1
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Hall CV, Twelves JL, Saxena M, Scapozza L, Gurry T. Effects of a diverse prebiotic fibre supplement on HbA1c, insulin sensitivity, and inflammatory biomarkers in pre-diabetes: a pilot placebo-controlled randomised clinical trial. Br J Nutr 2024:1-23. [PMID: 38654680 DOI: 10.1017/s0007114524000904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Prebiotic fibre represents a promising and efficacious treatment to manage pre-diabetes, acting via complementary pathways involving the gut microbiome and viscosity-related properties. In this study, we evaluated the effect of using a diverse prebiotic fibre supplement on glycaemic, lipid, and inflammatory biomarkers in patients with pre-diabetes. Sixty-six patients diagnosed with pre-diabetes (yet not receiving glucose-lowering medications) were randomised into treatment (n = 33) and placebo (n = 33) interventions. Participants in the treatment arm consumed 20g per day of a diverse prebiotic fibre supplement and participants in the placebo arm consumed 2g per day of cellulose for 24 weeks. A total of 51 and 48 participants completed the week 16 and week 24 visits, respectively. The intervention was well-tolerated, with a high average adherence rate across groups. Our results extend upon previous work, showing a significant change in glycated haemoglobin (HbA1c) in the treatment group, but only in participants with lower baseline HbA1c levels (<6% HbA1c) (P = 0.05; treatment -0.17 ± 0.27 vs. placebo 0.07 ± 0.29, mean ± SD). Within the whole cohort, we showed significant improvements in insulin sensitivity (P = 0.03; treatment 1.62 ± 5.79 v. placebo -0.77 ± 2.11), and C-reactive protein (P FWE = 0.03; treatment -2.02 ± 6.42 vs placebo 0.94 ± 2.28) in the treatment group compared with the placebo. Together, our results support the use of a diverse prebiotic fibre supplement for physiologically relevant biomarkers in pre-diabetes.
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Affiliation(s)
| | | | - Manish Saxena
- William Harvey Research Institute, Barts NIHR Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland
| | - Thomas Gurry
- Myota GmbH, London, UK
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland
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2
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Quinn-Bohmann N, Wilmanski T, Sarmiento KR, Levy L, Lampe JW, Gurry T, Rappaport N, Ostrem EM, Venturelli OS, Diener C, Gibbons SM. Microbial community-scale metabolic modeling predicts personalized short chain fatty acid production profiles in the human gut. bioRxiv 2023:2023.02.28.530516. [PMID: 36909644 PMCID: PMC10002715 DOI: 10.1101/2023.02.28.530516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Microbially-derived short chain fatty acids (SCFAs) in the human gut are tightly coupled to host metabolism, immune regulation, and integrity of the intestinal epithelium. However, the production of SCFAs can vary widely between individuals consuming the same diet, with lower levels often associated with disease. A systems-scale mechanistic understanding of this heterogeneity is lacking. We present a microbial community-scale metabolic modeling (MCMM) approach to predict individual-specific SCFA production profiles. We assess the quantitative accuracy of our MCMMs using in vitro, ex vivo, and in vivo data. Next, we show how MCMM SCFA predictions are significantly associated with blood-derived clinical chemistries, including cardiometabolic and immunological health markers, across a large human cohort. Finally, we demonstrate how MCMMs can be leveraged to design personalized dietary, prebiotic, and probiotic interventions that optimize SCFA production in the gut. Our results represent an important advance in engineering gut microbiome functional outputs for precision health and nutrition.
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Affiliation(s)
- Nick Quinn-Bohmann
- Institute for Systems Biology, Seattle, WA 98109, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA 98195, USA
| | | | | | - Lisa Levy
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Thomas Gurry
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland
- Myota GmbH, Berlin, Germany
| | - Noa Rappaport
- Center for Phenomic Health, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Erin M. Ostrem
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ophelia S. Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Sean M. Gibbons
- Institute for Systems Biology, Seattle, WA 98109, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- eScience Institute, University of Washington, Seattle, WA 98195, USA
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3
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Gibbons SM, Gurry T, Lampe JW, Chakrabarti A, Dam V, Everard A, Goas A, Gross G, Kleerebezem M, Lane J, Maukonen J, Penna ALB, Pot B, Valdes AM, Walton G, Weiss A, Zanzer YC, Venlet NV, Miani M. Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions. Adv Nutr 2022; 13:1450-1461. [PMID: 35776947 PMCID: PMC9526856 DOI: 10.1093/advances/nmac075] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 01/28/2023] Open
Abstract
Humans often show variable responses to dietary, prebiotic, and probiotic interventions. Emerging evidence indicates that the gut microbiota is a key determinant for this population heterogeneity. Here, we provide an overview of some of the major computational and experimental tools being applied to critical questions of microbiota-mediated personalized nutrition and health. First, we discuss the latest advances in in silico modeling of the microbiota-nutrition-health axis, including the application of statistical, mechanistic, and hybrid artificial intelligence models. Second, we address high-throughput in vitro techniques for assessing interindividual heterogeneity, from ex vivo batch culturing of stool and continuous culturing in anaerobic bioreactors, to more sophisticated organ-on-a-chip models that integrate both host and microbial compartments. Third, we explore in vivo approaches for better understanding of personalized, microbiota-mediated responses to diet, prebiotics, and probiotics, from nonhuman animal models and human observational studies, to human feeding trials and crossover interventions. We highlight examples of existing, consumer-facing precision nutrition platforms that are currently leveraging the gut microbiota. Furthermore, we discuss how the integration of a broader set of the tools and techniques described in this piece can generate the data necessary to support a greater diversity of precision nutrition strategies. Finally, we present a vision of a precision nutrition and healthcare future, which leverages the gut microbiota to design effective, individual-specific interventions.
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Affiliation(s)
| | - Thomas Gurry
- Pharmaceutical Biochemistry group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland (PSI-WS), University of Geneva/University of Lausanne, Geneva, Switzerland
| | - Johanna W Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Veerle Dam
- Sensus BV (Royal Cosun), Roosendaal, The Netherlands
| | - Amandine Everard
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), UCLouvain, Université Catholique de Louvain, Brussels, Belgium
| | - Almudena Goas
- Department of Food, Nutrition, and Exercise Sciences, University of Surrey, Guildford, United Kingdom
| | - Gabriele Gross
- Medical and Scientific Affairs, Reckitt| Mead Johnson Nutrition Institute, Nijmegen, The Netherlands
| | - Michiel Kleerebezem
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Jonathan Lane
- Health and Happiness Group, H&H Research, Cork, Ireland
| | | | - Ana Lucia Barretto Penna
- Department of Food Engineering and Technology, São Paulo State University, São José do Rio Preto, Brazil
| | - Bruno Pot
- Yakult Europe BV, Almere, The Netherlands
| | - Ana M Valdes
- Nottingham NIHR Biomedical Research Centre at the School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Gemma Walton
- Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Adrienne Weiss
- Yili Innovation Center Europe, Wageningen, The Netherlands
| | | | - Naomi V Venlet
- International Life Sciences Institute, European Branch, Brussels, Belgium
| | - Michela Miani
- International Life Sciences Institute, European Branch, Brussels, Belgium
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4
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Gurry T, Nguyen LTT, Yu X, Alm EJ. Functional heterogeneity in the fermentation capabilities of the healthy human gut microbiota. PLoS One 2021; 16:e0254004. [PMID: 34288919 PMCID: PMC8294568 DOI: 10.1371/journal.pone.0254004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiota is known for its highly heterogeneous composition across different individuals. However, relatively little is known about functional differences in its ability to ferment complex polysaccharides. Through ex vivo measurements from healthy human donors, we show that individuals vary markedly in their microbial metabolic phenotypes (MMPs), mirroring differences in their microbiota composition, and resulting in the production of different quantities and proportions of Short Chain Fatty Acids (SCFAs) from the same inputs. We also show that aspects of these MMPs can be predicted from composition using 16S rRNA sequencing. From experiments performed using the same dietary fibers in vivo, we demonstrate that an ingested bolus of fiber is almost entirely consumed by the microbiota upon passage. We leverage our ex vivo data to construct a model of SCFA production and absorption in vivo, and argue that inter-individual differences in quantities of absorbed SCFA are directly related to differences in production. Though in vivo studies are required to confirm these data in the context of the gut, in addition to in vivo read outs of SCFAs produced in response to specific fiber spike-ins, these data suggest that optimizing SCFA production in a given individual through targeted fiber supplementation requires quantitative understanding of their MMP.
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Affiliation(s)
- Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- Institute for Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Le Thanh Tu Nguyen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Xiaoqian Yu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Eric J. Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- * E-mail:
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5
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Marizzoni M, Gurry T, Lopizzo N, Salvatore M, Franzese M, Mirabelli P, Frisoni GB, Cattaneo A. Impact of bioinformatic pipelines and reference databases on 16S rRNA gene sequencing in patients with cognitive impairment. Alzheimers Dement 2020. [DOI: 10.1002/alz.042472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Moira Marizzoni
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy
| | - Thomas Gurry
- Broad Institute of Harvard and MIT Cambridge MA USA
| | - Nicola Lopizzo
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy
| | | | | | | | - Giovanni B Frisoni
- Memory Clinic and LANVIE‐Laboratory of Neuroimaging of Aging University Hospitals and University of Geneva Geneva Switzerland
| | - Annamaria Cattaneo
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy
- King’s College London London United Kingdom
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6
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Gurry T, Scapozza L. Exploiting the gut microbiota's fermentation capabilities towards disease prevention. J Pharm Biomed Anal 2020; 189:113469. [PMID: 32688211 DOI: 10.1016/j.jpba.2020.113469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022]
Abstract
One of the crucial roles played in the context of human physiology by the human gut microbiota is to ferment resistant polysaccharides and dietary fibres in the colon. Even though it has long been presumed that these processes play fundamental roles in regulating human health, we remain unable to treat or even diagnose deficiencies in microbial fermentation. In part, this relatively slow progress can be attributed to the fact that studying the gut microbiota and its metabolic properties has until now heavily relied on next generation sequencing and case-control cohorts to identify differentially abundant genes, pathways or organisms in the context of a particular clinical indication. Unfortunately, these methods and studies do not allow us to rigorously probe the functional and metabolic phenotype of a microbiota, or for elucidating its mechanisms of action on the host. To improve our clinical control over these fermentation processes, it is critical that we improve our quantitative, mechanistic understanding of their impact on host physiology. In this review, we provide an overview of our current understanding of the roles microbial fermentation processes play in human health in the context of disease prevention. We then describe the evidence linking these processes with depression and anxiety-related conditions, and use these complex disorders as a framework for illustrating the fact that achieving a clinical vision that exploits microbial fermentation towards human health will depend on thoughtful multi-disciplinary collaboration between clinical research, systems biology, and the pharmaceutical and analytical sciences.
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Affiliation(s)
- Thomas Gurry
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, (PSI-WS), University of Geneva, Switzerland.
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, (PSI-WS), University of Geneva, Switzerland
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7
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Yu X, Gurry T, Nguyen LTT, Richardson HS, Alm EJ. Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota. mBio 2020; 11:e00217-20. [PMID: 32900799 PMCID: PMC7482059 DOI: 10.1128/mbio.00217-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/31/2020] [Indexed: 01/01/2023] Open
Abstract
Prebiotics confer benefits to human health, often by promoting the growth of gut bacteria that produce metabolites valuable to the human body, such as short-chain fatty acids (SCFAs). While prebiotic selection has strongly focused on maximizing the production of SCFAs, less attention has been paid to gases, a by-product of SCFA production that also has physiological effects on the human body. Here, we investigate how the content and volume of gas production by human gut microbiota are affected by the chemical composition of the prebiotic and the community composition of the microbiota. We first constructed a linear system model based on mass and electron balance and compared the theoretical product ranges of two prebiotics, inulin and pectin. Modeling shows that pectin is more restricted in product space, with less potential for H2 but more potential for CO2 production. An ex vivo experimental system showed pectin degradation produced significantly less H2 than inulin, but CO2 production fell outside the theoretical product range, suggesting fermentation of fecal debris. Microbial community composition also impacted results: methane production was dependent on the presence of Methanobacteria, while interindividual differences in H2 production during inulin degradation were driven by a Lachnospiraceae taxon. Overall, these results suggest that both the chemistry of the prebiotic and the composition of the microbiota are relevant to gas production. Metabolic processes that are relatively prevalent in the microbiome, such as H2 production, will depend more on substrate, while rare metabolisms such as methanogenesis depend more strongly on microbiome composition.IMPORTANCE Prebiotic fermentation in the gut often leads to the coproduction of short-chain fatty acids (SCFAs) and gases. While excess gas production can be a potential problem for those with functional gut disorders, gas production is rarely considered during prebiotic design. In this study, we combined the use of theoretical models and an ex vivo experimental platform to illustrate that both the chemical composition of the prebiotic and the community composition of the human gut microbiota can affect the volume and content of gas production during prebiotic fermentation. Specifically, more prevalent metabolic processes such as hydrogen production were strongly affected by the oxidation state of the probiotic, while rare metabolisms such as methane production were less affected by the chemical nature of the substrate and entirely dependent on the presence of Methanobacteria in the microbiota.
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Affiliation(s)
- Xiaoqian Yu
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Le Thanh Tu Nguyen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hunter S Richardson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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8
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Marizzoni M, Gurry T, Provasi S, Greub G, Lopizzo N, Ribaldi F, Festari C, Mazzelli M, Mombelli E, Salvatore M, Mirabelli P, Franzese M, Soricelli A, Frisoni GB, Cattaneo A. Comparison of Bioinformatics Pipelines and Operating Systems for the Analyses of 16S rRNA Gene Amplicon Sequences in Human Fecal Samples. Front Microbiol 2020; 11:1262. [PMID: 32636817 PMCID: PMC7318847 DOI: 10.3389/fmicb.2020.01262] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/18/2020] [Indexed: 01/03/2023] Open
Abstract
Amplicon high-throughput sequencing of 16S ribosomal RNA (rRNA) gene is currently the most widely used technique to investigate complex gut microbial communities. Microbial identification might be influenced by several factors, including the choice of bioinformatic pipelines, making comparisons across studies difficult. Here, we compared four commonly used pipelines (QIIME2, Bioconductor, UPARSE and mothur) run on two operating systems (OS) (Linux and Mac), to evaluate the impact of bioinformatic pipeline and OS on the taxonomic classification of 40 human stool samples. We applied the SILVA 132 reference database for all the pipelines. We compared phyla and genera identification and relative abundances across the four pipelines using the Friedman rank sum test. QIIME2 and Bioconductor provided identical outputs on Linux and Mac OS, while UPARSE and mothur reported only minimal differences between OS. Taxa assignments were consistent at both phylum and genus level across all the pipelines. However, a difference in terms of relative abundance was identified for all phyla (p < 0.013) and for the majority of the most abundant genera (p < 0.028), such as Bacteroides (QIIME2: 24.5%, Bioconductor: 24.6%, UPARSE-linux: 23.6%, UPARSE-mac: 20.6%, mothur-linux: 22.2%, mothur-mac: 21.6%, p < 0.001). The use of different bioinformatic pipelines affects the estimation of the relative abundance of gut microbial community, indicating that studies using different pipelines cannot be directly compared. A harmonization procedure is needed to move the field forward.
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Affiliation(s)
- Moira Marizzoni
- Laboratory of Neuroimaging and Alzheimer's Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Thomas Gurry
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Stefania Provasi
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Gilbert Greub
- Institut de Microbiologie de l'Université de Lausanne, Lausanne, Switzerland
| | - Nicola Lopizzo
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Federica Ribaldi
- Laboratory of Neuroimaging and Alzheimer's Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.,Memory Clinic and LANVIE - Laboratory of Neuroimaging of Aging, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Cristina Festari
- Laboratory of Neuroimaging and Alzheimer's Epidemiology, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Monica Mazzelli
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Elisa Mombelli
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | | | | | | | | | - Giovanni B Frisoni
- Memory Clinic and LANVIE - Laboratory of Neuroimaging of Aging, University Hospitals and University of Geneva, Geneva, Switzerland
| | - Annamaria Cattaneo
- Laboratory of Biological Psychiatry, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
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9
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Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci Transl Med 2019; 10:10/472/eaap8914. [PMID: 30567928 DOI: 10.1126/scitranslmed.aap8914] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 04/06/2018] [Accepted: 07/16/2018] [Indexed: 12/15/2022]
Abstract
Changes in the gut microbiota have been associated with two of the most common gastrointestinal diseases, inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Here, we performed a case-control analysis using shotgun metagenomic sequencing of stool samples from 1792 individuals with IBD and IBS compared with control individuals in the general population. Despite substantial overlap between the gut microbiome of patients with IBD and IBS compared with control individuals, we were able to use gut microbiota composition differences to distinguish patients with IBD from those with IBS. By combining species-level profiles and strain-level profiles with bacterial growth rates, metabolic functions, antibiotic resistance, and virulence factor analyses, we identified key bacterial species that may be involved in two common gastrointestinal diseases.
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Affiliation(s)
- Arnau Vich Vila
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Floris Imhann
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Valerie Collij
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Soesma A Jankipersadsing
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Thomas Gurry
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zlatan Mujagic
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Alexander Kurilshikov
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Marc Jan Bonder
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Xiaofang Jiang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ettje F Tigchelaar
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Jackie Dekens
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Vera Peters
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Michiel D Voskuil
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Marijn C Visschedijk
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Hendrik M van Dullemen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Daniel Keszthelyi
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Morris A Swertz
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Lude Franke
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Rudi Alberts
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Eleonora A M Festen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Gerard Dijkstra
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Ad A M Masclee
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Marten H Hofker
- University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
| | - Ramnik J Xavier
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jingyuan Fu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
| | - Cisca Wijmenga
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Daisy M A E Jonkers
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Alexandra Zhernakova
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Rinse K Weersma
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.
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10
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Marizzoni M, Provasi S, Greub G, Gurry T, Lopizzo N, Ribaldi F, Salvatore M, Mirabelli P, Soricelli A, Frisoni GB, Cattaneo A. P4-125: BIOINFORMATIC PIPELINE COMPARISON FOR COMPOSITIONAL ANALYSIS OF THE GUT MICROBIOME IN ALZHEIMER'S PATIENTS. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.3786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Moira Marizzoni
- IRCCS Centro San Giovanni di Dio Fatebenefratelli; Brescia Italy
| | - Stefania Provasi
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli; Brescia Italy
| | - Gilbert Greub
- Institut de Microbiologie de l'Université de Lausanne; Lausanne Switzerland
| | - Thomas Gurry
- Center for Microbiome Informatics and Therapeutics; Massachusetts Institute of Technology; Cambridge MA USA
- Broad Institute of Harvard and MIT; Cambridge MA USA
| | - Nicola Lopizzo
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli; Brescia Italy
| | - Federica Ribaldi
- IRCCS Centro San Giovanni di Dio Fatebenefratelli; Brescia Italy
- University of Geneva; Geneva Switzerland
- University of Brescia; Brescia Italy
| | | | - Peppino Mirabelli
- Istituto di Ricovero e Cura a Carattere Scientifico SDN; Naples Italy
| | - Andrea Soricelli
- University of Naples Parthenope; Naples Italy
- IRCCS SDN; Naples Italy
| | - Giovanni B. Frisoni
- University Hospital of Geneva; Geneva Switzerland
- Lab Alzheimer's Neuroimaging & Epidemiology; IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli; Brescia Italy
- LANVIE - Laboratory of Neuroimaging of Aging; University of Geneva; Geneva Switzerland
| | - Annamaria Cattaneo
- IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli; Brescia Italy
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11
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Cui M, Qi Q, Gurry T, Zhao T, An B, Pu J, Gui X, Cheng AA, Zhang S, Xun D, Becce M, Briatico-Vangosa F, Liu C, Lu TK, Zhong C. Modular genetic design of multi-domain functional amyloids: insights into self-assembly and functional properties. Chem Sci 2019; 10:4004-4014. [PMID: 31015941 PMCID: PMC6461117 DOI: 10.1039/c9sc00208a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/14/2019] [Indexed: 01/16/2023] Open
Abstract
Engineering functional amyloids through a modular genetic strategy represents new opportunities for creating multifunctional molecular materials with tailored structures and performance. Despite important advances, how fusion modules affect the self-assembly and functional properties of amyloids remains elusive. Here, using Escherichia coli curli as a model system, we systematically studied the effect of flanking domains on the structures, assembly kinetics and functions of amyloids. The designed amyloids were composed of E. coli biofilm protein CsgA (as amyloidogenic cores) and one or two flanking domains, consisting of chitin-binding domains (CBDs) from Bacillus circulans chitinase, and/or mussel foot proteins (Mfps). Incorporation of fusion domains did not disrupt the typical β-sheet structures, but indeed affected assembly rate, morphology, and stiffness of resultant fibrils. Consequently, the CsgA-fusion fibrils, particularly those containing three domains, were much shorter than the CsgA-only fibrils. Furthermore, the stiffness of the resultant fibrils was heavily affected by the structural feature of fusion domains, with β-sheet-containing domains tending to increase the Young's modulus while random coil domains decreasing the Young's modulus. In addition, fibrils containing CBD domains showed higher chitin-binding activity compared to their CBD-free counterparts. The CBD-CsgA-Mfp3 construct exhibited significantly lower binding activity than Mfp5-CsgA-CBD due to inappropriate folding of the CBD domain in the former construct, in agreement with results based upon molecular dynamics modeling. Our study provides new insights into the assembly and functional properties of designer amyloid proteins with increasing complex domain structures and lays the foundation for the future design of functional amyloid-based structures and molecular materials.
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Affiliation(s)
- Mengkui Cui
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
- University of Chinese Academy of Sciences , Beijing 100049 , China
- Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Qi Qi
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Thomas Gurry
- Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139-4307 , USA
| | - Tianxin Zhao
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
- University of Chinese Academy of Sciences , Beijing 100049 , China
- Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Bolin An
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Jiahua Pu
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Xinrui Gui
- Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
- Interdisciplinary Research Center on Biology and Chemistry , Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Allen A Cheng
- Department of Electrical Engineering and Computer Science , Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139-4307 , USA
| | - Siyu Zhang
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Dongmin Xun
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
| | - Michele Becce
- Department of Electrical Engineering and Computer Science , Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139-4307 , USA
- Dipartimento di Chimica Materiali e Ingegneria Chimica G. Natta , Politecnico di Milano , Piazza Leonardo da Vinci 32 , 20133 Milano , Italy
- Department of Materials , Imperial College London , London SW7 2AZ , UK
| | - Francesco Briatico-Vangosa
- Dipartimento di Chimica Materiali e Ingegneria Chimica G. Natta , Politecnico di Milano , Piazza Leonardo da Vinci 32 , 20133 Milano , Italy
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry , Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 200032 , China
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science , Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139-4307 , USA
| | - Chao Zhong
- School of Physical Science and Technology , ShanghaiTech University , Shanghai 200120 , China .
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12
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Brito IL, Gurry T, Zhao S, Huang K, Young SK, Shea TP, Naisilisili W, Jenkins AP, Jupiter SD, Gevers D, Alm EJ. Transmission of human-associated microbiota along family and social networks. Nat Microbiol 2019; 4:964-971. [PMID: 30911128 DOI: 10.1038/s41564-019-0409-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 02/14/2019] [Indexed: 01/01/2023]
Abstract
The human microbiome, described as an accessory organ because of the crucial functions it provides, is composed of species that are uniquely found in humans1,2. Yet, surprisingly little is known about the impact of routine interpersonal contacts in shaping microbiome composition. In a relatively 'closed' cohort of 287 people from the Fiji Islands, where common barriers to bacterial transmission are absent, we examine putative bacterial transmission in individuals' gut and oral microbiomes using strain-level data from both core single-nucleotide polymorphisms and flexible genomic regions. We find a weak signal of transmission, defined by the inferred sharing of genotypes, across many organisms that, in aggregate, reveals strong transmission patterns, most notably within households and between spouses. We were unable to determine the directionality of transmission nor whether it was direct. We further find that women harbour strains more closely related to those harboured by their familial and social contacts than men, and that transmission patterns of oral-associated and gut-associated microbiota need not be the same. Using strain-level data alone, we are able to confidently predict a subset of spouses, highlighting the role of shared susceptibilities, behaviours or social interactions that distinguish specific links in the social network.
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Affiliation(s)
- Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| | - Thomas Gurry
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome, Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shijie Zhao
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome, Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | | - Aaron P Jenkins
- Edith Cowan University, Joondalup, Western Australia, Australia.,School of Public Health, University of Sydney, Sydney, New South Wales, Australia
| | | | - Dirk Gevers
- Janssen Human Microbiome Institute, Cambridge, MA, USA
| | - Eric J Alm
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Center for Microbiome, Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Broad Institute, Cambridge, MA, USA.
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13
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Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D’Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles. Gut Microbes 2018; 10:358-366. [PMID: 30373468 PMCID: PMC6546312 DOI: 10.1080/19490976.2018.1528822] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Several gastrointestinal diseases show a sex imbalance, although the underlying (patho)physiological mechanisms behind this are not well understood. The gut microbiome may be involved in this process, forming a complex interaction with host immune system, sex hormones, medication and other environmental factors. Here we performed sex-specific analyses of fecal microbiota composition in 1135 individuals from a population-based cohort. The overall gut microbiome composition of females and males was significantly different (p = 0.001), with females showing a greater microbial diversity (p = 0.009). After correcting for the effects of intrinsic factors, smoking, diet and medications, female hormonal factors such as the use of oral contraceptives and undergoing an ovariectomy were associated with microbial species and pathways. Females had a higher richness of antibiotic-resistance genes, with the most notable being resistance to the lincosamide nucleotidyltransferase (LNU) gene family. The higher abundance of resistance genes is consistent with the greater prescription of the Macrolide-Lincosamide-Streptogramin classes of antibiotics to females. Furthermore, we observed an increased resistance to aminoglycosides in females with self-reported irritable bowel syndrome. These results throw light upon the effects of common medications that are differentially prescribed between sexes and highlight the importance of sex-specific analysis when studying the gut microbiome and resistome.
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Affiliation(s)
- Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Soesma A. Jankipersadsing
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Floris Imhann
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xiaofang Jiang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric J. Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mauro D’Amato
- Gastrointestinal Genetics Unit, Biodonostia Health Research Institute, San Sebastian, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sicco Scherjon
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,CONTACT Alexandra Zhernakova, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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14
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Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ. Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort. Sci Rep 2018; 8:12699. [PMID: 30139999 PMCID: PMC6107591 DOI: 10.1038/s41598-018-30783-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/26/2018] [Indexed: 01/05/2023] Open
Abstract
Dietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host’s microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient’s microbiota.
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Affiliation(s)
- Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Le Thanh Tu Nguyen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sean M Kearney
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ashwin Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Xiaofang Jiang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Claire Duvallet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zain Kassam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,OpenBiome, Somerville, MA, 02143, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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15
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Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun 2017; 8:1784. [PMID: 29209090 PMCID: PMC5716994 DOI: 10.1038/s41467-017-01973-8] [Citation(s) in RCA: 564] [Impact Index Per Article: 80.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/30/2017] [Indexed: 12/16/2022] Open
Abstract
Hundreds of clinical studies have demonstrated associations between the human microbiome and disease, yet fundamental questions remain on how we can generalize this knowledge. Results from individual studies can be inconsistent, and comparing published data is further complicated by a lack of standard processing and analysis methods. Here we introduce the MicrobiomeHD database, which includes 28 published case–control gut microbiome studies spanning ten diseases. We perform a cross-disease meta-analysis of these studies using standardized methods. We find consistent patterns characterizing disease-associated microbiome changes. Some diseases are associated with over 50 genera, while most show only 10–15 genus-level changes. Some diseases are marked by the presence of potentially pathogenic microbes, whereas others are characterized by a depletion of health-associated bacteria. Furthermore, we show that about half of genera associated with individual studies are bacteria that respond to more than one disease. Thus, many associations found in case–control studies are likely not disease-specific but rather part of a non-specific, shared response to health and disease. Reported associations between the human microbiome and disease are often inconsistent. Here, Duvallet et al. perform a meta-analysis of 28 gut microbiome studies spanning ten diseases, and find associations that are likely not disease-specific but potentially part of a shared response to disease.
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Affiliation(s)
- Claire Duvallet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sean M Gibbons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
| | - Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA
| | - Rafael A Irizarry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA.
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16
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Bajaj JS, Kassam Z, Fagan A, Gavis EA, Liu E, Cox IJ, Kheradman R, Heuman D, Wang J, Gurry T, Williams R, Sikaroodi M, Fuchs M, Alm E, John B, Thacker LR, Riva A, Smith M, Taylor-Robinson SD, Gillevet PM. Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: A randomized clinical trial. Hepatology 2017; 66:1727-1738. [PMID: 28586116 PMCID: PMC6102730 DOI: 10.1002/hep.29306] [Citation(s) in RCA: 376] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/12/2017] [Accepted: 06/05/2017] [Indexed: 12/11/2022]
Abstract
UNLABELLED Recurrent hepatic encephalopathy (HE) is a leading cause of readmission despite standard of care (SOC) associated with microbial dysbiosis. Fecal microbiota transplantation (FMT) may improve dysbiosis; however, it has not been studied in HE. We aimed to define whether FMT using a rationally derived stool donor is safe in recurrent HE compared to SOC alone. An open-label, randomized clinical trial with a 5-month follow-up in outpatient men with cirrhosis with recurrent HE on SOC was conducted with 1:1 randomization. FMT-randomized patients received 5 days of broad-spectrum antibiotic pretreatment, then a single FMT enema from the same donor with the optimal microbiota deficient in HE. Follow-up occurred on days 5, 6, 12, 35, and 150 postrandomization. The primary outcome was safety of FMT compared to SOC using FMT-related serious adverse events (SAEs). Secondary outcomes were adverse events, cognition, microbiota, and metabolomic changes. Participants in both arms were similar on all baseline criteria and were followed until study end. FMT with antibiotic pretreatment was well tolerated. Eight (80%) SOC participants had a total of 11 SAEs compared to 2 (20%) FMT participants with SAEs (both FMT unrelated; P = 0.02). Five SOC and no FMT participants developed further HE (P = 0.03). Cognition improved in the FMT, but not the SOC, group. Model for End-Stage Liver Disease (MELD) score transiently worsened postantibiotics, but reverted to baseline post-FMT. Postantibiotics, beneficial taxa, and microbial diversity reduction occurred with Proteobacteria expansion. However, FMT increased diversity and beneficial taxa. SOC microbiota and MELD score remained similar throughout. CONCLUSION FMT from a rationally selected donor reduced hospitalizations, improved cognition, and dysbiosis in cirrhosis with recurrent HE. (Hepatology 2017;66:1727-1738).
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Affiliation(s)
- Jasmohan S. Bajaj
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Zain Kassam
- OpenBiome, Somerville, Massachusetts, USA,Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew Fagan
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Edith A. Gavis
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Eric Liu
- George Mason University, Manassas, Virginia, USA
| | - I. Jane Cox
- Institute of Hepatology London, Foundation for Liver Research, United Kingdom
| | | | - Douglas Heuman
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Jessica Wang
- George Mason University, Manassas, Virginia, USA
| | - Thomas Gurry
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Roger Williams
- Institute of Hepatology London, Foundation for Liver Research, United Kingdom
| | | | - Michael Fuchs
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Eric Alm
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Binu John
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Leroy R Thacker
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia, USA
| | - Antonio Riva
- Institute of Hepatology London, Foundation for Liver Research, United Kingdom
| | - Mark Smith
- OpenBiome, Somerville, Massachusetts, USA
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17
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Pakpour S, Bhanvadia A, Zhu R, Amarnani A, Gibbons SM, Gurry T, Alm EJ, Martello LA. Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment. Microbiome 2017; 5:148. [PMID: 29132405 PMCID: PMC5684761 DOI: 10.1186/s40168-017-0368-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/01/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Colonization by the pathogen Clostridium difficile often occurs in the background of a disrupted microbial community. Identifying specific organisms conferring resistance to invasion by C. difficile is desirable because diagnostic and therapeutic strategies based on the human microbiota have the potential to provide more precision to the management and treatment of Clostridium difficile infection (CDI) and its recurrence. METHODS We conducted a longitudinal study of adult patients diagnosed with their first CDI. We investigated the dynamics of the gut microbiota during antibiotic treatment, and we used microbial or demographic features at the time of diagnosis, or after treatment, to predict CDI recurrence. To check the validity of the predictions, a meta-analysis using a previously published dataset was performed. RESULTS We observed that patients' microbiota "before" antibiotic treatment was predictive of disease relapse, but surprisingly, post-antibiotic microbial community is indistinguishable between patients that recur or not. At the individual OTU level, we identified Veillonella dispar as a candidate organism for preventing CDI recurrence; however, we did not detect a corresponding signal in the conducted meta-analysis. CONCLUSION Although in our patient population, a candidate organism was identified for negatively predicting CDI recurrence, results suggest the need for larger cohort studies that include patients with diverse demographic characteristics to generalize species that robustly confer colonization resistance against C. difficile and accurately predict disease relapse.
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Affiliation(s)
- Sepideh Pakpour
- Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA USA
- MIT Center for Microbiome Informatics and Therapeutics, Cambridge, MA USA
| | - Amit Bhanvadia
- Division of Digestive Diseases, Lenox Hill Hospital/Northwell Health, New York, NY USA
- Medicine, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Roger Zhu
- Surgery, NewYork-Presbyterian/Queens, Flushing, NY USA
- Medicine, SUNY Downstate Medical Center, Brooklyn, NY USA
| | | | - Sean M. Gibbons
- Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA USA
- MIT Center for Microbiome Informatics and Therapeutics, Cambridge, MA USA
| | - Thomas Gurry
- Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA USA
- MIT Center for Microbiome Informatics and Therapeutics, Cambridge, MA USA
| | - Eric J. Alm
- Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA USA
- MIT Center for Microbiome Informatics and Therapeutics, Cambridge, MA USA
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18
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Bajaj JS, Kassam Z, Cox IJ, Gurry T, Williams R, Alm E, John B, Smith M, Taylor-Robinson SD, Gillevet PM. Reply. Hepatology 2017; 66:1355-1356. [PMID: 28714102 DOI: 10.1002/hep.29368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 07/11/2017] [Indexed: 12/07/2022]
Affiliation(s)
- Jasmohan S Bajaj
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
| | - Zain Kassam
- OpenBiome, Somerville, MA.,Massachusetts Institute of Technology, Cambridge, MA
| | - I Jane Cox
- Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Thomas Gurry
- Massachusetts Institute of Technology, Cambridge, MA
| | - Roger Williams
- Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Eric Alm
- Massachusetts Institute of Technology, Cambridge, MA
| | - Binu John
- Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA
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19
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Abstract
Synbiotics refer to combinations of probiotics and prebiotics that act synergistically to confer health benefits to the host. As a therapeutic strategy, they provide a gentle yet powerful method for modulating the composition and metabolic output of the human gut microbiota. In the context of achieving the UN Sustainable Development Goals, synbiotics have the potential to act as cost‐effective prophylactic measures against a variety of human ailments, ranging from infant diarrhoea to metabolic and inflammatory diseases in adults, by maintaining commensal microbial communities and metabolic networks that are conducive to human health.
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Affiliation(s)
- Thomas Gurry
- MIT Center for Microbiome Informatics and Therapeutics, Cambridge, MA, 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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20
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Olesen SW, Gurry T, Alm EJ. Designing fecal microbiota transplant trials that account for differences in donor stool efficacy. Stat Methods Med Res 2017; 27:2906-2917. [DOI: 10.1177/0962280216688502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fecal microbiota transplantation is a highly effective intervention for patients suffering from recurrent Clostridium difficile, a common hospital-acquired infection. Fecal microbiota transplantation’s success as a therapy for C. difficile has inspired interest in performing clinical trials that experiment with fecal microbiota transplantation as a therapy for other conditions like inflammatory bowel disease, obesity, diabetes, and Parkinson’s disease. Results from clinical trials that use fecal microbiota transplantation to treat inflammatory bowel disease suggest that, for at least one condition beyond C. difficile, most fecal microbiota transplantation donors produce stool that is not efficacious. The optimal strategies for identifying and using efficacious donors have not been investigated. We therefore examined the optimal Bayesian response-adaptive strategy for allocating patients to donors and formulated a computationally tractable myopic heuristic. This heuristic computes the probability that a donor is efficacious by updating prior expectations about the efficacy of fecal microbiota transplantation, the placebo rate, and the fraction of donors that produce efficacious stool. In simulations designed to mimic a recent fecal microbiota transplantation clinical trial, for which traditional power calculations predict [Formula: see text] statistical power, we found that accounting for differences in donor stool efficacy reduced the predicted statistical power to [Formula: see text]. For these simulations, using the heuristic Bayesian allocation strategy more than quadrupled the statistical power to [Formula: see text]. We use the results of similar simulations to make recommendations about the number of patients, the number of donors, and the choice of clinical endpoint that clinical trials should use to optimize their ability to detect if fecal microbiota transplantation is effective for treating a condition.
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Affiliation(s)
- Scott W Olesen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, USA
- The Broad Institute of MIT and Harvard, Cambridge, USA
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21
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Ziegler Z, Schmidt M, Gurry T, Burger V, Stultz CM. Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins. ACTA ACUST UNITED AC 2016; 32:2545-7. [PMID: 27153636 DOI: 10.1093/bioinformatics/btw200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/09/2016] [Indexed: 11/14/2022]
Abstract
UNLABELLED Intrinsically disordered proteins (IDPs) play central roles in many biological processes. Consequently, an accurate description of the disordered state is an important step towards a comprehensive understanding of a number of important biological functions. In this work we describe a new web server, Mollack, for the automated construction of unfolded ensembles that uses both experimental and molecular simulation data to construct models for the unfolded state. An important aspect of the method is that it calculates a quantitative estimate of the uncertainty in the constructed ensemble, thereby providing an objective measure of the quality of the final model. Overall, Mollack facilitates structure-function studies of disordered proteins. AVAILABILITY AND IMPLEMENTATION http://cmstultz-mollack.mit.edu CONTACT cmstultz@mit.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zachary Ziegler
- Cornell University, Ithaca, NY 14850, USA Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Molly Schmidt
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Thomas Gurry
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Virginia Burger
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Collin M Stultz
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA The Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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22
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Abstract
Intrinsically disordered proteins (IDPs) are notoriously difficult to study experimentally because they rapidly interconvert between many dissimilar conformations during their biological lifetime, and therefore cannot be described by a single structure. The importance of studying these systems, however, is underscored by the fact that they form toxic aggregates that play a role in the pathogenesis of many disorders. The first step towards a comprehensive understanding of the aggregation mechanism of these proteins involves a description of their thermally accessible states under physiologic conditions. The resulting conformational ensembles correspond to coarse-grained descriptions of their energy landscapes, where the number of structures in the ensemble is related to the resolution in which one views the free energy surface. Here, we provide step-by-step instructions on how to use experimental data to construct a conformational ensemble for an IDP using a Variational Bayesian Weighting (VBW) algorithm. We further discuss how to leverage this Bayesian approach to identify statistically significant ensemble-wide observations that can form the basis of further experimental studies.
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Affiliation(s)
- Thomas Gurry
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA
| | | | - Molly Schmidt
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA
| | - Collin M Stultz
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA.
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA.
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA.
- The Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, 02139-4307, USA.
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23
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Das A, Swedish T, Wahi A, Moufarrej M, Noland M, Gurry T, Aranda-Michel E, Aksel D, Wagh S, Sadashivaiah V, Zhang X, Raskar R. Mobile phone based mini-spectrometer for rapid screening of skin cancer. ACTA ACUST UNITED AC 2015. [DOI: 10.1117/12.2182191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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24
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DaSilva LC, Gurry T, Stultz CM. Toward a consensus in protein structure nomenclature. Intrinsically Disord Proteins 2014; 2:e970902. [PMID: 28232882 PMCID: PMC5314908 DOI: 10.4161/idp.29700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 06/23/2012] [Indexed: 11/19/2022]
Abstract
In a recent article, published in Intrinsically Disordered Proteins, a valuable consensus view regarding the nomenclature for disordered proteins was presented.1 In this work the authors present a thoughtful and systemic review of terms that have been used in the literature to describe proteins that sample a heterogeneous set of structures during their biological lifetime. We agree that the term "intrinsically disordered proteins" (IDPs) is an appropriate single descriptor to refer to this particular class of proteins, although it does not fully capture much of the nuanced complexities that are inherent to this class. In what follows we suggest a refinement to this nomenclature based on an analysis of the underlying ensemble that describes the thermally accessible states of a given IDP.
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Affiliation(s)
- Linder C DaSilva
- Research Laboratory of Electronics; Massachusetts Institute of Technology; Cambridge, MA USA; ICET-CUAl Federal University of Mato Grosso; Barra do Garças, Brazil
| | - Thomas Gurry
- Research Laboratory of Electronics; Massachusetts Institute of Technology; Cambridge, MA USA; Computational and Systems Biology Initiative; Massachusetts Institute of Technology; Cambridge, MA USA
| | - Collin M Stultz
- Research Laboratory of Electronics; Massachusetts Institute of Technology; Cambridge, MA USA; Computational and Systems Biology Initiative; Massachusetts Institute of Technology; Cambridge, MA USA; Dept. of Electrical Engineering and Computer Science & Institute for Medical Engineering and Sciences; Massachusetts Institute of Technology; Cambridge, MA USA
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25
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Abstract
Amyloid-β is an intrinsically disordered protein that forms fibrils in the brains of patients with Alzheimer's disease. To explore factors that affect the process of fibril growth, we computed the free energy associated with disordered amyloid-β monomers being added to growing amyloid fibrils using extensive molecular dynamics simulations coupled with umbrella sampling. We find that the mechanisms of Aβ40 and Aβ42 fibril elongation have many features in common, including the formation of an obligate on-pathway β-hairpin intermediate that hydrogen bonds to the fibril core. In addition, our data lead to new hypotheses for how fibrils may serve as secondary nucleation sites that can catalyze the formation of soluble oligomers, a finding in agreement with recent experimental observations. These data provide a detailed mechanistic description of amyloid-β fibril elongation and a structural link between the disordered free monomer and the growth of amyloid fibrils and soluble oligomers.
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Affiliation(s)
- Thomas Gurry
- Computational and Systems Biology Initiative and Research Laboratory of Electronics, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139-4307, United States
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26
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Zhong C, Gurry T, Cheng AA, Downey J, Deng Z, Stultz CM, Lu TK. Strong underwater adhesives made by self-assembling multi-protein nanofibres. Nat Nanotechnol 2014; 9:858-66. [PMID: 25240674 PMCID: PMC4191913 DOI: 10.1038/nnano.2014.199] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 08/14/2014] [Indexed: 05/20/2023]
Abstract
Many natural underwater adhesives harness hierarchically assembled amyloid nanostructures to achieve strong and robust interfacial adhesion under dynamic and turbulent environments. Despite recent advances, our understanding of the molecular design, self-assembly and structure-function relationships of these natural amyloid fibres remains limited. Thus, designing biomimetic amyloid-based adhesives remains challenging. Here, we report strong and multi-functional underwater adhesives obtained from fusing mussel foot proteins (Mfps) of Mytilus galloprovincialis with CsgA proteins, the major subunit of Escherichia coli amyloid curli fibres. These hybrid molecular materials hierarchically self-assemble into higher-order structures, in which, according to molecular dynamics simulations, disordered adhesive Mfp domains are exposed on the exterior of amyloid cores formed by CsgA. Our fibres have an underwater adhesion energy approaching 20.9 mJ m(-2), which is 1.5 times greater than the maximum of bio-inspired and bio-derived protein-based underwater adhesives reported thus far. Moreover, they outperform Mfps or curli fibres taken on their own and exhibit better tolerance to auto-oxidation than Mfps at pH ≥ 7.0.
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Affiliation(s)
- Chao Zhong
- Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Thomas Gurry
- Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Allen A Cheng
- Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Jordan Downey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Zhengtao Deng
- Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Collin M. Stultz
- Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- The Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Timothy K Lu
- Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
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27
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Gurry T, Stultz CM. The Mechanism of Amyloid-β42 Fibril Elongation. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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28
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Abstract
α-Synuclein, a protein that forms ordered aggregates in the brains of patients with Parkinson's disease, is intrinsically disordered in the monomeric state. Several studies, however, suggest that it can form soluble multimers in vivo that have significant secondary structure content. A number of studies demonstrate that α-synuclein can form β-strand-rich oligomers that are neurotoxic, and recent observations argue for the existence of soluble helical tetrameric species in cellulo that do not form toxic aggregates. To gain further insight into the different types of multimeric states that this protein can adopt, we generated an ensemble for an α-synuclein construct that contains a 10-residue N-terminal extension, which forms multimers when isolated from Escherichia coli. Data from NMR chemical shifts and residual dipolar couplings were used to guide the construction of the ensemble. Our data suggest that the dominant state of this ensemble is a disordered monomer, complemented by a small fraction of helical trimers and tetramers. Interestingly, the ensemble also contains trimeric and tetrameric oligomers that are rich in β-strand content. These data help to reconcile seemingly contradictory observations that indicate the presence of a helical tetramer in cellulo on the one hand, and a disordered monomer on the other. Furthermore, our findings are consistent with the notion that the helical tetrameric state provides a mechanism for storing α-synuclein when the protein concentration is high, thereby preventing non-membrane-bound monomers from aggregating.
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Affiliation(s)
- Thomas Gurry
- Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
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29
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Gurry T, Kahramanoğulları O, Endres RG. Biophysical mechanism for ras-nanocluster formation and signaling in plasma membrane. PLoS One 2009; 4:e6148. [PMID: 19587789 PMCID: PMC2704371 DOI: 10.1371/journal.pone.0006148] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 06/07/2009] [Indexed: 01/02/2023] Open
Abstract
Ras GTPases are lipid-anchored G proteins, which play a fundamental role in cell signaling processes. Electron micrographs of immunogold-labeled Ras have shown that membrane-bound Ras molecules segregate into nanocluster domains. Several models have been developed in attempts to obtain quantitative descriptions of nanocluster formation, but all have relied on assumptions such as a constant, expression-level independent ratio of Ras in clusters to Ras monomers (cluster/monomer ratio). However, this assumption is inconsistent with the law of mass action. Here, we present a biophysical model of Ras clustering based on short-range attraction and long-range repulsion between Ras molecules in the membrane. To test this model, we performed Monte Carlo simulations and compared statistical clustering properties with experimental data. We find that we can recover the experimentally-observed clustering across a range of Ras expression levels, without assuming a constant cluster/monomer ratio or the existence of lipid rafts. In addition, our model makes predictions about the signaling properties of Ras nanoclusters in support of the idea that Ras nanoclusters act as an analog-digital-analog converter for high fidelity signaling.
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Affiliation(s)
- Thomas Gurry
- Centre for Integrated Systems Biology at Imperial College, Imperial College London, London, United Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Ozan Kahramanoğulları
- Centre for Integrated Systems Biology at Imperial College, Imperial College London, London, United Kingdom
- Department of Computing, Imperial College London, London, United Kingdom
| | - Robert G. Endres
- Centre for Integrated Systems Biology at Imperial College, Imperial College London, London, United Kingdom
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
- * E-mail:
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