101
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Sinha R, Goedert JJ, Vogtmann E, Hua X, Porras C, Hayes R, Safaeian M, Yu G, Sampson J, Ahn J, Shi J. Quantification of Human Microbiome Stability Over 6 Months: Implications for Epidemiologic Studies. Am J Epidemiol 2018; 187:1282-1290. [PMID: 29608646 DOI: 10.1093/aje/kwy064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 12/21/2017] [Indexed: 12/13/2022] Open
Abstract
Temporal variation in microbiome measurements can reduce statistical power in research studies. Quantification of this variation is essential for designing studies of chronic disease. We analyzed 16S ribosomal RNA profiles in paired biological specimens separated by 6 months from 3 studies conducted during 1985-2013 (a National Cancer Institute colorectal cancer study, a Costa Rica study, and the Human Microbiome Project). We evaluated temporal stability by calculating intraclass correlation coefficients (ICCs). Sample sizes needed in order to detect microbiome differences between equal numbers of cases and controls for a nested case-control design were calculated on the basis of estimated ICCs. Across body sites, 12 phylum-level ICCs were greater than 0.5. Similarly, 11 alpha-diversity ICCs were greater than 0.5. Fecal beta-diversity estimates had ICCs over 0.5. For a single collection with most microbiome metrics, detecting an odds ratio of 2.0 would require 300-500 cases when matching 1 case to 1 control at P = 0.05. Use of 2 or 3 sequential specimens reduces the number of required subjects by 40%-50% for low-ICC metrics. Relative abundances of major phyla and alpha-diversity metrics have low temporal stability. Thus, detecting associations of moderate effect size with these metrics will require large sample sizes. Because beta diversity for feces is reasonably stable over time, smaller sample sizes can detect associations with community composition. Sequential prediagnostic specimens from thousands of prospectively ascertained cases are required to detect modest disease associations with particular microbiome metrics.
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Affiliation(s)
- Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Carolina Porras
- Costa Rican Agency for Biomedical Research-INCIENSA Foundation, San José, Costa Rica
| | - Richard Hayes
- Division of Epidemiology, Department of Population Health, School of Medicine, New York University, New York, New York
| | - Mahboobeh Safaeian
- Department of Medical and Scientific Affairs, Roche Molecular Systems, Inc., Pleasanton, California
| | - Guoqin Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jiyoung Ahn
- Division of Epidemiology, Department of Population Health, School of Medicine, New York University, New York, New York
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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102
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Zhao N, Zhan X, Guthrie KA, Mitchell CM, Larson J. Generalized Hotelling's test for paired compositional data with application to human microbiome studies. Genet Epidemiol 2018; 42:459-469. [PMID: 29737047 DOI: 10.1002/gepi.22127] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/12/2018] [Accepted: 03/29/2018] [Indexed: 02/06/2023]
Abstract
The human microbiome is a dynamic system that changes due to diseases, medication, change in diet, etc. The paired design is a common approach to evaluate the microbial changes while controlling for the inherent differences between people. For example, microbiome data may be collected from the same individuals before and after a treatment. Two challenges exist in analyzing this type of data. First, microbiome data are compositional such that the reads for all taxa in each sample are constrained to sum to a constant. Second, the number of taxa can be much larger than the sample size. Few statistical methods exist to analyze such data besides methods that test one taxon at a time. In this paper, we propose to first conduct a log-ratio transformation of the compositions, and then develop a generalized Hotelling's test (GHT) to evaluate whether the average microbiome compositions are equivalent in the paired samples. We replace the sample covariance matrix in standard Hotelling's statistic by a shrinkage-based covariance, calculated as a weighted average of the sample covariance and a positive definite target matrix. The optimal weighting can be obtained for many commonly used target matrices. We develop a permutation procedure to assess the statistical significance. Extensive simulations show that our proposed method has well-controlled type I error and better power than a few ad hoc approaches. We apply our method to examine the vaginal microbiome changes in response to treatments for menopausal hot flashes. An R package " GHT" is freely available at https://github.com/zhaoni153/GHT.
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Affiliation(s)
- Ni Zhao
- Departments of Biostatistics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Xiang Zhan
- Department of Public Health Sciences, Pennsylvania State University, Hershey, Pennsylvania, United States of America
| | - Katherine A Guthrie
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Caroline M Mitchell
- Vincent Center for Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joseph Larson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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103
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Chen L, Reeve J, Zhang L, Huang S, Wang X, Chen J. GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ 2018; 6:e4600. [PMID: 29629248 PMCID: PMC5885979 DOI: 10.7717/peerj.4600] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/21/2018] [Indexed: 12/21/2022] Open
Abstract
Normalization is the first critical step in microbiome sequencing data analysis used to account for variable library sizes. Current RNA-Seq based normalization methods that have been adapted for microbiome data fail to consider the unique characteristics of microbiome data, which contain a vast number of zeros due to the physical absence or under-sampling of the microbes. Normalization methods that specifically address the zero-inflation remain largely undeveloped. Here we propose geometric mean of pairwise ratios—a simple but effective normalization method—for zero-inflated sequencing data such as microbiome data. Simulation studies and real datasets analyses demonstrate that the proposed method is more robust than competing methods, leading to more powerful detection of differentially abundant taxa and higher reproducibility of the relative abundances of taxa.
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Affiliation(s)
- Li Chen
- Department of Health Outcomes Research and Policy, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - James Reeve
- Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, MN, USA
| | - Lujun Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shengbing Huang
- Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, MN, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Jun Chen
- Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, MN, USA.,Division of Biomedical Statistics and Informatics and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
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104
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Arcidiacono S, Soares JW, Philip Karl J, Chrisey L, Dancy CPTBCR, Goodson M, Gregory F, Hammamieh R, Loughnane NK, Kokoska R, Riddle CAPTM, Whitaker K, Racicot K. The current state and future direction of DoD gut microbiome research: a summary of the first DoD gut microbiome informational meeting. Stand Genomic Sci 2018. [PMCID: PMC5861724 DOI: 10.1186/s40793-018-0308-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The gut microbiome is increasingly recognized as integral to human health, and is emerging as a mediator of human physical and cognitive performance. This has led to the recognition that US Department of Defense (DoD) research supporting a healthy and resilient gut microbiome will be critical to optimizing the health and performance of future Warfighters. To facilitate knowledge dissemination and collaboration, identify resource capabilities and gaps, and maximize the positive impact of gut microbiome research on the Warfighter, DoD partners in microbiome research participated in a 2-day informational meeting co-hosted by the Natick Soldier Research, Engineering and Development Center (NSRDEC) and the US Army Research Institute of Environmental Medicine (USARIEM) on 16–17 November 2015. Attendee presentations and discussions demonstrated that multiple DoD organizations are actively advancing gut microbiome research. Common areas of research included the influence of military-relevant stressors on interactions between the microbiome and Warfighter biology, manipulation of the microbiome to influence Warfighter health, and use of the microbiome as a biomarker of Warfighter health status. Although resources and capabilities are available, they vary across laboratories and it was determined that centralizing certain DoD capabilities could accelerate progress. More significantly, the meeting created a foundation for a coordinated gut microbiome and nutrition research program aligning key DoD partners in the area of microbiome research. This report details the presentations and discussions presented during the 1st DoD Gut Microbiome Informational Meeting.
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105
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Raju SC, Lagström S, Ellonen P, de Vos WM, Eriksson JG, Weiderpass E, Rounge TB. Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling. J Microbiol Methods 2018; 147:76-86. [PMID: 29563060 DOI: 10.1016/j.mimet.2018.03.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 12/17/2022]
Abstract
Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.
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Affiliation(s)
- Sajan C Raju
- Folkhälsan Research Center, Helsinki, Finland; Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Sonja Lagström
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Willem M de Vos
- RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
| | - Johan G Eriksson
- Folkhälsan Research Center, Helsinki, Finland; Department of General Practice and Primary Health Care, University of Helsinki, Helsinki University Hospital, Helsinki, Finland; Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
| | - Elisabete Weiderpass
- Folkhälsan Research Center, Helsinki, Finland; Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Research, Cancer Registry of Norway, Oslo, Norway; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway.
| | - Trine B Rounge
- Folkhälsan Research Center, Helsinki, Finland; Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Research, Cancer Registry of Norway, Oslo, Norway.
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106
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Wu WK, Chen CC, Panyod S, Chen RA, Wu MS, Sheen LY, Chang SC. Optimization of fecal sample processing for microbiome study - The journey from bathroom to bench. J Formos Med Assoc 2018; 118:545-555. [PMID: 29490879 DOI: 10.1016/j.jfma.2018.02.005] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/23/2018] [Accepted: 02/05/2018] [Indexed: 12/30/2022] Open
Abstract
Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP). Third, we provide a useful information of collection kit with DNA stabilization buffers and compare their pros and cons for multi-omic study. Fourth, we offer technical strategies as well as information of novel tools for sample aliquoting before long-term storage. Fifth, we discuss the substantial impact of different DNA extraction protocols on technical variations of metagenomic analysis. And lastly, we point out the limitation of current methods and the unmet needs for better quality control of metagenomic analysis. We hope the information provided here will help investigators in this exciting field to advance their studies while avoiding experimental artifacts.
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Affiliation(s)
- Wei-Kai Wu
- Department of Internal Medicine, National Taiwan University Hospital Bei-Hu Branch, Taipei, Taiwan; Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chieh-Chang Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Suraphan Panyod
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Rou-An Chen
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Ming-Shiang Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Lee-Yan Sheen
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Shan-Chwen Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan.
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107
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Mahabir S, Willett WC, Friedenreich CM, Lai GY, Boushey CJ, Matthews CE, Sinha R, Colditz GA, Rothwell JA, Reedy J, Patel AV, Leitzmann MF, Fraser GE, Ross S, Hursting SD, Abnet CC, Kushi LH, Taylor PR, Prentice RL. Research Strategies for Nutritional and Physical Activity Epidemiology and Cancer Prevention. Cancer Epidemiol Biomarkers Prev 2018; 27:233-244. [PMID: 29254934 PMCID: PMC7992195 DOI: 10.1158/1055-9965.epi-17-0509] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/02/2017] [Accepted: 12/04/2017] [Indexed: 12/24/2022] Open
Abstract
Very large international and ethnic differences in cancer rates exist, are minimally explained by genetic factors, and show the huge potential for cancer prevention. A substantial portion of the differences in cancer rates can be explained by modifiable factors, and many important relationships have been documented between diet, physical activity, and obesity, and incidence of important cancers. Other related factors, such as the microbiome and the metabolome, are emerging as important intermediary components in cancer prevention. It is possible with the incorporation of newer technologies and studies including long follow-up and evaluation of effects across the life cycle, additional convincing results will be produced. However, several challenges exist for cancer researchers; for example, measurement of diet and physical activity, and lack of standardization of samples for microbiome collection, and validation of metabolomic studies. The United States National Cancer Institute convened the Research Strategies for Nutritional and Physical Activity Epidemiology and Cancer Prevention Workshop on June 28-29, 2016, in Rockville, Maryland, during which the experts addressed the state of the science and areas of emphasis. This current paper reflects the state of the science and priorities for future research. Cancer Epidemiol Biomarkers Prev; 27(3); 233-44. ©2017 AACR.
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Affiliation(s)
- Somdat Mahabir
- Environmental Epidemiology Branch, Epidemiology and Genomics Research Program (EGRP), Division of Cancer Control and Population Sciences (DCCPS), National Cancer Institute (NCI), Bethesda, Maryland.
| | - Walter C Willett
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
| | - Christine M Friedenreich
- Department of Cancer Epidemiology and Prevention Research, Cancer Control Alberta, Alberta Health Services, Edmonton, Alberta, Canada
| | - Gabriel Y Lai
- Environmental Epidemiology Branch, Epidemiology and Genomics Research Program (EGRP), Division of Cancer Control and Population Sciences (DCCPS), National Cancer Institute (NCI), Bethesda, Maryland
| | - Carol J Boushey
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Charles E Matthews
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), NCI, Bethesda, Maryland
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), NCI, Bethesda, Maryland
| | - Graham A Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University and Alvin J. Siteman Cancer Center, St. Louis, Missouri
| | - Joseph A Rothwell
- Nutrition and Metabolism Section, Biomarkers Group, International Agency for Cancer Research (IARC), Lyon, France
| | - Jill Reedy
- Risk Factor Assessment Branch, EGRP, DCCPS, NCI, Bethesda, Maryland
| | - Alpa V Patel
- Cancer Prevention Study-3, American Cancer Society, Atlanta, Georgia
| | - Michael F Leitzmann
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Gary E Fraser
- School of Public Health, School of Medicine, Loma Linda University, Loma Linda, California
| | - Sharon Ross
- Nutritional Science Research Group, Division of Cancer Prevention, NCI, Bethesda, Maryland
| | - Stephen D Hursting
- Nutrition Research Institute, Lineberger Comprehensive Cancer Center and University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Christian C Abnet
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), NCI, Bethesda, Maryland
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Philip R Taylor
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), NCI, Bethesda, Maryland
| | - Ross L Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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108
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Radjabzadeh D, Uitterlinden AG, Kraaij R. Microbiome measurement: Possibilities and pitfalls. Best Pract Res Clin Gastroenterol 2017; 31:619-623. [PMID: 29566904 DOI: 10.1016/j.bpg.2017.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 10/29/2017] [Indexed: 01/31/2023]
Abstract
Microbiome research is an emerging field in medical sciences. Several studies have made headways in understanding the influence of microbes on our health and disease states. Further progress in mapping microbiome populations across different body sites and understanding the underlying mechanisms of microbiome-host interactions depends critically on study design, collection protocols, analytical genetic techniques, and reference databases. In particular, a shift has appeared going from small sample collections to large-scale population studies (with extensive phenotypic information including disease status) which calls for some adaptions. In this review we will focus on gut microbiome profiling using the 16S ribosomal RNA approach in the setting of large-scale population studies, and discuss some novel developments.
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Affiliation(s)
| | - André G Uitterlinden
- Dept. Internal Medicine, Erasmus MC, Rotterdam, The Netherlands; Dept. Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Robert Kraaij
- Dept. Internal Medicine, Erasmus MC, Rotterdam, The Netherlands; Dept. Epidemiology, Erasmus MC, Rotterdam, The Netherlands.
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109
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Parthasarathy G, Chen J, Chia N, O'Connor HM, Gaskins HR, Bharucha AE. Reproducibility of assessing fecal microbiota in chronic constipation. Neurogastroenterol Motil 2017; 29:1-10. [PMID: 28752633 PMCID: PMC5593773 DOI: 10.1111/nmo.13172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/29/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND While limited data suggest that the fecal microbiota in healthy people is stable over time, the intraindividual variability of the fecal microbiota in constipated patients is unknown. METHODS This study evaluated the intraindividual reproducibility of fecal microbiota analyzed with 16S rRNA gene sequencing in two stool samples collected without and after a laxative, respectively, in 25 healthy people and 25 constipated women. Participants completed a food record for 3 d before the stool collection. Colonic transit was measured with scintigraphy. KEY RESULTS The constipated patients were older (48±15 vs 39±10 y, P=.02) than healthy participants but had a similar BMI. The total daily caloric intake was less (P=.005) in constipated (1265±350 kcal) than healthy participants (1597±402 kcal). Fourteen patients but only two controls (P<.005), had delayed colonic transit. For most measures of alpha (eg, Observed OTU number, Shannon index) and beta diversity (eg, Bray-Curtis dissimilarity, UniFrac, phyla level abundance), the ICCs between two stool samples were high, indicating moderate or strong agreement, and similar in healthy people and constipated patients. The ICC for the weighted UniFrac distance, which is weighted by abundance, was lower than its unweighted counterpart, indicating that the unweighted measure is more robust and reproducible. CONCLUSIONS AND INFERENCES The intraindividual reproducibility of fecal microbiota in constipated patients is high and comparable to healthy participants. For most purposes, evaluating the fecal microbiota in a single stool sample should generally suffice in adequately powered studies of healthy and constipated patients.
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Affiliation(s)
- Gopanandan Parthasarathy
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905 USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905 USA,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905 USA
| | - Nicholas Chia
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905 USA,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905 USA
| | - Helen M. O'Connor
- Clinical Research and Trials Unit, Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, 55905 USA
| | - H. Rex Gaskins
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801 USA
| | - Adil E. Bharucha
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, 55905 USA
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110
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Wong WS, Clemency N, Klein E, Provenzano M, Iyer R, Niederhuber JE, Hourigan SK. Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants. MICROBIOME 2017; 5:114. [PMID: 28870234 PMCID: PMC5583988 DOI: 10.1186/s40168-017-0333-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 08/25/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Effective methods are needed to collect fecal samples from children for large-scale microbiota studies. Stool collected on fecal occult blood test (FOBT) cards that can be mailed provides an effective solution; however, the quality of sequencing resulting from this method is unknown. The aim of this study is to compare microbiota metrics of 16S ribosomal RNA (rRNA) gene sequencing from stool and meconium collected on FOBT cards with stool collected in an Eppendorf tube (ET) under different conditions. METHODS Eight stool samples from children in diapers aged 0 month-2 years and three meconium samples were collected and stored as follows: (1) ≤ 2 days at room temperature (RT) in an ET, (2) 7 days at - 80 °C in an ET, (3) 3-5 days at RT on a FOBT card, (4) 7 days at RT on a FOBT card, and (5) 7 days at - 80 °C on a FOBT card. Samples stored at - 80 °C were frozen immediately. Each specimen/condition underwent 16S rRNA gene sequencing with replicates on the Illumina MiSeq. Alpha and beta diversity measures and relative abundance of major phyla were compared between storage conditions and container (ET vs. FOBT card), with pairwise comparison between different storage conditions and the "standard" of 7 days at - 80 °C in an ET and fresh stool in an ET. RESULTS Stool samples clustered mainly by individual diaper (P < 10-5, Adonis), rather than by storage condition (P = 0.42) or container (P = 0.16). However, meconium samples clustered more by container (P = 0.002) than by individual diaper (P = 0.009) and storage condition (P = 0.02). Additionally, there were no differences in alpha diversity measures and relative abundance of major phyla after Bonferroni correction between stool stored on a FOBT card at RT for 7 days with stool stored in an ET tube at - 80 °C; differences in alpha diversity were seen however when compared to fresh stool in an ET. Overall, based on the intraclass correlation coefficient (ICC), the different storage containers/conditions are reliable in preserving the microbial memberships and slightly less reliable in preserving the alpha diversity and relative microbial composition of infant stool. CONCLUSIONS Acknowledging certain limitations, FOBT cards may be a useful tool in large-scale stool microbiota studies in children requiring outpatient follow-up where only small amounts of stool can be obtained, but should not be used when studying meconium.
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Affiliation(s)
- Wendy S.W. Wong
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - Nicole Clemency
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - Elisabeth Klein
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - Marina Provenzano
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - Ramaswamy Iyer
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - John E. Niederhuber
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
- Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205 USA
| | - Suchitra K. Hourigan
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
- Inova Children’s Hospital, 3300 Gallows Road, Falls Church, VA 22042 USA
- Pediatric Specialists of Virginia, 3023 Hamaker Court, Suite 600, Fairfax, VA 22031 USA
- Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205 USA
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111
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Couto Furtado Albuquerque M, van Herwaarden Y, Kortman GAM, Dutilh BE, Bisseling T, Boleij A. Preservation of bacterial DNA in 10-year-old guaiac FOBT cards and FIT tubes. J Clin Pathol 2017; 70:994-996. [PMID: 28830908 PMCID: PMC5749348 DOI: 10.1136/jclinpath-2017-204592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/03/2022]
Affiliation(s)
| | | | - Guus A M Kortman
- Department of Laboratory Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Bas E Dutilh
- Department of Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.,Center for Molecular and Biomolecular Informatics (CMBI), Radboudumc, Nijmegen, The Netherlands
| | - Tanya Bisseling
- Department of Gastroenterology, Radboudumc, Nijmegen, The Netherlands
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Evaluation of Copan FecalSwab as Specimen Type for Use in Xpert C. difficile Assay. J Clin Microbiol 2017; 55:3123-3129. [PMID: 28794179 PMCID: PMC5625397 DOI: 10.1128/jcm.00369-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/03/2017] [Indexed: 12/18/2022] Open
Abstract
Liquid-based microbiology (LBM) devices incorporating flocked swabs and preservation medium ease transport of specimens and improve specimen yield compared to traditional fiber wound swabs; however, the performance of LBM collection devices has not been evaluated in many molecular assays. It is unclear how the differences in matrix and specimen loading with an LBM device will affect test performance compared to traditional collection devices. The purpose of this study was to evaluate the performance of specimens collected in FecalSwab transport medium (Copan Diagnostics, Murrieta, CA) compared to unpreserved stool using the Cepheid Xpert C. difficile assay (Cepheid, Sunnyvale, CA). Results equivalent to unpreserved stool samples were obtained when 400 μl of FecalSwab-preserved stool was employed in the Xpert assay. The positive and negative percent agreement of specimens inoculated with FecalSwab medium (n = 281) was 97.0% (95% confidence interval [CI], 90.9 to 96.4%) and 99.4% (95% CI, 96.4 to 99.9%), respectively, compared to reference results obtained using unpreserved stool. Throughout this study, only four discrepant results occurred when comparing preserved specimens to unpreserved stool specimens in the Xpert C. difficile PCR assay. Post discrepant analysis, using the BD MAX Cdiff assay, the specificity and sensitivity both increased to 100%. The high positive and negative percent agreements observed in this study suggest that stool preserved in FecalSwab media yields equivalent results to using unpreserved stool when tested on the Xpert C. difficile assay, allowing laboratories to adopt this liquid-based microbiology collection device.
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Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh. Appl Environ Microbiol 2017; 83:AEM.00361-17. [PMID: 28258145 DOI: 10.1128/aem.00361-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 02/27/2017] [Indexed: 12/17/2022] Open
Abstract
To our knowledge, fecal microbiota collection methods have not been evaluated in low- and middle-income countries. Therefore, we evaluated five different fecal sample collection methods for technical reproducibility, stability, and accuracy within the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Fifty participants from the HEALS provided fecal samples in the clinic which were aliquoted into no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT) tubes. Half of the aliquots were frozen immediately at -80°C (day 0) and the remaining samples were left at ambient temperature for 96 h and then frozen (day 4). Intraclass correlation coefficients (ICC) were calculated for the relative abundances of the top three phyla, for two alpha diversity measures, and for four beta diversity measures. The duplicate samples had relatively high ICCs for technical reproducibility at day 0 and day 4 (range, 0.79 to 0.99). The FOBT card and samples preserved in RNAlater and 95% ethanol had the highest ICCs for stability over 4 days. The FIT tube had lower stability measures overall. In comparison to the "gold standard" method using immediately frozen fecal samples with no solution, the ICCs for many of the microbial metrics were low, but the rank order appeared to be preserved as seen by the Spearman correlation. The FOBT cards, 95% ethanol, and RNAlater were effective fecal preservatives. These fecal collection methods are optimal for future cohort studies, particularly in low- and middle-income countries.IMPORTANCE The collection of fecal samples in prospective cohort studies is essential to provide the opportunity to study the effect of the human microbiota on numerous health conditions. However, these collection methods have not been adequately tested in low- and middle-income countries. We present estimates of technical reproducibility, stability at ambient temperature for 4 days, and accuracy comparing a "gold standard" for fecal samples in no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test cards, and fecal immunochemical test tubes in a study conducted in Bangladesh. Fecal occult blood test cards and fecal samples stored in 95% ethanol or RNAlater adequately preserve fecal samples in this setting. Therefore, new studies in low- and middle-income countries should include collection of fecal samples using fecal occult blood test cards, 95% ethanol, or RNAlater for prospective cohort studies.
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Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping. mSystems 2017; 2:mSystems00199-16. [PMID: 28289733 PMCID: PMC5340865 DOI: 10.1128/msystems.00199-16] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/06/2017] [Indexed: 01/24/2023] Open
Abstract
The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members of the class Gammaproteobacteria, grow at room temperature, sometimes confusing microbiome results, particularly when stability is assumed. Although comparative benchmarking has shown that several preservation methods, including the use of 95% ethanol, fecal occult blood test (FOBT) and FTA cards, and Omnigene-GUT kits, reduce changes in taxon abundance during room-temperature storage, these techniques all have drawbacks and cannot be applied retrospectively to samples that have already been collected. Here we performed a meta-analysis using several different microbiome sample storage condition studies, showing consistent trends in which specific bacteria grew (i.e., "bloomed") at room temperature, and introduce a procedure for removing the sequences that most distort analyses. In contrast to similarity-based clustering using operational taxonomic units (OTUs), we use a new technique called "Deblur" to identify the exact sequences corresponding to blooming taxa, greatly reducing false positives and also dramatically decreasing runtime. We show that applying this technique to samples collected for the American Gut Project (AGP), for which participants simply mail samples back without the use of ice packs or other preservatives, yields results consistent with published microbiome studies performed with frozen or otherwise preserved samples. IMPORTANCE In many microbiome studies, the necessity to store samples at room temperature (i.e., remote fieldwork) and the ability to ship samples without hazardous materials that require special handling training, such as ethanol (i.e., citizen science efforts), is paramount. However, although room-temperature storage for a few days has been shown not to obscure physiologically relevant microbiome differences between comparison groups, there are still changes in specific bacterial taxa, notably, in members of the class Gammaproteobacteria, that can make microbiome profiles difficult to interpret. Here we identify the most problematic taxa and show that removing sequences from just a few fast-growing taxa is sufficient to correct microbiome profiles.
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Vogtmann E, Chen J, Amir A, Shi J, Abnet CC, Nelson H, Knight R, Chia N, Sinha R. Comparison of Collection Methods for Fecal Samples in Microbiome Studies. Am J Epidemiol 2017; 185:115-123. [PMID: 27986704 DOI: 10.1093/aje/kww177] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/21/2016] [Indexed: 12/14/2022] Open
Abstract
Prospective cohort studies are needed to assess the relationship between the fecal microbiome and human health and disease. To evaluate fecal collection methods, we determined technical reproducibility, stability at ambient temperature, and accuracy of 5 fecal collection methods (no additive, 95% ethanol, RNAlater Stabilization Solution, fecal occult blood test cards, and fecal immunochemical test tubes). Fifty-two healthy volunteers provided fecal samples at the Mayo Clinic in Rochester, Minnesota, in 2014. One set from each sample collection method was frozen immediately, and a second set was incubated at room temperature for 96 hours and then frozen. Intraclass correlation coefficients (ICCs) were calculated for the relative abundance of 3 phyla, 2 alpha diversity metrics, and 4 beta diversity metrics. Technical reproducibility was high, with ICCs for duplicate fecal samples between 0.64 and 1.00. Stability for most methods was generally high, although the ICCs were below 0.60 for 95% ethanol in metrics that were more sensitive to relative abundance. When compared with fecal samples that were frozen immediately, the ICCs were below 0.60 for the metrics that were sensitive to relative abundance; however, the remaining 2 alpha diversity and 3 beta diversity metrics were all relatively accurate, with ICCs above 0.60. In conclusion, all fecal sample collection methods appear relatively reproducible, stable, and accurate. Future studies could use these collection methods for microbiome analyses.
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Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, Yuen E, Freiman H, Lustbader I, Salik J, Friedlander C, Hayes RB, Ahn J. The gut microbiota in conventional and serrated precursors of colorectal cancer. MICROBIOME 2016; 4:69. [PMID: 28038683 PMCID: PMC5203720 DOI: 10.1186/s40168-016-0218-6] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/03/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Colorectal cancer is a heterogeneous disease arising from at least two precursors-the conventional adenoma (CA) and the serrated polyp. We and others have previously shown a relationship between the human gut microbiota and colorectal cancer; however, its relationship to the different early precursors of colorectal cancer is understudied. We tested, for the first time, the relationship of the gut microbiota to specific colorectal polyp types. RESULTS Gut microbiota were assessed in 540 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples. Participants were categorized as CA cases (n = 144), serrated polyp cases (n = 73), or polyp-free controls (n = 323). CA cases were further classified as proximal (n = 87) or distal (n = 55) and as non-advanced (n = 121) or advanced (n = 22). Serrated polyp cases were further classified as hyperplastic polyp (HP; n = 40) or sessile serrated adenoma (SSA; n = 33). We compared gut microbiota diversity, overall composition, and normalized taxon abundance among these groups. CA cases had lower species richness in stool than controls (p = 0.03); in particular, this association was strongest for advanced CA cases (p = 0.004). In relation to overall microbiota composition, only distal or advanced CA cases differed significantly from controls (p = 0.02 and p = 0.002). In taxon-based analysis, stool of CA cases was depleted in a network of Clostridia operational taxonomic units from families Ruminococcaceae, Clostridiaceae, and Lachnospiraceae, and enriched in the classes Bacilli and Gammaproteobacteria, order Enterobacteriales, and genera Actinomyces and Streptococcus (all q < 0.10). SSA and HP cases did not differ in diversity or composition from controls, though sample size for these groups was small. Few taxa were differentially abundant between HP cases or SSA cases and controls; among them, class Erysipelotrichi was depleted in SSA cases. CONCLUSIONS Our results indicate that gut microbes may play a role in the early stages of colorectal carcinogenesis through the development of CAs. Findings may have implications for developing colorectal cancer prevention therapies targeting early microbial drivers of colorectal carcinogenesis.
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Affiliation(s)
- Brandilyn A Peters
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Christine Dominianni
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Jean A Shapiro
- Division of Cancer Prevention and Control, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Timothy R Church
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Jing Wu
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - George Miller
- Department of Surgery, New York University School of Medicine, New York, NY, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
- NYU Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | | | - Hal Freiman
- Kips Bay Endoscopy Center, New York, NY, USA
| | | | - James Salik
- Kips Bay Endoscopy Center, New York, NY, USA
| | | | - Richard B Hayes
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- NYU Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Jiyoung Ahn
- Department of Population Health, New York University School of Medicine, New York, NY, USA.
- NYU Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
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Taylor M, Wood HM, Halloran SP, Quirke P. Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing. J Clin Pathol 2016; 70:600-606. [DOI: 10.1136/jclinpath-2016-204165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 01/19/2023]
Abstract
AimsWith a growing interest in the influence the gut microbiome has on the development of colorectal cancer (CRC), we investigated the feasibility and stability of isolating and typing microbial DNA from guaiac faecal occult blood test (gFOBt) cards. This has the future potential to screen the microbial populations present in confirmed colorectal neoplasia cases with aims to predict the presence and development of CRC.MethodsFresh stool samples from three healthy volunteers were applied to gFOBt cards. DNA was extracted from both the cards and fresh stool samples. A series of additional cards were prepared from one volunteer, and extracted at time points between 2 weeks and 3 years. The V4 region of the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq at 2×250 bp read lengths. Data were analysed using QIIME software.ResultsSamples were grouped both by volunteer and by type (fresh or gFOBt), and compared a variety of ways: visual inspection of taxa, α and β diversity, intraclass correlation. In all comparisons, samples grouped by volunteer, and not by sample type. The different time points showed no appreciable differences with increased storage time.ConclusionsThis study has demonstrated that there is good concordance between microbial DNA isolated from fresh stool sample, and from the matched gFOBt card. Samples stored for up to 3 years showed no detrimental effect on measureable microbial DNA. This study has important future implications for investigating microbial influence on CRC development and other pathologies.
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Baxter NT, Koumpouras CC, Rogers MAM, Ruffin MT, Schloss PD. DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model. MICROBIOME 2016; 4:59. [PMID: 27842559 PMCID: PMC5109736 DOI: 10.1186/s40168-016-0205-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND There is a significant demand for colorectal cancer (CRC) screening methods that are noninvasive, inexpensive, and capable of accurately detecting early stage tumors. It has been shown that models based on the gut microbiota can complement the fecal occult blood test and fecal immunochemical test (FIT). However, a barrier to microbiota-based screening is the need to collect and store a patient's stool sample. RESULTS Using stool samples collected from 404 patients, we tested whether the residual buffer containing resuspended feces in FIT cartridges could be used in place of intact stool samples. We found that the bacterial DNA isolated from FIT cartridges largely recapitulated the community structure and membership of patients' stool microbiota and that the abundance of bacteria associated with CRC were conserved. We also found that models for detecting CRC that were generated using bacterial abundances from FIT cartridges were equally predictive as models generated using bacterial abundances from stool. CONCLUSIONS These findings demonstrate the potential for using residual buffer from FIT cartridges in place of stool for microbiota-based screening for CRC. This may reduce the need to collect and process separate stool samples and may facilitate combining FIT and microbiota-based biomarkers into a single test. Additionally, FIT cartridges could constitute a novel data source for studying the role of the microbiome in cancer and other diseases.
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Affiliation(s)
- Nielson T. Baxter
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI USA
| | - Charles C. Koumpouras
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI USA
| | - Mary A. M. Rogers
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI USA
| | - Mack T. Ruffin
- Department of Family and Community Medicine, Penn State Hershey Medical Center, Hershey, PA USA
| | - Patrick D. Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI USA
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Loftfield E, Vogtmann E, Sampson JN, Moore SC, Nelson H, Knight R, Chia N, Sinha R. Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies. Cancer Epidemiol Biomarkers Prev 2016; 25:1483-1490. [PMID: 27543620 PMCID: PMC5093035 DOI: 10.1158/1055-9965.epi-16-0409] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/05/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The gut metabolome may be associated with the incidence and progression of numerous diseases. The composition of the gut metabolome can be captured by measuring metabolite levels in the feces. However, there are little data describing the effect of fecal sample collection methods on metabolomic measures. METHODS We collected fecal samples from 18 volunteers using four methods: no solution, 95% ethanol, fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT). One set of samples was frozen after collection (day 0), and for 95% ethanol, FOBT, and FIT, a second set was frozen after 96 hours at room temperature. We evaluated (i) technical reproducibility within sample replicates, (ii) stability after 96 hours at room temperature for 95% ethanol, FOBT, and FIT, and (iii) concordance of metabolite measures with the putative "gold standard," day 0 samples without solution. RESULTS Intraclass correlation coefficients (ICC) estimating technical reproducibility were high for replicate samples for each collection method. ICCs estimating stability at room temperature were high for 95% ethanol and FOBT (median ICC > 0.87) but not FIT (median ICC = 0.52). Similarly, Spearman correlation coefficients (rs) estimating metabolite concordance with the "gold standard" were higher for 95% ethanol (median rs = 0.82) and FOBT (median rs = 0.70) than for FIT (median rs = 0.40). CONCLUSIONS Metabolomic measurements appear reproducible and stable in fecal samples collected with 95% ethanol or FOBT. Concordance with the "gold standard" is highest with 95% ethanol and acceptable with FOBT. IMPACT Future epidemiologic studies should collect feces using 95% ethanol or FOBT if interested in studying fecal metabolomics. Cancer Epidemiol Biomarkers Prev; 25(11); 1483-90. ©2016 AACR.
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Affiliation(s)
- Erikka Loftfield
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Joshua N Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven C Moore
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Heidi Nelson
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Rob Knight
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota
- Department of Pediatrics, University of California San Diego, San Diego, California
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
- Department of Computer Science and Engineering, University of California San Diego, San Diego, California
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Yu G, Phillips S, Gail MH, Goedert JJ, Humphrys M, Ravel J, Ren Y, Caporaso NE. Evaluation of Buccal Cell Samples for Studies of Oral Microbiota. Cancer Epidemiol Biomarkers Prev 2016; 26:249-253. [DOI: 10.1158/1055-9965.epi-16-0538] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/30/2016] [Accepted: 10/03/2016] [Indexed: 11/16/2022] Open
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Amato KR. An introduction to microbiome analysis for human biology applications. Am J Hum Biol 2016; 29. [PMID: 27762069 DOI: 10.1002/ajhb.22931] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/04/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022] Open
Abstract
Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health. However, much remains to be learned about the broader ecological and evolutionary contexts within which gut microbes and humans are affecting each other. Here, I outline the procedures for generating data describing the gut microbiota with the goal of facilitating the wider integration of microbiome analyses into studies of human biology. I describe the steps involved in sample collection, DNA extraction, PCR amplification, high-throughput sequencing, and bioinformatics. While this review serves only as an introduction to these topics, it provides sufficient resources for researchers interested in launching new microbiome initiatives. As knowledge of these methods spreads, microbiome analysis should become a standard tool in the arsenal of human biology research.
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Affiliation(s)
- Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, 60208
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122
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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: 104] [Impact Index Per Article: 13.0] [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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Hale VL, Chen J, Johnson S, Harrington SC, Yab TC, Smyrk TC, Nelson H, Boardman LA, Druliner BR, Levin TR, Rex DK, Ahnen DJ, Lance P, Ahlquist DA, Chia N. Shifts in the Fecal Microbiota Associated with Adenomatous Polyps. Cancer Epidemiol Biomarkers Prev 2016; 26:85-94. [PMID: 27672054 DOI: 10.1158/1055-9965.epi-16-0337] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Adenomatous polyps are the most common precursor to colorectal cancer, the second leading cause of cancer-related death in the United States. We sought to learn more about early events of carcinogenesis by investigating shifts in the gut microbiota of patients with adenomas. METHODS We analyzed 16S rRNA gene sequences from the fecal microbiota of patients with adenomas (n = 233) and without (n = 547). RESULTS Multiple taxa were significantly more abundant in patients with adenomas, including Bilophila, Desulfovibrio, proinflammatory bacteria in the genus Mogibacterium, and multiple Bacteroidetes species. Patients without adenomas had greater abundances of Veillonella, Firmicutes (Order Clostridia), and Actinobacteria (family Bifidobacteriales). Our findings were consistent with previously reported shifts in the gut microbiota of colorectal cancer patients. Importantly, the altered adenoma profile is predicted to increase primary and secondary bile acid production, as well as starch, sucrose, lipid, and phenylpropanoid metabolism. CONCLUSIONS These data hint that increased sugar, protein, and lipid metabolism along with increased bile acid production could promote a colonic environment that supports the growth of bile-tolerant microbes such as Bilophilia and Desulfovibrio In turn, these microbes may produce genotoxic or inflammatory metabolites such as H2S and secondary bile acids, which could play a role in catalyzing adenoma development and eventually colorectal cancer. IMPACT This study suggests a plausible biological mechanism to explain the links between shifts in the microbiota and colorectal cancer. This represents a first step toward resolving the complex interactions that shape the adenoma-carcinoma sequence of colorectal cancer and may facilitate personalized therapeutics focused on the microbiota. Cancer Epidemiol Biomarkers Prev; 26(1); 85-94. ©2016 AACR.
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Affiliation(s)
- Vanessa L Hale
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Stephen Johnson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Sean C Harrington
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Thomas C Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota
| | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brooke R Druliner
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Theodore R Levin
- Division of Gastroenterology, Kaiser Permanente, Oakland, California
| | - Douglas K Rex
- Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Dennis J Ahnen
- Denver Department of Veterans Affairs Medical Center, University of Colorado Denver School of Medicine, Denver, Colorado
| | - Peter Lance
- University of Arizona Cancer Center, Tucson, Arizona
| | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, Rochester, Minnesota.
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
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Sung J, Hale V, Merkel AC, Kim PJ, Chia N. Metabolic modeling with Big Data and the gut microbiome. Appl Transl Genom 2016; 10:10-5. [PMID: 27668170 PMCID: PMC5025471 DOI: 10.1016/j.atg.2016.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 01/19/2016] [Accepted: 02/02/2016] [Indexed: 12/20/2022]
Abstract
The recent advances in high-throughput omics technologies have enabled researchers to explore the intricacies of the human microbiome. On the clinical front, the gut microbial community has been the focus of many biomarker-discovery studies. While the recent deluge of high-throughput data in microbiome research has been vastly informative and groundbreaking, we have yet to capture the full potential of omics-based approaches. Realizing the promise of multi-omics data will require integration of disparate omics data, as well as a biologically relevant, mechanistic framework - or metabolic model - on which to overlay these data. Also, a new paradigm for metabolic model evaluation is necessary. Herein, we outline the need for multi-omics data integration, as well as the accompanying challenges. Furthermore, we present a framework for characterizing the ecology of the gut microbiome based on metabolic network modeling.
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Affiliation(s)
- Jaeyun Sung
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Vanessa Hale
- Center for Individualized Medicine, Microbiome Program, Mayo Clinic, Rochester, MN 55905, USA
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Annette C. Merkel
- Center for Individualized Medicine, Microbiome Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Pan-Jun Kim
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 37673, Republic of Korea
- Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Nicholas Chia
- Center for Individualized Medicine, Microbiome Program, Mayo Clinic, Rochester, MN 55905, USA
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biomedical Engineering, Mayo College, Rochester, MN 55905, USA
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125
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Blekhman R, Tang K, Archie EA, Barreiro LB, Johnson ZP, Wilson ME, Kohn J, Yuan ML, Gesquiere L, Grieneisen LE, Tung J. Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Sci Rep 2016; 6:31519. [PMID: 27528013 PMCID: PMC4985740 DOI: 10.1038/srep31519] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/20/2016] [Indexed: 02/01/2023] Open
Abstract
Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples—unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.
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Affiliation(s)
- Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55108, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55108, USA
| | - Karen Tang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55108, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55108, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 45665, USA.,Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya
| | - Luis B Barreiro
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Quebec, H3T 1C5 Canada
| | - Zachary P Johnson
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Mark E Wilson
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Jordan Kohn
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Michael L Yuan
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | | | - Laura E Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 45665, USA
| | - Jenny Tung
- Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Department of Biology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham NC 27708, USA
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126
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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: 440] [Impact Index Per Article: 55.0] [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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127
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Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems 2016; 1:mSystems00021-16. [PMID: 27822526 PMCID: PMC5069758 DOI: 10.1128/msystems.00021-16] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/05/2016] [Indexed: 01/10/2023] Open
Abstract
Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide excellent microbiome stability out to 8 weeks, opening up a range of field studies with humans and wildlife that would otherwise be cost-prohibitive. Immediate freezing at −20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible for many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including such types of variation as freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions. We found that three of the methods—95% ethanol, FTA cards, and the OMNIgene Gut kit—can preserve samples sufficiently well at ambient temperatures such that differences at 8 weeks are comparable to differences among technical replicates. However, even the worst methods, including those with no fixative, were able to reveal microbiome differences between species at 8 weeks and between individuals after a week, allowing meta-analyses of samples collected using various methods when the effect of interest is expected to be larger than interindividual variation (although use of a single method within a study is strongly recommended to reduce batch effects). Encouragingly for FTA cards, the differences caused by this method are systematic and can be detrended. As in other studies, we strongly caution against the use of 70% ethanol. The results, spanning 15 individuals and over 1,200 samples, provide our most comprehensive view to date of storage effects on stool and provide a paradigm for the future studies of other sample types that will be required to provide a global view of microbial diversity and its interaction among humans, animals, and the environment. IMPORTANCE Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide excellent microbiome stability out to 8 weeks, opening up a range of field studies with humans and wildlife that would otherwise be cost-prohibitive.
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128
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Fu BC, Randolph TW, Lim U, Monroe KR, Cheng I, Wilkens LR, Le Marchand L, Hullar MAJ, Lampe JW. Characterization of the gut microbiome in epidemiologic studies: the multiethnic cohort experience. Ann Epidemiol 2016; 26:373-9. [PMID: 27039047 PMCID: PMC4892953 DOI: 10.1016/j.annepidem.2016.02.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/03/2016] [Accepted: 02/26/2016] [Indexed: 12/30/2022]
Abstract
PURPOSE The development of next-generation sequencing and accompanying bioinformatics tools has revolutionized characterization of microbial communities. As interest grows in the role of the human microbiome in health and disease, so does the need for well-powered, robustly designed epidemiologic studies. Here, we discuss sources of bias that can arise in gut microbiome research. METHODS Research comparing methods of specimen collection, preservation, processing, and analysis of gut microbiome samples is reviewed. Although selected studies are primarily based on the gut, many of the same principles are applicable to samples derived from other anatomical sites. Methods for participant recruitment and sampling of the gut microbiome implemented in an ongoing population-based study, the Multiethnic Cohort (MEC), are also described. RESULTS Variation in methodologies can influence the results of human microbiome studies. To help minimize bias, techniques such as sample homogenization, addition of internal standards, and quality filtering should be adopted in protocols. Within the MEC, participant response rates to stool sample collection were comparable to other studies, and in-home stool sample collection yields sufficient high-quality DNA for gut microbiome analysis. CONCLUSIONS Application of standardized and quality controlled methods in human microbiome studies is necessary to ensure data quality and comparability among studies.
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Affiliation(s)
- Benjamin C Fu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Epidemiology, University of Washington, Seattle
| | - Timothy W Randolph
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu
| | - Kristine R Monroe
- Department of Preventive Medicine, University of Southern California, Los Angeles
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont; Stanford Cancer Institute, Stanford, CA
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu
| | - Meredith A J Hullar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Johanna W Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Epidemiology, University of Washington, Seattle.
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129
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Drew DA, Lochhead P, Abu-Ali G, Chan AT, Huttenhower C, Izard J. Fecal Microbiome in Epidemiologic Studies-Letter. Cancer Epidemiol Biomarkers Prev 2016; 25:869. [PMID: 26961995 DOI: 10.1158/1055-9965.epi-16-0063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 11/16/2022] Open
Affiliation(s)
- David A Drew
- Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
| | - Paul Lochhead
- Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Galeb Abu-Ali
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jacques Izard
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts
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130
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Sinha R, Vogtmann E, Chen J, Amir A, Shi J, Sampson J, Flores R, Knight R, Chia N. Fecal Microbiome in Epidemiologic Studies-Response. Cancer Epidemiol Biomarkers Prev 2016; 25:870-1. [PMID: 26961994 DOI: 10.1158/1055-9965.epi-16-0161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 02/18/2016] [Indexed: 11/16/2022] Open
Affiliation(s)
- Rashmi Sinha
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland.
| | - Emily Vogtmann
- Nutritional Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland. Cancer Prevention Fellowship Program, Division of Cancer Prevention, NIH, NCI, Bethesda, Maryland
| | - Jun Chen
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota. Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Joshua Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Roberto Flores
- Nutritional Science Research Group, Division of Cancer Prevention, NIH, NCI, Bethesda, Maryland
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California. Department of Computer Science & Engineering, University of California San Diego, La Jolla, California
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota. Health Sciences Research, Mayo Clinic, Rochester, Minnesota. Department of Surgery, Mayo Clinic, Rochester, Minnesota. Biomedical Engineering and Physiology, Mayo College, Rochester, Minnesota.
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