functional components of the genome. In this study, we analyzed next-generation sequencing data from 962 European Americans, and found that as expected approximately 60% of the top 1% of positive selection signals lie in intergenic regions, 33% in intronic regions, and slightly over 1% in coding regions. Several detailed functional annotation categories in intergenic regions showed statistically significant enrichment in positively selected loci when compared to the null distribution of the genomic span of ENCODE categories. There was a significant enrichment of purifying selection signals detected in enhancers, transcription factor binding sites, microRNAs and target sites, but not on lincRNA or piRNAs, suggesting different evolutionary constraints for these domains. Loci in “repressed or low activity regions” and loci near or overlapping the transcription start site were the most significantly over-represented annotations among the top 1% of signals for positive selection.
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Affiliation(s)
- Fuli Yu
- Human Genome Sequencing Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, United States of America
- Institute of Neurology, Tianjin Medical University General Hospital, Tianjin, China
- * E-mail: (FY); (EB)
| | - Jian Lu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
- College of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaoming Liu
- Human Genetic Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Elodie Gazave
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Diana Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Srilakshmi Raj
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Haley Hunter-Zinck
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Ran Blekhman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Leonardo Arbiza
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Cris Van Hout
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Alanna Morrison
- Human Genetic Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Andrew D. Johnson
- National Heart, Lung and Blood Institute (NHLBI) Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Joshua Bis
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, Washington, United States of America
| | - L. Adrienne Cupples
- National Heart, Lung and Blood Institute (NHLBI) Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, Washington, United States of America
| | - Donna Muzny
- Human Genome Sequencing Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jin Yu
- Human Genome Sequencing Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alon Keinan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, New York, United States of America
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genetic Center, University of Texas Health Science Center, Houston, Texas, United States of America
- * E-mail: (FY); (EB)
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Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, Ley RE. Human genetics shape the gut microbiome. Cell 2015; 159:789-99. [PMID: 25417156 DOI: 10.1016/j.cell.2014.09.053] [Citation(s) in RCA: 1942] [Impact Index Per Article: 215.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 07/10/2014] [Accepted: 09/24/2014] [Indexed: 12/13/2022]
Abstract
Host genetics and the gut microbiome can both influence metabolic phenotypes. However, whether host genetic variation shapes the gut microbiome and interacts with it to affect host phenotype is unclear. Here, we compared microbiotas across >1,000 fecal samples obtained from the TwinsUK population, including 416 twin pairs. We identified many microbial taxa whose abundances were influenced by host genetics. The most heritable taxon, the family Christensenellaceae, formed a co-occurrence network with other heritable Bacteria and with methanogenic Archaea. Furthermore, Christensenellaceae and its partners were enriched in individuals with low body mass index (BMI). An obese-associated microbiome was amended with Christensenella minuta, a cultured member of the Christensenellaceae, and transplanted to germ-free mice. C. minuta amendment reduced weight gain and altered the microbiome of recipient mice. Our findings indicate that host genetics influence the composition of the human gut microbiome and can do so in ways that impact host metabolism.
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Affiliation(s)
- Julia K Goodrich
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Jillian L Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Angela C Poole
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Jessica L Sutter
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Omry Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Ran Blekhman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michelle Beaumont
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - William Van Treuren
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA; Biofrontiers Institute, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Microbiology, Cornell University, Ithaca, NY 14853, USA.
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50
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Tung J, Barreiro LB, Burns MB, Grenier JC, Lynch J, Grieneisen LE, Altmann J, Alberts SC, Blekhman R, Archie EA. Social networks predict gut microbiome composition in wild baboons. eLife 2015; 4. [PMID: 25774601 PMCID: PMC4379495 DOI: 10.7554/elife.05224] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/27/2015] [Indexed: 12/31/2022] Open
Abstract
Social relationships have profound effects on health in humans and other primates, but the mechanisms that explain this relationship are not well understood. Using shotgun metagenomic data from wild baboons, we found that social group membership and social network relationships predicted both the taxonomic structure of the gut microbiome and the structure of genes encoded by gut microbial species. Rates of interaction directly explained variation in the gut microbiome, even after controlling for diet, kinship, and shared environments. They therefore strongly implicate direct physical contact among social partners in the transmission of gut microbial species. We identified 51 socially structured taxa, which were significantly enriched for anaerobic and non-spore-forming lifestyles. Our results argue that social interactions are an important determinant of gut microbiome composition in natural animal populations-a relationship with important ramifications for understanding how social relationships influence health, as well as the evolution of group living.
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Affiliation(s)
- Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, United States
| | - Luis B Barreiro
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
| | - Michael B Burns
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Jean-Christophe Grenier
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Canada
| | - Josh Lynch
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Laura E Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, United States
| | - Jeanne Altmann
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, United States
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Elizabeth A Archie
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
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