1
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Rajasekera TA, Galley JD, Mackos AR, Chen HJ, Mitchell JG, Kleinman JJ, Cappelucci P, Mashburn-Warren L, Lauber CL, Bailey MT, Worly BL, Gur TL. Stress and depression-associated shifts in gut microbiota: A pilot study of human pregnancy. Brain Behav Immun Health 2024; 36:100730. [PMID: 38323225 PMCID: PMC10844036 DOI: 10.1016/j.bbih.2024.100730] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
Background Psychosocial stress and mood-related disorders, such as depression, are prevalent and vulnerability to these conditions is heightened during pregnancy. Psychosocial stress induces consequences via several mechanisms including the gut microbiota-brain axis and associated signaling pathways. Previous preclinical work indicates that prenatal stress alters maternal gut microbial composition and impairs offspring development. Importantly, although the fecal and vaginal microenvironments undergo alterations across pregnancy, we lack consensus regarding which shifts are adaptive or maladaptive in the presence of prenatal stress and depression. Clinical studies interrogating these relationships have identified unique taxa but have been limited in study design. Methods We conducted a prospective cohort study of pregnant individuals consisting of repeated administration of psychometrics (Perceived Stress Scale (PSS) and Center for Epidemiological Studies Depression Scale (CES-D)) and collection of fecal and vaginal microbiome samples. Fecal and vaginal microbial community composition across psychometric responses were interrogated using full-length 16S rRNA sequencing followed by α and β-diversity metrics and taxonomic abundance. Results Early pregnancy stress was associated with increased abundance of fecal taxa not previously identified in related studies, and stress from late pregnancy through postpartum was associated with increased abundance of typical vaginal taxa and opportunistic pathogens in the fecal microenvironment. Additionally, in late pregnancy, maternal stress and depression scores were associated with each other and with elevated maternal C-C motif chemokine ligand 2 (CCL2) concentrations. At delivery, concordant with previous literature, umbilical CCL2 concentration was negatively correlated with relative abundance of maternal fecal Lactobacilli. Lastly, participants with more severe depressive symptoms experienced steeper decreases in prenatal vaginal α-diversity. Conclusion These findings a) underscore previous preclinical and clinical research demonstrating the effects of prenatal stress on maternal microbiome composition, b) suggest distinct biological pathways for the consequences of stress versus depression and c) extend the literature by identifying several taxa which may serve critical roles in mediating this relationship. Thus, further interrogation of the role of specific maternal microbial taxa in relation to psychosocial stress and its sequelae is warranted.
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Affiliation(s)
- Therese A. Rajasekera
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jeffrey D. Galley
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Amy R. Mackos
- College of Nursing, The Ohio State University, Columbus, OH, USA
| | - Helen J. Chen
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Medical Scientist Training Program, The Ohio State University, Columbus, OH, USA
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
| | | | | | - Paige Cappelucci
- College of Medicine, The Ohio State University, Columbus, OH, USA
| | | | - Christian L. Lauber
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Michael T. Bailey
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Center for Microbial Pathogenesis, The Research Institute, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Brett L. Worly
- Obstetrics and Gynecology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Tamar L. Gur
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Medical Scientist Training Program, The Ohio State University, Columbus, OH, USA
- College of Medicine, The Ohio State University, Columbus, OH, USA
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, USA
- Department of Neuroscience, The Ohio State University, Columbus, OH, USA
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2
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Galley JD, Mashburn-Warren L, Blalock LC, Lauber CL, Carroll JE, Ross KM, Hobel C, Coussons-Read M, Dunkel Schetter C, Gur TL. Maternal anxiety, depression and stress affects offspring gut microbiome diversity and bifidobacterial abundances. Brain Behav Immun 2023; 107:253-264. [PMID: 36240906 DOI: 10.1016/j.bbi.2022.10.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/22/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022] Open
Abstract
Uncovering mechanisms underlying fetal programming during pregnancy is of critical importance. Atypical neurodevelopment during the pre- and immediate postnatal period has been associated with long-term adverse health outcomes, including mood disorders and aberrant cognitive ability in offspring. Maternal factors that have been implicated in anomalous offspring development include maternal inflammation and tress, anxiety, and depression. One potential mechanism through which these factors perturb normal offspring postnatal development is through microbiome disruption. The mother is a primary source of early postnatal microbiome seeding for the offspring, and the transference of a healthy microbiome is key in normal neurodevelopment. Since psychological stress, mood disorders, and inflammation have all been implicated in altering maternal microbiome community structure, passing on aberrant microbial communities to the offspring that may then affect developmental outcomes. Therefore, we examined how maternal stress, anxiety and depression assessed with standardized instruments, and maternal inflammatory cytokine levels in the pre- and postnatal period are associated with the offspring microbiome within the first 13 months of life, utilizing full length 16S sequencing on infant stool samples, that allowed for species-level resolution. Results revealed that infants of mothers who reported higher anxiety and perceived stress had reduced alpha diversity. Additionally, the relative taxonomic quantitative abundances of Bifidobacterium dentium and other species that have been associated with either modulation of the gut-brain axis, or other beneficial health outcomes, were reduced in the offspring of mothers with higher anxiety, perceived stress, and depression. We also found associations between bifidobacteria and prenatal maternal pro-inflammatory cytokines IL-6, IL-8, and IL-10. In summary, specific microbial taxa involved in maintaining proper brain and immune function are lower in offspring born to mothers with anxiety, depression, or stress, providing strong evidence for a mechanism by which maternal factors may affect offspring health through microbiota dysregulation.
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Affiliation(s)
- Jeffrey D Galley
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Lexie C Blalock
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Christian L Lauber
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Judith E Carroll
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kharah M Ross
- Center for Social Sciences, Athabasca University, Athabasca, Alberta, Canada
| | - Calvin Hobel
- Cedars-Sinai Medical Centre, Los Angeles, CA, USA
| | - Mary Coussons-Read
- Department of Psychology, The University of Colorado, Colorado Springs, CO, USA
| | | | - Tamar L Gur
- Department of Psychiatry and Behavioral Health, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Neuroscience, The Ohio State University, Columbus, OH, USA; Obstetrics and Gynecology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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3
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Salman SS, Williams KC, Marte-Ortiz P, Rumpf W, Mashburn-Warren L, Lauber CL, Bailey MT, Maltz RM. Polyethylene Glycol 3350 Changes Stool Consistency and the Microbiome but not Behavior of CD1 Mice. J Pediatr Gastroenterol Nutr 2021; 73:499-506. [PMID: 34238825 DOI: 10.1097/mpg.0000000000003222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
OBJECTIVES Polyethylene Glycol 3350 (PEG3350) is a laxative commonly used to treat constipation in children. The Food and Drug Administration has received reports of increased anxiety, aggression, and obsessive--compulsive behaviors in children administered PEG3350. Thus, we assessed whether daily administration of PEG3350 leads to anxiety-like behavior in mice. METHODS Outbred CD-1 IGS mice were administered either a high or a low dose of PEG3350 via daily oral gavage for 2 weeks. As a laxative comparison and control, additional mice were given a high or low dose of magnesium citrate or vehicle (water). Weight and stool consistency were assessed after each gavage to determine laxative effectiveness. Anxiety-like behaviors were assessed using light/dark, open field, and elevated plus maze (EPM) tests at baseline, after 2 weeks of daily gavage, and after a 2 week washout in experiment 1, and after 2 weeks of daily gavage in experiment 2. Stool samples were collected for microbiome analysis in experiment 2 at baseline, after 2 weeks of daily gavage, and after 2 weeks washout. RESULTS PEG3350 and magnesium citrate significantly changed stool consistency, as well as microbiome alpha and beta diversity. Anxiety-like behaviors were not, however, different in mice administered low or high doses of PEG3350 or magnesium citrate. CONCLUSIONS Although changes in stool consistency and the gut microbiome occurred, administration of PEG3350 did not alter anxiety-like behaviors.
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Affiliation(s)
- Salman S Salman
- Division of Pediatric Gastroenterology, Nationwide Children's Hospital
| | - Kent C Williams
- Division of Pediatric Gastroenterology, Nationwide Children's Hospital.,Department of Pediatrics, The Ohio State University College of Medicine
| | - Pedro Marte-Ortiz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide at Nationwide Children's Hospital, Columbus, OH
| | | | | | - Christian L Lauber
- Department of Pediatrics, The Ohio State University College of Medicine.,Institute for Genomic Medicine.,Oral and Gastrointestinal Microbiology Research Affinity Group
| | - Michael T Bailey
- Department of Pediatrics, The Ohio State University College of Medicine.,Oral and Gastrointestinal Microbiology Research Affinity Group.,Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide at Nationwide Children's Hospital, Columbus, OH
| | - Ross M Maltz
- Division of Pediatric Gastroenterology, Nationwide Children's Hospital.,Department of Pediatrics, The Ohio State University College of Medicine.,Oral and Gastrointestinal Microbiology Research Affinity Group.,Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide at Nationwide Children's Hospital, Columbus, OH
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4
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Khodakivskyi PV, Lauber CL, Yevtodiyenko A, Bazhin AA, Bruce S, Ringel-Kulka T, Ringel Y, Bétrisey B, Torres J, Hu J, Chou CJ, Goun EA. Noninvasive imaging and quantification of bile salt hydrolase activity: From bacteria to humans. Sci Adv 2021; 7:7/6/eaaz9857. [PMID: 33536224 PMCID: PMC7857686 DOI: 10.1126/sciadv.aaz9857] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/16/2020] [Indexed: 05/07/2023]
Abstract
The microbiome-produced enzyme bile salt hydrolase (BSH) plays a central role in human health, but its function remains unclear due to the lack of suitable methods for measuring its activity. Here, we have developed a novel optical tool based on ultrasensitive bioluminescent imaging and demonstrated that this assay can be used for quick and cost-effective quantification of BSH activity across a broad range of biological settings including pure enzymes and bacteria, intact fecal slurries, and noninvasive imaging in live animals, as well as for the assessment of BSH activity in the entire gastrointestinal tract of mice and humans. Using this assay, we showed that certain types of prebiotics are capable of increasing BSH activity of the gut microbiota in vivo and successfully demonstrated potential application of this assay as a noninvasive diagnostic test to predict the clinical status of inflammatory bowel disease (IBD) patients.
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Affiliation(s)
- Pavlo V Khodakivskyi
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Christian L Lauber
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Aleksey Yevtodiyenko
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Arkadiy A Bazhin
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Stephen Bruce
- Clinical Chemistry Laboratory, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Tamar Ringel-Kulka
- UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599, USA
| | - Yehuda Ringel
- Division of Gastroenterology and Hepatology, Meir Medical Center, affiliated with Tel Aviv University, Kfar-Saba, Israel
- Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
- Biomica Ltd. 13 Gad Feinstein St. POB 4173, Rehovot 7414002, Israel
| | - Bertrand Bétrisey
- Cellular Metabolism, Department of Cell Biology, Nestlé Institute of Health Sciences, Nestlé Research, 1000 Lausanne, Switzerland
| | - Joana Torres
- Gastroenterology Division, Hospital Beatriz Ângelo, Loures, Portugal
- The Dr. Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chieh Jason Chou
- Department of Gastro-Intestinal Health and Microbiome, Nestlé Institute of Health Sciences, Nestlé Research, 1000 Lausanne, Switzerland
| | - Elena A Goun
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
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5
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Rabot S, Membrez M, Blancher F, Berger B, Moine D, Krause L, Bibiloni R, Bruneau A, Gérard P, Siddharth J, Lauber CL, Chou CJ. High fat diet drives obesity regardless the composition of gut microbiota in mice. Sci Rep 2016; 6:32484. [PMID: 27577172 PMCID: PMC5006052 DOI: 10.1038/srep32484] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [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: 08/08/2016] [Indexed: 02/08/2023] Open
Abstract
The gut microbiota is involved in many aspects of host physiology but its role in body weight and glucose metabolism remains unclear. Here we studied the compositional changes of gut microbiota in diet-induced obesity mice that were conventionally raised or received microbiota transplantation. In conventional mice, the diversity of the faecal microbiota was weakly associated with 1st week weight gain but transferring the microbiota of mice with contrasting weight gain to germfree mice did not change obesity development or feed efficiency of recipients regardless whether the microbiota was taken before or after 10 weeks high fat (HF) feeding. Interestingly, HF-induced glucose intolerance was influenced by microbiota inoculation and improved glucose tolerance was associated with a low Firmicutes to Bacteroidetes ratio. Transplantation of Bacteroidetes rich microbiota compared to a control microbiota ameliorated glucose intolerance caused by HF feeding. Altogether, our results demonstrate that gut microbiota is involved in the regulation of glucose metabolism and the abundance of Bacteroidetes significantly modulates HF-induced glucose intolerance but has limited impact on obesity in mice. Our results suggest that gut microbiota is a part of complex aetiology of insulin resistance syndrome, individual microbiota composition may cause phenotypic variation associated with HF feeding in mice.
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Affiliation(s)
- Sylvie Rabot
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | | | | | - Déborah Moine
- Nestlé Research Centre, Lausanne, Switzerland.,Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Lutz Krause
- Nestlé Research Centre, Lausanne, Switzerland
| | | | - Aurélia Bruneau
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Philippe Gérard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Jay Siddharth
- Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | | | - Chieh Jason Chou
- Nestlé Research Centre, Lausanne, Switzerland.,Nestlé Institute of Health Sciences, Lausanne, Switzerland
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6
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Lin P, Bach M, Asquith M, Lee AY, Akileswaran L, Stauffer P, Davin S, Pan Y, Cambronne ED, Dorris M, Debelius JW, Lauber CL, Ackermann G, Baeza YV, Gill T, Knight R, Colbert RA, Taurog JD, Van Gelder RN, Rosenbaum JT. HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats. PLoS One 2014; 9:e105684. [PMID: 25140823 PMCID: PMC4139385 DOI: 10.1371/journal.pone.0105684] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [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: 04/22/2014] [Accepted: 07/22/2014] [Indexed: 11/18/2022] Open
Abstract
The HLA-B27 gene is a major risk factor for clinical diseases including ankylosing spondylitis, acute anterior uveitis, reactive arthritis, and psoriatic arthritis, but its mechanism of risk enhancement is not completely understood. The gut microbiome has recently been shown to influence several HLA-linked diseases. However, the role of HLA-B27 in shaping the gut microbiome has not been previously investigated. In this study, we characterize the differences in the gut microbiota mediated by the presence of the HLA-B27 gene. We identified differences in the cecal microbiota of Lewis rats transgenic for HLA-B27 and human β2-microglobulin (hβ2m), compared with wild-type Lewis rats, using biome representational in situ karyotyping (BRISK) and 16S rRNA gene sequencing. 16S sequencing revealed significant differences between transgenic animals and wild type animals by principal coordinates analysis. Further analysis of the data set revealed an increase in Prevotella spp. and a decrease in Rikenellaceae relative abundance in the transgenic animals compared to the wild type animals. By BRISK analysis, species-specific differences included an increase in Bacteroides vulgatus abundance in HLA-B27/hβ2m and hβ2m compared to wild type rats. The finding that HLA-B27 is associated with altered cecal microbiota has not been shown before and can potentially provide a better understanding of the clinical diseases associated with this gene.
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Affiliation(s)
- Phoebe Lin
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
| | - Mary Bach
- Division of Rheumatology, University of Washington, VA Medical Center, Seattle, Washington, United States of America
| | - Mark Asquith
- Division of Rheumatology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Aaron Y. Lee
- Moorfield's Eye Institute of London, London, United Kingdom
| | - Lakshmi Akileswaran
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States of America
| | - Patrick Stauffer
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Sean Davin
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Yuzhen Pan
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Eric D. Cambronne
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Martha Dorris
- Department of Rheumatology, University of Texas Southwestern, Dallas, Texas, United States of America
| | | | | | - Gail Ackermann
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Yoshiki V. Baeza
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Tejpal Gill
- Pediatric Translational Research Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Rob Knight
- University of Colorado Boulder, Boulder, Colorado, United States of America
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Robert A. Colbert
- Pediatric Translational Research Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Joel D. Taurog
- Department of Rheumatology, University of Texas Southwestern, Dallas, Texas, United States of America
| | - Russell N. Van Gelder
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States of America
| | - James T. Rosenbaum
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Rheumatology, Oregon Health & Science University, Portland, Oregon, United States of America
- Dever's Eye Institute, Portland, Oregon, United States of America
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7
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Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B, Lusis AJ, Knight R, Caporaso JG, Svanbäck R. Individual diet has sex-dependent effects on vertebrate gut microbiota. Nat Commun 2014; 5:4500. [PMID: 25072318 PMCID: PMC4279269 DOI: 10.1038/ncomms5500] [Citation(s) in RCA: 349] [Impact Index Per Article: 34.9] [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: 12/03/2013] [Accepted: 06/25/2014] [Indexed: 02/06/2023] Open
Abstract
Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial composition ('dysbiosis'). However, it remains unclear whether diet effects are general or depend on host genotype. Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. Within each of two natural fish populations (threespine stickleback and Eurasian perch), among-individual diet variation is correlated with individual differences in gut microbiota. However, these diet-microbiota associations are sex dependent. We document similar sex-specific diet-microbiota correlations in humans. Experimental diet manipulations in laboratory stickleback and mice confirmed that diet affects microbiota differently in males versus females. The prevalence of such genotype by environment (sex by diet) interactions implies that therapies to treat dysbiosis might have sex-specific effects.
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Affiliation(s)
- Daniel I. Bolnick
- Howard Hughes Medical Institute and Department of Integrative Biology, University of Texas at Austin, One University Station C0990, Austin, Texas 78712, USA
| | - Lisa K. Snowberg
- Department of Integrative Biology, University of Texas at Austin, One University Station C0990, Austin, Texas 78712, USA
| | - Philipp E. Hirsch
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
- Program Man-Society-Environment, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland
| | - Christian L. Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309-0216, USA
| | - Elin Org
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, California 90095-1675, USA
| | - Brian Parks
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, California 90095-1675, USA
| | - Aldons J. Lusis
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, California 90095-1675, USA
| | - Rob Knight
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309-0215, USA
| | - J. Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011, USA
- Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Richard Svanbäck
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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8
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Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Front Microbiol 2014; 5:298. [PMID: 24995004 PMCID: PMC4063188 DOI: 10.3389/fmicb.2014.00298] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [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: 02/26/2014] [Accepted: 05/30/2014] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across environments.
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Affiliation(s)
| | - William A Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, CO, USA
| | - Christian L Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA
| | - Jose C Clemente
- Biofrontiers Institute, University of Colorado Boulder, CO, USA
| | | | | | | | | | | | | | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA ; Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA
| | - Jack A Gilbert
- Department of Ecology and Evolution, University of Chicago Chicago, IL, USA ; Institute of Genomic and Systems Biology, Argonne National Laboratory Argonne, IL, USA
| | - Rob Knight
- Biofrontiers Institute, University of Colorado Boulder, CO, USA ; Howard Hughes Medical Institute, University of Colorado Boulder, CO, USA
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9
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Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanbäck R. Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecol Lett 2014; 17:979-87. [PMID: 24847735 PMCID: PMC4084827 DOI: 10.1111/ele.12301] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [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: 12/04/2013] [Revised: 01/03/2014] [Accepted: 04/25/2014] [Indexed: 01/26/2023]
Abstract
Vertebrates' diets profoundly influence the composition of symbiotic gut microbial communities. Studies documenting diet-microbiota associations typically focus on univariate or categorical diet variables. However, in nature individuals often consume diverse combinations of foods. If diet components act independently, each providing distinct microbial colonists or nutrients, we expect a positive relationship between diet diversity and microbial diversity. We tested this prediction within each of two fish species (stickleback and perch), in which individuals vary in their propensity to eat littoral or pelagic invertebrates or mixtures of both prey. Unexpectedly, in most cases individuals with more generalised diets had less diverse microbiota than dietary specialists, in both natural and laboratory populations. This negative association between diet diversity and microbial diversity was small but significant, and most apparent after accounting for complex interactions between sex, size and diet. Our results suggest that multiple diet components can interact non-additively to influence gut microbial diversity.
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Affiliation(s)
- Daniel I Bolnick
- Howard Hughes Medical Institute and Section of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
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10
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Forsberg KJ, Patel S, Gibson MK, Lauber CL, Knight R, Fierer N, Dantas G. Bacterial phylogeny structures soil resistomes across habitats. Nature 2014; 509:612-6. [PMID: 24847883 PMCID: PMC4079543 DOI: 10.1038/nature13377] [Citation(s) in RCA: 752] [Impact Index Per Article: 75.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/14/2014] [Indexed: 12/16/2022]
Abstract
Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.
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Affiliation(s)
- Kevin J Forsberg
- 1] Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA [2]
| | - Sanket Patel
- 1] Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA [3]
| | - Molly K Gibson
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA
| | - Christian L Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA
| | - Rob Knight
- 1] Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA [2] Howard Hughes Medical Institute, Boulder, Colorado 80309, USA
| | - Noah Fierer
- 1] Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA [2] Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Gautam Dantas
- 1] Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA [2] Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA [3] Department of Biomedical Engineering, Washington University, St Louis, Missouri 63130, USA
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Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife 2013; 2:e01104. [PMID: 24137541 PMCID: PMC3796315 DOI: 10.7554/elife.01104] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [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: 06/19/2013] [Accepted: 09/20/2013] [Indexed: 12/13/2022] Open
Abstract
Establishing the time since death is critical in every death investigation, yet existing techniques are susceptible to a range of errors and biases. For example, forensic entomology is widely used to assess the postmortem interval (PMI), but errors can range from days to months. Microbes may provide a novel method for estimating PMI that avoids many of these limitations. Here we show that postmortem microbial community changes are dramatic, measurable, and repeatable in a mouse model system, allowing PMI to be estimated within approximately 3 days over 48 days. Our results provide a detailed understanding of bacterial and microbial eukaryotic ecology within a decomposing corpse system and suggest that microbial community data can be developed into a forensic tool for estimating PMI. DOI:http://dx.doi.org/10.7554/eLife.01104.001 Our bodies—especially our skin, our saliva, the lining of our mouth and our gastrointestinal tract—are home to a diverse collection of bacteria and other microorganisms called the microbiome. While the roles played by many of these microorganisms have yet to be identified, it is known that they contribute to the health and wellbeing of their host by metabolizing indigestible compounds, producing essential vitamins, and preventing the growth of harmful bacteria. They are important for nutrient and carbon cycling in the environment. The advent of advanced sequencing techniques has made it feasible to study the composition of this microbial community, and to monitor how it changes over time or how it responds to events such as antibiotic treatment. Sequencing studies have been used to highlight the significant differences between microbial communities found in different parts of the body, and to follow the evolution of the gut microbiome from birth. Most of these studies have focused on live animals, so little is known about what happens to the microbiome after its host dies. In particular, it is not known if the changes that occur after death are similar for all individuals. Moreover, the decomposing animal supplies nutrients and carbon to the surrounding ecosystem, but its influence on the microbial community of its immediate environment is not well understood. Now Metcalf et al. have used high-throughput sequencing to study the bacteria and other microorganisms (such as nematodes and fungi) in dead and decomposing mice, and also in the soil beneath them, over the course of 48 days. The changes were significant and also consistent across the corpses, with the microbial communities in the corpses influencing those in the soil, and vice versa. Metcalf et al. also showed that these measurements could be used to estimate the postmortem interval (the time since death) to within approximately 3 days, which suggests that the work could have applications in forensic science. DOI:http://dx.doi.org/10.7554/eLife.01104.002
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Affiliation(s)
- Jessica L Metcalf
- Biofrontiers Institute , University of Colorado at Boulder , Boulder , United States
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12
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Lauber CL, Ramirez KS, Aanderud Z, Lennon J, Fierer N. Temporal variability in soil microbial communities across land-use types. ISME J 2013; 7:1641-50. [PMID: 23552625 DOI: 10.1038/ismej.2013.50] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 02/09/2013] [Accepted: 02/13/2013] [Indexed: 02/01/2023]
Abstract
Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.
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Affiliation(s)
- Christian L Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309-0216, USA
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13
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Flores GE, Bates ST, Caporaso JG, Lauber CL, Leff JW, Knight R, Fierer N. Diversity, distribution and sources of bacteria in residential kitchens. Environ Microbiol 2012; 15:588-96. [PMID: 23171378 PMCID: PMC5100818 DOI: 10.1111/1462-2920.12036] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 09/26/2012] [Accepted: 10/12/2012] [Indexed: 02/01/2023]
Abstract
Bacteria readily colonize kitchen surfaces, and the exchange of microbes between humans and the kitchen environment can impact human health. However, we have a limited understanding of the overall diversity of these communities, how they differ across surfaces and sources of bacteria to kitchen surfaces. Here we used high-throughput sequencing of the 16S rRNA gene to explore biogeographical patterns of bacteria across > 80 surfaces within the kitchens of each of four households. In total, 34 bacterial and two archaeal phyla were identified, with most sequences belonging to the Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. Genera known to contain common food-borne pathogens were low in abundance but broadly distributed throughout the kitchens, with different taxa exhibiting distinct distribution patterns. The most diverse communities were associated with infrequently cleaned surfaces such as fans above stoves, refrigerator/freezer door seals and floors. In contrast, the least diverse communities were observed in and around sinks, which were dominated by biofilm-forming Gram-negative lineages. Community composition was influenced by conditions on individual surfaces, usage patterns and dispersal from source environments. Human skin was the primary source of bacteria across all kitchen surfaces, with contributions from food and faucet water dominating in a few specific locations. This study demonstrates that diverse bacterial communities are widely distributed in residential kitchens and that the composition of these communities is often predictable. These results also illustrate the ease with which human- and food-associated bacteria can be transferred in residential settings to kitchen surfaces.
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Affiliation(s)
- Gilberto E Flores
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
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14
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Lin X, McKinley J, Resch CT, Kaluzny R, Lauber CL, Fredrickson J, Knight R, Konopka A. Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer. ISME J 2012; 6:1665-76. [PMID: 22456444 DOI: 10.1038/ismej.2012.26] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Pyrosequencing analysis of 16S rRNA genes was used to study temporal dynamics of groundwater bacteria and archaea over 10 months within three well clusters separated by ~30 m and located 250 m from the Columbia River on the Hanford Site, WA. Each cluster contained three wells screened at different depths ranging from 10 to 17 m that differed in hydraulic conductivities. Representative samples were selected for analyses of prokaryotic 16S and eukaryotic 18S rRNA gene copy numbers. Temporal changes in community composition occurred in all nine wells over the 10-month sampling period. However, there were particularly strong effects near the top of the water table when the seasonal rise in the Columbia River caused river water intrusion at the top of the aquifer. The occurrence and disappearance of some microbial assemblages (such as Actinobacteria ACK-M1) were correlated with river water intrusion. This seasonal impact on microbial community structure was greater in the shallow saturated zone than deeper zone in the aquifer. Spatial and temporal patterns for several 16S rRNA gene operational taxonomic units associated with particular physiological functions (for example, methane oxidizers and metal reducers) suggests dynamic changes in fluxes of electron donors and acceptors over an annual cycle. In addition, temporal dynamics in eukaryotic 18S rRNA gene copies and the dominance of protozoa in 18S clone libraries suggest that bacterial community dynamics could be affected not only by the physical and chemical environment but also by top-down biological control.
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Affiliation(s)
- Xueju Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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15
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Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012; 6:1621-4. [PMID: 22402401 PMCID: PMC3400413 DOI: 10.1038/ismej.2012.8] [Citation(s) in RCA: 5111] [Impact Index Per Article: 425.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
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Affiliation(s)
- J Gregory Caporaso
- Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
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16
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Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R. Moving pictures of the human microbiome. Genome Biol 2012; 12:R50. [PMID: 21624126 PMCID: PMC3271711 DOI: 10.1186/gb-2011-12-5-r50] [Citation(s) in RCA: 742] [Impact Index Per Article: 61.8] [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: 03/07/2011] [Revised: 05/08/2011] [Accepted: 05/30/2011] [Indexed: 12/13/2022] Open
Abstract
Background Understanding the normal temporal variation in the human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing and computational technologies, however, have been a limiting factor in performing dense time series analysis of the human microbiome. Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints. Results We find that despite stable differences between body sites and individuals, there is pronounced variability in an individual's microbiota across months, weeks and even days. Additionally, only a small fraction of the total taxa found within a single body site appear to be present across all time points, suggesting that no core temporal microbiome exists at high abundance (although some microbes may be present but drop below the detection threshold). Many more taxa appear to be persistent but non-permanent community members. Conclusions DNA sequencing and computational advances described here provide the ability to go beyond infrequent snapshots of our human-associated microbial ecology to high-resolution assessments of temporal variations over protracted periods, within and between body habitats and individuals. This capacity will allow us to define normal variation and pathologic states, and assess responses to therapeutic interventions.
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Affiliation(s)
- J Gregory Caporaso
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
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Abstract
UNLABELLED As microbial ecologists take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses data and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing α -diversity, using taxonomic summaries; visualizing β -diversity, using results from multidimensional scaling methods; and animating relationships among microbial taxa or pathways overtime. SitePainter thus increases the visual power and ability to explore spatially explicit studies. AVAILABILITY https://sourceforge.net/projects/sitepainter SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT antoniog@colorado.edu, Rob.Knight@colorado.edu.
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Affiliation(s)
- Antonio Gonzalez
- Department of Computer Science, University of Colorado at Boulder and Howard Hughes Medical Institute, Boulder, CO 80309, USA.
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Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 2011; 6:1007-17. [PMID: 22134642 PMCID: PMC3329107 DOI: 10.1038/ismej.2011.159] [Citation(s) in RCA: 706] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.
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Affiliation(s)
- Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
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Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, Knight R, Fierer N. Microbial biogeography of public restroom surfaces. PLoS One 2011; 6:e28132. [PMID: 22132229 PMCID: PMC3223236 DOI: 10.1371/journal.pone.0028132] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [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: 09/12/2011] [Accepted: 11/01/2011] [Indexed: 12/11/2022] Open
Abstract
We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear linkages between communities on or in different body sites and those communities found on restroom surfaces. More generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching of surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determine sources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test the efficacy of hygiene practices.
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Affiliation(s)
- Gilberto E. Flores
- Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America
| | - Scott T. Bates
- Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America
| | - Dan Knights
- Department of Computer Science, University of Colorado, Boulder, Colorado, United States of America
| | - Christian L. Lauber
- Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America
| | - Jesse Stombaugh
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United States of America
- Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado, United States of America
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
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Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem 2011; 43:1450-1455. [PMID: 22267877 PMCID: PMC3260529 DOI: 10.1016/j.soilbio.2011.03.012] [Citation(s) in RCA: 348] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.
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Affiliation(s)
- Gaddy T. Bergmann
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
| | - Scott T. Bates
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
| | - Kathryn G. Eilers
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
| | - Christian L. Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
| | - J. Gregory Caporaso
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, Colorado 80309-0215, USA
| | - William A. Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Campus Box 347, Boulder, Colorado 80309-0347, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, Colorado 80309-0215, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
- Corresponding author: Dr. Noah Fierer Assistant professor University of Colorado at Boulder Department of Ecology and Evolutionary Biology CIRES Box 216 UCB Boulder, CO 80309-0216, USA Office: 303-492-5615 Lab: 303-492-2099 Fax: 303-492-1149
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Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 2011; 12:2998-3006. [PMID: 20561020 DOI: 10.1111/j.1462-2920.2010.02277.x] [Citation(s) in RCA: 314] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The severe environmental stresses of the Arctic may have promoted unique soil bacterial communities compared with those found in lower latitude environments. Here, we present a comprehensive analysis of the biogeography of soil bacterial communities in the Arctic using a high resolution bar-coded pyrosequencing technique. We also compared arctic soils with soils from a wide range of more temperate biomes to characterize variability in soil bacterial communities across the globe. We show that arctic soil bacterial community composition and diversity are structured according to local variation in soil pH rather than geographical proximity to neighboring sites, suggesting that local environmental heterogeneity is far more important than dispersal limitation in determining community-level differences. Furthermore, bacterial community composition had similar levels of variability, richness and phylogenetic diversity within arctic soils as across soils from a wide range of lower latitudes, strongly suggesting a common diversity structure within soil bacterial communities around the globe. These results contrast with the well-established latitudinal gradients in animal and plant diversity, suggesting that the controls on bacterial community distributions are fundamentally different from those observed for macro-organisms and that our biome definitions are not useful for predicting variability in soil bacterial communities across the globe.
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Affiliation(s)
- Haiyan Chu
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
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Ramirez KS, Lauber CL, Knight R, Bradford MA, Fierer N. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology 2011; 91:3463-70; discussion 3503-14. [PMID: 21302816 DOI: 10.1890/10-0426.1] [Citation(s) in RCA: 208] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) through anthropogenic activities. Although the effects of increased N inputs on plant communities have been reasonably well studied, few comparable studies have examined impacts on whole soil bacterial communities, though they play critical roles in ecosystem functioning. We sampled soils from two long-term ecological research (LTER) experimental N gradients, both of which have been amended with NH4NO3; a grassland at Cedar Creek (27 years of N additions) and an agricultural field at Kellogg Biological Station (8 years of N additions). By examining shifts in bacterial communities across these contrasting ecosystem types, we could test competing hypotheses about the direct and indirect factors that might drive bacterial responses to elevated N inputs. Bacterial community structure was highly responsive to N additions. We observed predictable and consistent changes in the structure of the bacterial communities across both ecosystem types. Our results suggest that bacterial communities across these gradients are more structured by N and/or soil carbon availability than by shifts in the plant community or soil pH associated with the elevated nitrogen inputs. In contrast to the pronounced shifts in bacterial community composition and in direct contrast to the patterns often observed in plant communities, increases in N availability did not have consistent effects on the richness and diversity of soil bacterial communities.
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Affiliation(s)
- Kelly S Ramirez
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA.
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Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R. PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. ACTA ACUST UNITED AC 2011; 27:1159-61. [PMID: 21349862 PMCID: PMC3072552 DOI: 10.1093/bioinformatics/btr087] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Motivation: PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task. Results: PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data. Availability: PrimerProspector is open-source software available at http://pprospector.sourceforge.net Contact:rob.knight@colorado.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- William A Walters
- Department of Molecular, Cellular, and Developmental Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, CO 80309, USA
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Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol 2010; 11:210. [PMID: 20441597 PMCID: PMC2898070 DOI: 10.1186/gb-2010-11-5-210] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Culture-independent studies of human microbiota by direct genomic sequencing reveal quite distinct differences among communities, indicating that improved sequencing capacity can be most wisely utilized to study more samples, rather than more sequences per sample.
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Affiliation(s)
- Justin Kuczynski
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett 2010; 307:80-6. [PMID: 20412303 DOI: 10.1111/j.1574-6968.2010.01965.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Storage conditions are considered to be a critical component of DNA-based microbial community analysis methods. However, whether differences in short-term sample storage conditions impact the assessment of bacterial community composition and diversity requires systematic and quantitative assessment. Therefore, we used barcoded pyrosequencing of bacterial 16S rRNA genes to survey communities, harvested from a variety of habitats [soil, human gut (feces) and human skin] and subsequently stored at 20, 4, -20 and -80 degrees C for 3 and 14 days. Our results indicate that the phylogenetic structure and diversity of communities in individual samples were not significantly influenced by the storage temperature or the duration of storage. Likewise, the relative abundances of most taxa were largely unaffected by temperature even after 14 days of storage. Our results indicate that environmental factors and biases in molecular techniques likely confer greater amounts of variation to microbial communities than do differences in short-term storage conditions, including storage for up to 2 weeks at room temperature. These results suggest that many samples collected and stored under field conditions without refrigeration may be useful for microbial community analyses.
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Affiliation(s)
- Christian L Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309-0216, USA.
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Abstract
Elucidating the biogeography of bacterial communities on the human body is critical for establishing healthy baselines from which to detect differences associated with diseases. To obtain an integrated view of the spatial and temporal distribution of the human microbiota, we surveyed bacteria from up to 27 sites in seven to nine healthy adults on four occasions. We found that community composition was determined primarily by body habitat. Within habitats, interpersonal variability was high, whereas individuals exhibited minimal temporal variability. Several skin locations harbored more diverse communities than the gut and mouth, and skin locations differed in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.
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Affiliation(s)
- Elizabeth K Costello
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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Bowers RM, Lauber CL, Wiedinmyer C, Hamady M, Hallar AG, Fall R, Knight R, Fierer N. Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei. Appl Environ Microbiol 2009; 75:5121-30. [PMID: 19502432 PMCID: PMC2725505 DOI: 10.1128/aem.00447-09] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [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] [Received: 02/23/2009] [Accepted: 06/02/2009] [Indexed: 02/01/2023] Open
Abstract
Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 x 10(5) to 6.6 x 10(6) cells m(-3) of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups Burkholderiales and Moraxellaceae (particularly the genus Psychrobacter) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria.
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MESH Headings
- Air Microbiology
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Biodiversity
- Cluster Analysis
- Colony Count, Microbial
- Colorado
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fungi/classification
- Fungi/genetics
- Fungi/isolation & purification
- Ice
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Robert M Bowers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 80309, USA.
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Lauber CL, Sinsabaugh RL, Zak DR. Laccase gene composition and relative abundance in oak forest soil is not affected by short-term nitrogen fertilization. Microb Ecol 2009; 57:50-57. [PMID: 18758844 DOI: 10.1007/s00248-008-9437-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 07/25/2008] [Indexed: 05/26/2023]
Abstract
Anthropogenic nitrogen (N) deposition affects a wide range of soil processes including phenol oxidase (PO) activity and soil organic matter dynamics. Depression of phenol oxidase activity in response to N saturation is believed to be mediated by the activity of white-rot basidiomycetes, whose production of extracellular oxidative enzymes can be limited by high N availability. We examined the effect of short-term N deposition on basidiomycete laccase gene diversity and relative abundance in temperate oak forest soil in which significant decreases in phenol oxidase and increased SOM have been recorded in response to experimental N deposition. UniFrac was used to compare the composition of laccase genes between three control- and three nitrogen-fertilized (80 kg(-1) ha(-1) per year) oak forest soils. The relative abundance of laccase genes was determined from qPCR analysis of laccase and basidiomycete ITS gene abundances. Our results indicate that there was no significant shift in the composition of laccase genes between control- and N-fertilized soils, nor was there a significant change in the relative abundance of laccase genes. These data suggest that N deposition effects on mineral soil PO activity do not result from changes in laccase gene diversity of white-rot basidiomycetes but are likely the result of altered microbial abundance or expression in this ecosystem type. Furthermore, laccase gene composition may be tied to factors that structure microbial communities in general, as soil laccase gene communities are more similar to other forest soils than with the corresponding litter.
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Affiliation(s)
- Christian L Lauber
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131-0001, USA.
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Sinsabaugh RL, Lauber CL, Weintraub MN, Ahmed B, Allison SD, Crenshaw C, Contosta AR, Cusack D, Frey S, Gallo ME, Gartner TB, Hobbie SE, Holland K, Keeler BL, Powers JS, Stursova M, Takacs-Vesbach C, Waldrop MP, Wallenstein MD, Zak DR, Zeglin LH. Stoichiometry of soil enzyme activity at global scale. Ecol Lett 2008; 11:1252-1264. [DOI: 10.1111/j.1461-0248.2008.01245.x] [Citation(s) in RCA: 1254] [Impact Index Per Article: 78.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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