Seasonal Variation in Human Gut Microbiome Composition
Publication Date
March 11, 2014
Journal
PLOS ONE
Authors
Emily R. Davenport, Orna Mizrahi Man, Katelyn Michelini, Luis B. Barreiro, et al
Volume
9
Issue
3
Pages
e90731
DOI
https://dx.plos.org/10.1371/journal.pone.0090731
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0090731
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24618913
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3949691
Europe PMC
http://europepmc.org/abstract/MED/24618913
Web of Science
000332842400027
Scopus
84897475563
Mendeley
http://www.mendeley.com/research/seasonal-variation-human-gut-microbiome-composition-3
Events
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Mendeley | Further Information

{"title"=>"Seasonal variation in human gut microbiome composition", "type"=>"journal", "authors"=>[{"first_name"=>"Emily R.", "last_name"=>"Davenport", "scopus_author_id"=>"55551674600"}, {"first_name"=>"Orna", "last_name"=>"Mizrahi-Man", "scopus_author_id"=>"24067640200"}, {"first_name"=>"Katelyn", "last_name"=>"Michelini", "scopus_author_id"=>"54950098500"}, {"first_name"=>"Luis B.", "last_name"=>"Barreiro", "scopus_author_id"=>"8857481700"}, {"first_name"=>"Carole", "last_name"=>"Ober", "scopus_author_id"=>"7102639601"}, {"first_name"=>"Yoav", "last_name"=>"Gilad", "scopus_author_id"=>"6602166624"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84897475563", "sgr"=>"84897475563", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0090731", "pmid"=>"24618913", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"372764239"}, "id"=>"86532e3e-15ee-32a2-abcd-afb430be5c79", "abstract"=>"The composition of the human gut microbiome is influenced by many environmental factors. Diet is thought to be one of the most important determinants, though we have limited understanding of the extent to which dietary fluctuations alter variation in the gut microbiome between individuals. In this study, we examined variation in gut microbiome composition between winter and summer over the course of one year in 60 members of a founder population, the Hutterites. Because of their communal lifestyle, Hutterite diets are similar across individuals and remarkably stable throughout the year, with the exception that fresh produce is primarily served during the summer and autumn months. Our data indicate that despite overall gut microbiome stability within individuals over time, there are consistent and significant population-wide shifts in microbiome composition across seasons. We found seasonal differences in both (i) the abundance of particular taxa (false discovery rate <0.05), including highly abundant phyla Bacteroidetes and Firmicutes, and (ii) overall gut microbiome diversity (by Shannon diversity; P = 0.001). It is likely that the dietary fluctuations between seasons with respect to produce availability explain, at least in part, these differences in microbiome composition. For example, high levels of produce containing complex carbohydrates consumed during the summer months might explain increased abundance of Bacteroidetes, which contain complex carbohydrate digesters, and decreased levels of Actinobacteria, which have been negatively correlated to fiber content in food questionnaires. Our observations demonstrate the plastic nature of the human gut microbiome in response to variation in diet.", "link"=>"http://www.mendeley.com/research/seasonal-variation-human-gut-microbiome-composition-3", "reader_count"=>240, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>8, "Librarian"=>1, "Student > Doctoral Student"=>14, "Researcher"=>45, "Student > Ph. D. Student"=>64, "Student > Postgraduate"=>12, "Student > Master"=>40, "Other"=>13, "Student > Bachelor"=>28, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>8, "Librarian"=>1, "Student > Doctoral Student"=>14, "Researcher"=>45, "Student > Ph. D. Student"=>64, "Student > Postgraduate"=>12, "Student > Master"=>40, "Other"=>13, "Student > Bachelor"=>28, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>10, "Agricultural and Biological Sciences"=>124, "Arts and Humanities"=>2, "Veterinary Science and Veterinary Medicine"=>2, "Chemical Engineering"=>2, "Chemistry"=>1, "Computer Science"=>1, "Engineering"=>1, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>25, "Nursing and Health Professions"=>3, "Materials Science"=>1, "Mathematics"=>2, "Medicine and Dentistry"=>31, "Sports and Recreations"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Psychology"=>4, "Social Sciences"=>11, "Immunology and Microbiology"=>13}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>31}, "Social Sciences"=>{"Social Sciences"=>11}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Psychology"=>{"Psychology"=>4}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>10}, "Environmental Science"=>{"Environmental Science"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>2}, "Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>13}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>124}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>25}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"United States"=>8, "Japan"=>1, "United Kingdom"=>4, "Switzerland"=>1, "Spain"=>1, "India"=>3, "New Zealand"=>1, "Canada"=>1, "Austria"=>1, "Netherlands"=>2, "Norway"=>1, "Finland"=>1, "Germany"=>2, "Croatia"=>1}, "group_count"=>11}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1414931"], "description"=>"<p>Principal components analysis (PCA) of data obtained from samples collected in the summer (red triangle) and winter (blue circle), at the phylum (A), class (B), order (C), family (D), and genus (E) level across samples. F) Individual shifts in microbiome composition along PC1 (y-axis). Data from the same individual across seasons is connected by a line (gray lines represent individuals showing seasonal trend, black lines highlight individuals showing the opposite trend). G) The average pairwise distance along the PC1/PC2 plane is shorter where points are from the same season than points between seasons (t-test <i>P</i> = 3.38×10<sup>−78</sup>), supporting seasonal clustering along the first two principle components.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Species interactions", "biota", "microbial ecology", "genomics", "microbiology", "Population biology", "Anatomy and physiology", "Digestive system", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Gastroenterology and hepatology", "temporal", "shifts", "observed", "microbiome"], "article_id"=>957830, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Emily R. Davenport", "Orna Mizrahi-Man", "Katelyn Michelini", "Luis B. Barreiro", "Carole Ober", "Yoav Gilad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090731.g002", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Consistent_temporal_shifts_observed_in_microbiome_composition_/957830", "title"=>"Consistent temporal shifts observed in microbiome composition.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-11 02:54:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1414929"], "description"=>"<p>Boxplots of pairwise Spearman correlation (y-axis) of bacterial abundance is shown for data at each taxonomic level (x-axis) across different classification levels. ‘Replicates’ refer to technical replicates derived from separate DNA extractions and library preparations from the same sample.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Species interactions", "biota", "microbial ecology", "genomics", "microbiology", "Population biology", "Anatomy and physiology", "Digestive system", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Gastroenterology and hepatology", "microbiome"], "article_id"=>957828, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Emily R. Davenport", "Orna Mizrahi-Man", "Katelyn Michelini", "Luis B. Barreiro", "Carole Ober", "Yoav Gilad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090731.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_of_microbiome_composition_between_replicates_individuals_and_over_time_/957828", "title"=>"Correlation of microbiome composition between replicates, individuals, and over time.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-11 02:54:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1414934"], "description"=>"<p>A) A significant difference (paired t-test <i>P</i><0.002) in Shannon diversity (H′, y-axis), between season (x-axis). B) H′ between sexes is not significantly different in either winter (t-test <i>P</i> = 0.46) or summer (<i>P</i> = 0.38). C) Diversity significantly decreases with age based on the data collected from winter samples (r<sup>2</sup> = 0.1267, <i>P</i><0.006), but not based on the data collected from the summer samples (r<sup>2</sup> = 0.01653, <i>P</i> = 0.33).</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Species interactions", "biota", "microbial ecology", "genomics", "microbiology", "Population biology", "Anatomy and physiology", "Digestive system", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Gastroenterology and hepatology"], "article_id"=>957833, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Emily R. Davenport", "Orna Mizrahi-Man", "Katelyn Michelini", "Luis B. Barreiro", "Carole Ober", "Yoav Gilad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090731.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_between_seasons_sexes_and_age_/957833", "title"=>"Diversity between seasons, sexes, and age.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-11 02:54:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1414935"], "description"=>"<p>In summer, when fruits and vegetables are grown in colony gardens, consumption of fresh produce is higher than in winter. Conversely, when fresh produce is not as available, a higher proportion of canned or frozen fruits and vegetables are eaten. Bars indicate standard error measurements. *** P<0.001 (t-test, adjusted for multiple tests using Benjamin Hochberg correction). See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090731#pone.0090731.s016\" target=\"_blank\">Table S6</a> for a list of all tests performed.</p>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Species interactions", "biota", "microbial ecology", "genomics", "microbiology", "Population biology", "Anatomy and physiology", "Digestive system", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Gastroenterology and hepatology", "varies"], "article_id"=>957834, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Emily R. Davenport", "Orna Mizrahi-Man", "Katelyn Michelini", "Luis B. Barreiro", "Carole Ober", "Yoav Gilad"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0090731.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Produce_consumption_varies_by_season_/957834", "title"=>"Produce consumption varies by season.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-11 02:54:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/1414942", "https://ndownloader.figshare.com/files/1414943", "https://ndownloader.figshare.com/files/1414944", "https://ndownloader.figshare.com/files/1414945", "https://ndownloader.figshare.com/files/1414946", "https://ndownloader.figshare.com/files/1414947", "https://ndownloader.figshare.com/files/1414948", "https://ndownloader.figshare.com/files/1414949", "https://ndownloader.figshare.com/files/1414950", "https://ndownloader.figshare.com/files/1414951", "https://ndownloader.figshare.com/files/1414952", "https://ndownloader.figshare.com/files/1414953", "https://ndownloader.figshare.com/files/1414954", "https://ndownloader.figshare.com/files/1414955", "https://ndownloader.figshare.com/files/1414956", "https://ndownloader.figshare.com/files/1414957", "https://ndownloader.figshare.com/files/1414958"], "description"=>"<div><p>The composition of the human gut microbiome is influenced by many environmental factors. Diet is thought to be one of the most important determinants, though we have limited understanding of the extent to which dietary fluctuations alter variation in the gut microbiome between individuals. In this study, we examined variation in gut microbiome composition between winter and summer over the course of one year in 60 members of a founder population, the Hutterites. Because of their communal lifestyle, Hutterite diets are similar across individuals and remarkably stable throughout the year, with the exception that fresh produce is primarily served during the summer and autumn months. Our data indicate that despite overall gut microbiome stability within individuals over time, there are consistent and significant population-wide shifts in microbiome composition across seasons. We found seasonal differences in both (<i>i</i>) the abundance of particular taxa (false discovery rate <0.05), including highly abundant phyla Bacteroidetes and Firmicutes, and (<i>ii</i>) overall gut microbiome diversity (by Shannon diversity; <i>P</i> = 0.001). It is likely that the dietary fluctuations between seasons with respect to produce availability explain, at least in part, these differences in microbiome composition. For example, high levels of produce containing complex carbohydrates consumed during the summer months might explain increased abundance of Bacteroidetes, which contain complex carbohydrate digesters, and decreased levels of Actinobacteria, which have been negatively correlated to fiber content in food questionnaires. Our observations demonstrate the plastic nature of the human gut microbiome in response to variation in diet.</p></div>", "links"=>[], "tags"=>["ecology", "Community Ecology", "Species interactions", "biota", "microbial ecology", "genomics", "microbiology", "Population biology", "Anatomy and physiology", "Digestive system", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Gastroenterology and hepatology", "microbiome"], "article_id"=>957841, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Emily R. Davenport", "Orna Mizrahi-Man", "Katelyn Michelini", "Luis B. Barreiro", "Carole Ober", "Yoav Gilad"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0090731.s001", "https://dx.doi.org/10.1371/journal.pone.0090731.s002", "https://dx.doi.org/10.1371/journal.pone.0090731.s003", "https://dx.doi.org/10.1371/journal.pone.0090731.s004", "https://dx.doi.org/10.1371/journal.pone.0090731.s005", "https://dx.doi.org/10.1371/journal.pone.0090731.s006", "https://dx.doi.org/10.1371/journal.pone.0090731.s007", "https://dx.doi.org/10.1371/journal.pone.0090731.s008", "https://dx.doi.org/10.1371/journal.pone.0090731.s009", "https://dx.doi.org/10.1371/journal.pone.0090731.s010", "https://dx.doi.org/10.1371/journal.pone.0090731.s011", "https://dx.doi.org/10.1371/journal.pone.0090731.s012", "https://dx.doi.org/10.1371/journal.pone.0090731.s013", "https://dx.doi.org/10.1371/journal.pone.0090731.s014", "https://dx.doi.org/10.1371/journal.pone.0090731.s015", "https://dx.doi.org/10.1371/journal.pone.0090731.s016", "https://dx.doi.org/10.1371/journal.pone.0090731.s017"], "stats"=>{"downloads"=>30, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Seasonal_Variation_in_Human_Gut_Microbiome_Composition_/957841", "title"=>"Seasonal Variation in Human Gut Microbiome Composition", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-11 02:54:34"}

PMC Usage Stats | Further Information

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