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Björk JR, Bolte LA, Maltez Thomas A, Lee KA, Rossi N, Wind TT, Smit LM, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Spector TD, Bataille V, Segata N, Hospers GAP, Weersma RK. Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. Nat Med 2024; 30:785-796. [PMID: 38365950 PMCID: PMC10957474 DOI: 10.1038/s41591-024-02803-3] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/03/2024] [Indexed: 02/18/2024]
Abstract
Multiple clinical trials targeting the gut microbiome are being conducted to optimize treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these interventions, understanding gut microbiome changes during ICB is urgently needed. Here through longitudinal microbiome profiling of 175 patients treated with ICB for advanced melanoma, we show that several microbial species-level genome bins (SGBs) and pathways exhibit distinct patterns from baseline in patients achieving progression-free survival (PFS) of 12 months or longer (PFS ≥12) versus patients with PFS shorter than 12 months (PFS <12). Out of 99 SGBs that could discriminate between these two groups, 20 were differentially abundant only at baseline, while 42 were differentially abundant only after treatment initiation. We identify five and four SGBs that had consistently higher abundances in patients with PFS ≥12 and <12 months, respectively. Constructing a log ratio of these SGBs, we find an association with overall survival. Finally, we find different microbial dynamics in different clinical contexts including the type of ICB regimen, development of immune-related adverse events and concomitant medication use. Insights into the longitudinal dynamics of the gut microbiome in association with host factors and treatment regimens will be critical for guiding rational microbiome-targeted therapies aimed at enhancing ICB efficacy.
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Affiliation(s)
- Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
| | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Andrew Maltez Thomas
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Niccolo Rossi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Thijs T Wind
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Lotte M Smit
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Federica Armanini
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Francesco Asnicar
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Aitor Blanco-Miguez
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Preston, UK
| | - Neus Calbet-Llopart
- Department of Dermatology, Melanoma Group, Hospital Clínic Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Lisa Derosa
- Gustave Roussy Cancer Center, U1015 INSERM and Oncobiome Network, University Paris Saclay, Villejuif-Grand-Paris, France
| | - Nathalie Dhomen
- Division of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Kelly Brooks
- Division of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Mark Harries
- Department of Medical Oncology, Guys Cancer Centre, Guy's and St Thomas' NHS Trust, London, UK
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona and IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Paolo Manghi
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Richard Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Luigi Nezi
- European Institute of Oncology (Istituto Europeo di Oncologia), Milan, Italy
| | - Federica Pinto
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Miriam Potrony
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona and IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Susana Puig
- Department of Dermatology, Melanoma Group, Hospital Clínic Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | | | - Heather M Shaw
- Department of Medical Oncology, Mount Vernon Cancer Centre, East and North Herts NHS Trust, Northwood, UK
| | - Sabrina Tamburini
- European Institute of Oncology (Istituto Europeo di Oncologia), Milan, Italy
| | - Sara Valpione
- Division of Immunology, Immunity to Infection and Respiratory Medicine, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Levi Waldron
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Laurence Zitvogel
- Gustave Roussy Cancer Center, U1015 INSERM and Oncobiome Network, University Paris Saclay, Villejuif-Grand-Paris, France
| | - Moreno Zolfo
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
| | - Elisabeth G E de Vries
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Paul Nathan
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona and IDIBAPS, University of Barcelona, Barcelona, Spain
- Department of Medical Oncology, Mount Vernon Cancer Centre, East and North Herts NHS Trust, Northwood, UK
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Véronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, Mount Vernon Cancer Centre, Northwood, UK
- Department of Dermatology, Hemel Hempstead Hospital, West Hertfordshire NHS Trust, Hemel Hempstead, UK
| | - Nicola Segata
- Department of CellularComputational and Integrative Biology, University of Trento, Trento, Italy
- European Institute of Oncology (Istituto Europeo di Oncologia), Milan, Italy
| | - Geke A P Hospers
- Department of Medical Oncology, Groningen University of Groningen and University Medical Center Groningen, Groningent, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
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2
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Hu S, Bourgonje AR, Gacesa R, Jansen BH, Björk JR, Bangma A, Hidding IJ, van Dullemen HM, Visschedijk MC, Faber KN, Dijkstra G, Harmsen HJM, Festen EAM, Vich Vila A, Spekhorst LM, Weersma RK. Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease. Nat Commun 2024; 15:1470. [PMID: 38368394 PMCID: PMC10874382 DOI: 10.1038/s41467-024-45855-2] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/05/2024] [Indexed: 02/19/2024] Open
Abstract
Disrupted host-microbe interactions at the mucosal level are key to the pathophysiology of IBD. This study aimed to comprehensively examine crosstalk between mucosal gene expression and microbiota in patients with IBD. To study tissue-specific interactions, we perform transcriptomic (RNA-seq) and microbial (16S-rRNA-seq) profiling of 697 intestinal biopsies (645 derived from 335 patients with IBD and 52 from 16 non-IBD controls). Mucosal gene expression patterns in IBD are mainly determined by tissue location and inflammation, whereas the mucosal microbiota composition shows a high degree of individual specificity. Analysis of transcript-bacteria interactions identifies six distinct groups of inflammation-related pathways that are associated with intestinal microbiota (adjusted P < 0.05). An increased abundance of Bifidobacterium is associated with higher expression of genes involved in fatty acid metabolism, while Bacteroides correlates with increased metallothionein signaling. In patients with fibrostenosis, a transcriptional network dominated by immunoregulatory genes is associated with Lachnoclostridium bacteria in non-stenotic tissue (adjusted P < 0.05), while being absent in CD without fibrostenosis. In patients using TNF-α-antagonists, a transcriptional network dominated by fatty acid metabolism genes is linked to Ruminococcaceae (adjusted P < 0.05). Mucosal microbiota composition correlates with enrichment of intestinal epithelial cells, macrophages, and NK-cells. Overall, these data demonstrate the presence of context-specific mucosal host-microbe interactions in IBD, revealing significantly altered inflammation-associated gene-taxa modules, particularly in patients with fibrostenotic CD and patients using TNF-α-antagonists. This study provides compelling insights into host-microbe interactions that may guide microbiota-directed precision medicine and fuels the rationale for microbiota-targeted therapeutics as a strategy to alter disease course in IBD.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Institute of Precision Medicine, the First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Amber Bangma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iwan J Hidding
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lieke M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, Medisch Spectrum Twente, Enschede, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Swarte JC, Knobbe TJ, Björk JR, Gacesa R, Nieuwenhuis LM, Zhang S, Vila AV, Kremer D, Douwes RM, Post A, Quint EE, Pol RA, Jansen BH, de Borst MH, de Meijer VE, Blokzijl H, Berger SP, Festen EAM, Zhernakova A, Fu J, Harmsen HJM, Bakker SJL, Weersma RK. Health-related quality of life is linked to the gut microbiome in kidney transplant recipients. Nat Commun 2023; 14:7968. [PMID: 38042820 PMCID: PMC10693618 DOI: 10.1038/s41467-023-43431-8] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 11/08/2023] [Indexed: 12/04/2023] Open
Abstract
Kidney transplant recipients (KTR) have impaired health-related quality of life (HRQoL) and suffer from intestinal dysbiosis. Increasing evidence shows that gut health and HRQoL are tightly related in the general population. Here, we investigate the association between the gut microbiome and HRQoL in KTR, using metagenomic sequencing data from fecal samples collected from 507 KTR. Multiple bacterial species are associated with lower HRQoL, many of which have previously been associated with adverse health conditions. Gut microbiome distance to the general population is highest among KTR with an impaired physical HRQoL (R = -0.20, P = 2.3 × 10-65) and mental HRQoL (R = -0.14, P = 1.3 × 10-3). Physical and mental HRQoL explain a significant part of variance in the gut microbiome (R2 = 0.58%, FDR = 5.43 × 10-4 and R2 = 0.37%, FDR = 1.38 × 10-3, respectively). Additionally, multiple metabolic and neuroactive pathways (gut brain modules) are associated with lower HRQoL. While the observational design of our study does not allow us to analyze causality, we provide a comprehensive overview of the associations between the gut microbiome and HRQoL while controlling for confounders.
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Affiliation(s)
- J Casper Swarte
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tim J Knobbe
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lianne M Nieuwenhuis
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shuyan Zhang
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Daan Kremer
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rianne M Douwes
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adrian Post
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Evelien E Quint
- Department of Surgery, division of Transplantation Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Robert A Pol
- Department of Surgery, division of Transplantation Surgery, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Vincent E de Meijer
- Department of Surgery, section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Stefan P Berger
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- 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
| | - 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
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Stephan J L Bakker
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Visconti A, Rossi N, Deriš H, Lee KA, Hanić M, Trbojević-Akmačić I, Thomas AM, Bolte LA, Björk JR, Hooiveld-Noeken JS, Board R, Harland M, Newton-Bishop J, Harries M, Sacco JJ, Lorigan P, Shaw HM, de Vries EGE, Fehrmann RSN, Weersma RK, Spector TD, Nathan P, Hospers GAP, Sasieni P, Bataille V, Lauc G, Falchi M. Total serum N-glycans associate with response to immune checkpoint inhibition therapy and survival in patients with advanced melanoma. BMC Cancer 2023; 23:166. [PMID: 36805683 PMCID: PMC9938582 DOI: 10.1186/s12885-023-10511-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/04/2023] [Indexed: 02/20/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of melanoma and other cancers. However, no reliable biomarker of survival or response has entered the clinic to identify those patients with melanoma who are most likely to benefit from ICIs. Glycosylation affects proteins and lipids' structure and functions. Tumours are characterized by aberrant glycosylation which may contribute to their progression and hinder an effective antitumour immune response. METHODS We aim at identifying novel glyco-markers of response and survival by leveraging the N-glycome of total serum proteins collected in 88 ICI-naive patients with advanced melanoma from two European countries. Samples were collected before and during ICI treatment. RESULTS We observe that responders to ICIs present with a pre-treatment N-glycome profile significantly shifted towards higher abundancy of low-branched structures containing lower abundances of antennary fucose, and that this profile is positively associated with survival and a better predictor of response than clinical variables alone. CONCLUSION While changes in serum protein glycosylation have been previously implicated in a pro-metastatic melanoma behaviour, we show here that they are also associated with response to ICI, opening new avenues for the stratification of patients and the design of adjunct therapies aiming at improving immune response.
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Affiliation(s)
- Alessia Visconti
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK
| | - Niccolò Rossi
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK
| | - Helena Deriš
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Karla A Lee
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK
| | - Maja Hanić
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | | | | | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center, Groningen, The Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center, Groningen, The Netherlands
| | | | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Chorley, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St. James', University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St. James', University of Leeds, Leeds, UK
| | - Mark Harries
- Department of Medical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Joseph J Sacco
- Liverpool Clatterbridge Cancer Centre, Liverpool, UK
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, UK
| | - Heather M Shaw
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center, Groningen, The Netherlands
| | - Tim D Spector
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK
| | - Paul Nathan
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Geke A P Hospers
- Department of Medical Oncology, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter Sasieni
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Veronique Bataille
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK.
- Department of Dermatology, Mount Vernon Cancer Centre, Northwood, UK.
- Department of Dermatology, West Herts NHS Trust, Herts, UK.
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mario Falchi
- Department of Twins Research & Genetics Epidemiology, King's College London, London, UK.
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5
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Bolte LA, Lee KA, Björk JR, Leeming ER, Campmans-Kuijpers MJE, de Haan JJ, Vila AV, Maltez-Thomas A, Segata N, Board R, Harries M, Lorigan P, de Vries EGE, Nathan P, Fehrmann R, Bataille V, Spector TD, Hospers GAP, Weersma RK. Association of a Mediterranean Diet With Outcomes for Patients Treated With Immune Checkpoint Blockade for Advanced Melanoma. JAMA Oncol 2023; 9:705-709. [PMID: 36795408 PMCID: PMC9936383 DOI: 10.1001/jamaoncol.2022.7753] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Importance Immune checkpoint blockade (ICB) has improved the survival of patients with advanced melanoma. Durable responses are observed for 40% to 60% of patients, depending on treatment regimens. However, there is still large variability in the response to treatment with ICB, and patients experience a range of immune-related adverse events of differing severity. Nutrition, through its association with the immune system and gut microbiome, is a poorly explored but appealing target with potential to improve the efficacy and tolerability of ICB. Objective To investigate the association between habitual diet and response to treatment with ICB. Design, Setting, and Participants This multicenter cohort study (the PRIMM study) was conducted in cancer centers in the Netherlands and UK and included 91 ICB-naive patients with advanced melanoma who were receiving ICB between 2018 and 2021. Exposures Patients were treated with anti-programmed cell death 1 and anti-cytotoxic T lymphocyte-associated antigen 4 monotherapy or combination therapy. Dietary intake was assessed through food frequency questionnaires before treatment. Main Outcomes and Measures Clinical end points were defined as overall response rate (ORR), progression-free survival at 12 months (PFS-12), and immune-related adverse events that were grade 2 or higher. Results There were a total of 44 Dutch participants (mean [SD] age, 59.43 [12.74] years; 22 women [50%]) and 47 British participants (mean [SD] age, 66.21 [16.63] years; 15 women [32%]). Dietary and clinical data were prospectively collected from 91 patients receiving ICB between 2018 and 2021 for advanced melanoma in the UK and the Netherlands. Logistic generalized additive models revealed positive linear associations between a Mediterranean dietary pattern that was high in whole grains, fish, nuts, fruit, and vegetables and the probability of ORR and PFS-12 (probability of 0.77 for ORR; P = .02; false discovery rate, 0.032; effective degrees of freedom, 0.83; probability of 0.74 for PFS-12; P = .01; false discovery rate, 0.021; effective degrees of freedom, 1.54). Conclusions and Relevance This cohort study found a positive association between a Mediterranean diet, a widely recommended model of healthy eating, and response to treatment with ICB. Large prospective studies from different geographies are needed to confirm the findings and further elucidate the role of diet in the context of ICB.
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Affiliation(s)
- Laura A. Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Karla A. Lee
- Department of Twin Research and Genetic Epidemiology, King’s College London, England
| | - Johannes R. Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Emily R. Leeming
- Department of Twin Research and Genetic Epidemiology, King’s College London, England
| | - Marjo J. E. Campmans-Kuijpers
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Jacco J. de Haan
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Andrew Maltez-Thomas
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy,European Institute of Oncology, IRCSS, Milan, Italy
| | - Ruth Board
- Department of Medical Oncology, Royal Preston Hospital, Lancashire National Health Service (NHS) Foundation Trust, Fulwood, England
| | - Mark Harries
- Department of Medical Oncology, Guys Cancer Centre, Guys, and St Thomas’s NHS Trust, London, England
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, England
| | - Elisabeth G. E. de Vries
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Paul Nathan
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, England
| | - Rudolf Fehrmann
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Véronique Bataille
- Department of Twin Research and Genetic Epidemiology, King’s College London, England,Department of Dermatology, West Hertfordshire NHS Trust, England
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, England
| | - Geke A. P. Hospers
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
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6
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Swarte JC, Li Y, Hu S, Björk JR, Gacesa R, Vich Vila A, Douwes RM, Collij V, Kurilshikov A, Post A, Klaassen MAY, Eisenga MF, Gomes-Neto AW, Kremer D, Jansen BH, Knobbe TJ, Berger SP, Sanders JSF, Heiner-Fokkema MR, Porte RJ, Cuperus FJC, de Meijer VE, Wijmenga C, Festen EAM, Zhernakova A, Fu J, Harmsen HJM, Blokzijl H, Bakker SJL, Weersma RK. Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation. Sci Transl Med 2022; 14:eabn7566. [PMID: 36044594 DOI: 10.1126/scitranslmed.abn7566] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Organ transplantation is a life-saving treatment for patients with end-stage disease, but survival rates after transplantation vary considerably. There is now increasing evidence that the gut microbiome is linked to the survival of patients undergoing hematopoietic cell transplant, yet little is known about the role of the gut microbiome in solid organ transplantation. We analyzed 1370 fecal samples from 415 liver and 672 renal transplant recipients using shotgun metagenomic sequencing to assess microbial taxonomy, metabolic pathways, antibiotic resistance genes, and virulence factors. To quantify taxonomic and metabolic dysbiosis, we also analyzed 1183 age-, sex-, and body mass index-matched controls from the same population. In addition, a subset of 78 renal transplant recipients was followed longitudinally from pretransplantation to 24 months after transplantation. Our data showed that both liver and kidney transplant recipients suffered from gut dysbiosis, including lower microbial diversity, increased abundance of unhealthy microbial species, decreased abundance of important metabolic pathways, and increased prevalence and diversity of antibiotic resistance genes and virulence factors. These changes were found to persist up to 20 years after transplantation. Last, we demonstrated that the use of immunosuppressive drugs was associated with the observed dysbiosis and that the extent of dysbiosis was associated with increased mortality after transplantation. This study represents a step toward potential microbiome-targeted interventions that might influence the outcomes of recipients of solid organ transplantation.
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Affiliation(s)
- J Casper Swarte
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Yanni Li
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Rianne M Douwes
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Adrian Post
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Marjolein A Y Klaassen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Michele F Eisenga
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - António W Gomes-Neto
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Daan Kremer
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Tim J Knobbe
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Stefan P Berger
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Jan-Stephan F Sanders
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - M Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Robert J Porte
- Department of Surgery, Section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Frans J C Cuperus
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Vincent E de Meijer
- Department of Surgery, Section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Stephan J L Bakker
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
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7
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Rossi N, Lee KA, Bermudez MV, Visconti A, Thomas AM, Bolte LA, Björk JR, de Ruijter LK, Newton-Bishop J, Harland M, Shaw HM, Harries M, Sacco J, Board R, Lorigan P, de Vries EGE, Segata N, Taams L, Papa S, Spector TD, Nathan P, Weersma RK, Hospers GAP, Fehrmann RSN, Bataille V, Falchi M. Circulating inflammatory proteins associate with response to immune checkpoint inhibition therapy in patients with advanced melanoma. EBioMedicine 2022; 83:104235. [PMID: 36007304 PMCID: PMC9421308 DOI: 10.1016/j.ebiom.2022.104235] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 03/11/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Inflammation can modulate tumour growth and progression, and influence clinical response to treatment. We investigated the potential of circulating inflammatory proteins for response stratification of immune checkpoint inhibitor (ICI) therapy for advanced melanoma. METHODS Study subjects were 87 patients with unresectable stage III or IV cutaneous melanoma from the multiple centres across the United Kingdom (UK) and the Netherlands (NL) who received ipilimumab, nivolumab, or pembrolizumab, or a combination of ipilimumab and nivolumab. Serum samples were collected before and during ICI therapy at follow-up visits scheduled every third week over a 12-week period. We performed targeted quantification of 92 proteins involved in inflammation and tested for association of their pre-treatment and on-treatment levels, as well as longitudinal changes, with overall response rate, progression-free survival, and overall survival. FINDINGS We observed consistently higher pre-treatment levels of interleukin-6 (IL-6), hepatocyte growth factor (HGF), and monocyte chemotactic protein 2 (MCP-2), in non-responders compared to responders (meta-analysis p=3.31 × 10-4, 2.29 × 10-4, and 1.02 × 10-3, respectively). Patients' stratification according to the median value of IL-6, HGF, and MCP-2 highlighted a cumulative negative effect of pre-treatment levels of the three proteins on response (p=1.13 × 10-2), with overall response rate among patients presenting with combined elevated IL-6, HGF, and MCP-2 levels being three-fold lower (26.7%) compared to patients with none of the three proteins elevated (80.0%, p=9.22 × 10-3). Longitudinal data analysis showed that on-treatment changes in circulating inflammatory proteins are not correlated with response. INTERPRETATION Our findings are in line with an increasing body of evidence that the pro-inflammatory cytokine IL-6 can influence response to ICI in advanced melanoma, and further support a role of circulating HGF and MCP-2 levels as prognostic biomarkers as suggested by previous smaller studies. Inflammatory proteins may serve as predictive biomarkers of ICI response and valuable targets for combination therapy. FUNDING This work was supported by the Seerave Foundation and Dutch Cancer Society.
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Affiliation(s)
- Niccolò Rossi
- Department of Twin Research and Genetic Epidemiology, King's College London, UK
| | - Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, UK
| | - Maria V Bermudez
- Centre for Inflammation Biology and Cancer Immunology, King's College London, UK
| | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, UK
| | | | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, the Netherlands
| | - Laura Kist de Ruijter
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St James's, University of Leeds, UK
| | - Heather M Shaw
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Mark Harries
- Department of Medical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Joseph Sacco
- Liverpool Clatterbridge Cancer Centre, Liverpool, UK
| | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Preston, UK
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, UK; Division of Cancer Sciences, University of Manchester, UK
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Leonie Taams
- Centre for Inflammation Biology and Cancer Immunology, King's College London, UK
| | - Sophie Papa
- Department of Medical Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK; School of Cancer and Pharmaceutical Studies, King's College London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, UK
| | - Paul Nathan
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, the Netherlands
| | - Geke A P Hospers
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, UK; Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK.
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, UK.
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8
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Gacesa R, Kurilshikov A, Vich Vila A, Sinha T, Klaassen MAY, Bolte LA, Andreu-Sánchez S, Chen L, Collij V, Hu S, Dekens JAM, Lenters VC, Björk JR, Swarte JC, Swertz MA, Jansen BH, Gelderloos-Arends J, Jankipersadsing S, Hofker M, Vermeulen RCH, Sanna S, Harmsen HJM, Wijmenga C, Fu J, Zhernakova A, Weersma RK. Environmental factors shaping the gut microbiome in a Dutch population. Nature 2022; 604:732-739. [PMID: 35418674 DOI: 10.1038/s41586-022-04567-7] [Citation(s) in RCA: 198] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/18/2022] [Indexed: 12/22/2022]
Abstract
The gut microbiome is associated with diverse diseases1-3, but a universal signature of a healthy or unhealthy microbiome has not been identified, and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. Here we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We correlated these to 241 host and environmental factors, including physical and mental health, use of medication, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is shaped primarily by the environment and cohabitation. Only around 6.6% of taxa are heritable, whereas the variance of around 48.6% of taxa is significantly explained by cohabitation. By identifying 2,856 associations between the microbiome and health, we find that seemingly unrelated diseases share a common microbiome signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, with numerous early-life and current factors being significantly associated with microbiome function and composition. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.
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Affiliation(s)
- R Gacesa
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - A Kurilshikov
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - A Vich Vila
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - T Sinha
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M A Y Klaassen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - L A Bolte
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Andreu-Sánchez
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - L Chen
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - V Collij
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Hu
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J A M Dekens
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Center of Development and Innovation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - V C Lenters
- University Medical Centre Utrecht, Julius Center for Health Sciences and Primary Care, Utrecht, The Netherlands
| | - J R Björk
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J C Swarte
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M A Swertz
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - B H Jansen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J Gelderloos-Arends
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Jankipersadsing
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M Hofker
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - R C H Vermeulen
- University Medical Centre Utrecht, Julius Center for Health Sciences and Primary Care, Utrecht, The Netherlands.,Utrecht University, Institute for Risk Assessment Sciences (IRAS), Department of Population Health Sciences, Utrecht, The Netherlands
| | - S Sanna
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy
| | - H J M Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - C Wijmenga
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J Fu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands. .,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
| | - A Zhernakova
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
| | - R K Weersma
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.
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9
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Lee KA, Thomas AM, Bolte LA, Björk JR, de Ruijter LK, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Leeming ER, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Vijay A, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Bataille V, Hospers GAP, Spector TD, Weersma RK, Segata N. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nat Med 2022; 28:535-544. [PMID: 35228751 PMCID: PMC8938272 DOI: 10.1038/s41591-022-01695-5] [Citation(s) in RCA: 134] [Impact Index Per Article: 67.0] [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: 03/24/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022]
Abstract
The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on the specific microbiome characteristics linked to the clinical benefits of ICIs. We performed shotgun metagenomic sequencing of stool samples collected before ICI initiation from five observational cohorts recruiting ICI-naive patients with advanced cutaneous melanoma (n = 165). Integrating the dataset with 147 metagenomic samples from previously published studies, we found that the gut microbiome has a relevant, but cohort-dependent, association with the response to ICIs. A machine learning analysis confirmed the link between the microbiome and overall response rates (ORRs) and progression-free survival (PFS) with ICIs but also revealed limited reproducibility of microbiome-based signatures across cohorts. Accordingly, a panel of species, including Bifidobacterium pseudocatenulatum, Roseburia spp. and Akkermansia muciniphila, associated with responders was identified, but no single species could be regarded as a fully consistent biomarker across studies. Overall, the role of the human gut microbiome in ICI response appears more complex than previously thought, extending beyond differing microbial species simply present or absent in responders and nonresponders. Future studies should adopt larger sample sizes and take into account the complex interplay of clinical factors with the gut microbiome over the treatment course.
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Affiliation(s)
- Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Laura Kist de Ruijter
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | | | | | | | - Ruth Board
- Department of Oncology, Lancashire Teaching Hospitals NHS Trust, Preston, UK
| | - Neus Calbet-Llopart
- Dermatology Department, Hospital Clínic Barcelona, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Lisa Derosa
- U1015 INSERM, University Paris Saclay, Gustave Roussy Cancer Center and Oncobiome Network, Villejuif-Grand-Paris, France
| | - Nathalie Dhomen
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Kelly Brooks
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Mark Harland
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Mark Harries
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
- Department of Medical Oncology, Guys Cancer Centre, Guys and St Thomas's NHS Trust, London, UK
| | - Emily R Leeming
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Paul Lorigan
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Richard Marais
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
| | - Julia Newton-Bishop
- Division of Haematology and Immunology, Institute of Medical Research at St. James's, University of Leeds, Leeds, UK
| | - Luigi Nezi
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy
| | | | - Miriam Potrony
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Susana Puig
- Centro de Investigación Biomédica en Red en Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | | | - Heather M Shaw
- Department of Medical Oncology, Mount Vernon Cancer Centre, Northwood, UK
| | - Sabrina Tamburini
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy
| | - Sara Valpione
- Molecular Oncology Group, CRUK Manchester Institute, University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Amrita Vijay
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Rheumatology & Orthopaedics Division, School of Medicine, University of Nottingham, Nottingham, UK
| | - Levi Waldron
- Department CIBIO, University of Trento, Trento, Italy
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA
| | - Laurence Zitvogel
- U1015 INSERM, University Paris Saclay, Gustave Roussy Cancer Center and Oncobiome Network, Villejuif-Grand-Paris, France
| | - Moreno Zolfo
- Department CIBIO, University of Trento, Trento, Italy
| | - Elisabeth G E de Vries
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Paul Nathan
- Biochemical and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS and University of Barcelona, Barcelona, Spain
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Véronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, Mount Vernon Cancer Centre, Northwood, UK
| | - Geke A P Hospers
- Department of Medical Oncology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.
- European Institute of Oncology (Istituto Europeo di Oncologia, IRCSS), Milan, Italy.
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10
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Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Gut microbiome heritability is nearly universal but environmentally contingent. Science 2021; 373:181-186. [PMID: 34244407 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022]
Abstract
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada.,Research Center, Montreal Heart Institute, Montréal, Quebec H1T 1C8, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Neil Gottel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jacob B Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Kenya.,The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Kenya
| | | | | | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
| | - Jack A Gilbert
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada.,Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA. .,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA.,Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA. .,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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11
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Björk JR, Dasari M, Grieneisen L, Archie EA. Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research. Am J Primatol 2019; 81:e22970. [PMID: 30941803 PMCID: PMC7193701 DOI: 10.1002/ajp.22970] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/05/2019] [Accepted: 03/07/2019] [Indexed: 12/16/2022]
Abstract
To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field-based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
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12
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Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T. Erratum to: The sponge microbiome project. Gigascience 2018; 7:5232346. [PMID: 30521034 PMCID: PMC6283209 DOI: 10.1093/gigascience/giy145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Amnon Amir
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Gail L Ackermann
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Carlo Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | | | - Cole Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA
| | - Detmer Sipkema
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Fang Liu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Georg Steinert
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giorgos Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Grace P McCormack
- Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland
| | - Guofang Feng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Jan Vicente
- Hawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI 96744-1346
| | - Johannes R Björk
- Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jose M Montoya
- Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France
| | - Julie B Olson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Julie Reveillaud
- INRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, 34398 Montpellier, France
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Mari-Carmen Pineda
- Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia
| | - Maria V Marra
- Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paraskevi Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Patrick M Erwin
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Rachel L Simister
- Department of Microbiology and Immunology, University of British Columbia, Canada, V6T 1Z3
| | - Rob Knight
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA.,Department of Computer Science and Engineering, and Center for Microbiome Innovation, University of California - San Diego, La Jolla, CA 92093, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook NY 11794, USA
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, Portugal
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Susanna Lopez-Legentil
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA
| | - Thanos Dailianis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, and Christian-Albrechts-University of Kiel, Germany
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Nicole S Webster
- Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
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13
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Björk JR, Hui FKC, O’Hara RB, Montoya JM. Uncovering the drivers of host-associated microbiota with joint species distribution modelling. Mol Ecol 2018; 27:2714-2724. [PMID: 29761593 PMCID: PMC6025780 DOI: 10.1111/mec.14718] [Citation(s) in RCA: 29] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 01/07/2023]
Abstract
In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models (JSDMs) which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates such as diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including (a) model-based ordination to visualize and quantify the main patterns in the data; (b) variance partitioning to assess how influential the included host-specific factors are in structuring the microbiota; and (c) co-occurrence networks to visualize microbe-to-microbe associations.
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Affiliation(s)
- Johannes R. Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
- Theoretical and Experimental Ecology Station, CNRS-University Paul Sabatier, Moulis, France
| | - Francis K. C. Hui
- Mathematical Sciences Institute, The Australian National University, Canberra, Australia
| | - Robert B. O’Hara
- Department of Mathematical Sciences, NTNU, Trondheim, Norway
- Biodiversity and Climate Research Centre, Frankfurt, Germany
| | - Jose M. Montoya
- Theoretical and Experimental Ecology Station, CNRS-University Paul Sabatier, Moulis, France
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14
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Moitinho-Silva L, Nielsen S, Amir A, Gonzalez A, Ackermann GL, Cerrano C, Astudillo-Garcia C, Easson C, Sipkema D, Liu F, Steinert G, Kotoulas G, McCormack GP, Feng G, Bell JJ, Vicente J, Björk JR, Montoya JM, Olson JB, Reveillaud J, Steindler L, Pineda MC, Marra MV, Ilan M, Taylor MW, Polymenakou P, Erwin PM, Schupp PJ, Simister RL, Knight R, Thacker RW, Costa R, Hill RT, Lopez-Legentil S, Dailianis T, Ravasi T, Hentschel U, Li Z, Webster NS, Thomas T. The sponge microbiome project. Gigascience 2017; 6:1-7. [PMID: 29020741 PMCID: PMC5632291 DOI: 10.1093/gigascience/gix077] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/28/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022] Open
Abstract
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Amnon Amir
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Gail L Ackermann
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
| | - Carlo Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | | | - Cole Easson
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA
| | - Detmer Sipkema
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Fang Liu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Georg Steinert
- Wageningen University, Laboratory of Microbiology, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giorgos Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Grace P McCormack
- Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland
| | - Guofang Feng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Jan Vicente
- Hawaii Institute of Marine Biology, 46-007 Lilipuna Road, Kaneohe, HI 96744-1346
| | - Johannes R Björk
- Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jose M Montoya
- Ecological Networks and Global Change Group, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, Moulis, France
| | - Julie B Olson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Julie Reveillaud
- INRA, UMR1309 CMAEE; Cirad, UMR15 CMAEE, 34398 Montpellier, France
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Mari-Carmen Pineda
- Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia
| | - Maria V Marra
- Zoology, School of Natural Sciences, Ryan Institute, National University of Ireland Galway, University Rd., Galway, Ireland
| | - Micha Ilan
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paraskevi Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Patrick M Erwin
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky and University Oldenburg, Schleusenstr. 1, 26382 Wilhelmshaven, Germany
| | - Rachel L Simister
- Department of Microbiology and Immunology, University of British Columbia, Canada, V6T 1Z3
| | - Rob Knight
- Department of Pediatrics, University of California - San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, and Center for Microbiome Innovation, University of California - San Diego, La Jolla, CA 92093, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook NY 11794, USA
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (IBB), Department of Bioengineering, IST, Universidade de Lisboa, Lisbon, Portugal
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Susanna Lopez-Legentil
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington NC 28409, USA
| | - Thanos Dailianis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Thalassocosmos, 71500 Heraklion, Greece
| | - Timothy Ravasi
- KAUST Environmental Epigenetic Program (KEEP), Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, and Christian-Albrechts-University of Kiel, Germany
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P.R. China
| | - Nicole S Webster
- Australian Institute of Marine Science (AIMS), Townsville, 4810, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, 2052, Australia
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15
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Abstract
Microbes are known to form intricate and intimate relationships with most animal and plant taxa. Microbe--host symbiotic associations are poorly explored in comparison with other species interaction networks. The current paradigm on symbiosis research stems from species-poor systems where pairwise and reciprocally specialized interactions between a single microbe and a single host that coevolve are the norm. These symbioses involving just a few species are fascinating in their own right, but more diverse and complex host-associated microbial communities are increasingly found, with new emerging questions that require new paradigms and approaches. Here we adopt an intermediate complexity approach to study the specificity, phylogenetic community structure, and temporal variability of the subset of the most abundant bacteria associated with different sponge host species with diverse eco-evolutionary characteristics. We do so by using a monthly resolved annual temporal series of host-associated and free-living bacteria. Bacteria are very abundant and diverse within marine sponges, and these symbiotic interactions are hypothesized to have a very ancient origin. We show that host-bacteria reciprocal specialization depends on the temporal scale and level of taxonomic aggregation considered. Sponge hosts with similar eco-evolutionary characteristics (e.g., volume of tissue corresponding to microbes, water filtering rates, and microbial transmission type) have similar bacterial phylogenetic community structure when looking at interactions aggregated over time. In general, sponge hosts hypothesized to form more intricate relationships with bacteria show a remarkably persistent bacterial community over time. Other hosts, however, show a large turnover similar to that observed for free-living bacterioplankton. Our study highlights the importance of exploring temporal variability in host--microbe interaction networks if we aim to determine how specific and persistent these poorly explored but extremely common interactions are.
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Affiliation(s)
- Johannes R Björk
- Instituto de Ciencias del Mar, Agencia Estatal Consejo Superior de Investigaciones Científicas, Passeig Maritim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - C Díez-Vives
- Instituto de Ciencias del Mar, Agencia Estatal Consejo Superior de Investigaciones Científicas, Passeig Maritim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Rafel Coma
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain
| | - Marta Ribes
- Instituto de Ciencias del Mar, Agencia Estatal Consejo Superior de Investigaciones Científicas, Passeig Maritim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - José M Montoya
- Instituto de Ciencias del Mar, Agencia Estatal Consejo Superior de Investigaciones Científicas, Passeig Maritim de la Barceloneta 37-49, 08003, Barcelona, Spain
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16
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