1
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Maghini DG, Dvorak M, Dahlen A, Roos M, Kuersten S, Bhatt AS. Quantifying bias introduced by sample collection in relative and absolute microbiome measurements. Nat Biotechnol 2024; 42:328-338. [PMID: 37106038 DOI: 10.1038/s41587-023-01754-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.
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Affiliation(s)
- Dylan G Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mai Dvorak
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alex Dahlen
- Quantitative Sciences Unit, Stanford University, Stanford, CA, USA
| | | | | | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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2
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Rodger G, Chau K, Aranega-Bou P, Roohi A, Moore G, Hopkins KL, Hopkins S, Walker AS, Stoesser N. A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing. J Hosp Infect 2024; 144:128-136. [PMID: 38145816 DOI: 10.1016/j.jhin.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Hospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterize these factors are lacking. AIMS To validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ('resistome') composition of sink trap samples for metagenomic sequencing. METHODS Antibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a 'real-world' pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at ∼22 °C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0). FINDINGS The limits of detection for each antibiotic were: 3 μg/L (ampicillin), 10 μg/L (doxycycline), 20 μg/L (sulfamethoxazole) and 8 μg/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterized 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulphonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at ∼22 °C for up to five days. CONCLUSIONS Dipsticks can be used to detect antibiotic residues and characterize water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.
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Affiliation(s)
- G Rodger
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - K Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - P Aranega-Bou
- Biosafety, Air and Water Microbiology Group, UK Health Security Agency, Porton Down, UK
| | - A Roohi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK
| | - G Moore
- Biosafety, Air and Water Microbiology Group, UK Health Security Agency, Porton Down, UK
| | | | - S Hopkins
- UK Health Security Agency, Colindale, UK
| | - A S Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - N Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Health Protection Unit in Antimicrobial Resistance and Healthcare-associated Infection, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
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3
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Pang S, Chen X, Lu Z, Meng L, Huang Y, Yu X, Huang L, Ye P, Chen X, Liang J, Peng T, Luo W, Wang S. Longevity of centenarians is reflected by the gut microbiome with youth-associated signatures. NATURE AGING 2023; 3:436-449. [PMID: 37117794 DOI: 10.1038/s43587-023-00389-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/27/2023] [Indexed: 04/30/2023]
Abstract
Centenarians are an excellent model to study the relationship between the gut microbiome and longevity. To characterize the gut microbiome signatures of aging, we conducted a cross-sectional investigation of 1,575 individuals (20-117 years) from Guangxi province of China, including 297 centenarians (n = 45 with longitudinal sampling). Compared to their old adult counterparts, centenarians displayed youth-associated features in the gut microbiome characterized by an over-representation of a Bacteroides-dominated enterotype, increase in species evenness, enrichment of potentially beneficial Bacteroidetes and depletion of potential pathobionts. Health status stratification in older individuals did not alter the directional trends for these signature comparisons but revealed more apparent associations in less healthy individuals. Importantly, longitudinal analysis of centenarians across a 1.5-year period indicated that the youth-associated gut microbial signatures were enhanced with regard to increased evenness, reduction in interindividual variation and stability of Bacteroides, and that centenarians with low microbial evenness were prone to large microbiome instability during aging. These results together highlight a youth-related aging pattern of the gut microbiome for long-lived individuals.
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Affiliation(s)
- Shifu Pang
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China
| | - Xiaodong Chen
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China
- The Grand Health Industry Research Institute, Guangxi Academy of Sciences, Nanning, China
| | - Zhilong Lu
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China
| | - Lili Meng
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China
| | - Yu Huang
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China
| | - Xiuqi Yu
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China
| | - Lianfei Huang
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengpeng Ye
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China
| | - Xiaochun Chen
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China
| | - Jian Liang
- Medical College, Guangxi University, Nanning, China
| | - Tao Peng
- Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Weifei Luo
- AIage Life Science Corporation Ltd., Guangxi Free Trade Zone Aisheng Biotechnology Corporation Ltd., Nanning, China.
- The Grand Health Industry Research Institute, Guangxi Academy of Sciences, Nanning, China.
- State Key Laboratory of Non-food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, China.
| | - Shuai Wang
- The Grand Health Industry Research Institute, Guangxi Academy of Sciences, Nanning, China.
- State Key Laboratory of Veterinary Etiological Biology, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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4
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Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Sci Alliance 2023; 6:6/3/e202201833. [PMID: 36522135 PMCID: PMC9756366 DOI: 10.26508/lsa.202201833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Füssy
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth H Richardson
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikola Zarevski
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Nastasia J Freyria
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Federico M Ibarbalz
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Juan Jose Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robyn E Edgar
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Lori Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John McFarlane
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Charlotte Nef
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Anna Mg Novák Vanclová
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Yi Peng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marianne Potvin
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colomban de Vargas
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Pelletier
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Patrick Wincker
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
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5
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Chapman JA, Stewart CJ. Methodological challenges in neonatal microbiome research. Gut Microbes 2023; 15:2183687. [PMID: 36843005 PMCID: PMC9980642 DOI: 10.1080/19490976.2023.2183687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 02/16/2023] [Indexed: 02/28/2023] Open
Abstract
Following microbial colonization at birth, the gut microbiome plays a vital role in the healthy development of human neonates and impacts both health and disease in later life. Understanding the development of the neonatal gut microbiome and how it interacts with the neonatal host are therefore important areas of study. However, research within this field must address a range of specific challenges that impact the design and implementation of research methods. If not considered ahead of time, these challenges have the potential to introduce biases into studies, negatively affecting the relevance, reproducibility, and impact of any findings. This review outlines the nature of these challenges and points to current and future solutions, as outlined in the literature, to assist researchers in the early stages of study design.
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Affiliation(s)
- Jonathan A Chapman
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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6
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Steiner HE, Patterson HK, Giles JB, Karnes JH. Bringing pharmacomicrobiomics to the clinic through well-designed studies. Clin Transl Sci 2022; 15:2303-2315. [PMID: 35899413 PMCID: PMC9579385 DOI: 10.1111/cts.13381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 01/25/2023] Open
Abstract
Pharmacomicrobiomic studies investigate drug-microbiome interactions, such as the effect of microbial variation on drug response and disposition. Studying and understanding the interactions between the gut microbiome and drugs is becoming increasingly relevant to clinical practice due to its potential for avoiding adverse drug reactions or predicting variability in drug response. The highly variable nature of the human microbiome presents significant challenges to assessing microbes' influence. Studies aiming to explore drug-microbiome interactions should be well-designed to account for variation in the microbiome over time and collect data on confounders such as diet, disease, concomitant drugs, and other environmental factors. Here, we assemble a set of important considerations and recommendations for the methodological features required for performing a pharmacomicrobiomic study in humans with a focus on the gut microbiome. Consideration of these factors enable discovery, reproducibility, and more accurate characterization of the relationships between a given drug and the microbiome. Furthermore, appropriate interpretation and dissemination of results from well-designed studies will push the field closer to clinical relevance and implementation.
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Affiliation(s)
- Heidi E. Steiner
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Hayley K. Patterson
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Jason B. Giles
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Jason H. Karnes
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA,Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
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7
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Orwoll ES, Parimi N, Wiedrick J, Lapidus J, Napoli N, Wilkinson JE, Huttenhower C, Langsetmo L, Kiel DP. Analysis of the Associations Between the Human Fecal Microbiome and Bone Density, Structure, and Strength: The Osteoporotic Fractures in Men (MrOS) Cohort. J Bone Miner Res 2022; 37:597-607. [PMID: 35119137 PMCID: PMC9605688 DOI: 10.1002/jbmr.4518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/27/2021] [Accepted: 01/13/2022] [Indexed: 11/08/2022]
Abstract
In preclinical models, the composition and function of the gut microbiota have been linked to bone growth and homeostasis, but there are few available data from studies of human populations. In a hypothesis-generating experiment in a large cohort of community-dwelling older men (n = 831; age range, 78-98 years), we explored the associations between fecal microbial profiles and bone density, microarchitecture, and strength measured with total hip dual-energy X-ray absorptiometry (DXA) and high-resolution peripheral quantitative computed tomography (HRpQCT) (distal radius, distal and diaphyseal tibia). Fecal samples were collected and the 16S rRNA gene V4 hypervariable region sequenced. Sequences were bioinformatically processed through the DADA2 pipeline and then taxonomically assigned using SILVA. Generalized linear models as implemented in microbiome multivariable association with linear models (MaAsLin 2) were used to test for associations between skeletal measures and specific microbial genera. The abundances of four bacterial genera were weakly associated with bone density, structure, or strength (false discovery rate [FDR] ≤ 0.05), and the measured directions of associations of genera were generally consistent across multiple bone measures, supporting a role for microbiota on skeletal homeostasis. However, the associated effect sizes were small (log2 fold change < ±0.35), limiting power to confidently identify these associations even with high resolution skeletal imaging phenotypes, and we assessed the resulting implications for the design of future cohort-based studies. As in analogous examples from genomewide association studies, we find that larger cohort sizes will likely be needed to confidently identify associations between the fecal microbiota and skeletal health relying on 16S sequencing. Our findings bolster the view that the gut microbiome is associated with clinically important measures of bone health, while also indicating the challenges in the design of cohort-based microbiome studies. © 2022 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Eric S Orwoll
- Department of Medicine, Oregon Health & Sciences University, Portland, OR, USA
| | - Neeta Parimi
- San Francisco Coordinating Center, San Francisco, CA, USA
| | - Jack Wiedrick
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA
| | - Jodi Lapidus
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA.,Oregon Health & Science University - Portland State University School of Public Health, Portland, OR, USA
| | - Nicola Napoli
- Department of Medicine, Unit of Endocrinology and Diabetes, Campus Bio-Medico University of Rome, Rome, Italy.,Division of Bone and Mineral Diseases, Washington University, St Louis, MO, USA
| | - Jeremy E Wilkinson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lisa Langsetmo
- School of Public Health, University of Minnesota, Twin Cities, Minneapolis, MN, USA
| | - Douglas P Kiel
- Hinda and Arthur Marcus Institute for Aging Research, Hebrew Senior Life, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT & Harvard, Cambridge, MA, USA
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8
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Monger XC, Saucier L, Gilbert AA, Vincent AT. Stabilization of swine faecal samples influences taxonomic and functional results in microbiome analyses. MethodsX 2022; 9:101716. [PMID: 35601955 PMCID: PMC9118172 DOI: 10.1016/j.mex.2022.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
Stabilization of faecal samples improves the integrity of extracted DNA. Microbiome results are affected by sample stabilization. Results are similar for samples that were stabilized when frozen, to samples that were stabilized before freezing.
Studies on the microbiome of different species are on the rise, due to a growing interest in animal health and the safety of food products of animal origin. A challenge with studying animals’ microbiomes is to find methods that obtain a good representation of the microbial community of interest. Good unbiased sampling protocols are the basis for a solid experimental design, but may need to be done in environments where sample preservation could be difficult. In this study, we evaluate by shotgun sequencing the impact of stabilizing swine faeces samples using a commercial stabilizer (PERFORMAbiome • GUT | PB-200, DNA Genotek). Using stabilizer makes it possible to obtain DNA that is significantly less degraded than when the samples are not stabilized. Also, the results on the taxonomy and on the bacterial functions encoded in the microbiome are impacted by whether or not the samples are stabilized. Finally, the stabilization of samples that had already been frozen and stored at -80°C led to extraction and DNA quality results similar to those obtained from samples that were stabilized before freezing.
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9
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Harder CB, Persson S, Christensen J, Ljubic A, Nielsen EM, Hoorfar J. Molecular diagnostics of Salmonella and Campylobacter in human/animal fecal samples remain feasible after long-term sample storage without specific requirements. AIMS Microbiol 2022; 7:399-414. [PMID: 35071939 PMCID: PMC8712530 DOI: 10.3934/microbiol.2021024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/05/2021] [Indexed: 11/27/2022] Open
Abstract
Rapid advances in the development of sequencing technologies, numbers of commercial providers and diminishing costs have made DNA-based identification and diagnostics increasingly accessible to doctors and laboratories, eliminating the need for local investments in expensive technology and training or hiring of skilled technicians. However, reliable and comparable molecular analyses of bacteria in stool samples are dependent on storage and workflow conditions that do not introduce post-sampling bias, the most important factor being the need to keep the DNA at a stable detectable level. For that reason, there may remain other prohibitively costly requirements for cooling or freezing equipment or special chemical additives. This study investigates the diagnostic detectability of Salmonella and Campylobacter DNA in human, pig and chicken stool samples, stored at different temperatures and with different preservation methods. Stool samples were spiked with 106 CFU/mL of both Salmonella and Campylobacter strains stored at −20 °C, 5 °C and 20 °C (Room temperature, RT) and treated with either RNAlater, EDTA or Silica/ethanol. DNA was extracted at 9 different time points within 30 days and quantified by Qubit (total DNA) and qPCR (Salmonella and Campylobacter DNA). We found no statistically significant differences among the different preservation methods, and DNA from both species was easily detected at all time points and at all temperatures, both with and without preservation. This suggests that infections by these bacteria can be diagnosed and possibly also analysed in further detail simply by taking a stool sample in any suitable sealed container that can be transported to laboratory analysis without special storage or preservation requirements. We briefly discuss how this finding can benefit infection control in both developed and developing countries.
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Affiliation(s)
- C B Harder
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark.,Molecular Ecology, Microbial Ecology and Evolutionary Genetics, Lund University, Sölvegatan 37, 223 62 Lund
| | - S Persson
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark
| | - J Christensen
- Danish Veterinary and Food Administration, Microbiological department, Søndervang 4, 4100 Ringsted
| | - A Ljubic
- AGC Biologics, Process Transfer, Vandtårnsvej 83, 2860 Søborg, Denmark
| | - E M Nielsen
- Statens Serum institut, Dept. Bacteriology, Parasitology and Fungi, Artillerivej 5, 2300 Copenhagen, Denmark
| | - J Hoorfar
- Technical University of Denmark, National Food Institute, 2800 Kgs. Lyngby, Denmark
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10
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Abstract
Integrative analysis of high-quality metagenomics and metabolomics data from fecal samples provides novel clues for the mechanism underpinning gut microbe-human interactions. However, data regarding the influence of fecal collection methods on both metagenomics and metabolomics are sparse. Six fecal collection methods (the gold standard [GS] [i.e., immediate freezing at −80°C with no solution], 95% ethanol, RNAlater, OMNIgene Gut, fecal occult blood test [FOBT] cards, and Microlution) were used to collect 88 fecal samples from eight healthy volunteers for whole-genome shotgun sequencing (WGSS) and untargeted metabolomic profiling. Metrics assessed included the abundances of predominant phyla and α- and β-diversity at the species, gene, and pathway levels. Intraclass correlation coefficients (ICCs) were calculated for microbes and metabolites to estimate (i) stability (day 4 versus day 0 within each method), (ii) concordance (day 0 for each method versus the GS), and (iii) reliability (day 4 for each method versus the GS). For the top 4 phyla and microbial diversity metrics at the species, gene, and pathway levels, generally high stability and reliability were observed for most methods except for 95% ethanol; similar concordances were seen for different methods. For metabolomics data, 95% ethanol showed the highest stability, concordance, and reliability (median ICCs = 0.71, 0.71, and 0.65, respectively). Taken together, OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles. We recommend using separate collecting methods for gut metagenomic sequencing and fecal metabolomic profiling in large population studies. IMPORTANCE The choice of fecal collection method is essential for studying gut microbe-human interactions in large-scale population-based research. In this study, we examined the effects of fecal collection methods and storage time at ambient temperature on variations in the gut microbiome community composition; microbial diversity metrics at the species, gene, and pathway levels; antibiotic resistance genes; and metabolome profiling. Our findings suggest using different fecal sample collection methods for different data generation purposes. OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles.
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11
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Orsso CE, Peng Y, Deehan EC, Tan Q, Field CJ, Madsen KL, Walter J, Prado CM, Tun HM, Haqq AM. Composition and Functions of the Gut Microbiome in Pediatric Obesity: Relationships with Markers of Insulin Resistance. Microorganisms 2021; 9:1490. [PMID: 34361925 PMCID: PMC8304481 DOI: 10.3390/microorganisms9071490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022] Open
Abstract
The gut microbiome is hypothesized to play a crucial role in the development of obesity and insulin resistance (IR); the pathways linking the microbiome to IR in pediatrics have yet to be precisely characterized. We aimed to determine the relationship between the gut microbiome composition and metabolic functions and IR in children with obesity. In a cross-sectional study, fecal samples from children with obesity (10-16 years old) were collected for taxonomical and functional analysis of the fecal microbiome using shotgun metagenomics. The homeostatic model assessment for insulin resistance (HOMA-IR) was determined using fasting glucose and insulin. Associations between HOMA-IR and α-diversity measures as well as metabolic pathways were evaluated using Spearman correlations; relationships between HOMA-IR and β-diversity were assessed by permutational multivariate analysis of variance. Twenty-one children (nine males; median: age = 12.0 years; BMI z-score = 2.9; HOMA-IR = 3.6) completed the study. HOMA-IR was significantly associated with measures of α-diversity but not with β-diversity. Children with higher HOMA-IR exhibited lower overall species richness, Firmicutes species richness, and overall Proteobacteria species Shannon diversity. Furthermore, HOMA-IR was inversely correlated with the abundance of pathways related to the biosynthesis of lipopolysaccharides, amino acids, and short-chain fatty acids, whereas positive correlations between HOMA-IR and the peptidoglycan biosynthesis pathways were observed. In conclusion, insulin resistance was associated with decreased microbial α-diversity measures and abundance of genes related to the metabolic pathways. Our study provides a framework for understanding the microbial alterations in pediatric obesity.
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Affiliation(s)
- Camila E. Orsso
- Human Nutrition Research Unit, Department of Agricultural, Food and Nutritional Science, 4-002 Li Ka Shing Centre for Health Innovation, University of Alberta, Edmonton, AB T6G 2E1, Canada; (C.E.O.); (C.M.P.)
| | - Ye Peng
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Hong Kong 999077, China;
| | - Edward C. Deehan
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2C2, Canada; (E.C.D.); (K.L.M.)
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Qiming Tan
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Catherine J. Field
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1, Canada;
| | - Karen L. Madsen
- Department of Medicine, University of Alberta, Edmonton, AB T6G 2C2, Canada; (E.C.D.); (K.L.M.)
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology, and Department of Medicine, University College Cork—National University of Ireland, T12 YT20 Cork, Ireland;
| | - Carla M. Prado
- Human Nutrition Research Unit, Department of Agricultural, Food and Nutritional Science, 4-002 Li Ka Shing Centre for Health Innovation, University of Alberta, Edmonton, AB T6G 2E1, Canada; (C.E.O.); (C.M.P.)
| | - Hein M. Tun
- HKU-Pasteur Research Pole, School of Public Health, University of Hong Kong, Hong Kong 999077, China;
| | - Andrea M. Haqq
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada;
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1, Canada;
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12
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Pribyl AL, Parks DH, Angel NZ, Boyd JA, Hasson AG, Fang L, MacDonald SL, Wills BA, Wood DLA, Krause L, Tyson GW, Hugenholtz P. Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME COMMUNICATIONS 2021; 1:14. [PMID: 37938632 PMCID: PMC9645250 DOI: 10.1038/s43705-021-00014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
Abstract
The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.
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Affiliation(s)
| | | | | | - Joel A Boyd
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | - Liang Fang
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | | | | | - Lutz Krause
- Microba Life Sciences, Brisbane, QLD, Australia
| | - Gene W Tyson
- Microba Life Sciences, Brisbane, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Science, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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13
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Everett C, Li C, Wilkinson JE, Nguyen LH, McIver LJ, Ivey K, Izard J, Palacios N, Eliassen AH, Willett WC, Ascherio A, Sun Q, Tworoger SS, Chan AT, Garrett WS, Huttenhower C, Rimm EB, Song M. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies. Nat Protoc 2021; 16:2724-2731. [PMID: 33883746 DOI: 10.1038/s41596-021-00519-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/16/2021] [Indexed: 02/06/2023]
Abstract
A lack of prospective studies has been a major barrier for assessing the role of the microbiome in human health and disease on a population-wide scale. To address this significant knowledge gap, we have launched a large-scale collection targeting fecal and oral microbiome specimens from 20,000 women within the Nurses' Health Study II cohort (the Microbiome Among Nurses study, or Micro-N). Leveraging the rich epidemiologic data that have been repeatedly collected from this cohort since 1989; the established biorepository of archived blood, urine, buccal cell, and tumor tissue specimens; the available genetic and biomarker data; the cohort's ongoing follow-up; and the BIOM-Mass microbiome research platform, Micro-N furnishes unparalleled resources for future prospective studies to interrogate the interplay between host, environmental factors, and the microbiome in human health. These prospectively collected materials will provide much-needed evidence to infer causality in microbiome-associated outcomes, paving the way toward development of microbiota-targeted modulators, preventives, diagnostics and therapeutics. Here, we describe a generalizable, scalable and cost-effective platform used for stool and oral microbiome specimen and metadata collection in the Micro-N study as an example of how prospective studies of the microbiome may be carried out.
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Affiliation(s)
- Christine Everett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Chengchen Li
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy E Wilkinson
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren J McIver
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kerry Ivey
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,South Australian Health and Medical Research Institute, Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia.,Department of Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Jacques Izard
- Food Science and Technology Department, Institute of Agriculture and Natural Resources, University of Nebraska, Lincoln, NE, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Natalia Palacios
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Public Health, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - A Heather Eliassen
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Walter C Willett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Alberto Ascherio
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Qi Sun
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Shelley S Tworoger
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Andrew T Chan
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Wendy S Garrett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric B Rimm
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mingyang Song
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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14
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Westaway JAF, Huerlimann R, Miller CM, Kandasamy Y, Norton R, Rudd D. Methods for exploring the faecal microbiome of premature infants: a review. Matern Health Neonatol Perinatol 2021; 7:11. [PMID: 33685524 PMCID: PMC7941982 DOI: 10.1186/s40748-021-00131-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration.
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Affiliation(s)
- Jacob A F Westaway
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Roger Huerlimann
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
| | - Catherine M Miller
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia
| | - Yoga Kandasamy
- Townsville University Hospital, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Robert Norton
- Pathology Queensland, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Donna Rudd
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
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15
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Doludin YV, Limonova AS, Kozlova VA, Efimova AI, Borisova AL, Meshkov AN, Pokrovskaya MS, Drapkina OM. Collection and storage of DNA-containing biomaterial and isolated DNA. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2020. [DOI: 10.15829/1728-8800-2020-2730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The advances of biomedicine include the new technologies, diagnosis and treatment techniques, as well as the practical use of new types of biological targets, in particular, nucleic acids. Genomic deoxyribonucleic acid (DNA), extracellular DNA (exDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. The use of new technologies for DNA analysis required the development of standardized methods for processing biological samples in order to obtain high-quality DNA samples. The research uses various methods for collecting, preparing samples and storing various DNA-containing biomaterials and isolated DNA, as well as methods for assessing the quality of samples and biobank standards. It is obvious that the use of uniform standards will allow large-scale genetic research on the basis of biobanks and research laboratories. Specialists from professional organizations such as International Society for Biological and Environmental Repositories (ISBER), Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), European, Middle Eastern & African Society for Biopreservationa and Biobanking (ESBB) and the Russian National Association of Biobanks and Biobanking Professionals.
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Affiliation(s)
- Yu. V. Doludin
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. S. Limonova
- National Medical Research Center for Therapy and Preventive Medicine
| | - V. A. Kozlova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. I. Efimova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. L. Borisova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine
| | - M. S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
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16
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Bai Y, Li H, Liu Y. Visualizing research trends and research theme evolution in E-learning field: 1999–2018. Scientometrics 2020. [DOI: 10.1007/s11192-020-03760-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractThis paper aims to provide a comprehensive understanding of the evolution of major research themes and trends in e-learning research. A co-word analysis is applied for the analysis of the 21,656 keywords collected from 7214 articles published in 10 journals in the field of e-learning from the years 1999 to 2018. Specifically, a cluster analysis, social network analysis, strategic diagram, and graph theory were applied in the analysis for two time periods: 1999–2008 and 2009–2018. The study detects the bridging, popular, and core topics in e-learning research for the two periods. The research results indicate that e-learning research has undergone a health evolution over the past two decades. There is a temporal continuity of e-learning research because some research topics have kept their continuity over the studied 20 years. Meanwhile, the research traditions in the e-learning field are also continuously evolving with the development of new technologies. The results also offer useful hints on the future direction of how the field may evolve.
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17
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Mandal R, Cano R, Davis CD, Hayashi D, Jackson SA, Jones CM, Lampe JW, Latulippe ME, Lin NJ, Lippa KA, Piotrowski P, Da Silva SM, Swanson KS, Wishart DS. Workshop report: Toward the development of a human whole stool reference material for metabolomic and metagenomic gut microbiome measurements. Metabolomics 2020; 16:119. [PMID: 33164148 PMCID: PMC7649161 DOI: 10.1007/s11306-020-01744-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION To date, there has been little effort to develop standards for metabolome-based gut microbiome measurements despite the significant efforts toward standard development for DNA-based microbiome measurements. OBJECTIVES The National Institute of Standards and Technology (NIST), The BioCollective (TBC), and the North America Branch of the International Life Sciences Institute (ILSI North America) are collaborating to extend NIST's efforts to develop a Human Whole Stool Reference Material for the purpose of method harmonization and eventual quality control. METHODS The reference material will be rationally designed for adequate quality assurance and quality control (QA/QC) for underlying measurements in the study of the impact of diet and nutrition on functional aspects of the host gut microbiome and relationships of those functions to health. To identify which metabolites deserve priority in their value assignment, NIST, TBC, and ILSI North America jointly conducted a workshop on September 12, 2019 at the NIST campus in Gaithersburg, Maryland. The objective of the workshop was to identify metabolites for which evidence indicates relevance to health and disease and to decide on the appropriate course of action to develop a fit-for-purpose reference material. RESULTS This document represents the consensus opinions of workshop participants and co-authors of this manuscript, and provides additional supporting information. In addition to developing general criteria for metabolite selection and a preliminary list of proposed metabolites, this paper describes some of the strengths and limitations of this initiative given the current state of microbiome research. CONCLUSIONS Given the rapidly evolving nature of gut microbiome science and the current state of knowledge, an RM (as opposed to a CRM) measured for multiple metabolites is appropriate at this stage. As the science evolves, the RM can evolve to match the needs of the research community. Ultimately, the stool RM may exist in sequential versions. Beneficial to this evolution will be a clear line of communication between NIST and the stakeholder community to ensure alignment with current scientific understanding and community needs.
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Affiliation(s)
- Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Raul Cano
- The BioCollective, LLC, 5650 N Washington St, Denver, CO, 80216, USA
| | - Cindy D Davis
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD, 20852, USA
| | | | - Scott A Jackson
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Christina M Jones
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Johanna W Lampe
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, M4-B802, PO Box 19024, Seattle, WA, 98109, USA
| | - Marie E Latulippe
- North American Branch of the International Life Sciences Institute (ILSI North America), 740 15th Street NW, Suite 600, Washington, DC, 20005, USA.
| | - Nancy J Lin
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Katrice A Lippa
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Paulina Piotrowski
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Sandra M Da Silva
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Kelly S Swanson
- University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
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18
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An ambient temperature collection and stabilization strategy for canine microbiota studies. Sci Rep 2020; 10:13383. [PMID: 32770113 PMCID: PMC7414149 DOI: 10.1038/s41598-020-70232-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Similar to humans, the fecal microbiome of dogs may be useful in diagnosing diseases or assessing dietary interventions. The accuracy and reproducibility of microbiome data depend on sample integrity, which can be affected by storage methods. Here, we evaluated the ability of a stabilization device to preserve canine fecal samples under various storage conditions simulating shipping in hot or cold climates. Microbiota data from unstabilized samples stored at room temperature (RT) and samples placed in PERFORMAbiome·GUT collection devices (PB-200) (DNA Genotek, Inc. Ottawa, Canada) and stored at RT, 37 °C, 50 °C, or undergoing repeated freeze-thaw cycles, were compared with freshly extracted samples. Alpha- and beta diversity indices were not affected in stabilized samples, regardless of storage temperature. Unstabilized samples stored at RT, however, had higher alpha diversity. Moreover, the relative abundance of dominant bacterial phyla (Firmicutes, Fusobacteria, Bacteriodetes, and Actinobacteria) and 24 genera were altered in unstabilized samples stored at RT, while microbiota abundance was not significantly changed in stabilized samples stored at RT. Our results suggest that storage method is important in microbiota studies and that the stabilization device may be useful in maintaining microbial profile integrity, especially for samples collected off-site and/or those undergoing temperature changes during shipment or storage.
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19
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The Gut Microbiota Profile in Children with Prader-Willi Syndrome. Genes (Basel) 2020; 11:genes11080904. [PMID: 32784572 PMCID: PMC7463799 DOI: 10.3390/genes11080904] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Although gut microbiota has been suggested to play a role in disease phenotypes of Prader-Willi syndrome (PWS), little is known about its composition in affected children and how it relates to hyperphagia. This cross-sectional study aimed to characterize the gut bacterial and fungal communities of children with PWS, and to determine associations with hyperphagia. Fecal samples were collected from 25 children with PWS and 25 age-, sex-, and body mass index-matched controls. Dietary intake data, hyperphagia scores, and relevant clinical information were also obtained. Fecal bacterial and fungal communities were characterized by 16S rRNA and ITS2 sequencing, respectively. Overall bacterial α-diversity and compositions of PWS were not different from those of the controls, but 13 bacterial genera were identified to be differentially abundant. Interestingly, the fungal community, as well as specific genera, were different between PWS and controls. The majority of the variation in the gut microbiota was not attributed to differences in dietary intake or the impact of genotype. Hyperphagia scores were associated with fungal α-diversity and relative abundance of several taxa, such as Staphylococcus, Clostridium, SMB53, and Candida. Further longitudinal studies correlating changes in the microbiome with the degree of hyperphagia and studies integrating multi-omics data are warranted.
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Luan Z, Sun G, Huang Y, Yang Y, Yang R, Li C, Wang T, Tan D, Qi S, Jun C, Wang C, Wang S, Zhao Y, Jing Y. Metagenomics Study Reveals Changes in Gut Microbiota in Centenarians: A Cohort Study of Hainan Centenarians. Front Microbiol 2020; 11:1474. [PMID: 32714309 PMCID: PMC7343713 DOI: 10.3389/fmicb.2020.01474] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 06/05/2020] [Indexed: 12/21/2022] Open
Abstract
Several studies based on 16SrDNA analysis have revealed certain unique characteristics of gut microbiome in centenarians. We established a prospective cohort of fecal microbiota and conducted the first metagenomics-based study among centenarians. The objective was to explore the dynamic changes of gut microbiota in healthy centenarians and centenarians approaching end of life and to unravel the characteristics of aging-associated microbiome. Seventy-five healthy centenarians residing in three regions of Hainan participated in follow-up surveys and collection of fecal samples at intervals of 3 months. Data pertaining to dietary status, health status scores, cause of disease and death, and fecal specimens were collected for 15 months. Twenty participants died within 20 months during the follow-up period. The median survival time was 8-9 months (range, 1-17) and the mortality rate was 14.7% per year. The health status scores before death were significantly lower than those at 3 months before the end of the follow-up period [median score: 3 (range, 1-5), P < 0.05]. At this time, the participants mainly exhibited symptoms of anorexia and reduced dietary intake and physical activity. Metagenomics sequencing and analysis were carried out to characterize the gut microbiota changes in the centenarians during their transition from healthy status to death. Anosim analysis showed a significant change in gut microbiota from 7 months prior to death (R = 0.10, P = 0.02). All participants were grouped with 7 months before death as cut-off; no significant difference in α diversity was found between the two groups (P = 0.45). Semi-supervised monitoring and log rank sum analysis revealed significant changes in the abundance of ten bacterial species before death; of these, eight species were significantly reduced (Akkermansia muciniphila, Alistipes finegoldii, Alistipes shahii, Bacteroides faecis, Bacteroides intestinalis, Butyrivibrio crossotus, Bacteroides stercoris, and Prevotella stercorea) while two were significantly increased before death (Bifidobacterium longum and Ruminococcus bromii). Compared to centenarians in northern Italy, Hainan centenarians exhibited unique characteristics of gut microbiome. The abundance of ten bacterial species showed significant changes starting from 7 months before death. We speculate that these changes might occur before the clinical symptoms of deterioration in health status.
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Affiliation(s)
- Zhe Luan
- Chinese PLA General Hospital, Beijing, China
| | - Gang Sun
- Chinese PLA General Hospital, Beijing, China
| | - Yun Huang
- Realbio Technology Co., Ltd., Hangzhou, China
| | | | - Ruifu Yang
- Academy of Military Medical Sciences, Beijing, China
| | - Congyong Li
- Chinese PLA General Hospital, Beijing, China
| | | | - Di Tan
- Realbio Technology Co., Ltd., Hangzhou, China
| | - Shirui Qi
- Tianjin First Central Hospital, Tianjin, China
| | - Chen Jun
- Chinese PLA General Hospital, Beijing, China
| | - Cong Wang
- Chinese PLA General Hospital, Beijing, China
| | | | - Yiming Zhao
- Hainan Branch of Chinese PLA General Hospital, Sanya, China
| | - Yujia Jing
- Chinese PLA General Hospital, Beijing, China
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21
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Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R, Thiele I. Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions. BMC Biol 2020; 18:62. [PMID: 32517799 PMCID: PMC7285525 DOI: 10.1186/s12915-020-00775-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/27/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a systemic disease clinically defined by the degeneration of dopaminergic neurons in the brain. While alterations in the gut microbiome composition have been reported in PD, their functional consequences remain unclear. Herein, we addressed this question by an analysis of stool samples from the Luxembourg Parkinson's Study (n = 147 typical PD cases, n = 162 controls). RESULTS All individuals underwent detailed clinical assessment, including neurological examinations and neuropsychological tests followed by self-reporting questionnaires. Stool samples from these individuals were first analysed by 16S rRNA gene sequencing. Second, we predicted the potential secretion for 129 microbial metabolites through personalised metabolic modelling using the microbiome data and genome-scale metabolic reconstructions of human gut microbes. Our key results include the following. Eight genera and seven species changed significantly in their relative abundances between PD patients and healthy controls. PD-associated microbial patterns statistically depended on sex, age, BMI, and constipation. Particularly, the relative abundances of Bilophila and Paraprevotella were significantly associated with the Hoehn and Yahr staging after controlling for the disease duration. Furthermore, personalised metabolic modelling of the gut microbiomes revealed PD-associated metabolic patterns in the predicted secretion potential of nine microbial metabolites in PD, including increased methionine and cysteinylglycine. The predicted microbial pantothenic acid production potential was linked to the presence of specific non-motor symptoms. CONCLUSION Our results suggest that PD-associated alterations of the gut microbiome can translate into substantial functional differences affecting host metabolism and disease phenotype.
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Affiliation(s)
- Federico Baldini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, Ireland
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Estelle Sandt
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Lukas Pavelka
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg City, Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg City, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg.
- School of Medicine, National University of Ireland, Galway, Ireland.
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
- APC Microbiome, Cork, Ireland.
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22
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Chen CC, Wu WK, Chang CM, Panyod S, Lu TP, Liou JM, Fang YJ, Chuang EY, Wu MS. Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles. J Formos Med Assoc 2020; 119:1791-1798. [PMID: 32111519 DOI: 10.1016/j.jfma.2020.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/04/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND/PURPOSE Appropriate storage of fecal samples is a critical step for the unbiased analysis of microbial communities in metagenomic studies. Rapid freezing at -80 °C is usually considered to be best practice, but this approach is challenging. DNA stabilizing kits may provide a more convenient method to preserve and store clinical samples. We evaluated the reliability of two collection kits (Stratec stool collection tube with stabilizer, #1038111200 and OMNIgene.GUT OMR-200) on preserving fecal microbiota. METHODS Samples were collected from two locations of the fecal specimen, in four healthy volunteers. The samples were sub-aliquoted and stored in a -80 °C freezer, in Stratec and OMNIgene.GUT (incubation at ambient temperature for 0, 3, or 7 days). The fecal microbial composition was assessed by 16S rRNA sequencing. RESULTS We found that alpha diversity was not significantly affected by storage conditions. Samples stored in DNA stabilizers were still representative of the original microbial community after 7 days at ambient temperature. Individual differences were found to have a greater contribution to the differences in microbial community composition than storage conditions or sampling location. Samples subjected to stabilizers displayed microbial community shifts compared with immediately frozen samples. A linear discriminant analysis effect size (LEfSe) analysis showed that the relative abundances of Faecalibacterium were significantly higher in samples stored in Stratec kits. CONCLUSION Our study reveals that both Stratec and OMNIgene.GUT kits provide good microbiome preservation for up to 7 days in ambient temperature and would represent good options for fecal sample collection in large scale, population-based studies.
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Affiliation(s)
- Chieh-Chang Chen
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - 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
| | - Chih-Min Chang
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taiwan; Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taiwan
| | - Suraphan Panyod
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taiwan
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taiwan; Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taiwan
| | - Jyh-Ming Liou
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Jen Fang
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yun-Lin, Taiwan
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taiwan; Institute of Epidemiology and Preventive Medicine, Department of Public Health, National Taiwan University, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Ming-Shiang Wu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
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Neuberger-Castillo L, Hamot G, Marchese M, Sanchez I, Ammerlaan W, Betsou F. Method Validation for Extraction of DNA from Human Stool Samples for Downstream Microbiome Analysis. Biopreserv Biobank 2020; 18:102-116. [PMID: 31999474 DOI: 10.1089/bio.2019.0112] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background: A formal method validation for biospecimen processing in the context of accreditation in laboratories and biobanks is lacking. A previously optimized stool processing protocol was validated for fitness-for-purpose for downstream microbiome analysis. Materials and Methods: DNA extraction from human stool was validated with various collection tubes, stabilizing solutions and storage conditions in terms of fitness-for-purpose for downstream microbiome analysis, robustness, and sample stability. Acceptance criteria were based on accurate identification of a reference material, homogeneity of extracted samples, and sample stability in a 2-year period. Results: The automated DNA extraction using the chemagic™ Magnetic Separation Module I (MSM I) extracted 8 out of 8 bacteria in the ZymoBIOMICS® Microbial Community Standard. Seven tested stabilizing solutions (OMNIgene®•GUT, RNAlater®, AquaStool™, RNAssist, PerkinElmer SEB lysis buffer, and DNA Genotek's CP-150) were all compatible with the chemagic MSM I and showed no significant difference in microbiome alpha diversity and no significant difference in the overall microbiome composition compared to the baseline snap-frozen stool sample. None of the stabilizing solutions showed intensive polymerase chain reaction (PCR) inhibition in the SPUD assay. However, when we take into account more stringent criteria which include a higher double-stranded DNA yield, higher DNA purity, and absence of PCR inhibition, we recommend the use of OMNIgene•GUT, RNAlater, or AquaStool as alternatives to rapid freezing of samples. The highest sample homogeneity was achieved with RNAlater- and OMNIgene•GUT -stabilized samples. Sample stability after a 2-year storage in -80°C was seen with OMNIgene•GUT -stabilized samples. Conclusions: We validated a combination of a stool processing method with various collection methods, suitable for downstream microbiome applications. Sample collection, storage conditions and DNA extraction methods can influence the microbiome profile results. Laboratories and biobanks should ensure that these conditions are systematically recorded in the scope of accreditation.
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Affiliation(s)
| | - Gaël Hamot
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Monica Marchese
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Ignacio Sanchez
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Wim Ammerlaan
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
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24
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Shomorony I, Cirulli ET, Huang L, Napier LA, Heister RR, Hicks M, Cohen IV, Yu HC, Swisher CL, Schenker-Ahmed NM, Li W, Nelson KE, Brar P, Kahn AM, Spector TD, Caskey CT, Venter JC, Karow DS, Kirkness EF, Shah N. An unsupervised learning approach to identify novel signatures of health and disease from multimodal data. Genome Med 2020; 12:7. [PMID: 31924279 PMCID: PMC6953286 DOI: 10.1186/s13073-019-0705-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/12/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Modern medicine is rapidly moving towards a data-driven paradigm based on comprehensive multimodal health assessments. Integrated analysis of data from different modalities has the potential of uncovering novel biomarkers and disease signatures. METHODS We collected 1385 data features from diverse modalities, including metabolome, microbiome, genetics, and advanced imaging, from 1253 individuals and from a longitudinal validation cohort of 1083 individuals. We utilized a combination of unsupervised machine learning methods to identify multimodal biomarker signatures of health and disease risk. RESULTS Our method identified a set of cardiometabolic biomarkers that goes beyond standard clinical biomarkers. Stratification of individuals based on the signatures of these biomarkers identified distinct subsets of individuals with similar health statuses. Subset membership was a better predictor for diabetes than established clinical biomarkers such as glucose, insulin resistance, and body mass index. The novel biomarkers in the diabetes signature included 1-stearoyl-2-dihomo-linolenoyl-GPC and 1-(1-enyl-palmitoyl)-2-oleoyl-GPC. Another metabolite, cinnamoylglycine, was identified as a potential biomarker for both gut microbiome health and lean mass percentage. We identified potential early signatures for hypertension and a poor metabolic health outcome. Additionally, we found novel associations between a uremic toxin, p-cresol sulfate, and the abundance of the microbiome genera Intestinimonas and an unclassified genus in the Erysipelotrichaceae family. CONCLUSIONS Our methodology and results demonstrate the potential of multimodal data integration, from the identification of novel biomarker signatures to a data-driven stratification of individuals into disease subtypes and stages-an essential step towards personalized, preventative health risk assessment.
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Affiliation(s)
- Ilan Shomorony
- Human Longevity, Inc., San Diego, CA, 92121, USA
- Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA
| | | | - Lei Huang
- Human Longevity, Inc., San Diego, CA, 92121, USA
| | | | | | | | | | - Hung-Chun Yu
- Human Longevity, Inc., San Diego, CA, 92121, USA
| | | | | | - Weizhong Li
- Human Longevity, Inc., San Diego, CA, 92121, USA
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Karen E Nelson
- Human Longevity, Inc., San Diego, CA, 92121, USA
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Pamila Brar
- Human Longevity, Inc., San Diego, CA, 92121, USA
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Andrew M Kahn
- Human Longevity, Inc., San Diego, CA, 92121, USA
- Division of Cardiovascular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - C Thomas Caskey
- Human Longevity, Inc., San Diego, CA, 92121, USA
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - J Craig Venter
- Human Longevity, Inc., San Diego, CA, 92121, USA
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | | | - Ewen F Kirkness
- Human Longevity, Inc., San Diego, CA, 92121, USA
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Naisha Shah
- Human Longevity, Inc., San Diego, CA, 92121, USA.
- J. Craig Venter Institute, La Jolla, CA, 92037, USA.
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25
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Watson EJ, Giles J, Scherer BL, Blatchford P. Human faecal collection methods demonstrate a bias in microbiome composition by cell wall structure. Sci Rep 2019; 9:16831. [PMID: 31727963 PMCID: PMC6856092 DOI: 10.1038/s41598-019-53183-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 10/24/2019] [Indexed: 12/14/2022] Open
Abstract
Clinical trial faecal collections present challenges through geographical spread and inexperienced participants. Collection techniques have been developed and tested to overcome these challenges, but previous studies investigating these techniques have demonstrated a highly variable capacity for sample preservation. Furthermore, these studies typically only examine either preservation of genetic content or metabolites, not both. This study investigated the Stool Nucleic Acid Collection and Preservation Tube (Norgen BioTek Corp) for the preservation of both microbial DNA and microbial organic acid metabolites in human faecal samples when compared to frozen samples. Twenty six healthy adult participants were instructed to collect a bowel movement, subsample into collection tubes and immediately transfer the remaining bulk to −20 °C storage. Resulting organic acid concentrations remained comparable across methods when the preservation tubes were used correctly. The 16S rRNA gene sequencing data revealed twenty significantly different bacterial genera between the two collection methods. Ten Gram-negative genera were more abundant in the collection tubes, and ten Gram-positive genera were more abundant in the fresh frozen samples. This study has illustrated that faecal collection methods bias the microbial community profile according to Gram status and this should be considered when designing studies that collect and store human faecal samples.
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Affiliation(s)
- Emma-Jane Watson
- CSIRO Health and Biosecurity, Gate 13 Kintore Avenue, Adelaide, South Australia, 5000, Australia
| | - Jennifer Giles
- CSIRO Health and Biosecurity, Gate 13 Kintore Avenue, Adelaide, South Australia, 5000, Australia
| | - Benjamin L Scherer
- CSIRO Health and Biosecurity, Gate 13 Kintore Avenue, Adelaide, South Australia, 5000, Australia
| | - Paul Blatchford
- CSIRO Health and Biosecurity, Gate 13 Kintore Avenue, Adelaide, South Australia, 5000, Australia. .,Zespri International Limited, 400 Maunganui Road, Mt Maunganui, 3149, New Zealand.
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26
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Ilett EE, Jørgensen M, Noguera-Julian M, Daugaard G, Murray DD, Helleberg M, Paredes R, Lundgren J, Sengeløv H, MacPherson C. Gut microbiome comparability of fresh-frozen versus stabilized-frozen samples from hospitalized patients using 16S rRNA gene and shotgun metagenomic sequencing. Sci Rep 2019; 9:13351. [PMID: 31527823 PMCID: PMC6746779 DOI: 10.1038/s41598-019-49956-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/04/2019] [Indexed: 02/06/2023] Open
Abstract
Collection of faecal samples for microbiome analysis in acutely sick patients is logistically difficult, particularly if immediate freezing is required (i.e. fresh-frozen, or FF sampling). Previous studies in healthy/non-hospitalized volunteers have shown that chemical stabilization (i.e. stabilized-frozen, or SF sampling) allows room-temperature storage with comparable results to FF samples. To test this in a hospital setting we compared FF and SF approaches across 17 patients undergoing haematopoietic stem cell transplantation (HSCT) using both 16S rRNA gene and shotgun metagenomic sequencing. A paired (same stool specimen) comparison of FF and SF samples was made, with an overall comparable level in relative taxonomic abundances between the two sampling techniques. Though shotgun metagenomic sequencing found significant differences for certain bacterial genera (P < 0.001), these were considered minor methodological effects. Within-sample diversity of either method was not significantly different (Shannon diversity P16SrRNA = 0.68 and Pshotgun = 0.89) and we could not reject the null hypothesis that between-sample variation in FF and SF were equivalent (P16SrRNA = 0.98 and Pshotgun = 1.0). This indicates that SF samples can be used to reliably study the microbiome in acutely sick patient populations, thus creating and enabling further outcomes-based metagenomic studies on similarly valuable cohorts.
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Affiliation(s)
- Emma E Ilett
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark.
| | - Mette Jørgensen
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA - IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Gedske Daugaard
- Department of Oncology, Rigshospitalet Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Daniel D Murray
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Marie Helleberg
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Roger Paredes
- Institut de Recerca de la SIDA - IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain.,Infectious Diseases Service, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Jens Lundgren
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Henrik Sengeløv
- Department of Haematology, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
| | - Cameron MacPherson
- PERSIMUNE Centre of Excellence, Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark
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27
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Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study. PLoS One 2019; 14:e0216557. [PMID: 31188837 PMCID: PMC6561628 DOI: 10.1371/journal.pone.0216557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/23/2019] [Indexed: 12/30/2022] Open
Abstract
Background Understanding the role of the gut microbiome is pivotal for the future development of therapies for the prevention and management of autoimmune conditions such as type 1 diabetes when sampling during early life may be particularly important. The current standard methods for collecting gut microbiome samples for research is to extract fresh samples or freeze samples immediately after collection. This is often impractical however for population-based studies. The aim of this study was to determine the optimal method for the stabilization of stool bacterial DNA obtained from nappies and transported by post in ambient conditions to the research centre for a national birth cohort study. Methods Four methods to collect samples were compared to immediate freezing of samples: 1) collecting faeces onto a swab which was immediately frozen, 2) using a commercially available kit with stabilisation solution (OMNIgene•GUT kit) at ambient temperature, 3) collecting onto a swab and 4) collecting into a sterile plain tube. Samples 3) and 4) were returned to the laboratory by post at ambient temperatures. A Bland Altman analysis was used to assess the agreement between the different methods and the frozen standard. Results Stool samples were collected by parents. For samples transported in ambient conditions, the limits of agreement showed that the OMNIgene•GUT kit had the narrowest 95% limits of agreement with the frozen standard as measured by the number of operational taxonomic units and the Shannon diversity index. Conclusions All methods assessed for preserving samples collected from nappies at a distance and delivered by post for gut microbiome analysis showed variation / disagreement from the frozen standard. Overall, the OMNIgene•GUT kit preserved the samples with minimal changes compared to other methods and was practical for parents to use.
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28
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Keohane DM, Woods T, O'Connor P, Underwood S, Cronin O, Whiston R, O'Sullivan O, Cotter P, Shanahan F, Molloy MGM. Four men in a boat: Ultra-endurance exercise alters the gut microbiome. J Sci Med Sport 2019; 22:1059-1064. [PMID: 31053425 DOI: 10.1016/j.jsams.2019.04.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/28/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Compositional and functional adaptions occur in the gut microbiome in response to habitual physical activity. The response of the gut microbiome to sustained, intense exercise in previously active individuals, however, is unknown. This study aimed to prospectively explore the gut microbiome response of four well-trained male athletes to prolonged, high intensity trans-oceanic rowing, describing changes in microbial diversity, abundance and metabolic capacity. DESIGN A prospective, repeated-measures, within-subject report. METHODS Serial stool samples were obtained from four male athletes for metagenomic whole-genome shotgun sequencing to record microbial community structure and relevant functional gene profiles before, during and after a continuous, unsupported 33-day, 5000 km transoceanic rowing race. Calorific intake and macronutrient composition were recorded by validated food frequency questionnaire and anthropometry was determined by body composition analysis and cardiorespiratory testing. RESULTS Microbial diversity increased throughout the ultra-endurance event. Variations in taxonomic composition included increased abundance of butyrate producing species and species associated with improved metabolic health, including improved insulin sensitivity. The functional potential of bacterial species involved in specific amino and fatty acid biosynthesis also increased. Many of the adaptions in microbial community structure and metaproteomics persisted at three months follow up. CONCLUSIONS These findings demonstrate that prolonged, intense exercise positively influences gut microbial diversity, increases the relative abundance of some bacterial species and up-regulates the metabolic potential of specific pathways expressing microbial gene products. These adaptions may play a compensatory role in controlling the physiological stress associated with sustained exertion as well as negating the deleterious consequences accompanying endurance exercise.
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Affiliation(s)
- David M Keohane
- Department of Medicine, Cork University Hospital, Ireland; APC Microbiome Ireland, University College Cork, Ireland; Irish Centre for Arthritic Research and Education (I.C.A.R.E), Cork University Hospital, Ireland; School Of Medicine, University College Cork, Brookfield Health Science Complex, Ireland.
| | - Trevor Woods
- Human Performance Laboratory, Mardyke Arena, University College Cork, Ireland
| | - Pat O'Connor
- Department of Medicine, Cork University Hospital, Ireland
| | - Sean Underwood
- Department of Medicine, Cork University Hospital, Ireland
| | - Owen Cronin
- Department of Medicine, Cork University Hospital, Ireland; APC Microbiome Ireland, University College Cork, Ireland; Irish Centre for Arthritic Research and Education (I.C.A.R.E), Cork University Hospital, Ireland
| | | | - Orla O'Sullivan
- APC Microbiome Ireland, University College Cork, Ireland; Teagasc Sequencing Facility, Moorepark, Ireland
| | - Paul Cotter
- APC Microbiome Ireland, University College Cork, Ireland; Teagasc Sequencing Facility, Moorepark, Ireland
| | - Fergus Shanahan
- Department of Medicine, Cork University Hospital, Ireland; APC Microbiome Ireland, University College Cork, Ireland; Irish Centre for Arthritic Research and Education (I.C.A.R.E), Cork University Hospital, Ireland; School Of Medicine, University College Cork, Brookfield Health Science Complex, Ireland
| | - Michael G M Molloy
- Department of Medicine, Cork University Hospital, Ireland; APC Microbiome Ireland, University College Cork, Ireland; Irish Centre for Arthritic Research and Education (I.C.A.R.E), Cork University Hospital, Ireland; School Of Medicine, University College Cork, Brookfield Health Science Complex, Ireland
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Alpizar-Rodriguez D, Lesker TR, Gronow A, Gilbert B, Raemy E, Lamacchia C, Gabay C, Finckh A, Strowig T. Prevotella copri in individuals at risk for rheumatoid arthritis. Ann Rheum Dis 2019; 78:590-593. [PMID: 30760471 DOI: 10.1136/annrheumdis-2018-214514] [Citation(s) in RCA: 237] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/27/2019] [Accepted: 01/30/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Rheumatoid arthritis (RA) has been associated with a relative expansion of faecal Prevotellaceae. To determine the microbiome composition and prevalence of Prevotella spp. in a group of individuals at increased risk for RA, but prior to the development of the disease. METHODS In an ongoing cohort study of first-degree relatives (FDRs) of patients with RA, we identified 'FDR controls', asymptomatic and without autoantibodies, and individuals in pre-clinical RA stages, who had either developed anticitrullinated peptide antibodies or rheumatoid factor positivity and/or symptoms and signs associated with possible RA. Stool sampling and culture-independent microbiota analyses were performed followed by descriptive statistics and statistical analyses of community structures. RESULTS A total of 133 participants were included, of which 50 were categorised as 'FDR controls' and 83 in 'pre-clinical RA stages'. The microbiota of individuals in 'pre-clinical RA stages' was significantly altered compared with FDR controls. We found a significant enrichment of the bacterial family Prevotellaceae, particularly Prevotella spp., in the 'pre-clinical RA' group (p=0.04). CONCLUSIONS Prevotella spp. enrichment in individuals in pre-clinical stages of RA, before the onset of RA, suggests a role of intestinal dysbiosis in the development of RA.
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Affiliation(s)
| | - Till Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Achim Gronow
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Benoît Gilbert
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Elena Raemy
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Celine Lamacchia
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Cem Gabay
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Axel Finckh
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany .,Hannover Medical School, Hannover, Germany
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Lee KM, Adams M, Klassen JL. Evaluation of DESS as a storage medium for microbial community analysis. PeerJ 2019; 7:e6414. [PMID: 30740279 PMCID: PMC6368006 DOI: 10.7717/peerj.6414] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/24/2018] [Indexed: 12/14/2022] Open
Abstract
Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.
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Affiliation(s)
- Kevin M Lee
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Madison Adams
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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31
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Flannery J, Callaghan B, Sharpton T, Fisher P, Pfeifer J. Is adolescence the missing developmental link in Microbiome-Gut-Brain axis communication? Dev Psychobiol 2019; 61:783-795. [PMID: 30690712 DOI: 10.1002/dev.21821] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/12/2018] [Accepted: 11/26/2018] [Indexed: 12/21/2022]
Abstract
Gut microbial research has recently opened new frontiers in neuroscience and potentiated novel therapies for mental health problems (Mayer, et al., 2014). Much of our understanding of the gut microbiome's role in brain function and behavior, however, has been largely derived from research on nonhuman animals. Even less is known about how the development of the gut microbiome influences critical periods of neural and behavioral development, particularly adolescence. In this review, we first discuss why the gut microbiome has become increasingly relevant to developmental cognitive neuroscience and provide a synopsis of the known connections of the gut microbiome with social-affective brain function and behavior, specifically highlighting human developmental work when possible. We then focus on adolescence, a key period of neurobiological and social-affective development. Specifically, we review the links between the gut microbiome and six overarching domains of change during adolescence: (a) social processes, (b) motivation and behavior, (c) neural development, (d) cognition, (e) neuroendocrine function, and (f) physical health and wellness. Using a developmental science perspective, we summarize key changes across these six domains to underscore the promise for the gut microbiome to bidirectionally influence and transform adolescent development.
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Coello K, Hansen TH, Sørensen N, Munkholm K, Kessing LV, Pedersen O, Vinberg M. Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives. Brain Behav Immun 2019; 75:112-118. [PMID: 30261302 DOI: 10.1016/j.bbi.2018.09.026] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/23/2018] [Accepted: 09/24/2018] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE An aberrant gut microbiota may be associated with a broad spectrum of diseases including mental illness. The gut microbiota is scarcely studied in bipolar disorder (BD). We examined the gut microbiota composition in patients with newly diagnosed BD, their unaffected first-degree relatives and healthy individuals. METHODS Stool samples were collected from 113 patients with BD, 39 unaffected first-degree relatives and 77 healthy individuals and the microbiota was profiled using 16S rRNA gene amplicon sequencing. RESULTS The gut microbiota community membership of patients with BD differed from that of healthy individuals (R2 = 1.0%, P = 0.008), whereas the community membership of unaffected first-degree relatives did not. Flavonifractor was present in 61% of patients with BD, 42% of their unaffected relatives and 39% of healthy individuals. Presence of Flavonifractor was associated with an odds ratio of 2.9 (95%CI: 1.6-5.2, P = 5.8 × 10-4, Q = 0.036) for having BD. When excluding smokers, presence of Flavonifractor was associated with an odds ratio of 2.3 (95%CI: 1.1-5.3, P = 0.019) for having BD. However, when considering the subsample of non-smokers only, BD and presence of Flavonifractor were no longer associated when adjusted for all possible tests at genus level (Q = 0.6). Presence of Flavonifractor in patients with BD was associated with smoking and female sex, but not with age, waist circumference, exercise level, high-sensitive C-reactive protein, current affective state, subtype of BD, illness duration or psychotropic medication, respectively. CONCLUSION Flavonifractor, a bacterial genus that may induce oxidative stress and inflammation in its host, was associated with BD. Higher prevalence of smoking among patients with BD contributed to our findings, and it cannot be excluded that findings are influenced by residual confounding.
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Affiliation(s)
- Klara Coello
- Copenhagen Affective Disorders Research Centre (CADIC), Psychiatric Center Copenhagen, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Tue Haldor Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Klaus Munkholm
- Copenhagen Affective Disorders Research Centre (CADIC), Psychiatric Center Copenhagen, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lars Vedel Kessing
- Copenhagen Affective Disorders Research Centre (CADIC), Psychiatric Center Copenhagen, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Maj Vinberg
- Copenhagen Affective Disorders Research Centre (CADIC), Psychiatric Center Copenhagen, Rigshospitalet, and Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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Progress of analytical tools and techniques for human gut microbiome research. J Microbiol 2018; 56:693-705. [DOI: 10.1007/s12275-018-8238-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/07/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022]
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Methodology challenges in studying human gut microbiota - effects of collection, storage, DNA extraction and next generation sequencing technologies. Sci Rep 2018; 8:5143. [PMID: 29572539 PMCID: PMC5865204 DOI: 10.1038/s41598-018-23296-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/09/2018] [Indexed: 12/25/2022] Open
Abstract
The information on microbiota composition in the human gastrointestinal tract predominantly originates from the analyses of human faeces by application of next generation sequencing (NGS). However, the detected composition of the faecal bacterial community can be affected by various factors including experimental design and procedures. This study evaluated the performance of different protocols for collection and storage of faecal samples (native and OMNIgene.GUT system) and bacterial DNA extraction (MP Biomedicals, QIAGEN and MO BIO kits), using two NGS platforms for 16S rRNA gene sequencing (Ilumina MiSeq and Ion Torrent PGM). OMNIgene.GUT proved as a reliable and convenient system for collection and storage of faecal samples although favouring Sutterella genus. MP provided superior DNA yield and quality, MO BIO depleted Gram positive organisms while using QIAGEN with OMNIgene.GUT resulted in greatest variability compared to other two kits. MiSeq and IT platforms in their supplier recommended setups provided comparable reproducibility of donor faecal microbiota. The differences included higher diversity observed with MiSeq and increased capacity of MiSeq to detect Akkermansia muciniphila, [Odoribacteraceae], Erysipelotrichaceae and Ruminococcaceae (primarily Faecalibacterium prausnitzii). The results of our study could assist the investigators using NGS technologies to make informed decisions on appropriate tools for their experimental pipelines.
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Penington JS, Penno MAS, Ngui KM, Ajami NJ, Roth-Schulze AJ, Wilcox SA, Bandala-Sanchez E, Wentworth JM, Barry SC, Brown CY, Couper JJ, Petrosino JF, Papenfuss AT, Harrison LC. Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis. Sci Rep 2018; 8:4386. [PMID: 29531234 PMCID: PMC5847573 DOI: 10.1038/s41598-018-22491-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/22/2018] [Indexed: 12/14/2022] Open
Abstract
To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at -80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline. Variation in gut microbiome was dominated by differences between individuals. Minor differences in the abundance of taxa were found between collection-processing methods and day of collection, and between the two centers. We conclude that collection with storage and transport at 4 °C within 24 h is adequate for 16S rRNA analysis of the gut microbiome. Other factors including differences in PCR and sequencing methods account for relatively minor variation compared to differences between individuals.
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Affiliation(s)
| | - Megan A S Penno
- Robinson Research Institute, University of Adelaide, Adelaide, 5006, South Australia, Australia
| | - Katrina M Ngui
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alexandra J Roth-Schulze
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Victoria, 3010, Australia
| | - Stephen A Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Victoria, 3010, Australia
| | - Esther Bandala-Sanchez
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Victoria, 3010, Australia
| | - John M Wentworth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
- Department of Medical Biology, University of Melbourne, Victoria, 3010, Australia
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, 5006, South Australia, Australia
| | - Cheryl Y Brown
- Robinson Research Institute, University of Adelaide, Adelaide, 5006, South Australia, Australia
| | - Jennifer J Couper
- Robinson Research Institute, University of Adelaide, Adelaide, 5006, South Australia, Australia
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anthony T Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Victoria, 3010, Australia.
| | - Leonard C Harrison
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Victoria, 3010, Australia.
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Abstract
Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while metagenome sequencing data was successfully generated for samples from 49 participants. Although 16S rDNA sequencing was more sensitive, metagenome sequencing allowed for a more comprehensive and unbiased representation of the microbial flora, including eukarya and viral pathogens, and of bacterial virulence factors. Urine samples positive by metagenome sequencing contained a plethora of bacterial (median 41 genera/sample), eukarya (median 2 species/sample) and viral sequences (median 3 viruses/sample). Genomic analyses suggested cases of infection with potential pathogens that are often missed during routine urine culture due to species specific growth requirements. While conventional microbiological methods are inadequate to identify a large diversity of microbial species that are present in urine, genomic approaches appear to more comprehensively and quantitatively describe the urinary microbiome.
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Han M, Hao L, Lin Y, Li F, Wang J, Yang H, Xiao L, Kristiansen K, Jia H, Li J. A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses. MICROBIOME 2018; 6:43. [PMID: 29482661 PMCID: PMC5828344 DOI: 10.1186/s40168-018-0429-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for large-scale metagenomic studies and the development of clinical/commercial personal metagenomic sequencing. RESULTS In this study, we systematically tested a novel N-octylpyridinium bromide-based fecal sample preservation method and compared it with other currently used storage methods. We found that the N-octylpyridinium bromide-based method enabled preservation of the bacterial composition in fecal samples transported and stored at room temperature for up to at least 14 days. CONCLUSIONS We describe a novel chemical stabilizer that allows cost-effective transportation and storage at room temperature for several days with preservation of bacterial composition. This method will facilitate sample collection even in remote area and also enable transport via normal commercial transportation routes.
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Affiliation(s)
- Mo Han
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Lilan Hao
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yuxiang Lin
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Fang Li
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, 518083, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China.
- Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China.
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China.
- Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Shenzhen, 518083, China.
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Fawkner-Corbett D, Simmons A, Parikh K. Microbiome, pattern recognition receptor function in health and inflammation. Best Pract Res Clin Gastroenterol 2017; 31:683-691. [PMID: 29566912 DOI: 10.1016/j.bpg.2017.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/05/2017] [Indexed: 01/31/2023]
Abstract
The innate immune system plays an important role in shaping the microbiota into configurations that are tolerated and beneficial to the host, thereby playing a crucial role in human health. Innate immunity is based on the fundamental principle that Pattern Recognition Receptors (PRRs) recognise pathogen associated molecular patterns as non-self-entities and trigger intracellular signalling pathways that lead to the induction of numerous cytokines and chemokines that help maintain host resistance to infections. Dysregulation of this interaction has been identified as the core defect that leads to chronic intestinal inflammation allowing certain microbiota to be harmful to host health. This dysbiosis of the microbiome is found associated with numerous chronic diseases. A logical explanation would be that genetic defects in the recognition and response pathways that the host uses to identify these microbial pathogens could lead to altered microbial colonisation or mis-recognition of normal bacteria leading to diseases. The interaction between pattern recognition receptors, microbial traits and human health with respect to the gut are now rapidly resolved and will be the subject of this review.
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Affiliation(s)
- David Fawkner-Corbett
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK; Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK; Academic Paediatric Surgery Unit (APSU), Nuffield Department of Surgical Sciences, University of Oxford, UK
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK; Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Kaushal Parikh
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK; Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
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Abstract
Microbiome analysis involves determining the composition and function of a community of microorganisms in a particular location. For the gastroenterologist, this technology opens up a rapidly evolving set of challenges and opportunities for generating novel insights into the health of patients on the basis of microbiota characterizations from intestinal, hepatic or extraintestinal samples. Alterations in gut microbiota composition correlate with intestinal and extraintestinal disease and, although only a few mechanisms are known, the microbiota are still an attractive target for developing biomarkers for disease detection and management as well as potential therapeutic applications. In this Review, we summarize the major decision points confronting new entrants to the field or for those designing new projects in microbiome research. We provide recommendations based on current technology options and our experience of sequencing platform choices. We also offer perspectives on future applications of microbiome research, which we hope convey the promise of this technology for clinical applications.
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40
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Vandeputte D, Tito RY, Vanleeuwen R, Falony G, Raes J. Practical considerations for large-scale gut microbiome studies. FEMS Microbiol Rev 2017; 41:S154-S167. [PMID: 28830090 PMCID: PMC7207147 DOI: 10.1093/femsre/fux027] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/19/2017] [Indexed: 12/14/2022] Open
Abstract
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.
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Affiliation(s)
- Doris Vandeputte
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Raul Y. Tito
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Rianne Vanleeuwen
- Universiteit Antwerpen, Productontwikkeling, Ambtmanstraat 1, B-2000 Antwerpen, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
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Abrahamson M, Hooker E, Ajami NJ, Petrosino JF, Orwoll ES. Successful collection of stool samples for microbiome analyses from a large community-based population of elderly men. Contemp Clin Trials Commun 2017; 7:158-162. [PMID: 29250605 PMCID: PMC5726580 DOI: 10.1016/j.conctc.2017.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The relationship of the gastrointestinal microbiome to health and disease is of major research interest, including the effects of the gut microbiota on age related conditions. Here we report on the outcome of a project to collect stool samples on a large number of community dwelling elderly men using the OMNIgene-GUT stool/feces collection kit (OMR-200, DNA Genotek, Ottawa, Canada). Among 1,328 men who were eligible for stool collection, 982 (74%) agreed to participate and 951 submitted samples. The collection process was reported to be acceptable, almost all samples obtained were adequate, the process of sample handling by mail was uniformly successful. The DNA obtained provided excellent results in microbiome analyses, yielding an abundance of species and a diversity of taxa as would be predicted. Our results suggest that population studies of older participants involving remote stool sample collection are feasible. These approaches would allow large scale research projects of the association of the gut microbiota with important clinical outcomes.
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Affiliation(s)
| | | | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Eric S Orwoll
- Oregon Health & Science University, Portland, Oregon, USA
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Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet? Nat Rev Gastroenterol Hepatol 2017; 14:315-320. [PMID: 28356581 DOI: 10.1038/nrgastro.2017.29] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Spurred on by ever-evolving developments in analytical methodology, the microbiome, and the gut microbiome in particular, has become the hot topic in biomedical research. Ingenious experiments in animal models have revealed the extent to which the gut microbiota sustains health and how its disruption might contribute to disease pathogenesis. Not surprisingly, associations between the microbiota and disease states in humans have been the subject of considerable interest and many links proposed. However, with rare exceptions, the incrimination of an altered microbiota in disease pathogenesis seems premature at this time given our incomplete understanding of the composition of the gut microbiota in health and the effect of many confounding factors in the interpretation of supposedly abnormal microbial signatures. Future studies must account for these variables and the bidirectionality of host-microorganism interactions in health and disease. In this Perspectives, the status of microbiota signatures in the clinical arena (for facilitating diagnosis or refining prognosis) will be critically assessed and guidance toward future progress provided.
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Wiehlmann L, Pienkowska K, Hedtfeld S, Dorda M, Tümmler B. Impact of sample processing on human airways microbial metagenomes. J Biotechnol 2017; 250:51-55. [PMID: 28119120 DOI: 10.1016/j.jbiotec.2017.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 11/19/2022]
Abstract
Whole metagenome shotgun sequencing provides information about the gene content and the composition of microbial communities provided that the processing of the samples does not introduce a methodology-driven bias. We tested the impact of DNA isolation and storage period on the metagenome profile. Deep throat swabs were collected from healthy adults and an infected infant. DNA was isolated by sonification or enzymatic lysis either immediately or after 24h storage in agar gel Amies transport medium at room temperature. Disruption of cells and subsequent fragmentation of DNA by sonification was as suitable as the common enzymatic lysis to generate high-quality metagenomes particularly for low total DNA input of less than ten nanograms. Conversely, storage of samples for 24h produced severely distorted metagenomes. The majority of species became less abundant or even extinct, whereas a few Streptococcus, Neisseria and Haemophilus spp. proliferated so that the total number of bacterial reads increased at the expense of human reads. We recommend that samples for metagenome analysis should be immediately processed or frozen at -80°C.
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Affiliation(s)
- Lutz Wiehlmann
- Clinical Research Group, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany; Core Unit 'Next Generation Sequencing', Medizinische Hochschule Hannover, D-30625 Hannover, Germany; Institute for Human Genetics, Medizinische Hochschule Hannover, D-30625 Hannover, Germany.
| | - Katarzyna Pienkowska
- Clinical Research Group, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany.
| | - Silke Hedtfeld
- Clinical Research Group, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany.
| | - Marie Dorda
- Clinical Research Group, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany; Core Unit 'Next Generation Sequencing', Medizinische Hochschule Hannover, D-30625 Hannover, Germany.
| | - Burkhard Tümmler
- Clinical Research Group, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research, D-30625 Hannover, Germany.
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