901
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Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. Nature 2017; 551:340-345. [PMID: 29144460 DOI: 10.1038/nature24302] [Citation(s) in RCA: 366] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/22/2017] [Indexed: 12/15/2022]
Abstract
The role of adaptive immunity in early cancer development is controversial. Here we show that chronic inflammation and fibrosis in humans and mice with non-alcoholic fatty liver disease is accompanied by accumulation of liver-resident immunoglobulin-A-producing (IgA+) cells. These cells also express programmed death ligand 1 (PD-L1) and interleukin-10, and directly suppress liver cytotoxic CD8+ T lymphocytes, which prevent emergence of hepatocellular carcinoma and express a limited repertoire of T-cell receptors against tumour-associated antigens. Whereas CD8+ T-cell ablation accelerates hepatocellular carcinoma, genetic or pharmacological interference with IgA+ cell generation attenuates liver carcinogenesis and induces cytotoxic T-lymphocyte-mediated regression of established hepatocellular carcinoma. These findings establish the importance of inflammation-induced suppression of cytotoxic CD8+ T-lymphocyte activation as a tumour-promoting mechanism.
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902
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Kaul A, Mandal S, Davidov O, Peddada SD. Analysis of Microbiome Data in the Presence of Excess Zeros. Front Microbiol 2017; 8:2114. [PMID: 29163406 PMCID: PMC5682008 DOI: 10.3389/fmicb.2017.02114] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/17/2017] [Indexed: 01/12/2023] Open
Abstract
Motivation: An important feature of microbiome count data is the presence of a large number of zeros. A common strategy to handle these excess zeros is to add a small number called pseudo-count (e.g., 1). Other strategies include using various probability models to model the excess zero counts. Although adding a pseudo-count is simple and widely used, as demonstrated in this paper, it is not ideal. On the other hand, methods that model excess zeros using a probability model often make an implicit assumption that all zeros can be explained by a common probability models. As described in this article, this is not always recommended as there are potentially three types/sources of zeros in a microbiome data. The purpose of this paper is to develop a simple methodology to identify and accomodate three different types of zeros and to test hypotheses regarding the relative abundance of taxa in two or more experimental groups. Another major contribution of this paper is to perform constrained (directional or ordered) inference when there are more than two ordered experimental groups (e.g., subjects ordered by diet or age groups or environmental exposure groups). As far as we know this is the first paper that addresses such problems in the analysis of microbiome data. Results: Using extensive simulation studies, we demonstrate that the proposed methodology not only controls the false discovery rate at a desired level of significance while competing well in terms of power with DESeq2, a popular procedure derived from RNASeq literature. As expected, the method using pseudo-counts tends to be very conservative and the classical t-test that ignores the underlying simplex structure in the data has an inflated FDR.
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Affiliation(s)
- Abhishek Kaul
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIH), Durham, NC, United States
| | | | - Ori Davidov
- Department of Statistics, University of Haifa, Haifa, Israel
| | - Shyamal D. Peddada
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIH), Durham, NC, United States
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903
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Schwendner P, Mahnert A, Koskinen K, Moissl-Eichinger C, Barczyk S, Wirth R, Berg G, Rettberg P. Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing. MICROBIOME 2017; 5:129. [PMID: 28974259 PMCID: PMC5627443 DOI: 10.1186/s40168-017-0345-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/18/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND The Mars500 project was conceived as the first full duration simulation of a crewed return flight to Mars. For 520 days, six crew members lived confined in a specifically designed spacecraft mock-up. The herein described "MIcrobial ecology of Confined Habitats and humAn health" (MICHA) experiment was implemented to acquire comprehensive microbiota data from this unique, confined manned habitat, to retrieve important information on the occurring microbiota dynamics, the microbial load and diversity in the air and on various surfaces. In total, 360 samples from 20 (9 air, 11 surface) locations were taken at 18 time-points and processed by extensive cultivation, PhyloChip and next generation sequencing (NGS) of 16S rRNA gene amplicons. RESULTS Cultivation assays revealed a Staphylococcus and Bacillus-dominated microbial community on various surfaces, with an average microbial load that did not exceed the allowed limits for ISS in-flight requirements indicating adequate maintenance of the facility. Areas with high human activity were identified as hotspots for microbial accumulation. Despite substantial fluctuation with respect to microbial diversity and abundance throughout the experiment, the location within the facility and the confinement duration were identified as factors significantly shaping the microbial diversity and composition, with the crew representing the main source for microbial dispersal. Opportunistic pathogens, stress-tolerant or potentially mobile element-bearing microorganisms were predicted to be prevalent throughout the confinement, while the overall microbial diversity dropped significantly over time. CONCLUSIONS Our findings clearly indicate that under confined conditions, the community structure remains a highly dynamic system which adapts to the prevailing habitat and micro-conditions. Since a sterile environment is not achievable, these dynamics need to be monitored to avoid spreading of highly resistant or potentially pathogenic microorganisms and a potentially harmful decrease of microbial diversity. If necessary, countermeasures are required, to maintain a healthy, diverse balance of beneficial, neutral and opportunistic pathogenic microorganisms. Our results serve as an important data collection for (i) future risk estimations of crewed space flight, (ii) an optimized design and planning of a spacecraft mission and (iii) for the selection of appropriate microbial monitoring approaches and potential countermeasures, to ensure a microbiologically safe space-flight environment.
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Affiliation(s)
- Petra Schwendner
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
- Institute for Microbiology, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
- Present address: UK Center for Astrobiology, University of Edinburgh, School of Physics and Astronomy, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
| | - Kaisa Koskinen
- Medical University of Graz, Department of Internal Medicine, Auenbruggerplatz 15, 8036 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Christine Moissl-Eichinger
- Medical University of Graz, Department of Internal Medicine, Auenbruggerplatz 15, 8036 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Simon Barczyk
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
| | - Reinhard Wirth
- Institute for Microbiology, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
| | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
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904
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Stewart CJ, Mansbach JM, Wong MC, Ajami NJ, Petrosino JF, Camargo CA, Hasegawa K. Associations of Nasopharyngeal Metabolome and Microbiome with Severity among Infants with Bronchiolitis. A Multiomic Analysis. Am J Respir Crit Care Med 2017; 196:882-891. [PMID: 28530140 PMCID: PMC5649976 DOI: 10.1164/rccm.201701-0071oc] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/30/2017] [Indexed: 12/19/2022] Open
Abstract
RATIONALE Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, although emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity. OBJECTIVES To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis. METHODS We conducted a multicenter prospective cohort study of infants (age <1 yr) hospitalized with bronchiolitis. By applying metabolomic and metagenomic (16S ribosomal RNA gene and whole-genome shotgun sequencing) approaches to 144 nasopharyngeal airway samples collected within 24 hours of hospitalization, we determined metabolome and microbiome profiles and their association with higher severity, defined by the use of positive pressure ventilation (i.e., continuous positive airway pressure and/or intubation). MEASUREMENTS AND MAIN RESULTS Nasopharyngeal airway metabolome profiles significantly differed by bronchiolitis severity (P < 0.001). Among 254 metabolites identified, a panel of 25 metabolites showed high sensitivity (84%) and specificity (86%) in predicting the use of positive pressure ventilation. The intensity of these metabolites was correlated with relative abundance of Streptococcus pneumoniae. In the pathway analysis, sphingolipid metabolism was the most significantly enriched subpathway in infants with positive pressure ventilation use compared with those without (P < 0.001). Enrichment of sphingolipid metabolites was positively correlated with the relative abundance of S. pneumoniae. CONCLUSIONS Although further validation is needed, our multiomic analyses demonstrate the potential of metabolomics to predict bronchiolitis severity and better understand microbe-host interaction.
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Affiliation(s)
- Christopher J. Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas; and
| | | | - Matthew C. Wong
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas; and
| | - Nadim J. Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas; and
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas; and
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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905
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Heintz-Buschart A, Pandey U, Wicke T, Sixel-Döring F, Janzen A, Sittig-Wiegand E, Trenkwalder C, Oertel WH, Mollenhauer B, Wilmes P. The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder. Mov Disord 2017; 33:88-98. [PMID: 28843021 PMCID: PMC5811909 DOI: 10.1002/mds.27105] [Citation(s) in RCA: 330] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 12/13/2022] Open
Abstract
Background Increasing evidence connects the gut microbiota and the onset and/or phenotype of Parkinson's disease (PD). Differences in the abundances of specific bacterial taxa have been reported in PD patients. It is, however, unknown whether these differences can be observed in individuals at high risk, for example, with idiopathic rapid eye movement sleep behavior disorder, a prodromal condition of α‐synuclein aggregation disorders including PD. Objectives To compare microbiota in carefully preserved nasal wash and stool samples of subjects with idiopathic rapid eye movement sleep behavior disorder, manifest PD, and healthy individuals. Methods Microbiota of flash‐frozen stool and nasal wash samples from 76 PD patients, 21 idiopathic rapid eye movement sleep behavior disorder patients, and 78 healthy controls were assessed by 16S and 18S ribosomal RNA amplicon sequencing. Seventy variables, related to demographics, clinical parameters including nonmotor symptoms, and sample processing, were analyzed in relation to microbiome variability and controlled differential analyses were performed. Results Differentially abundant gut microbes, such as Akkermansia, were observed in PD, but no strong differences in nasal microbiota. Eighty percent of the differential gut microbes in PD versus healthy controls showed similar trends in idiopathic rapid eye movement sleep behavior disorder, for example, Anaerotruncus and several Bacteroides spp., and correlated with nonmotor symptoms. Metagenomic sequencing of select samples enabled the reconstruction of genomes of so far uncharacterized differentially abundant organisms. Conclusion Our study reveals differential abundances of gut microbial taxa in PD and its prodrome idiopathic rapid eye movement sleep behavior disorder in comparison to the healthy controls, and highlights the potential of metagenomics to identify and characterize microbial taxa, which are enriched or depleted in PD and/or idiopathic rapid eye movement sleep behavior disorder. © 2017 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Anna Heintz-Buschart
- Eco-Systems Biology Research Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Urvashi Pandey
- Eco-Systems Biology Research Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tamara Wicke
- Paracelsus-Elena-Klinik, Kassel, Germany.,Department of Neurology, Philipps University Marburg, Germany
| | - Friederike Sixel-Döring
- Paracelsus-Elena-Klinik, Kassel, Germany.,Department of Neurology, Philipps University Marburg, Germany
| | - Annette Janzen
- Department of Neurology, Philipps University Marburg, Germany
| | | | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kassel, Germany.,University Medical Center Goettingen, Department of Neurosurgery, Goettingen, Germany
| | | | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Kassel, Germany.,University Medical Center Goettingen, Department of Neurology, Goettingen, Germany
| | - Paul Wilmes
- Eco-Systems Biology Research Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
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906
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Rathore R, Dowling DN, Forristal PD, Spink J, Cotter PD, Bulgarelli D, Germaine KJ. Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape ( Brassica napus). Front Microbiol 2017; 8:1489. [PMID: 28848510 PMCID: PMC5553296 DOI: 10.3389/fmicb.2017.01489] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/24/2017] [Indexed: 02/01/2023] Open
Abstract
Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil's physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip-tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited 'rhizosphere effect' in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.
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Affiliation(s)
- Ridhdhi Rathore
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
| | - David N Dowling
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
| | | | - John Spink
- Teagasc Crops Research CentreCarlow, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, and the APC Microbiome InstituteCork, Ireland
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton InstituteInvergowrie, Scotland
| | - Kieran J Germaine
- Envirocore, Dargan Research Centre, Institute of TechnologyCarlow, Ireland
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907
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Ganda EK, Gaeta N, Sipka A, Pomeroy B, Oikonomou G, Schukken YH, Bicalho RC. Normal milk microbiome is reestablished following experimental infection with Escherichia coli independent of intramammary antibiotic treatment with a third-generation cephalosporin in bovines. MICROBIOME 2017; 5:74. [PMID: 28701174 PMCID: PMC5506599 DOI: 10.1186/s40168-017-0291-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/20/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND The use of antimicrobials in food animals and the emergence of antimicrobial resistance are global concerns. Ceftiofur is the only third-generation cephalosporin labeled for veterinary use in the USA, and it is the drug of choice in the majority of dairy farms for the treatment of mastitis. Here, we use next-generation sequencing to describe longitudinal changes that occur in the milk microbiome before, during, and after infection and treatment with ceftiofur. Twelve animals were intramammary challenged with Escherichia coli in one quarter and randomly allocated to receive intramammary treatment with ceftiofur (5d) or untreated controls. Serial samples were collected from -72 to 216 h relative to challenge from the challenged quarter, an ipsilateral quarter assigned to the same treatment group, and from a third quarter that did not undergo intervention. RESULTS Infection with E. coli dramatically impacted microbial diversity. Ceftiofur significantly decreased LogCFUs but had no significant effect on the milk microbiome, rate of pathogen clearance, or somatic cell count. At the end of the study, the microbial profile of infected quarters was indistinguishable from pre-challenge samples in both treated and untreated animals. Intramammary infusion with ceftiofur did not alter the healthy milk (i.e., milk devoid of clots or serous appearance and collected from a mammary gland that shows no clinical signs of mastitis) microbiome. CONCLUSIONS Our results indicate that the mammary gland harbors a resilient microbiome, capable of reestablishing itself after experimental infection with E. coli independent of antimicrobial treatment.
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Affiliation(s)
- Erika K Ganda
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Natalia Gaeta
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil
| | - Anja Sipka
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Brianna Pomeroy
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Georgios Oikonomou
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Ynte H Schukken
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- GD Animal Health, Deventer, The Netherlands
| | - Rodrigo C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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908
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Abstract
After the initiation of Human Microbiome Project in 2008, various biostatistic and bioinformatic tools for data analysis and computational methods have been developed and applied to microbiome studies. In this review and perspective, we discuss the research and statistical hypotheses in gut microbiome studies, focusing on mechanistic concepts that underlie the complex relationships among host, microbiome, and environment. We review the current available statistic tools and highlight recent progress of newly developed statistical methods and models. Given the current challenges and limitations in biostatistic approaches and tools, we discuss the future direction in developing statistical methods and models for the microbiome studies.
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Affiliation(s)
- Yinglin Xia
- Division of Academic Internal Medicine and Geriatrics, Department of Medicine University of Illinois at Chicago, Chicago, IL.,Division of Gastroenterology and Hepatology, Department of Medicine University of Illinois at Chicago, Chicago, IL
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine University of Illinois at Chicago, Chicago, IL
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909
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Khanna S, Vazquez-Baeza Y, González A, Weiss S, Schmidt B, Muñiz-Pedrogo DA, Rainey JF, Kammer P, Nelson H, Sadowsky M, Khoruts A, Farrugia SL, Knight R, Pardi DS, Kashyap PC. Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. MICROBIOME 2017; 5:55. [PMID: 28506317 PMCID: PMC5433077 DOI: 10.1186/s40168-017-0269-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 04/23/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND Gut microbiota play a key role in maintaining homeostasis in the human gut. Alterations in the gut microbial ecosystem predispose to Clostridium difficile infection (CDI) and gut inflammatory disorders such as inflammatory bowel disease (IBD). Fecal microbiota transplantation (FMT) from a healthy donor can restore gut microbial diversity and pathogen colonization resistance; consequently, it is now being investigated for its ability to improve inflammatory gut conditions such as IBD. In this study, we investigated changes in gut microbiota following FMT in 38 patients with CDI with or without underlying IBD. RESULTS There was a significant change in gut microbial composition towards the donor microbiota and an overall increase in microbial diversity consistent with previous studies after FMT. FMT was successful in treating CDI using a diverse set of donors, and varying degrees of donor stool engraftment suggesting that donor type and degree of engraftment are not drivers of a successful FMT treatment of CDI. However, patients with underlying IBD experienced an increased number of CDI relapses (during a 24-month follow-up) and a decreased growth of new taxa, as compared to the subjects without IBD. Moreover, the need for IBD therapy did not change following FMT. These results underscore the importance of the existing gut microbial landscape as a decisive factor to successfully treat CDI and potentially for improvement of the underlying pathophysiology in IBD. CONCLUSIONS FMT leads to a significant change in microbial diversity in patients with recurrent CDI and complete resolution of symptoms. Stool donor type (related or unrelated) and degree of engraftment are not the key for successful treatment of CDI by FMT. However, CDI patients with IBD have higher proportion of the original community after FMT and lack of improvement of their IBD symptoms and increased episodes of CDI on long-term follow-up.
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Affiliation(s)
- Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yoshiki Vazquez-Baeza
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Antonio González
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA
| | - Bradley Schmidt
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - John F Rainey
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Patricia Kammer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Heidi Nelson
- Division of Colorectal Surgery, Mayo Clinic, Rochester, MN, USA
| | - Michael Sadowsky
- BioTechnology Institute, University of Minnesota, Minneapolis, MN, USA
| | - Alexander Khoruts
- Division of Gastroenterology, University of Minnesota, Minneapolis, MN, USA
| | - Stefan L Farrugia
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Darrell S Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA.
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910
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Hill-Burns EM, Debelius JW, Morton JT, Wissemann WT, Lewis MR, Wallen ZD, Peddada SD, Factor SA, Molho E, Zabetian CP, Knight R, Payami H. Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome. Mov Disord 2017; 32:739-749. [PMID: 28195358 PMCID: PMC5469442 DOI: 10.1002/mds.26942] [Citation(s) in RCA: 565] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND There is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota could explain several features of PD. OBJECTIVE The objective of this study was to determine if PD involves dysbiosis of gut microbiome, disentangle effects of confounders, and identify candidate taxa and functional pathways to guide research. METHODS A total of 197 PD cases and 130 controls were studied. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from stool. Metadata were collected on 39 potential confounders including medications, diet, gastrointestinal symptoms, and demographics. Statistical analyses were conducted while controlling for potential confounders and correcting for multiple testing. We tested differences in the overall microbial composition, taxa abundance, and functional pathways. RESULTS Independent microbial signatures were detected for PD (P = 4E-5), participants' region of residence within the United States (P = 3E-3), age (P = 0.03), sex (P = 1E-3), and dietary fruits/vegetables (P = 0.01). Among patients, independent signals were detected for catechol-O-methyltransferase-inhibitors (P = 4E-4), anticholinergics (P = 5E-3), and possibly carbidopa/levodopa (P = 0.05). We found significantly altered abundances of the Bifidobacteriaceae, Christensenellaceae, [Tissierellaceae], Lachnospiraceae, Lactobacillaceae, Pasteurellaceae, and Verrucomicrobiaceae families. Functional predictions revealed changes in numerous pathways, including the metabolism of plant-derived compounds and xenobiotics degradation. CONCLUSION PD is accompanied by dysbiosis of gut microbiome. Results coalesce divergent findings of prior studies, reveal altered abundance of several taxa, nominate functional pathways, and demonstrate independent effects of PD medications on the microbiome. The findings provide new leads and testable hypotheses on the pathophysiology and treatment of PD. © 2017 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Erin M. Hill-Burns
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
| | - Justine W. Debelius
- Department of Pediatrics, University of California San Diego, La Jolla, California, 92093, USA
| | - James T. Morton
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, 92093, USA
| | - William T. Wissemann
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
| | - Matthew R. Lewis
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
| | - Zachary D. Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
| | - Shyamal D. Peddada
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences (NIH/NIEHS), RTP, North Carolina, 27709, USA
| | - Stewart A. Factor
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric Molho
- Department of Neurology, Albany Medical College, Albany, NY, 12208, USA
| | - Cyrus P. Zabetian
- VA Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, WA, 98108, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, 92093, USA
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
- Center for Genomic Medicine, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
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911
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Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients. Genome Med 2017; 9:39. [PMID: 28449715 PMCID: PMC5408370 DOI: 10.1186/s13073-017-0428-y] [Citation(s) in RCA: 358] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/08/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker. METHODS We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naïve PD patients to 28 age-matched controls. RESULTS We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the ẞ-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions. CONCLUSIONS Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.
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Affiliation(s)
- J R Bedarf
- Department of Neurology, University of Bonn, Bonn, Germany.,German Centre for neurodegenerative disease research (DZNE), Bonn, Germany
| | - F Hildebrand
- European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
| | - L P Coelho
- European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
| | - S Sunagawa
- European Molecular Biology Laboratory, EMBL, Heidelberg, Germany.,ETH Zurich, Institute of Microbiology, Vladimir-Prelog-1-5/10, 8093, Zurich, Switzerland
| | - M Bahram
- Evolutionary Biology Centre, Uppsala University, Norbyva ̈gen 18D, 75236, Uppsala, Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005, Tartu, Estonia
| | - F Goeser
- Department of Internal Medicine I, University of Bonn, Bonn, Germany.,German Center for Infection Research (DZIF), Bonn-Cologne, Germany
| | - P Bork
- European Molecular Biology Laboratory, EMBL, Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany. .,Max Delbrück Centre for Molecular Medicine, 13125, Berlin, Germany. .,Department of Bioinformatics, University of Würzburg, 97074, Würzburg, Germany. .,, Meyerhofstraße 1, 69117, Heidelberg, Germany.
| | - U Wüllner
- Department of Neurology, University of Bonn, Bonn, Germany. .,German Centre for neurodegenerative disease research (DZNE), Bonn, Germany. .,, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
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912
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Koh H, Blaser MJ, Li H. A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping. MICROBIOME 2017; 5:45. [PMID: 28438217 PMCID: PMC5402681 DOI: 10.1186/s40168-017-0262-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 04/10/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbes is necessary to better understand the mechanisms involved in diseases related to microbiome perturbations. METHODS Here, we introduce a new microbiome-based group association testing method, optimal microbiome-based association test (OMiAT). OMiAT is a data-driven testing method which takes an optimal test throughout different tests from the sum of powered score tests (SPU) and microbiome regression-based kernel association test (MiRKAT). We illustrate that OMiAT efficiently discovers significant association signals arising from varying microbial abundances and different relative contributions from microbial abundance and phylogenetic information. We also propose a way to apply it to fine-mapping of diverse upper-level taxa at different taxonomic ranks (e.g., phylum, class, order, family, and genus), as well as the entire microbial community, within a newly introduced microbial taxa discovery framework, microbiome comprehensive association mapping (MiCAM). RESULTS Our extensive simulations demonstrate that OMiAT is highly robust and powerful compared with other existing methods, while correctly controlling type I error rates. Our real data analyses also confirm that MiCAM is especially efficient for the assessment of upper-level taxa by integrating OMiAT as a group analytic method. CONCLUSIONS OMiAT is attractive in practice due to the high complexity of microbiome data and the unknown true nature of the state. MiCAM also provides a hierarchical association map for numerous microbial taxa and can also be used as a guideline for further investigation on the roles of discovered taxa in human health and disease.
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Affiliation(s)
- Hyunwook Koh
- Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Martin J. Blaser
- Department of Medicine and Microbiology, New York University Langone Medical Center, New York, NY 10010 USA
| | - Huilin Li
- Department of Population Health and Environmental Medicine, New York University School of Medicine, New York, NY 10016 USA
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913
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Shi P, Li H. A model for paired-multinomial data and its application to analysis of data on a taxonomic tree. Biometrics 2017; 73:1266-1278. [PMID: 28369713 DOI: 10.1111/biom.12681] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 01/03/2023]
Abstract
In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This article considers the problem of analyzing two repeated measurements of microbiome data from the same subjects. Such data are often collected to assess the change of microbial composition after certain treatment, or the difference in microbial compositions across body sites. Existing models for such count data are limited in modeling the covariance structure of the counts and in handling paired multinomial count data. A new probability distribution is proposed for paired-multinomial count data, which allows flexible covariance structure and can be used to model repeatedly measured multivariate count data. Based on this distribution, a test statistic is developed for testing the difference in compositions based on paired multinomial count data. The proposed test can be applied to the count data observed on a taxonomic tree in order to test difference in microbiome compositions and to identify the subtrees with different subcompositions. Simulation results indicate that proposed test has correct type 1 errors and increased power compared to some commonly used methods. An analysis of an upper respiratory tract microbiome data set is used to illustrate the proposed methods.
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Affiliation(s)
- Pixu Shi
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, U.S.A
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, U.S.A
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914
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Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R. Normalization and microbial differential abundance strategies depend upon data characteristics. MICROBIOME 2017; 5:27. [PMID: 28253908 PMCID: PMC5335496 DOI: 10.1186/s40168-017-0237-y] [Citation(s) in RCA: 1027] [Impact Index Per Article: 146.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/27/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses. RESULTS Effects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average library size, rarefying lowers the false discovery rate. DESeq2, without addition of a constant, increased sensitivity on smaller datasets (<20 samples per group) but tends towards a higher false discovery rate with more samples, very uneven (~10×) library sizes, and/or compositional effects. For drawing inferences regarding taxon abundance in the ecosystem, analysis of composition of microbiomes (ANCOM) is not only very sensitive (for >20 samples per group) but also critically the only method tested that has a good control of false discovery rate. CONCLUSIONS These findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study.
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Affiliation(s)
- Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - Zhenjiang Zech Xu
- Departments of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093, USA
| | - Shyamal Peddada
- Biostatistics and Computational Biology Branch, NIEHS, NIH, Research Triangle Park Durham, NC, USA
| | - Amnon Amir
- Departments of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093, USA
| | - Kyle Bittinger
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 18014, USA
| | - Antonio Gonzalez
- Departments of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093, USA
| | | | - Jesse R Zaneveld
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Yoshiki Vázquez-Baeza
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, Dept. of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Embriette R Hyde
- Departments of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093, USA
| | - Rob Knight
- Departments of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093, USA.
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA.
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915
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Silverman JD, Washburne AD, Mukherjee S, David LA. A phylogenetic transform enhances analysis of compositional microbiota data. eLife 2017; 6:e21887. [PMID: 28198697 PMCID: PMC5328592 DOI: 10.7554/elife.21887] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/13/2017] [Indexed: 12/17/2022] Open
Abstract
Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.
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Affiliation(s)
- Justin D Silverman
- Program in Computational Biology and Bioinformatics, Duke University, Durham, United States
- Medical Scientist Training Program, Duke University, Durham, United States
- Center for Genomic and Computational Biology, Duke University, Durham, United States
| | - Alex D Washburne
- Nicholas School of the Environment, Duke University, Durham, United States
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, United States
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke University, Durham, United States
- Department of Statistical Science, Duke University, Durham, United States
- Department of Mathematics, Duke University, Durham, United States
- Department of Biostatistics and Bioinformatics, Duke University, Durham, United States
- Department of Computer Science, Duke University, Durham, United States
| | - Lawrence A David
- Program in Computational Biology and Bioinformatics, Duke University, Durham, United States
- Center for Genomic and Computational Biology, Duke University, Durham, United States
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
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916
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Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions. mBio 2017; 8:mBio.01703-16. [PMID: 28119466 PMCID: PMC5263242 DOI: 10.1128/mbio.01703-16] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Obesity has become a health epidemic in both humans and pets. A dysbiotic gut microbiota has been associated with obesity and other metabolic disorders. High-protein, low-carbohydrate (HPLC) diets have been recommended for body weight loss, but little is known about their effects on the canine gut microbiome. Sixty-three obese and lean Labrador retrievers and Beagles (mean age, 5.72 years) were fed a common baseline diet for 4 weeks in phase 1, followed by 4 weeks of a treatment diet, specifically, the HPLC diet (49.4% protein, 10.9% carbohydrate) or a low-protein, high-carbohydrate (LPHC) diet (25.5% protein, 38.8% carbohydrate) in phase 2. 16S rRNA gene profiling revealed that dietary protein and carbohydrate ratios have significant impacts on gut microbial compositions. This effect appeared to be more evident in obese dogs than in lean dogs but was independent of breed. Consumption of either diet increased the bacterial evenness, but not the richness, of the gut compared to that after consumption of the baseline diet. Macronutrient composition affected taxon abundances, mainly within the predominant phyla, Firmicutes and Bacteroidetes. The LPHC diet appeared to favor the growth of Bacteroides uniformis and Clostridium butyricum, while the HPLC diet increased the abundances of Clostridium hiranonis, Clostridium perfringens, and Ruminococcus gnavus and enriched microbial gene networks associated with weight maintenance. In addition, we observed a decrease in the Bacteroidetes to Firmicutes ratio and an increase in the Bacteroides to Prevotella ratio in the HPLC diet-fed dogs compared to these ratios in dogs fed other diets. Finally, analysis of the effect of diet on the predicted microbial gene network was performed using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). More than 50% of dogs are either overweight or obese in the United States. A dysbiotic gut microbiota is associated with obesity and other metabolic problems in humans. HPLC diets have been promoted as an effective weight loss strategy for many years, and potential effects were reported for both humans and dogs. In this study, we explored the influence of the protein and carbohydrate ratio on the gut microbiome in dogs with different body conditions. We demonstrated significant dietary effects on the gut microbiome, with greater changes in obese dogs than in lean dogs. The HPLC diet-fed dogs showed greater abundances of Firmicutes but fewer numbers of Bacteroidetes than other dogs. This knowledge will enable us to use prebiotics, probiotics, and other nutritional interventions to modulate the gut microbiota and to provide an alternative therapy for canine obesity.
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917
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Clark JS, Nemergut D, Seyednasrollah B, Turner PJ, Zhang S. Generalized joint attribute modeling for biodiversity analysis: median‐zero, multivariate, multifarious data. ECOL MONOGR 2017. [DOI: 10.1002/ecm.1241] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- James S. Clark
- Nicholas School of the Environment Duke University Durham North Carolina 27708 USA
- Department of Statistical Science Duke University Durham North Carolina 27708 USA
| | - Diana Nemergut
- Department of Biology Duke University Durham North Carolina 27708 USA
| | - Bijan Seyednasrollah
- Nicholas School of the Environment Duke University Durham North Carolina 27708 USA
| | - Phillip J. Turner
- Division of Marine Science and Conservation Nicholas School of the Environment Duke University Beaufort North Carolina 28516 USA
| | - Stacy Zhang
- Division of Marine Science and Conservation Nicholas School of the Environment Duke University Beaufort North Carolina 28516 USA
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918
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Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome Datasets Are Compositional: And This Is Not Optional. Front Microbiol 2017. [PMID: 29187837 DOI: 10.1080/01904168209363016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, and the built environment. There is increasing awareness that microbiome datasets generated by HTS are compositional because they have an arbitrary total imposed by the instrument. However, many investigators are either unaware of this or assume specific properties of the compositional data. The purpose of this review is to alert investigators to the dangers inherent in ignoring the compositional nature of the data, and point out that HTS datasets derived from microbiome studies can and should be treated as compositions at all stages of analysis. We briefly introduce compositional data, illustrate the pathologies that occur when compositional data are analyzed inappropriately, and finally give guidance and point to resources and examples for the analysis of microbiome datasets using compositional data analysis.
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Affiliation(s)
- Gregory B Gloor
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | - Jean M Macklaim
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | - Vera Pawlowsky-Glahn
- Departments of Computer Science, Applied Mathematics, and Statistics, Universitat de Girona, Girona, Spain
| | - Juan J Egozcue
- Department of Applied Mathematics, Universitat Politècnica de Catalunya, Barcelona, Spain
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919
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Alaimo S, Marceca GP, Giugno R, Ferro A, Pulvirenti A. Current Knowledge and Computational Techniques for Grapevine Meta-Omics Analysis. FRONTIERS IN PLANT SCIENCE 2017; 8:2241. [PMID: 29375610 PMCID: PMC5767322 DOI: 10.3389/fpls.2017.02241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 12/20/2017] [Indexed: 05/03/2023]
Abstract
Growing grapevine (Vitis vinifera) is a key contribution to the economy of many countries. Tools provided by genomics and bioinformatics did help researchers in obtaining biological knowledge about the different cultivars. Several genetic markers for common diseases were identified. Recently, the impact of microbiome has been proved to be of fundamental importance both in humans and in plants for its ability to confer protection or induce diseases. In this review we report current knowledge about grapevine microbiome, together with a description of the available computational methodologies for meta-omics analysis.
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Affiliation(s)
- Salvatore Alaimo
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Gioacchino P. Marceca
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Rosalba Giugno
- Department of Computer Science, University of Verona, Verona, Italy
| | - Alfredo Ferro
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Alfredo Pulvirenti
- Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
- *Correspondence: Alfredo Pulvirenti
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920
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Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R. Balance Trees Reveal Microbial Niche Differentiation. mSystems 2017; 2:e00162-16. [PMID: 28144630 PMCID: PMC5264246 DOI: 10.1128/msystems.00162-16] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/22/2016] [Indexed: 11/20/2022] Open
Abstract
Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss. Author Video: An author video summary of this article is available.
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Affiliation(s)
- James T. Morton
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Jon Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Robert A. Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA, and Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Daniel McDonald
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Antonio Gonzalez
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Jose A. Navas-Molina
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Jessica L. Metcalf
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy, University of California San Diego, La Jolla, California, USA, and Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Embriette R. Hyde
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - Manuel Lladser
- Department of Applied Mathematics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Pieter C. Dorrestein
- Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
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921
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Sampson TR, Debelius JW, Thron T, Janssen S, Shastri GG, Ilhan ZE, Challis C, Schretter CE, Rocha S, Gradinaru V, Chesselet MF, Keshavarzian A, Shannon KM, Krajmalnik-Brown R, Wittung-Stafshede P, Knight R, Mazmanian SK. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease. Cell 2016; 167:1469-1480.e12. [PMID: 27912057 PMCID: PMC5718049 DOI: 10.1016/j.cell.2016.11.018] [Citation(s) in RCA: 2112] [Impact Index Per Article: 264.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/12/2016] [Accepted: 11/10/2016] [Indexed: 02/06/2023]
Abstract
The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by aggregation of the protein α-synuclein (αSyn), often resulting in motor dysfunction as exemplified by Parkinson's disease (PD). Using mice that overexpress αSyn, we report herein that gut microbiota are required for motor deficits, microglia activation, and αSyn pathology. Antibiotic treatment ameliorates, while microbial re-colonization promotes, pathophysiology in adult animals, suggesting that postnatal signaling between the gut and the brain modulates disease. Indeed, oral administration of specific microbial metabolites to germ-free mice promotes neuroinflammation and motor symptoms. Remarkably, colonization of αSyn-overexpressing mice with microbiota from PD-affected patients enhances physical impairments compared to microbiota transplants from healthy human donors. These findings reveal that gut bacteria regulate movement disorders in mice and suggest that alterations in the human microbiome represent a risk factor for PD.
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Affiliation(s)
- Timothy R Sampson
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Justine W Debelius
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92110, USA
| | - Taren Thron
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stefan Janssen
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92110, USA
| | - Gauri G Shastri
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zehra Esra Ilhan
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Collin Challis
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Catherine E Schretter
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sandra Rocha
- Biology and Biological Engineering Department, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Viviana Gradinaru
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Kathleen M Shannon
- Department of Neurological Sciences, Section of Movement Disorders, Rush University Medical Center, Chicago, IL 60612, USA
| | - Rosa Krajmalnik-Brown
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Pernilla Wittung-Stafshede
- Biology and Biological Engineering Department, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92110, USA; Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA 92093, USA
| | - Sarkis K Mazmanian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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922
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Debelius J, Song SJ, Vazquez-Baeza Y, Xu ZZ, Gonzalez A, Knight R. Tiny microbes, enormous impacts: what matters in gut microbiome studies? Genome Biol 2016; 17:217. [PMID: 27760558 PMCID: PMC5072314 DOI: 10.1186/s13059-016-1086-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect sizes of both biological and technical covariates can help improve study design and the quality of biological conclusions. Care must be taken to avoid technical bias that can lead to incorrect biological conclusions. The presentation of quantitative effect sizes in addition to P values will improve our ability to perform meta-analysis and to evaluate potentially relevant biological effects. A better consideration of effect size and statistical power will lead to more robust biological conclusions in microbiome studies.
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Affiliation(s)
- Justine Debelius
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Yoshiki Vazquez-Baeza
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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923
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Mandal S, Godfrey KM, McDonald D, Treuren WV, Bjørnholt JV, Midtvedt T, Moen B, Rudi K, Knight R, Brantsæter AL, Peddada SD, Eggesbø M. Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake. MICROBIOME 2016; 4:55. [PMID: 27756413 PMCID: PMC5070355 DOI: 10.1186/s40168-016-0200-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 10/03/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Although diet is known to have a major modulatory influence on gut microbiota, knowledge of the specific roles of particular vitamins, minerals, and other nutrients is limited. Modulation of the composition of the microbiota in pregnant women is especially important as maternal microbes are transferred during delivery and initiate the colonization process in the infant. We studied the associations between intake of specific dietary nutrients during pregnancy and gut microbiota composition. METHODS Utilizing the Norwegian NoMIC cohort, we examined the relations between intakes of 28 dietary macro- and micronutrients during pregnancy, derived from food frequency questionnaires administered to 60 women in the second trimester, and observed taxonomic differences in their gut microbiota four days after delivery (assessed through Illumina 16S rRNA amplicon analysis). RESULTS Higher dietary intakes of fat-soluble vitamins, especially vitamin D, were associated with reduced microbial alpha diversity (p value <0.001). Furthermore, using recently developed statistical methodology, we discovered that the variations in fat-soluble vitamins, saturated and mono-unsaturated fat, and cholesterol intake, were associated with changes in phyla composition. Specifically, vitamin D, mono-unsaturated fat, cholesterol, and retinol were associated with relative increases in Proteobacteria, which is a phylum known to encompass multiple pathogens and to have pro-inflammatory properties. In contrast, saturated fat, vitamin E, and protein were associated with relative decreases in Proteobacteria. CONCLUSIONS The results in this article indicate that fats and fat-soluble vitamins are among the most potent dietary modulators of gut microbiota in mothers. The shifts in microbiota due to diet need to be further studied alongside gut microbiota changes during pregnancy to better understand the impact on infant gut microbiota.
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Affiliation(s)
- Siddhartha Mandal
- Department of Environmental Exposure and Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
- Present address: Public Health Foundation of India, Gurgaon, India
| | - Keith M. Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Daniel McDonald
- Department of Pediatrics at the University of California San Diego, San Diego, CA USA
| | - Will V. Treuren
- Department of Microbiology and Immunology, Stanford University, Stanford, CA USA
| | - Jørgen V. Bjørnholt
- Department of Environmental Exposure and Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
- Microbiological Department Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tore Midtvedt
- Department of Microbiology, Tumor and Cell biology (MTC), Karolinska Institute, Stockholm, Sweden
| | - Birgitte Moen
- The Norwegian Institute of Food Fisheries and Aquaculture, Aas, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, Norwegian Institute of Life Sciences, Aas, Norway
| | - Rob Knight
- Department of Pediatrics at the University of California San Diego, San Diego, CA USA
- Department of Computer Science, UC San Diego, San Diego, CA USA
| | - Anne Lise Brantsæter
- Department of Environmental Exposure and Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Shyamal D. Peddada
- Biostatistics and Computational Biology Branch, National Institute for Environmental Health Sciences, Durham, NC USA
| | - Merete Eggesbø
- Department of Environmental Exposure and Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
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924
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Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort. mSystems 2016; 1:mSystems00105-16. [PMID: 27822557 PMCID: PMC5080405 DOI: 10.1128/msystems.00105-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/19/2016] [Indexed: 11/21/2022] Open
Abstract
Recent work has demonstrated a potentially symbiotic relationship between oral commensal bacteria and humans through the salivary nitrate-nitrite-nitric oxide pathway (C. Duncan et al., Nat Med 1:546–551, 1995, http://dx.doi.org/10.1038/nm0695-546). Oral nitrate-reducing bacteria contribute physiologically relevant levels of nitrite and nitric oxide to the human host that may have positive downstream effects on cardiovascular health (V. Kapil et al., Free Radic Biol Med 55:93–100, 2013, http://dx.doi.org/10.1016/j.freeradbiomed.2012.11.013). In the work presented here, we used 16S rRNA Illumina sequencing to determine whether a connection exists between oral nitrate-reducing bacteria, nitrates for cardiovascular disease, and migraines, which are a common side effect of nitrate medications (U. Thadani and T. Rodgers, Expert Opin Drug Saf 5:667–674, 2006, http://dx.doi.org/10.1517/14740338.5.5.667). Nitrates, such as cardiac therapeutics and food additives, are common headache triggers, with nitric oxide playing an important role. Facultative anaerobic bacteria in the oral cavity may contribute migraine-triggering levels of nitric oxide through the salivary nitrate-nitrite-nitric oxide pathway. Using high-throughput sequencing technologies, we detected observable and significantly higher abundances of nitrate, nitrite, and nitric oxide reductase genes in migraineurs versus nonmigraineurs in samples collected from the oral cavity and a slight but significant difference in fecal samples. IMPORTANCE Recent work has demonstrated a potentially symbiotic relationship between oral commensal bacteria and humans through the salivary nitrate-nitrite-nitric oxide pathway (C. Duncan et al., Nat Med 1:546–551, 1995, http://dx.doi.org/10.1038/nm0695-546). Oral nitrate-reducing bacteria contribute physiologically relevant levels of nitrite and nitric oxide to the human host that may have positive downstream effects on cardiovascular health (V. Kapil et al., Free Radic Biol Med 55:93–100, 2013, http://dx.doi.org/10.1016/j.freeradbiomed.2012.11.013). In the work presented here, we used 16S rRNA Illumina sequencing to determine whether a connection exists between oral nitrate-reducing bacteria, nitrates for cardiovascular disease, and migraines, which are a common side effect of nitrate medications (U. Thadani and T. Rodgers, Expert Opin Drug Saf 5:667–674, 2006, http://dx.doi.org/10.1517/14740338.5.5.667).
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925
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Slattery J, MacFabe DF, Frye RE. The Significance of the Enteric Microbiome on the Development of Childhood Disease: A Review of Prebiotic and Probiotic Therapies in Disorders of Childhood. Clin Med Insights Pediatr 2016; 10:91-107. [PMID: 27774001 PMCID: PMC5063840 DOI: 10.4137/cmped.s38338] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/30/2016] [Accepted: 09/05/2016] [Indexed: 02/07/2023] Open
Abstract
Recent studies have highlighted the fact that the enteric microbiome, the trillions of microbes that inhabit the human digestive tract, has a significant effect on health and disease. Methods for manipulating the enteric microbiome, particularly through probiotics and microbial ecosystem transplantation, have undergone some study in clinical trials. We review some of the evidence for microbiome alteration in relation to childhood disease and discuss the clinical trials that have examined the manipulation of the microbiome in an effort to prevent or treat childhood disease with a primary focus on probiotics, prebiotics, and/or synbiotics (ie, probiotics + prebiotics). Studies show that alterations in the microbiome may be a consequence of events occurring during infancy and/or childhood such as prematurity, C-sections, and nosocomial infections. In addition, certain childhood diseases have been associated with microbiome alterations, namely necrotizing enterocolitis, infantile colic, asthma, atopic disease, gastrointestinal disease, diabetes, malnutrition, mood/anxiety disorders, and autism spectrum disorders. Treatment studies suggest that probiotics are potentially protective against the development of some of these diseases. Timing and duration of treatment, the optimal probiotic strain(s), and factors that may alter the composition and function of the microbiome are still in need of further research. Other treatments such as prebiotics, fecal microbial transplantation, and antibiotics have limited evidence. Future translational work, in vitro models, long-term and follow-up studies, and guidelines for the composition and viability of probiotic and microbial therapies need to be developed. Overall, there is promising evidence that manipulating the microbiome with probiotics early in life can help prevent or reduce the severity of some childhood diseases, but further research is needed to elucidate biological mechanisms and determine optimal treatments.
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Affiliation(s)
- John Slattery
- Arkansas Children’s Research Institute, Little Rock, AR, USA
- Division of Neurology, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Derrick F. MacFabe
- The Kilee Patchell-Evans Autism Research Group, Departments of Psychology (Neuroscience) and Psychiatry, Division of Developmental Disabilities, University of Western Ontario, London, ON, Canada
| | - Richard E. Frye
- Arkansas Children’s Research Institute, Little Rock, AR, USA
- Division of Neurology, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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926
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Extreme Dysbiosis of the Microbiome in Critical Illness. mSphere 2016; 1:mSphere00199-16. [PMID: 27602409 PMCID: PMC5007431 DOI: 10.1128/msphere.00199-16] [Citation(s) in RCA: 248] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 08/06/2016] [Indexed: 01/21/2023] Open
Abstract
Critical illness may be associated with the loss of normal, “health promoting” bacteria, allowing overgrowth of disease-promoting pathogenic bacteria (dysbiosis), which, in turn, makes patients susceptible to hospital-acquired infections, sepsis, and organ failure. This has significant world health implications, because sepsis is becoming a leading cause of death worldwide, and hospital-acquired infections contribute to significant illness and increased costs. Thus, a trial that monitors the ICU patient microbiome to confirm and characterize this hypothesis is urgently needed. Our study analyzed the microbiomes of 115 critically ill subjects and demonstrated rapid dysbiosis from unexpected environmental sources after ICU admission. These data may provide the first steps toward defining targeted therapies that correct potentially “illness-promoting” dysbiosis with probiotics or with targeted, multimicrobe synthetic “stool pills” that restore a healthy microbiome in the ICU setting to improve patient outcomes. Critical illness is hypothesized to associate with loss of “health-promoting” commensal microbes and overgrowth of pathogenic bacteria (dysbiosis). This dysbiosis is believed to increase susceptibility to nosocomial infections, sepsis, and organ failure. A trial with prospective monitoring of the intensive care unit (ICU) patient microbiome using culture-independent techniques to confirm and characterize this dysbiosis is thus urgently needed. Characterizing ICU patient microbiome changes may provide first steps toward the development of diagnostic and therapeutic interventions using microbiome signatures. To characterize the ICU patient microbiome, we collected fecal, oral, and skin samples from 115 mixed ICU patients across four centers in the United States and Canada. Samples were collected at two time points: within 48 h of ICU admission, and at ICU discharge or on ICU day 10. Sample collection and processing were performed according to Earth Microbiome Project protocols. We applied SourceTracker to assess the source composition of ICU patient samples by using Qiita, including samples from the American Gut Project (AGP), mammalian corpse decomposition samples, childhood (Global Gut study), and house surfaces. Our results demonstrate that critical illness leads to significant and rapid dysbiosis. Many taxons significantly depleted from ICU patients versus AGP healthy controls are key “health-promoting” organisms, and overgrowth of known pathogens was frequent. Source compositions of ICU patient samples are largely uncharacteristic of the expected community type. Between time points and within a patient, the source composition changed dramatically. Our initial results show great promise for microbiome signatures as diagnostic markers and guides to therapeutic interventions in the ICU to repopulate the normal, “health-promoting” microbiome and thereby improve patient outcomes. IMPORTANCE Critical illness may be associated with the loss of normal, “health promoting” bacteria, allowing overgrowth of disease-promoting pathogenic bacteria (dysbiosis), which, in turn, makes patients susceptible to hospital-acquired infections, sepsis, and organ failure. This has significant world health implications, because sepsis is becoming a leading cause of death worldwide, and hospital-acquired infections contribute to significant illness and increased costs. Thus, a trial that monitors the ICU patient microbiome to confirm and characterize this hypothesis is urgently needed. Our study analyzed the microbiomes of 115 critically ill subjects and demonstrated rapid dysbiosis from unexpected environmental sources after ICU admission. These data may provide the first steps toward defining targeted therapies that correct potentially “illness-promoting” dysbiosis with probiotics or with targeted, multimicrobe synthetic “stool pills” that restore a healthy microbiome in the ICU setting to improve patient outcomes. Podcast: A podcast concerning this article is available.
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927
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MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities. PLoS One 2016; 11:e0160169. [PMID: 27513472 PMCID: PMC4981383 DOI: 10.1371/journal.pone.0160169] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/14/2016] [Indexed: 12/14/2022] Open
Abstract
Culture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we can examine microbial communities. Recently, changes in microbial community structure and dynamics have been associated with a growing list of human diseases. The identification and comparison of bacteria driving those changes requires the development of sound statistical tools, especially if microbial biomarkers are to be used in a clinical setting. We present mixMC, a novel multivariate data analysis framework for metagenomic biomarker discovery. mixMC accounts for the compositional nature of 16S data and enables detection of subtle differences when high inter-subject variability is present due to microbial sampling performed repeatedly on the same subjects, but in multiple habitats. Through data dimension reduction the multivariate methods provide insightful graphical visualisations to characterise each type of environment in a detailed manner. We applied mixMC to 16S microbiome studies focusing on multiple body sites in healthy individuals, compared our results with existing statistical tools and illustrated added value of using multivariate methodologies to fully characterise and compare microbial communities.
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928
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Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 2016; 535:94-103. [PMID: 27383984 DOI: 10.1038/nature18850] [Citation(s) in RCA: 438] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/06/2016] [Indexed: 12/16/2022]
Abstract
Rapid advances in DNA sequencing, metabolomics, proteomics and computational tools are dramatically increasing access to the microbiome and identification of its links with disease. In particular, time-series studies and multiple molecular perspectives are facilitating microbiome-wide association studies, which are analogous to genome-wide association studies. Early findings point to actionable outcomes of microbiome-wide association studies, although their clinical application has yet to be approved. An appreciation of the complexity of interactions among the microbiome and the host's diet, chemistry and health, as well as determining the frequency of observations that are needed to capture and integrate this dynamic interface, is paramount for developing precision diagnostics and therapies that are based on the microbiome.
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Affiliation(s)
- Jack A Gilbert
- Department of Surgery, University of Chicago, Chicago, Illinois 60637, USA
| | - Robert A Quinn
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Justine Debelius
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - Zhenjiang Z Xu
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - James Morton
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
| | - Neha Garg
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Pieter C Dorrestein
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA.,Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, California 92093, USA.,Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, California 92093, USA.,Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA.,Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California 92093, USA
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929
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Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L. Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol Rev 2016; 40:686-700. [DOI: 10.1093/femsre/fuw017] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
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930
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Wu C, Chen J, Kim J, Pan W. An adaptive association test for microbiome data. Genome Med 2016; 8:56. [PMID: 27198579 PMCID: PMC4872356 DOI: 10.1186/s13073-016-0302-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/12/2016] [Indexed: 02/07/2023] Open
Abstract
There is increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. Although existing methods have identified many associations, a proper choice of a phylogenetic distance is critical for the power of these methods. To assess an overall association between the composition of a microbial community and an outcome of interest, we present a novel multivariate testing method called aMiSPU, that is joint and highly adaptive over all observed taxa and thus high powered across various scenarios, alleviating the issue with the choice of a phylogenetic distance. Our simulations and real-data analyses demonstrated that the aMiSPU test was often more powerful than several competing methods while correctly controlling type I error rates. The R package MiSPU is available at https://github.com/ChongWu-Biostat/MiSPU
and CRAN.
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Affiliation(s)
- Chong Wu
- Division of Biostatistics, University of Minnesota, 420 Delaware St. SE, Minneapolis, 55455, USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, 55905, USA
| | - Junghi Kim
- Division of Biostatistics, University of Minnesota, 420 Delaware St. SE, Minneapolis, 55455, USA
| | - Wei Pan
- Division of Biostatistics, University of Minnesota, 420 Delaware St. SE, Minneapolis, 55455, USA.
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931
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Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice. Proc Natl Acad Sci U S A 2016; 113:E3130-9. [PMID: 27185913 DOI: 10.1073/pnas.1600324113] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The prevalence of inflammatory diseases is increasing in modern urban societies. Inflammation increases risk of stress-related pathology; consequently, immunoregulatory or antiinflammatory approaches may protect against negative stress-related outcomes. We show that stress disrupts the homeostatic relationship between the microbiota and the host, resulting in exaggerated inflammation. Repeated immunization with a heat-killed preparation of Mycobacterium vaccae, an immunoregulatory environmental microorganism, reduced subordinate, flight, and avoiding behavioral responses to a dominant aggressor in a murine model of chronic psychosocial stress when tested 1-2 wk following the final immunization. Furthermore, immunization with M. vaccae prevented stress-induced spontaneous colitis and, in stressed mice, induced anxiolytic or fear-reducing effects as measured on the elevated plus-maze, despite stress-induced gut microbiota changes characteristic of gut infection and colitis. Immunization with M. vaccae also prevented stress-induced aggravation of colitis in a model of inflammatory bowel disease. Depletion of regulatory T cells negated protective effects of immunization with M. vaccae on stress-induced colitis and anxiety-like or fear behaviors. These data provide a framework for developing microbiome- and immunoregulation-based strategies for prevention of stress-related pathologies.
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932
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Geography and Location Are the Primary Drivers of Office Microbiome Composition. mSystems 2016; 1:mSystems00022-16. [PMID: 27822521 PMCID: PMC5069741 DOI: 10.1128/msystems.00022-16] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 12/21/2022] Open
Abstract
Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, disturbance due to repeated sampling, though detectable, is small compared to that due to other variables, opening up a range of longitudinal study designs in the BE. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples in all of the sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities. In the United States, humans spend the majority of their time indoors, where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidate several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ on the basis of surface material (e.g., ceiling tile or carpet) but do differ on the basis of the location in a room (e.g., ceiling or floor), two features that are often conflated but that we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material was likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work, which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces. IMPORTANCE Our study highlights several points that should impact the design of future studies of the microbiology of BEs. First, projects tracking changes in BE bacterial communities should focus sampling efforts on surveying different locations in offices and in different cities but not necessarily different materials or different offices in the same city. Next, disturbance due to repeated sampling, though detectable, is small compared to that due to other variables, opening up a range of longitudinal study designs in the BE. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples in all of the sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities.
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933
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Gloor GB, Reid G. Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data. Can J Microbiol 2016; 62:692-703. [PMID: 27314511 DOI: 10.1139/cjm-2015-0821] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A workshop held at the 2015 annual meeting of the Canadian Society of Microbiologists highlighted compositional data analysis methods and the importance of exploratory data analysis for the analysis of microbiome data sets generated by high-throughput DNA sequencing. A summary of the content of that workshop, a review of new methods of analysis, and information on the importance of careful analyses are presented herein. The workshop focussed on explaining the rationale behind the use of compositional data analysis, and a demonstration of these methods for the examination of 2 microbiome data sets. A clear understanding of bioinformatics methodologies and the type of data being analyzed is essential, given the growing number of studies uncovering the critical role of the microbiome in health and disease and the need to understand alterations to its composition and function following intervention with fecal transplant, probiotics, diet, and pharmaceutical agents.
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Affiliation(s)
- Gregory B Gloor
- a Department of Biochemistry, Western University, London, Ontario, Canada.,b Canadian Center for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, Ontario, Canada
| | - Gregor Reid
- b Canadian Center for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, Ontario, Canada.,c Department of Microbiology and Immunology, and Department of Surgery, Western University, London, Ontario, Canada
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934
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Faust K, Lima-Mendez G, Lerat JS, Sathirapongsasuti JF, Knight R, Huttenhower C, Lenaerts T, Raes J. Cross-biome comparison of microbial association networks. Front Microbiol 2015; 6:1200. [PMID: 26579106 PMCID: PMC4621437 DOI: 10.3389/fmicb.2015.01200] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/15/2015] [Indexed: 12/22/2022] Open
Abstract
Clinical and environmental meta-omics studies are accumulating an ever-growing amount of microbial abundance data over a wide range of ecosystems. With a sufficiently large sample number, these microbial communities can be explored by constructing and analyzing co-occurrence networks, which detect taxon associations from abundance data and can give insights into community structure. Here, we investigate how co-occurrence networks differ across biomes and which other factors influence their properties. For this, we inferred microbial association networks from 20 different 16S rDNA sequencing data sets and observed that soil microbial networks harbor proportionally fewer positive associations and are less densely interconnected than host-associated networks. After excluding sample number, sequencing depth and beta-diversity as possible drivers, we found a negative correlation between community evenness and positive edge percentage. This correlation likely results from a skewed distribution of negative interactions, which take place preferentially between less prevalent taxa. Overall, our results suggest an under-appreciated role of evenness in shaping microbial association networks.
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Affiliation(s)
- Karoline Faust
- Center for the Biology of Disease, VIBLeuven, Belgium
- Department of Microbiology and Immunology, REGA Institute, KU LeuvenLeuven, Belgium
- Department of Applied Biological Sciences, Vrije Universiteit BrusselBrussels, Belgium
| | - Gipsi Lima-Mendez
- Center for the Biology of Disease, VIBLeuven, Belgium
- Department of Microbiology and Immunology, REGA Institute, KU LeuvenLeuven, Belgium
- Department of Applied Biological Sciences, Vrije Universiteit BrusselBrussels, Belgium
| | - Jean-Sébastien Lerat
- Machine Learning Group, Department of Computer Science, Université Libre de BruxellesBrussels, Belgium
| | | | - Rob Knight
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, BoulderCO, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, BostonMA, USA
| | - Tom Lenaerts
- Machine Learning Group, Department of Computer Science, Université Libre de BruxellesBrussels, Belgium
- Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit BrusselBrussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles–Vrije Universiteit BrusselBrussels, Belgium
| | - Jeroen Raes
- Center for the Biology of Disease, VIBLeuven, Belgium
- Department of Microbiology and Immunology, REGA Institute, KU LeuvenLeuven, Belgium
- Department of Applied Biological Sciences, Vrije Universiteit BrusselBrussels, Belgium
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