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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe 2024; 32:739-754.e4. [PMID: 38565143 PMCID: PMC11081829 DOI: 10.1016/j.chom.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/06/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA
| | - Andrew J Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA.
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Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.06.561241. [PMID: 37873088 PMCID: PMC10592638 DOI: 10.1101/2023.10.06.561241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to insertion "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain level variation within the microbiota impacts human health.
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Affiliation(s)
- Joshua M. Kirsch
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
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Lea AJ, Clark AG, Dahl AW, Devinsky O, Garcia AR, Golden CD, Kamau J, Kraft TS, Lim YAL, Martins DJ, Mogoi D, Pajukanta P, Perry GH, Pontzer H, Trumble BC, Urlacher SS, Venkataraman VV, Wallace IJ, Gurven M, Lieberman DE, Ayroles JF. Applying an evolutionary mismatch framework to understand disease susceptibility. PLoS Biol 2023; 21:e3002311. [PMID: 37695771 PMCID: PMC10513379 DOI: 10.1371/journal.pbio.3002311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/21/2023] [Indexed: 09/13/2023] Open
Abstract
Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.
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Affiliation(s)
- Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Andrew G. Clark
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, New York, United States of America
| | - Andrew W. Dahl
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Orrin Devinsky
- Department of Neurology, NYU Langone Comprehensive Epilepsy Center, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Angela R. Garcia
- Department of Anthropology, Stanford University, Stanford, California, United States of America
| | - Christopher D. Golden
- Department of Nutrition, Harvard T H Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joseph Kamau
- One Health Centre, Institute of Primate Research, Karen, Nairobi, Kenya
| | - Thomas S. Kraft
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Yvonne A. L. Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Dino J. Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, New York, United States of America
| | - Donald Mogoi
- Department of Medical Services and Public Health, Ministry of Health Laikipia County, Nanyuki, Kenya
| | - Päivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, California, United States of America
| | - George H. Perry
- Departments of Anthropology and Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Herman Pontzer
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - Benjamin C. Trumble
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, United States of America
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Samuel S. Urlacher
- Department of Anthropology, Baylor University, Waco, Texas, United States of America
| | - Vivek V. Venkataraman
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Ian J. Wallace
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Michael Gurven
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Daniel E. Lieberman
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Julien F. Ayroles
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
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Lea AJ, Clark AG, Dahl AW, Devinsky O, Garcia AR, Golden CD, Kamau J, Kraft TS, Lim YAL, Martins D, Mogoi D, Pajukanta P, Perry G, Pontzer H, Trumble BC, Urlacher SS, Venkataraman VV, Wallace IJ, Gurven M, Lieberman D, Ayroles JF. Evolutionary mismatch and the role of GxE interactions in human disease. ARXIV 2023:arXiv:2301.05255v2. [PMID: 36713247 PMCID: PMC9882586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases that were rare throughout human history but are now common. A key idea from anthropology and evolutionary biology-the evolutionary mismatch hypothesis-seeks to explain this phenomenon. It posits that humans evolved in environments that radically differ from the ones experienced by most people today, and thus traits that were advantageous in past environments may now be "mismatched" and disease-causing. This hypothesis is, at its core, a genetic one: it predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions and have differential health effects in ancestral versus modern environments. Here, we discuss how this concept could be leveraged to uncover the genetic architecture of NCDs in a principled way. Specifically, we advocate for partnering with small-scale, subsistence-level groups that are currently transitioning from environments that are arguably more "matched" with their recent evolutionary history to those that are more "mismatched". These populations provide diverse genetic backgrounds as well as the needed levels and types of environmental variation necessary for mapping GxE interactions in an explicit mismatch framework. Such work would make important contributions to our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and sociocultural contexts.
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Affiliation(s)
- Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Child and Brain Development, Canadian Institute for Advanced Research, Toronto, Canada
| | - Andrew G. Clark
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Andrew W. Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Orrin Devinsky
- Department of Neurology, NYU Langone Medical Center, New York, NY, USA
- Comprehensive Epilepsy Center, NYU Langone Medical Center, New York, NY, USA
| | - Angela R. Garcia
- Center for Evolution and Medicine, Arizona State University, Tempe, United States
| | | | - Joseph Kamau
- Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - Thomas S. Kraft
- Department of Anthropology, University of Utah, Salt Lake City, USA
| | - Yvonne A. L. Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Dino Martins
- Turkana Basin Research Institute, Turkana, Kenya
- Department of Ecology and Evolution, Princeton University, Princeton, NJ, USA
| | - Donald Mogoi
- Director at County Government of Laikipia, Nanyuki, Kenya
| | - Paivi Pajukanta
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Institute for Precision Health, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - George Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Herman Pontzer
- Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Benjamin C. Trumble
- School of Human Evolution and Social Change, Arizona State University, Tempe, US
- Center for Evolution and Medicine, Arizona State University, Tempe, United States
| | - Samuel S. Urlacher
- Department of Anthropology, Baylor University, Waco, TX, USA
- Child and Brain Development, Canadian Institute for Advanced Research, Toronto, Canada
| | | | - Ian J. Wallace
- Department of Anthropology, University of New Mexico, Albuquerque, USA
| | - Michael Gurven
- Department of Anthropology, University of California: Santa Barbara, Santa Barbara, CA, USA
| | - Daniel Lieberman
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Julien F. Ayroles
- Department of Ecology and Evolution, Princeton University, Princeton, NJ, USA
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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Prasoodanan P K V, Sharma AK, Mahajan S, Dhakan DB, Maji A, Scaria J, Sharma VK. Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth-gut axis. NPJ Biofilms Microbiomes 2021; 7:77. [PMID: 34620880 PMCID: PMC8497558 DOI: 10.1038/s41522-021-00248-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/09/2021] [Indexed: 01/22/2023] Open
Abstract
The abundance and diversity of host-associated Prevotella species have a profound impact on human health. To investigate the composition, diversity, and functional roles of Prevotella in the human gut, a population-wide analysis was carried out on 586 healthy samples from western and non-western populations including the largest Indian cohort comprising of 200 samples, and 189 Inflammatory Bowel Disease samples from western populations. A higher abundance and diversity of Prevotella copri species enriched in complex plant polysaccharides metabolizing enzymes, particularly pullulanase containing polysaccharide-utilization-loci (PUL), were found in Indian and non-western populations. A higher diversity of oral inflammations-associated Prevotella species and an enrichment of virulence factors and antibiotic resistance genes in the gut microbiome of western populations speculates an existence of a mouth-gut axis. The study revealed the landscape of Prevotella composition in the human gut microbiome and its impact on health in western and non-western populations.
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Affiliation(s)
- Vishnu Prasoodanan P K
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Ashok K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
- Department of Animal Science, Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN, 55455, USA
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Darshan B Dhakan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
- Behaviour and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Lisboa, Portugal
| | - Abhijit Maji
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
- Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, SD, 57007, USA
| | - Joy Scaria
- Animal Disease Research & Diagnostic Laboratory, South Dakota State University, Brookings, SD, 57007, USA
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India.
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Annapragada A, Brook CE, Luskin MS, Rahariniaina RP, Helin M, Razafinarivo O, Ambinintsoa Ralaiarison R, Randriamady HJ, Olson LE, Goodman SM, Golden CD. Evaluation of tenrec population viability and potential sustainable management under hunting pressure in northeastern Madagascar. Anim Conserv 2021. [DOI: 10.1111/acv.12714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- A. Annapragada
- Harvard John A. Paulson School of Engineering and Applied Sciences Cambridge MA 02138 USA
| | - C. E. Brook
- Department of Integrative Biology University of California Berkeley, Berkeley CA 94720 USA
| | - M. S. Luskin
- School of Biological Sciences The University of Queensland St Lucia, Brisbane QLD 4072 Australia
| | - R. P. Rahariniaina
- Madagascar Health and Environmental Research (MAHERY) Maroantsetra 512 Madagascar
| | - M. Helin
- Madagascar Health and Environmental Research (MAHERY) Maroantsetra 512 Madagascar
| | - O. Razafinarivo
- Madagascar Health and Environmental Research (MAHERY) Maroantsetra 512 Madagascar
| | | | - H. J. Randriamady
- Madagascar Health and Environmental Research (MAHERY) Maroantsetra 512 Madagascar
- Department of Nutrition Harvard TH Chan School of Public Health Boston MA 02115 USA
| | - L. E. Olson
- University of Alaska Museum 1962 Yukon Drive Fairbanks AK 99775 USA
- Field Museum of Natural History 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - S. M. Goodman
- Field Museum of Natural History 1400 South Lake Shore Drive Chicago IL 60605 USA
- Association Vahatra BP 3972 Antananarivo 101 Madagascar
| | - C. D. Golden
- Madagascar Health and Environmental Research (MAHERY) Maroantsetra 512 Madagascar
- Department of Nutrition Harvard TH Chan School of Public Health Boston MA 02115 USA
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Rice BL, Golden CD, Randriamady HJ, Rakotomalala AANA, Vonona MA, Anjaranirina EJG, Hazen J, Castro MC, Metcalf CJE, Hartl DL. Fine-scale variation in malaria prevalence across ecological regions in Madagascar: a cross-sectional study. BMC Public Health 2021; 21:1018. [PMID: 34051786 PMCID: PMC8164762 DOI: 10.1186/s12889-021-11090-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/10/2021] [Indexed: 11/23/2022] Open
Abstract
Background Large-scale variation in ecological parameters across Madagascar is hypothesized to drive varying spatial patterns of malaria infection. However, to date, few studies of parasite prevalence with resolution at finer, sub-regional spatial scales are available. As a result, there is a poor understanding of how Madagascar’s diverse local ecologies link with variation in the distribution of infections at the community and household level. Efforts to preserve Madagascar’s ecological diversity often focus on improving livelihoods in rural communities near remaining forested areas but are limited by a lack of data on their infectious disease burden. Methods To investigate spatial variation in malaria prevalence at the sub-regional scale in Madagascar, we sampled 1476 households (7117 total individuals, all ages) from 31 rural communities divided among five ecologically distinct regions. The sampled regions range from tropical rainforest to semi-arid, spiny forest and include communities near protected areas including the Masoala, Makira, and Mikea forests. Malaria prevalence was estimated by rapid diagnostic test (RDT) cross-sectional surveys performed during malaria transmission seasons over 2013–2017. Results Indicative of localized hotspots, malaria prevalence varied more than 10-fold between nearby (< 50 km) communities in some cases. Prevalence was highest on average in the west coast region (Morombe district, average community prevalence 29.4%), situated near protected dry deciduous forest habitat. At the household level, communities in southeast Madagascar (Mananjary district) were observed with over 50% of households containing multiple infected individuals at the time of sampling. From simulations accounting for variation in household size and prevalence at the community level, we observed a significant excess of households with multiple infections in rural communities in southwest and southeast Madagascar, suggesting variation in risk within communities. Conclusions Our data suggest that the malaria infection burden experienced by rural communities in Madagascar varies greatly at smaller spatial scales (i.e., at the community and household level) and that the southeast and west coast ecological regions warrant further attention from disease control efforts. Conservation and development efforts in these regions may benefit from consideration of the high, and variable, malaria prevalences among communities in these areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-021-11090-3.
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Affiliation(s)
- Benjamin L Rice
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA. .,Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar. .,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Christopher D Golden
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar.,Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Hervet J Randriamady
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar.,Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Anjaharinony Andry Ny Aina Rakotomalala
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar.,Department of Entomology, University of Antananarivo, Antananarivo, Madagascar
| | | | | | - James Hazen
- Catholic Relief Services (CRS) Madagascar, Antananarivo, Madagascar
| | - Marcia C Castro
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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Golden CD, Rice BL, Randriamady HJ, Vonona AM, Randrianasolo JF, Tafangy AN, Andrianantenaina MY, Arisco NJ, Emile GN, Lainandrasana F, Mahonjolaza RFF, Raelson HP, Rakotoarilalao VR, Rakotomalala AANA, Rasamison AD, Mahery R, Tantely ML, Girod R, Annapragada A, Wesolowski A, Winter A, Hartl DL, Hazen J, Metcalf CJE. Study Protocol: A Cross-Sectional Examination of Socio-Demographic and Ecological Determinants of Nutrition and Disease Across Madagascar. Front Public Health 2020; 8:500. [PMID: 33042943 PMCID: PMC7527467 DOI: 10.3389/fpubh.2020.00500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/04/2020] [Indexed: 11/13/2022] Open
Abstract
Madagascar has experienced significant environmental change since 1960, particularly through forest clearing for agricultural expansion. Climatic patterns are undergoing change in Madagascar as well, with increasing temperatures, droughts, and cyclonic activity. The impact of these environmental and climatic changes will pose threats to food availability, income generation, and local ecosystems, with significant potential effects on the spatial and temporal distribution of disease burden. This study seeks to describe the health status of a large sample of geographically and socially diverse Malagasy communities through multiple clinical measurements, detailed social surveys, and paired data on regional variation in local ecologies. With an increased understanding of the current patterns of variation in human health and nutrition, future studies will be better able to identify associations with climate and anticipate and mitigate the burdens expected from larger, longer-term changes. Our mixed-method approach included an observational cross-sectional study. Research subjects were men, women, and children from 1,125 households evenly distributed across 24 communities in four ecologically and socio-demographically distinct regions of Madagascar. For these 1,125 households, all persons of both sexes and all ages therein (for a total of 6,292 individuals) were recruited into the research study and a total of 5,882 individuals were enrolled. Through repeated social survey recalls and focus group meetings, we obtained social and demographic data, including broad categories of seasonal movements, and characterized the fluctuation of income generation, food production and dietary consumption. Through collection of clinical and biological samples for both point-of-care diagnoses and laboratory analyses, we obtained detailed occurrence (and importantly co-occurrence) data on micronutrient nutritional, infectious disease, and non-communicable disease status. Our research highlights the highly variable social, cultural, and environmental contexts of health conditions in Madagascar, and the tremendous inter-regional, inter-community, and intra-community variation in nutritional and disease status. More than 30% of the surveyed population was afflicted by anemia and 14% of the population had a current malaria infection. This type of rich metadata associated with a suite of biological samples and nutritional and disease outcome data should allow disentangling some of the underlying drivers of ill health across the changing landscapes of Madagascar.
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Affiliation(s)
- Christopher D. Golden
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, United States
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA, United States
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar
| | - Benjamin L. Rice
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | | | | | | | | | | | - Nicholas J. Arisco
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Gauthier N. Emile
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar
| | | | | | | | | | | | | | - Rebaliha Mahery
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar
| | - M. Luciano Tantely
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Akshaya Annapragada
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Amy Winter
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - James Hazen
- Madagascar Country Program, Catholic Relief Services, Antananarivo, Madagascar
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, United States
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Annapragada A, Borgerson C, Iams S, Ravelomanantsoa MA, Crawford GC, Helin M, Anjaranirina EJG, Randriamady HJ, Golden CD. Modeling the Impact of Newcastle Disease Virus Vaccinations on Chicken Production Systems in Northeastern Madagascar. Front Vet Sci 2019; 6:305. [PMID: 31612142 PMCID: PMC6775217 DOI: 10.3389/fvets.2019.00305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/28/2019] [Indexed: 11/13/2022] Open
Abstract
Chickens are a key source of nutrition for rural Malagasy communities. Due to high endemic rates of Newcastle disease, it remains challenging to raise sustainable chicken flocks as a consistent food source. Here, we explore the impact of triannual Newcastle disease virus (NDV) vaccine interventions on the growth and herd immunity acquisition of Malagasy chicken flocks. Between 2011 and 2018 we collected longitudinal data to assess the population dynamics of chicken populations in remote Malagasy communities. In 2016, we launched a pilot campaign for vaccination in six rural communities to determine the impacts on chicken survivorship and productivity. We used these data to specify a mathematical model of realistic Malagasy chicken population dynamics under a triannual vaccination regime. The mathematical model represents an extension to conventional SIR models that allows for modeling the impact of specific vaccinations on chicken flock dynamics, rather than estimation of parameters. Understanding chicken population dynamics is important for realizing the potential for domestic chicken flocks to serve as sustainable food sources. The results suggested that vaccination coverage of at least ~40% is necessary over 5+ years to achieve population doubling, while complete herd immunity may not be possible given the short duration of effectiveness of vaccination, and the high levels of births and deaths in the chicken flocks.
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Affiliation(s)
- Akshaya Annapragada
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Cortni Borgerson
- Department of Anthropology, Montclair State University, Montclair, NJ, United States
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar
| | - Sarah Iams
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - M. Ando Ravelomanantsoa
- Departement Production et Partenariat, Institut Malgache des Vaccins Vétérinaires (IMVAVET), Ampandrianomby, Antananarivo, Madagascar
| | | | - Marika Helin
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar
| | | | | | - Christopher D. Golden
- Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, United States
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10
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Golden CD, Borgerson C, Rice BL, Allen LH, Anjaranirina EJG, Barrett CB, Boateng G, Gephart JA, Hampel D, Hartl DL, Knippenberg E, Myers SS, Ralalason DH, Ramihantaniarivo H, Randriamady H, Shahab-Ferdows S, Vaitla B, Volkman SK, Vonona MA. Cohort Description of the Madagascar Health and Environmental Research-Antongil (MAHERY-Antongil) Study in Madagascar. Front Nutr 2019; 6:109. [PMID: 31428615 PMCID: PMC6690017 DOI: 10.3389/fnut.2019.00109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 07/01/2019] [Indexed: 12/19/2022] Open
Abstract
The Madagascar Health and Environmental Research-Antongil (MAHERY-Antongil) study cohort was set up in September 2015 to assess the nutritional value of seafood for the coastal Malagasy population living along Antongil Bay in northeastern Madagascar. Over 28 months of surveillance, we aimed to understand the relationships among different marine resource governance models, local people's fish catch, the consumption of seafood, and nutritional status. In the Antongil Bay, fisheries governance takes three general forms: traditional management, marine national parks, and co-management. Traditional management involves little to no involvement by the national government or non-governmental organizations, and focuses on culturally accepted Malagasy community practices. Co-management and marine national parks involve management support from either an non-govermental organization (NGO) or the national government. Five communities of varying governance strategies were enrolled into the study including 225 households and 1031 individuals whose diets, resource acquisition strategies, fisheries and agricultural practices, and other social, demographic and economic indicators were measured over the span of 3 years. Clinical visits with each individual were conducted at two points during the study to measure disease and nutritional status. By analyzing differences in fish catch arising from variation in governance (in addition to intra-annual seasonal changes and minor inter-annual changes), the project will allow us to calculate the public health value of sustainable fisheries management approaches for local populations. There is hope that coastal zones that are managed sustainably can increase the productivity of fisheries, increasing the catch of seafood products for poor, undernourished populations.
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Affiliation(s)
- Christopher D. Golden
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Madagascar Health and Environmental Research, Maroantsetra, Madagascar
| | - Cortni Borgerson
- Madagascar Health and Environmental Research, Maroantsetra, Madagascar
- Department of Anthropology, Montclair State University, Montclair, NJ, United States
| | - Benjamin L. Rice
- Madagascar Health and Environmental Research, Maroantsetra, Madagascar
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Lindsay H. Allen
- ARS Western Human Nutrition Research Center, United States Department of Agriculture, Davis, CA, United States
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | | | - Christopher B. Barrett
- CH Dyson School of Applied Economics & Management, Cornell University, Cornell, NY, United States
| | - Godfred Boateng
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Jessica A. Gephart
- National Center for Socio-Environmental Synthesis (SESYNC), Annapolis, MD, United States
| | - Daniela Hampel
- ARS Western Human Nutrition Research Center, United States Department of Agriculture, Davis, CA, United States
- Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | | | - Samuel S. Myers
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Dera H. Ralalason
- Service de District de la Santé Publique de Maroantsetra, Ministère de la Santé Publique d'Analanjirofo, Maroantsetra, Madagascar
| | | | | | - Setareh Shahab-Ferdows
- ARS Western Human Nutrition Research Center, United States Department of Agriculture, Davis, CA, United States
| | - Bapu Vaitla
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Sarah K. Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, United States
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11
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Seasonal trends of nutrient intake in rainforest communities of north-eastern Madagascar. Public Health Nutr 2019; 22:2200-2209. [PMID: 31112110 DOI: 10.1017/s1368980019001083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE We collected dietary records over the course of nine months to comprehensively characterize the consumption patterns of Malagasy people living in remote rainforest areas of north-eastern Madagascar. DESIGN The present study was a prospective longitudinal cohort study to estimate dietary diversity and nutrient intake for a suite of macronutrients, micronutrients and vitamins for 152 randomly selected households in two communities. SETTING Madagascar, with over 25 million people living in an area the size of France, faces a multitude of nutritional challenges. Micronutrient-poor staples, especially rice, roots and tubers, comprise nearly 80 % of the Malagasy diet by weight. The remaining dietary components (including wild foods and animal-source foods) are critical for nutrition. We focus our study in north-eastern Madagascar, characterized by access to rainforest, rice paddies and local agriculture. PARTICIPANTS We enrolled men, women and children of both sexes and all ages in a randomized sample of households in two communities. RESULTS Although the Household Dietary Diversity Score and Food Consumption Score reflect high dietary diversity, the Minimum Dietary Diversity-Women indicator suggests poor micronutrient adequacy. The food intake data confirm a mixed nutritional picture. We found that the median individual consumed less than 50 % of his/her age/sex-specific Estimated Average Requirement (EAR) for vitamins A, B12, D and E, and Ca, and less than 100 % of his/her EAR for energy, riboflavin, folate and Na. CONCLUSIONS Malnutrition in remote communities of north-eastern Madagascar is pervasive and multidimensional, indicating an urgent need for comprehensive public health and development interventions focused on providing nutritional security.
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Bustamante ND, Golden CD, Randrianasolo JF, Parmar P. A qualitative evaluation of health care in the Maroantsetra region of Madagascar. Int Health 2019; 11:185-192. [PMID: 30265340 DOI: 10.1093/inthealth/ihy070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/10/2018] [Accepted: 09/18/2018] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Individuals in rural communities in Madagascar must frequently travel long distances, over difficult terrain, to obtain basic care. The quality of care is often inconsistent and inadequate. METHODS An exploratory mixed-methods study was conducted in select coastal communities in the Maroantsetra region of Madagascar to generate a more robust understanding of community and health care provider perceptions and how patients decide to seek health care, including the decision to use traditional medicine vs allopathic medicine. A total of 69 free-listing exercises and 21 facility assessments were conducted in eight communities. RESULTS Symptoms most commonly reported as reasons to seek health care included headaches, fever and cough. Decisions to access allopathic health care facilities depended on the intersection of geographic and financial access to health care facilities, perceived severity of the illness and the availability and confidence in traditional plant-based medications. Traveling salespeople, staff at local stores and pharmacy workers very often lacked formal training. CONCLUSIONS The decision to use allopathic medicine was determined by the perception of disease severity and when vulnerable populations, such as children and the elderly, were involved. Results provide insight into patterns, motivations and obstacles to health care utilization and decision making in the Maroantsetra region of Madagascar.
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Affiliation(s)
- Nirma D Bustamante
- Department of Emergency Medicine, Brigham and Women's Hospital, Harvard University, Boston, MA, USA
| | - Christopher D Golden
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Madagascar Health and Environmental Research, Maroantsetra, Madagascar
| | | | - Parveen Parmar
- Department of Emergency Medicine, University of Southern California, Los Angeles, CA, USA
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13
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Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell 2019; 176:649-662.e20. [PMID: 30661755 PMCID: PMC6349461 DOI: 10.1016/j.cell.2019.01.001] [Citation(s) in RCA: 794] [Impact Index Per Article: 158.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/15/2018] [Accepted: 12/28/2018] [Indexed: 02/06/2023]
Abstract
The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.
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Affiliation(s)
| | | | - Serena Manara
- CIBIO Department, University of Trento, Trento, Italy
| | - Moreno Zolfo
- CIBIO Department, University of Trento, Trento, Italy
| | | | | | | | - Paolo Manghi
- CIBIO Department, University of Trento, Trento, Italy
| | - Adrian Tett
- CIBIO Department, University of Trento, Trento, Italy
| | - Paolo Ghensi
- CIBIO Department, University of Trento, Trento, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council, Valencia, Spain
| | | | - Casey DuLong
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | | | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA
| | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy.
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