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Delanote J, Correa Rojo A, Wells PM, Steves CJ, Ertaylan G. Systematic identification of the role of gut microbiota in mental disorders: a TwinsUK cohort study. Sci Rep 2024; 14:3626. [PMID: 38351227 PMCID: PMC10864280 DOI: 10.1038/s41598-024-53929-w] [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: 11/11/2022] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
Mental disorders are complex disorders influenced by multiple genetic, environmental, and biological factors. Specific microbiota imbalances seem to affect mental health status. However, the mechanisms by which microbiota disturbances impact the presence of depression, stress, anxiety, and eating disorders remain poorly understood. Currently, there are no robust biomarkers identified. We proposed a novel pyramid-layer design to accurately identify microbial/metabolomic signatures underlying mental disorders in the TwinsUK registry. Monozygotic and dizygotic twins discordant for mental disorders were screened, in a pairwise manner, for differentially abundant bacterial genera and circulating metabolites. In addition, multivariate analyses were performed, accounting for individual-level confounders. Our pyramid-layer study design allowed us to overcome the limitations of cross-sectional study designs with significant confounder effects and resulted in an association of the abundance of genus Parabacteroides with the diagnosis of mental disorders. Future research should explore the potential role of Parabacteroides as a mediator of mental health status. Our results indicate the potential role of the microbiome as a modifier in mental disorders that might contribute to the development of novel methodologies to assess personal risk and intervention strategies.
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Affiliation(s)
- Julie Delanote
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Alejandro Correa Rojo
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Data Science Institute, Interuniversity Institute for Biostatistics and Statistical Bioinformatics (I-BioStat), Hasselt University, Diepenbeek, Belgium
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, 3-4th Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK
- Department of Ageing and Health, St Thomas' Hospital, 9th floor, North Wing, Westminster Bridge Road, London, SE1 7EH, UK
| | - Gökhan Ertaylan
- Sustainable Health, Flemish Institute for Technological Research (VITO), Mol, Belgium.
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Danckert NP, Freidin MB, Smith IG, Wells PM, Naeini MK, Visconti A, Compte R, MacGregor A, Williams FMK. Treatment response in rheumatoid arthritis is predicted by the microbiome: a large observational study in UK DMARD-naïve patients. Rheumatology (Oxford) 2024:keae045. [PMID: 38291926 DOI: 10.1093/rheumatology/keae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 02/01/2024] Open
Abstract
OBJECTIVES Disease-modifying antirheumatic drugs (DMARDs) are first line treatment in rheumatoid arthritis (RA). Treatment response to DMARDs is patient-specific, dose efficacy is difficult to predict and long-term results variable. The gut microbiota are known to play a pivotal role in prodromal and early-disease RA, manifested by Prevotella spp. enrichment. The clinical response to therapy may be mediated by microbiota, and large-scale studies assessing the microbiome are few. This study assessed whether microbiome signals were associated with, and predictive of, patient response to DMARD-treatment. Accurate early identification of those who will respond poorly to DMARD therapy would allow selection of alternative treatment (e.g. biologic therapy), and potentially improve patient outcome. METHODS A multicentre, longitudinal, observational study of stool- and saliva microbiome was performed in DMARD-naïve, newly diagnosed RA patients during introduction of DMARD treatment. Clinical data and samples were collected at baseline (n = 144) in DMARD-naïve patients and at six weeks (n = 117) and 12 weeks (n = 95) into DMARD-therapy. Samples collected (n = 365 stool, n = 365 saliva) underwent shotgun sequencing. Disease activity measures were collected at each timepoint and minimal clinically important improvement determined. RESULTS In total, 26 stool microbes were found to decrease in those manifesting a minimal clinically important improvement. Prevotella spp. and Streptococcus spp. were the predominant taxa to decline following six weeks and 12 weeks of DMARDs, respectively. Furthermore, baseline microbiota of DMARD-naïve patients were indicative of future response. CONCLUSION DMARDs appear to restore a perturbed microbiome to a eubiotic state. Moreover, microbiome status can be used to predict likelihood of patient response to DMARD.
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Affiliation(s)
- Nathan P Danckert
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, King's College London, London, UK
| | - Maxim B Freidin
- Department of Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Isabelle Granville Smith
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, King's College London, London, UK
| | - Philippa M Wells
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Maryam Kazemi Naeini
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, King's College London, London, UK
| | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, King's College London, London, UK
| | - Roger Compte
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, King's College London, London, UK
| | - Alexander MacGregor
- Norwich Medical School, University of East Anglia, Norwich, UK
- Rheumatology Department, Norfolk and Norwich University Hospitals NHS Trust, Norwich, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, King's College London, London, UK
- Guy's and St Thomas' NHS Trust, London, UK
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Wells PM, Sprockett DD, Bowyer RCE, Kurushima Y, Relman DA, Williams FMK, Steves CJ. Influential factors of saliva microbiota composition. Sci Rep 2022; 12:18894. [PMID: 36344584 PMCID: PMC9640688 DOI: 10.1038/s41598-022-23266-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
Abstract
The oral microbiota is emerging as an influential factor of host physiology and disease state. Factors influencing oral microbiota composition have not been well characterised. In particular, there is a lack of population-based studies. We undertook a large hypothesis-free study of the saliva microbiota, considering potential influential factors of host health (frailty; diet; periodontal disease), demographics (age; sex; BMI) and sample processing (storage time), in a sample (n = 679) of the TwinsUK cohort of adult twins. Alpha and beta diversity of the saliva microbiota was associated most strongly with frailty (alpha diversity: β = -0.16, Q = 0.003, Observed; β = -0.16, Q = 0.002, Shannon; β = -0.16, Q = 0.003, Simpson; Beta diversity: Q = 0.002, Bray Curtis dissimilarity) and age (alpha diversity: β = 0.15, Q = 0.006, Shannon; β = 0.12, Q = 0.003, Simpson; beta diversity: Q = 0.002, Bray Curtis dissimilarity; Q = 0.032, Weighted UniFrac) in multivariate models including age, frailty, sex, BMI, frailty and diet, and adjustment for multiple testing. Those with a more advanced age were more likely to be dissimilar in the saliva microbiota composition than younger participants (P = 5.125e-06, ANOVA). In subsample analyses, including consideration of periodontal disease (total n = 138, periodontal disease n = 66), the association with frailty remained for alpha diversity (Q = 0.002, Observed ASVs; Q = 0.04 Shannon Index), but not beta diversity, whilst age was not demonstrated to associate with alpha or beta diversity in this subsample, potentially due to insufficient statistical power. Length of time that samples were stored prior to sequencing was associated with beta diversity (Q = 0.002, Bray Curtis dissimilarity). Six bacterial taxa were associated with age after adjustment for frailty and diet. Of the factors studied, frailty and age emerged as the most influential with regards to saliva microbiota composition. Whilst age and frailty are correlates, the associations were independent of each other, giving precedence to both biological and chronological ageing as processes of potential importance when considering saliva microbiota composition.
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Affiliation(s)
- Philippa M Wells
- Department of Twin Research, St Thomas Hospital, King's College London, London, UK
| | - Daniel D Sprockett
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ruth C E Bowyer
- Department of Twin Research, St Thomas Hospital, King's College London, London, UK
| | - Yuko Kurushima
- Department of Twin Research, St Thomas Hospital, King's College London, London, UK
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Frances M K Williams
- Department of Twin Research, St Thomas Hospital, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research, St Thomas Hospital, King's College London, London, UK.
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Stoll ML, Sawhney H, Wells PM, Sternes PR, Reveille JD, Morrow CD, Steves CJ, Brown MA, Gensler LS. The faecal microbiota is distinct in HLA-B27+ ankylosing spondylitis patients versus HLA-B27+ healthy controls. Clin Exp Rheumatol 2022; 41:1096-1104. [PMID: 36441657 DOI: 10.55563/clinexprheumatol/nlsj0o] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/01/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Spondyloarthritis (SpA) results from the interplay between genetic and environmental factors. An emerging modifiable factor is the human intestinal microbiota, which multiple studies in children and adults have shown to be abnormal in SpA patients, including enthesitis related arthritis and ankylosing spondylitis (AS). However, HLA-B27 itself appears to impact the contents of the microbiota and is more common in SpA patients versus controls, thus serving as a confounding factor in most comparative studies. METHODS This was a cross-sectional study that evaluated the contents of the faecal microbiota among 29 patients with HLA-B27+ AS and 43 healthy adults who underwent 16S sequencing and genotyping as part of the TwinsUK Programme. RESULTS HLA-B27 positive+ patients and healthy controls demonstrated substantial clustering based upon diagnosis. Decreased richness was observed among the AS patients, although measures of evenness were similar. After correction for multiple comparisons, several taxa - including Faecalibacterium prausnitzii and Coprococcus - were elevated in AS patients compared to controls, even when restricted to female subjects, while Bacteroides fragilis, Ruminococcus, and Akkermansia muciniphila were depleted in AS patients. CONCLUSIONS Consistent with some previous studies, our study demonstrates in patients with AS associations with Coprococcus, Bacteroides, and Ruminococcus. Other findings, including increased Faecalibacterium, are inconsistent with previous studies and thus potentially underscore the necessity of evaluating HLA-B27 positive controls in studies evaluating the impact of the intestinal microbiota on SpA.
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Affiliation(s)
- Matthew L. Stoll
- Department of Pediatrics, University of Alabama at Birmingham (UAB), AL, USA.
| | - Henna Sawhney
- Department of Medicine, University of California at San Francisco, CA, USA
| | | | - Peter R. Sternes
- Centre for Microbiome Research, Queensland University of Technology, Brisbane, Australia
| | - John D. Reveille
- Department of Internal Medicine, University of Texas at Houston, TX, USA
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, UAB, Birmingham, AL, USA
| | | | - Matthew A. Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, UK; Genomics England Ltd, London, UK
| | - Lianne S. Gensler
- Department of Medicine, University of California at San Francisco, CA, USA
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Bowyer RCE, Twohig-Bennett C, Coombes E, Wells PM, Spector TD, Jones AP, Steves CJ. Microbiota composition is moderately associated with greenspace composition in a UK cohort of twins. Sci Total Environ 2022; 813:152321. [PMID: 34915018 DOI: 10.1016/j.scitotenv.2021.152321] [Citation(s) in RCA: 8] [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] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
Exposure to natural environments, known as greenspace, appears to positively influence health, yet the mechanisms are unclear. Given that gut microbiota are associated with inflammatory disorders more prevalent in urban areas and individuals with lower greenspace exposure, microbiota may act as a mediator between greenspace and health. Using 2443 participants of the TwinsUK cohort, microbiota differences were compared in relation to rural/urban living and with quantiles of area-level greenspace at three different neighbourhood distances: 800 m, 3000 m and 5000 m. Using microbiota data captured from faecal samples using 16S rRNA marker gene sequencing, small compositional differences in association with 3000 m greenspace (p = 0.003) in models adjusted for confounders of microbiota variance (sequencing depth, antibiotics use, body mass index, frailty, age, diet, region and socioeconomic variables) were observed. Differences in abundances of genus were observed for all measures of greenspace in adjusted models; a key pathogenic genus was increased in abundance in association with urbanicity (Escherichia/Shigella, logFC = 0.73742, padj <0.001). Further, utilising the twin structure, within-pair differences in microbiota composition were compared and associations with 800 m greenspace observed (factor level significance in association with greatest difference, β = 0.08, p = 0.0162) as were differences in Escherichia/Shigella. The microbiota signature of those with a greater exposure to greenspace, but not necessarily explicitly rural individuals, was distinct from other individuals, suggesting microbiota as a potential mediator for greenspace and health.
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Affiliation(s)
- Ruth C E Bowyer
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | | | - Emma Coombes
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Andy P Jones
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK.
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK; Department of Ageing and Health, St Thomas' Hospital, 9th floor, North Wing, Westminster Bridge Road, London SE1 7EH, UK.
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Louca P, Nogal A, Wells PM, Asnicar F, Wolf J, Steves CJ, Spector TD, Segata N, Berry SE, Valdes AM, Menni C. Gut microbiome diversity and composition is associated with hypertension in women. J Hypertens 2021; 39:1810-1816. [PMID: 33973959 PMCID: PMC7611529 DOI: 10.1097/hjh.0000000000002878] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Animal studies support a role for the gut microbiota in hypertension development, but large human studies are lacking. Here, we investigated the relationship between hypertension prevalence and gut microbial composition in two cohorts. METHODS We included 871 unrelated TwinsUK women with faecal microbiome data (16s rRNA gene sequencing). Multivariable linear models adjusted for age, age2 and BMI as well as MiRKAT models, were used to estimate the association of hypertension with alpha- and beta-diversity metrics. To identify taxa associated with hypertension, a generalized additive model for location scale and shape was computed adjusting for covariates and multiple testing. Results were replicated in 448 women from PREDICT-1. RESULTS We found that measures of alpha diversity are significantly lower in hypertensive cases [Beta(95% confidence interval, 95% CI) = -0.05 (-0.095 to -0.004), P = 0.03] and a significant association between beta diversity and hypertension (FDR < 0.05). We identified and replicated two genera associated with hypertension. The genus, Ruminiclostridium 6 was less abundant in hypertension cases [meta-analysis (95% CI) = -0.31 (-0.5 to -0.13), P = 1 × 10-3]. The uncultured microbe Erysipelotrichacea-UCG003 was more abundant in hypertensive cases [meta-analysis (95% CI) = 0.46 (0.3-0.62), P = 1 × 10-4]. We genomically analysed the 16 s rRNA sequence and established a 100% identity match with the 16 s rRNA sequence of the genus Faecalibacillus. We functionally annotated Ruminiclostridium, identifying 83 metabolic pathways, including pathways previously linked to blood pressure regulation. CONCLUSION In this large human observation, we show that gut microbiome diversity and composition are associated with hypertension. Our results suggest that targeting the microbiome may be a novel means to prevent or treat hypertension.
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Affiliation(s)
- Panayiotis Louca
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ana Nogal
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Philippa M. Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | | | - Claire J. Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicola Segata
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sarah E. Berry
- Department of Nutritional Sciences, King's College London, London, United Kingdom
| | - Ana M. Valdes
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Academic Rheumatology Clinical Sciences Building, Nottingham City Hospital, University of Nottingham, Nottingham, UK
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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Freidin MB, Stalteri MA, Wells PM, Lachance G, Baleanu AF, Bowyer RCE, Kurilshikov A, Zhernakova A, Steves CJ, Williams FMK. An association between chronic widespread pain and the gut microbiome. Rheumatology (Oxford) 2021; 60:3727-3737. [PMID: 33331911 PMCID: PMC8328510 DOI: 10.1093/rheumatology/keaa847] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 05/21/2020] [Revised: 11/12/2020] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES Chronic widespread musculoskeletal pain (CWP) is a characteristic symptom of fibromyalgia, which has been shown to be associated with an altered gut microbiome. Microbiome studies to date have not examined the milder CWP phenotype specifically nor have they explored the role of raised BMI. The aim of this study was to investigate whether the microbiome is abnormal in CWP. METHODS CWP was assessed using a standardized screening questionnaire in female volunteers from the TwinsUK cohort including 113 CWP cases and 1623 controls. The stool microbiome was characterized using 16S rRNA amplicon sequencing and amplicon sequence variants, and associations with CWP examined using linear mixed-effects models adjusting for BMI, age, diet, family relatedness and technical factors. RESULTS Alpha diversity was significantly lower in CWP cases than controls (Mann-Whitney test, P-values 2.3e-04 and 1.2e-02, for Shannon and Simpson indices respectively). The species Coprococcus comes was significantly depleted in CWP cases (Padj = 3.04e-03). A genome-wide association study (GWAS) performed for C. comes in TwinsUK followed by meta-analysis with three Dutch cohorts (total n = 3521) resulted in nine suggestive regions, with the most convincing on chromosome 4 near the TRAM1L1 gene (rs76957229, P = 7.4e-8). A Mendelian randomization study based on the results of the GWAS did not support a causal role for C. comes on the development of CWP. CONCLUSIONS We have demonstrated reduced diversity in the microbiome in CWP, indicating an involvement of the gut microbiota in CWP; prospectively the microbiome may offer therapeutic opportunities for this condition.
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Affiliation(s)
- Maxim B Freidin
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Maria A Stalteri
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Genevieve Lachance
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Andrei-Florin Baleanu
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Ruth C E Bowyer
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
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Zouiouich S, Loftfield E, Huybrechts I, Viallon V, Louca P, Vogtmann E, Wells PM, Steves CJ, Herzig KH, Menni C, Jarvelin MR, Sinha R, Gunter MJ. Markers of metabolic health and gut microbiome diversity: findings from two population-based cohort studies. Diabetologia 2021; 64:1749-1759. [PMID: 34110438 PMCID: PMC8245388 DOI: 10.1007/s00125-021-05464-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/08/2021] [Indexed: 12/17/2022]
Abstract
AIMS/HYPOTHESIS The gut microbiome is hypothesised to be related to insulin resistance and other metabolic variables. However, data from population-based studies are limited. We investigated associations between serologic measures of metabolic health and the gut microbiome in the Northern Finland Birth Cohort 1966 (NFBC1966) and the TwinsUK cohort. METHODS Among 506 individuals from the NFBC1966 with available faecal microbiome (16S rRNA gene sequence) data, we estimated associations between gut microbiome diversity metrics and serologic levels of HOMA for insulin resistance (HOMA-IR), HbA1c and C-reactive protein (CRP) using multivariable linear regression models adjusted for sex, smoking status and BMI. Associations between gut microbiome diversity measures and HOMA-IR and CRP were replicated in 1140 adult participants from TwinsUK, with available faecal microbiome (16S rRNA gene sequence) data. For both cohorts, we used general linear models with a quasi-Poisson distribution and Microbiome Regression-based Kernel Association Test (MiRKAT) to estimate associations of metabolic variables with alpha- and beta diversity metrics, respectively, and generalised additive models for location scale and shape (GAMLSS) fitted with the zero-inflated beta distribution to identify taxa associated with the metabolic markers. RESULTS In NFBC1966, alpha diversity was lower in individuals with higher HOMA-IR with a mean of 74.4 (95% CI 70.7, 78.3) amplicon sequence variants (ASVs) for the first quartile of HOMA-IR and 66.6 (95% CI 62.9, 70.4) for the fourth quartile of HOMA-IR. Alpha diversity was also lower with higher HbA1c (number of ASVs and Shannon's diversity, p < 0.001 and p = 0.003, respectively) and higher CRP (number of ASVs, p = 0.025), even after adjustment for BMI and other potential confounders. In TwinsUK, alpha diversity measures were also lower among participants with higher measures of HOMA-IR and CRP. When considering beta diversity measures, we found that microbial community profiles were associated with HOMA-IR in NFBC1966 and TwinsUK, using multivariate MiRKAT models, with binomial deviance dissimilarity p values of <0.001. In GAMLSS models, the relative abundances of individual genera Prevotella and Blautia were associated with HOMA-IR in both cohorts. CONCLUSIONS/INTERPRETATION Overall, higher levels of HOMA-IR, CRP and HbA1c were associated with lower microbiome diversity in both the NFBC1966 and TwinsUK cohorts, even after adjustment for BMI and other variables. These results from two distinct population-based cohorts provide evidence for an association between metabolic variables and gut microbial diversity. Further experimental and mechanistic insights are now needed to provide understanding of the potential causal mechanisms that may link the gut microbiota with metabolic health.
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Affiliation(s)
- Semi Zouiouich
- Section of Nutrition and Metabolism, International Agency for Research on Cancer-WHO, Lyon, France.
| | - Erikka Loftfield
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Inge Huybrechts
- Section of Nutrition and Metabolism, International Agency for Research on Cancer-WHO, Lyon, France
| | - Vivian Viallon
- Section of Nutrition and Metabolism, International Agency for Research on Cancer-WHO, Lyon, France
| | | | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Claire J Steves
- Department of Twin Research, King's College London, London, UK
| | - Karl-Heinz Herzig
- Research Unit of Biomedicine, Medical Research Center (MRC), University of Oulu, University Hospital, Oulu, Finland
- Department of Gastroenterology and Metabolism, Poznan University of Medical Sciences, Poznan, Poland
| | - Cristina Menni
- Department of Twin Research, King's College London, London, UK
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer-WHO, Lyon, France
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Nogal A, Louca P, Zhang X, Wells PM, Steves CJ, Spector TD, Falchi M, Valdes AM, Menni C. Circulating Levels of the Short-Chain Fatty Acid Acetate Mediate the Effect of the Gut Microbiome on Visceral Fat. Front Microbiol 2021; 12:711359. [PMID: 34335546 PMCID: PMC8320334 DOI: 10.3389/fmicb.2021.711359] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background Acetate is a short-chain fatty acid (SCFA) produced by gut bacteria, which has been implicated in cardio-metabolic health. Here we examine the relationships of circulating acetate levels with gut microbiome composition and diversity and with visceral fat in a large population-based cohort. Results Microbiome alpha-diversity was positively correlated with circulating acetate levels (Shannon, Beta [95%CI] = 0.12 [0.06, 0.18], P = 0.002) after adjustment for covariates. Six serum acetate-associated bacterial genera were also identified, including positive correlations with Coprococcus, Barnesiella, Ruminococcus, and Ruminococcaceae NK4A21 and negative correlations were observed with Lachnoclostridium and Bacteroides. We also identified a correlation between visceral fat and serum acetate levels (Beta [95%CI] = −0.07 [−0.11, −0.04], P = 2.8 × 10–4) and between visceral fat and Lachnoclostridium (Beta [95%CI] = 0.076 [0.042, 0.11], P = 1.44 × 10–5). Formal mediation analysis revealed that acetate mediates ∼10% of the total effect of Lachnoclostridium on visceral fat. The taxonomic diversity showed that Lachnoclostridium and Coprococcus comprise at least 18 and 9 species, respectively, including novel bacterial species. By predicting the functional capabilities, we found that Coprococcus spp. present pathways involved in acetate production and metabolism of vitamins B, whereas we identified pathways related to the biosynthesis of trimethylamine (TMA) and CDP-diacylglycerol in Lachnoclostridium spp. Conclusions Our data indicates that gut microbiota composition and diversity may influence circulating acetate levels and that acetate might exert benefits on certain cardio-metabolic disease risk by decreasing visceral fat. Coprococcus may play an important role in host health by its production of vitamins B and SCFAs, whereas Lachnoclostridium might have an opposing effect by influencing negatively the circulating levels of acetate and being involved in the biosynthesis of detrimental lipid compounds.
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Affiliation(s)
- Ana Nogal
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Panayiotis Louca
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Xinyuan Zhang
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Ana M Valdes
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom.,Nottingham NIHR Biomedical Research Centre at the School of Medicine, Nottingham City Hospital, University of Nottingham, Nottingham, United Kingdom
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
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10
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Nag A, Kurushima Y, Bowyer RCE, Wells PM, Weiss S, Pietzner M, Kocher T, Raffler J, Völker U, Mangino M, Spector TD, Milburn MV, Kastenmüller G, Mohney RP, Suhre K, Menni C, Steves CJ. Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels. Hum Mol Genet 2021; 29:864-875. [PMID: 31960908 PMCID: PMC7104674 DOI: 10.1093/hmg/ddz308] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/05/2019] [Accepted: 12/11/2019] [Indexed: 12/26/2022] Open
Abstract
Saliva, as a biofluid, is inexpensive and non-invasive to obtain, and provides a vital tool to investigate oral health and its interaction with systemic health conditions. There is growing interest in salivary biomarkers for systemic diseases, notably cardiovascular disease. Whereas hundreds of genetic loci have been shown to be involved in the regulation of blood metabolites, leading to significant insights into the pathogenesis of complex human diseases, little is known about the impact of host genetics on salivary metabolites. Here we report the first genome-wide association study exploring 476 salivary metabolites in 1419 subjects from the TwinsUK cohort (discovery phase), followed by replication in the Study of Health in Pomerania (SHIP-2) cohort. A total of 14 distinct locus-metabolite associations were identified in the discovery phase, most of which were replicated in SHIP-2. While only a limited number of the loci that are known to regulate blood metabolites were also associated with salivary metabolites in our study, we identified several novel saliva-specific locus-metabolite associations, including associations for the AGMAT (with the metabolites 4-guanidinobutanoate and beta-guanidinopropanoate), ATP13A5 (with the metabolite creatinine) and DPYS (with the metabolites 3-ureidopropionate and 3-ureidoisobutyrate) loci. Our study suggests that there may be regulatory pathways of particular relevance to the salivary metabolome. In addition, some of our findings may have clinical significance, such as the utility of the pyrimidine (uracil) degradation metabolites in predicting 5-fluorouracil toxicity and the role of the agmatine pathway metabolites as biomarkers of oral health.
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Affiliation(s)
- Abhishek Nag
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK.,Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Yuko Kurushima
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Ruth C E Bowyer
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Stefan Weiss
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald & University of Greifswald, 17489 Greifswald, Germany
| | - Maik Pietzner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Thomas Kocher
- Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Johannes Raffler
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764 Neuherberg, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald & University of Greifswald, 17489 Greifswald, Germany
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Michael V Milburn
- Discovery and Translational Sciences, Metabolon, Inc., Morrisville, NC 27560, USA
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, D-85764 Neuherberg, Germany
| | - Robert P Mohney
- Discovery and Translational Sciences, Metabolon, Inc., Morrisville, NC 27560, USA
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha 24144, Qatar
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London SE1 7EH, UK
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11
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Cox NJ, Bowyer RCE, Ni Lochlainn M, Wells PM, Roberts HC, Steves CJ. The composition of the gut microbiome differs among community dwelling older people with good and poor appetite. J Cachexia Sarcopenia Muscle 2021; 12:368-377. [PMID: 33580637 PMCID: PMC8061352 DOI: 10.1002/jcsm.12683] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/07/2020] [Accepted: 01/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Anorexia of ageing is common and important in the development of sarcopenia in older individuals. Links have been proposed between the gut microbiota and sarcopenia. Disordered gut function is also recognized in anorexia of ageing, but how this may relate to resident gut microbiota is unexplored. Understanding this relationship may provide a basis for novel interventions for anorexia of ageing and sarcopenia. This study explores compositional differences of the gut microbiota between community dwelling healthy older adults with good or poor appetite, and associated differences in sarcopenia. METHODS We assessed appetite by the Simplified Nutritional Appetite Questionnaire (SNAQ) in members of the TwinsUK cohort aged ≥65 years. Using a pool of 776 individuals with existing microbiome data estimated from 16S rRNA sequencing data, we identified 102 cases (SNAQ score < 14) (95% female, mean age 68 years) matched to controls (SNAQ > 14) on body mass index, gender, age, diet, calorie consumption, frailty, antibiotic use, socio-economic status, and technical variables to minimize confounding microbiota associations. Species abundance and diversity, compositional differences, and paired differences in taxa abundance were compared between cases and controls. Additionally, we compared case and controls for sarcopenia as measured by muscle mass (appendicular lean mass/height2 ) and strength (chair stand time in seconds). RESULTS Cases with poor appetite had reduced species richness and diversity of their gut microbiome (adjusted OBSERVED: beta = -0.2, P < 0.001; adjusted SHANNON: beta = -0.17, P = 0.0135), significant compositional differences (adjusted non-parametric multivariate analysis of variance, P = 0.0095), and significant differences in taxa abundance including reduction of genus Lachnospira (logFC = -1.015, q = 0.023). In all-female subgroup analysis, cases with poor appetite demonstrated reduction in muscle strength (11.03 s vs. 9.26 s, P = 0.02). CONCLUSIONS This study is the first to observe differences in the composition of gut microbiota between healthy community dwelling older individuals with good and poor appetite. We found female individuals with reduced muscle strength had poor appetite compared with those with normal strength. These associations require further examination to understand causality and mechanisms of interaction, to inform potential strategies targeting the gut microbiota as a novel intervention for anorexia of ageing and sarcopenia.
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Affiliation(s)
- Natalie J Cox
- Academic Geriatric Medicine, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Ruth C E Bowyer
- Department of Twins Research and Genetic Epidemiology, Kings College London, St Thomas' Hospital, London, UK
| | - Mary Ni Lochlainn
- Department of Twins Research and Genetic Epidemiology, Kings College London, St Thomas' Hospital, London, UK
| | - Philippa M Wells
- Department of Twins Research and Genetic Epidemiology, Kings College London, St Thomas' Hospital, London, UK
| | - Helen C Roberts
- Academic Geriatric Medicine, Faculty of Medicine, University of Southampton, Tremona Road, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK.,NIHR Applied Research Collaboration (ARC) Wessex, Southampton, UK
| | - Claire J Steves
- Department of Twins Research and Genetic Epidemiology, Kings College London, St Thomas' Hospital, London, UK.,Department of Ageing and Health, Guy's and St Thomas' NHS Foundation Trust, London, UK
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12
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Zazzara MB, Wells PM, Bowyer RCE, Lochlainn MN, Thompson EJ, Penfold RS, Steves CJ. 103 Periodontal Health and Sarcopenia: Cross-Sectional Evidence From A Cohort of 2040 Twin Volunteers. Age Ageing 2021. [DOI: 10.1093/ageing/afab030.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
Periodontitis is a chronic inflammatory disease affecting the periodontium, ultimately leading to looseness and/or loss of teeth. Sarcopenia refers to age-related reduction in muscle mass and strength. Similar to periodontitis, chronic low-grade inflammation is thought to play a key role in its development. In addition, both increase in prevalence with advancing age. Despite known associations with other diseases involving a dysregulated inflammatory response, for example rheumatoid arthritis,, the relationship between periodontitis and sarcopenia, and whether they could be driven by similar processes, remains uncertain. The aim of this study was to explore the association between periodontitis and sarcopenia.
Methods
Observational study of 2040 adult volunteers [age 67.18 (12.17)] enrolled in the TwinsUK cohort study. Presence of tooth mobility and number of teeth lost were used to assess periodontal health. A binary variable was created to define periodontitis. Measurements of muscle strength, muscle quality/quantity and physical performance were used to assess sarcopenia. A categorical variable was created according to the European Working Group on Sarcopenia in Older People (EWGSOP2) consensus, to define sarcopenia (1: probable; 2: positive; 3: severe). Generalised linear mixed model analysis used on complete cases and age-matched (n = 1,288) samples to ascertain associations between periodontitis and sarcopenia.
Results
No significant association was found between periodontitis and sarcopenia in both the complete cases analysis and age-matched analysis. Results were consistent when analysis was adjusted for potential confounders including body mass index, frailty index, Mini Mental State Examination smoking, nutritional status and educational level.
Conclusions
This study found no significant association between periodontitis and sarcopenia in a cohort of 2040 adults. Although both periodontitis and sarcopenia have been linked to a dysregulated immune response and demonstrate an increase in prevalence with increasing age, our work is inconclusive due to the plethora of possible aetiopathogenetic pathways.
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Affiliation(s)
- M B Zazzara
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital, London UK
- Department of Gerontology, Neuroscience and Orthopedics, Sacred Heart Catholic University, Rome, Italy
| | - P M Wells
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital, London UK
| | - R C E Bowyer
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital, London UK
| | - M N Lochlainn
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital, London UK
| | - E J Thompson
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital, London UK
| | - R S Penfold
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital, London UK
| | - C J Steves
- Department of Twin Research and Genetic Epidemiology, King’s College London, St Thomas’ Hospital, London UK
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13
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Wells PM, Doores KJ, Couvreur S, Nunez RM, Seow J, Graham C, Acors S, Kouphou N, Neil SJD, Tedder RS, Matos PM, Poulton K, Lista MJ, Dickenson RE, Sertkaya H, Maguire TJA, Scourfield EJ, Bowyer RCE, Hart D, O'Byrne A, Steel KJA, Hemmings O, Rosadas C, McClure MO, Capedevilla-Pujol J, Wolf J, Ourselin S, Brown MA, Malim MH, Spector T, Steves CJ. Estimates of the rate of infection and asymptomatic COVID-19 disease in a population sample from SE England. J Infect 2020; 81:931-936. [PMID: 33068628 PMCID: PMC7557299 DOI: 10.1016/j.jinf.2020.10.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/11/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Understanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. METHODS We undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged 19-86 (median age 48; 85% female). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. FINDINGS We demonstrated a seroprevalence of 12% (51 participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic, and 16 (27%) were asymptomatic for core COVID-19 symptoms: fever, cough or anosmia. Specificity of anosmia for seropositivity was 95%, compared to 88% for fever cough and anosmia combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. INTERPRETATION Seroprevalence amongst adults from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic throughout the study. Anosmia demonstrated the highest symptom specificity for SARS-CoV-2 antibody response. FUNDING NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC.
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Affiliation(s)
- Philippa M Wells
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Simon Couvreur
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Rocio Martinez Nunez
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sam Acors
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Neophytos Kouphou
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Stuart J D Neil
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | | | - Pedro M Matos
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Kate Poulton
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Maria Jose Lista
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ruth E Dickenson
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Helin Sertkaya
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Thomas J A Maguire
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Edward J Scourfield
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ruth C E Bowyer
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Deborah Hart
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Aoife O'Byrne
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Kathryn J A Steel
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Oliver Hemmings
- Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Myra O McClure
- Department of Infectious Disease, Imperial College London, UK
| | | | | | - Sebastien Ourselin
- School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK
| | - Matthew A Brown
- Department of Medical & Molecular Genetics, Guy's and St Thomas' Hospital NHS Trust and King's College London NIHR Biomedical Research Centre, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Tim Spector
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Claire J Steves
- Department of Twin Research, King's College London, St Thomas' Hospital, London SE1 7EH, UK.
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14
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Ni Y, Yu G, Chen H, Deng Y, Wells PM, Steves CJ, Ju F, Fu J. M2IA: a web server for microbiome and metabolome integrative analysis. Bioinformatics 2020; 36:3493-3498. [PMID: 32176258 DOI: 10.1093/bioinformatics/btaa188] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/21/2020] [Accepted: 03/13/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION Microbiome-metabolome association studies have experienced exponential growth for an in-depth understanding of the impact of microbiota on human health over the last decade. However, analyzing the resulting multi-omics data and their correlations remains a significant challenge due to the lack of a comprehensive computational tool that can facilitate data integration and interpretation. In this study, an automated microbiome and metabolome integrative analysis pipeline (M2IA) has been developed to meet the urgent needs for tools that can effectively integrate microbiome and metabolome data to derive biological insights. RESULTS M2IA streamlines the integrative data analysis between metabolome and microbiome, from data preprocessing, univariate and multivariate statistical analyses, advanced functional analysis for biological interpretation, to a summary report. The functionality of M2IA was demonstrated using TwinsUK cohort datasets consisting of 1116 fecal metabolites and 16s rRNA microbiome from 786 individuals. Moreover, two important metabolic pathways, i.e. benzoate degradation and phosphotransferase system, were identified to be closely associated with obesity. AVAILABILITY AND IMPLEMENTATION M2IA is public available at http://m2ia.met-bioinformatics.cn. CONTACT yanni617@zju.edu.cn or fjf68@zju.edu.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yan Ni
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Gang Yu
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Huan Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Yongqiong Deng
- Department of Dermatology and STD, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | | | - Claire J Steves
- Department of Twin Research, Kings College London.,Department of Ageing and Health, St Thomas' Hospital, London SE1 7EH, UK
| | - Feng Ju
- School of Engineering, Westlake University.,Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Junfen Fu
- National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
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15
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Bowyer RCE, Schillereff DN, Jackson MA, Le Roy C, Wells PM, Spector TD, Steves CJ. Associations between UK tap water and gut microbiota composition suggest the gut microbiome as a potential mediator of health differences linked to water quality. Sci Total Environ 2020; 739:139697. [PMID: 32758933 DOI: 10.1016/j.scitotenv.2020.139697] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Tap water composition has been widely linked to differences in human health, however the biological pathways underlying this association are less clearly defined. We provide the first investigation of the potential for the gut microbiota to mediate this association. Tap water samples and drinking habits from 85 Mono-zygotic twins with existing faecal microbiota profiles from around the UK were used to assess associations of water composition with the gut microbiome. Water composition was captured using the first 3 principle components (PCs) from multiple factor analysis of ion concentrations, additionally estimating average daily dose (ADD) of the primary three solutes contributing to its variance: chloride, sulphate and sodium. Geographic differences in water composition were assessed. We used measures of faecal microbial diversity, between-individual differences in composition and differences in taxa abundance estimated from 16S rRNA sequencing data. Differences between twin pairs were also considered. We observed significant associations of sodium ADD with microbiota diversity (Chao1), chloride, sodium and sulphate ADD with dissimilarity between samples, and significant associations for all PCs and ADD-adjusted solutes with abundances of individual microbial taxa. These results support the hypothesis that the gut microbiota could mediate the effects of tap water composition on host health, warranting further investigation into tap-water as an influencer of microbiota composition.
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Affiliation(s)
- Ruth C E Bowyer
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Daniel N Schillereff
- Department of Geography, King's College London, Bush House North East Wing, 30 Aldwych, WC2B 4BG, UK.
| | - Matthew A Jackson
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK; Kennedy Institute of Rheumatology, University of Oxford, Oxford OX1 3QR, UK.
| | - Caroline Le Roy
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, 3-4th Floor South Wing Block D, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK; Department of Ageing and Health, St Thomas' Hospital, 9th floor, North Wing, Westminster Bridge Road, London SE1 7EH, UK.
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16
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Wells PM, Adebayo AS, Bowyer RCE, Freidin MB, Finckh A, Strowig T, Lesker TR, Alpizar-Rodriguez D, Gilbert B, Kirkham B, Cope AP, Steves CJ, Williams FMK. Associations between gut microbiota and genetic risk for rheumatoid arthritis in the absence of disease: a cross-sectional study. Lancet Rheumatol 2020; 2:e418-e427. [PMID: 33345197 PMCID: PMC7729822 DOI: 10.1016/s2665-9913(20)30064-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Rheumatoid arthritis is a chronic inflammatory autoimmune disease that is associated with reduced life expectancy. The disease is heritable and an extensive repertoire of genetic variants have been identified. The gut microbiota might represent an environmental risk factor for rheumatoid arthritis. We aimed to assess whether known rheumatoid arthritis risk alleles were associated with the gut microbiota in a large population who do not have rheumatoid arthritis. Methods In this cross-sectional study done in the UK and Switzerland, we used genotyping and microbiota data from previous studies of the TwinsUK cohort, excluding participants who had ever had a diagnosis of rheumatoid arthritis, as well as their unaffected co-twins. We used blood samples for genotyping and stool samples for the assessment of the gut microbiota. We generated a polygenic risk score (PRS) for rheumatoid arthritis in 1650 TwinsUK participants without the disease, based on 233 GWAS-identified single nucleotide polymorphisms associated with rheumatoid arthritis. We validated the PRS using logistic regression against rheumatoid arthritis diagnosis in 2686 UK Biobank individuals with a confirmed diagnosis of rheumatoid arthritis. Amplicon sequence variants (ASVs) were generated from 16S rRNA gene sequencing of stool samples and assessed for association with the PRS for rheumatoid arthritis. We validated the findings in an independent sample comprised of first-degree relatives of patients with rheumatoid arthritis from the SCREEN-RA cohort. Differential abundance of ASVs present in more than 5% of samples, grouped by ASV taxon annotation, against the rheumatoid arthritis PRS as a continuous variable was assessed using fixed-effects covariates. To account for multiple testing, the false discovery rate calculation was applied to all p values to generate q values, with a significance threshold of 0·05 determined a priori. Findings We found that presence of Prevotella spp were positively associated with the rheumatoid arthritis PRS in TwinsUK participants (q<1 × 10−7). This finding was validated in SCREEN-RA participants (n=133) carrying established shared epitope risk alleles (q=0·0011). We also found an association between Prevotella spp and presence of preclinical rheumatoid arthritis phases (q=0·021). Interpretation Prevotella spp in the gut microbiota are associated with the rheumatoid arthritis genotype in the absence of rheumatoid arthritis, including in individuals at high risk of developing rheumatoid arthritis. Our findings suggest that host genotype is associated with microbiota profile before disease onset. Funding Versus Arthritis.
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Affiliation(s)
- Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Adewale S Adebayo
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ruth C E Bowyer
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Maxim B Freidin
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Axel Finckh
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Hannover Medical School, Hannover, Germany
| | - Till Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Benoit Gilbert
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Bruce Kirkham
- Department of Rheumatology, Guy's and St Thomas' NHS Trust, London, UK
| | - Andrew P Cope
- Centre for Rheumatic Diseases, King's College London, London, UK.,Centre for Inflammation Biology and Cancer Immunology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.,Department of Ageing and Health, St Thomas' Hospital, London, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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Fabre MA, McKerrell T, Zwiebel M, Vijayabaskar MS, Park N, Wells PM, Rad R, Deloukas P, Small K, Steves CJ, Vassiliou GS. Concordance for clonal hematopoiesis is limited in elderly twins. Blood 2020; 135:269-273. [PMID: 31697828 PMCID: PMC6978156 DOI: 10.1182/blood.2019001807] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/06/2019] [Indexed: 12/14/2022] Open
Abstract
Although acquisition of leukemia-associated somatic mutations by 1 or more hematopoietic stem cells is inevitable with advancing age, its consequences are highly variable, ranging from clinically silent clonal hematopoiesis (CH) to leukemic progression. To investigate the influence of heritable factors on CH, we performed deep targeted sequencing of blood DNA from 52 monozygotic (MZ) and 27 dizygotic (DZ) twin pairs (aged 70-99 years). Using this highly sensitive approach, we identified CH (variant allele frequency ≥0.5%) in 62% of individuals. We did not observe higher concordance for CH within MZ twin pairs as compared with that within DZ twin pairs, or to that expected by chance. However, we did identify 2 MZ pairs in which both twins harbored identical rare somatic mutations, suggesting a shared cell of origin. Finally, in 3 MZ twin pairs harboring mutations in the same driver genes, serial blood samples taken 4 to 5 years apart showed substantial twin-to-twin variability in clonal trajectories. Our findings propose that the inherited genome does not exert a dominant influence on the behavior of adult CH and provide evidence that CH mutations may be acquired in utero.
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Affiliation(s)
- Margarete A Fabre
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service (NHS) Trust, Cambridge, United Kingdom
| | - Thomas McKerrell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service (NHS) Trust, Cambridge, United Kingdom
| | - Maximillian Zwiebel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- German Consortium for Translational Cancer Research (DKTK), Partnering Site Munich, Munich, Germany
| | - M S Vijayabaskar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Naomi Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, United Kingdom; and
| | - Roland Rad
- German Consortium for Translational Cancer Research (DKTK), Partnering Site Munich, Munich, Germany
| | - Panagiotis Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Kerrin Small
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, United Kingdom; and
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, United Kingdom; and
| | - George S Vassiliou
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome-Medical Research Council (MRC) Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, Cambridge University Hospitals National Health Service (NHS) Trust, Cambridge, United Kingdom
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Le Roy CI, Wells PM, Si J, Raes J, Bell JT, Spector TD. Red Wine Consumption Associated With Increased Gut Microbiota α-Diversity in 3 Independent Cohorts. Gastroenterology 2020; 158:270-272.e2. [PMID: 31472153 DOI: 10.1053/j.gastro.2019.08.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/29/2019] [Accepted: 08/10/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Caroline I Le Roy
- Department of Twin Research Genetic Epidemiology, King's College London, London, UK
| | - Philippa M Wells
- Department of Twin Research Genetic Epidemiology, King's College London, London, UK
| | - Jiyeon Si
- Vlaams Instituut voor Biotechnologie, Center for Microbiology Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology Rega Institute for Medical Research, Leuven, Belgium
| | - Jeroen Raes
- Vlaams Instituut voor Biotechnologie, Center for Microbiology Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology Rega Institute for Medical Research, Leuven, Belgium
| | - Jordana T Bell
- Department of Twin Research Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research Genetic Epidemiology, King's College London, London, UK.
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Wells PM, Williams FMK, Matey-Hernandez ML, Menni C, Steves CJ. 'RA and the microbiome: do host genetic factors provide the link? J Autoimmun 2019; 99:104-115. [PMID: 30850234 PMCID: PMC6470121 DOI: 10.1016/j.jaut.2019.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 11/12/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 12/29/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease, characterised by painful synovium inflammation, bony erosions, immune activation and the circulation of autoantibodies. Despite recent advances in therapeutics enabling disease suppression, there is a considerable demand for alternative therapeutic strategies as well as optimising those available at present. The relatively low concordance rate between monozygotic twins, 20–30% contrasts with heritability estimates of ∼65%, indicating a substantive role of other risk factors in RA pathogenesis. There is established evidence that RA has an infective component to its aetiology. More recently, differences in the commensal microbiota in RA compared to controls have been identified. Studies have shown that the gut, oral and lung microbiota is different in new onset treatment naïve, and established RA patients, compared to controls. Key taxonomic associations are an increase in abundance of Porphyromonas gingivalis and Prevotella copri in RA patients, compared to healthy controls. Host genetics may provide the link between disease and the microbiome. Genetic influence may be mediated by the host immune system; a differential response to RA associated taxa is suggested. The gut microbiome contains elements which are as much as 30% heritable. A better understanding of the influence of host genetics will shed light onto the role of the microbiome in RA. Here we review the role of the microbiome in RA through the lens of host genetics, and consider future research areas addressing microbiome study design and bioinformatics approaches. Rheumatoid arthritis (RA) affects 1% of the population and is highly debilitating. RA is ~65% heritable, yet the concordance rate between monozygotic twins is just 20–30%, indicating a substantive role of other risk factors. Studies have shown that the gut, oral and lung microbiome is different in treatment naïve and established RA patients, compared to controls. Current findings suggest an important influence of host genetics on the microbiome, which may contribute to RA via the host immune system. Associations of the microbiome with RA described thus far are confounded by host genetics, and future studies need to take account of this.
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Affiliation(s)
- Philippa M Wells
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK.
| | - Frances M K Williams
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - M L Matey-Hernandez
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - Cristina Menni
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - Claire J Steves
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK; Clinical Age Research Unit, Kings College Hospital Foundation Trust, London, UK
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Wood CR, Reynolds DR, Wells PM, Barlow JF, Woiwod IP, Chapman JW. Flight periodicity and the vertical distribution of high-altitude moth migration over southern Britain. Bull Entomol Res 2009; 99:525-535. [PMID: 19224662 DOI: 10.1017/s0007485308006548] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The continuous operation of insect-monitoring radars in the UK has permitted, for the first time, the characterization of various phenomena associated with high-altitude migration of large insects over this part of northern Europe. Previous studies have taken a case-study approach, concentrating on a small number of nights of particular interest. Here, combining data from two radars, and from an extensive suction- and light-trapping network, we have undertaken a more systematic, longer-term study of diel flight periodicity and vertical distribution of macro-insects in the atmosphere. Firstly, we identify general features of insect abundance and stratification, occurring during the 24-hour cycle, which emerge from four years' aggregated radar data for the summer months in southern Britain. These features include mass emigrations at dusk and, to a lesser extent, at dawn and daytime concentrations associated with thermal convection. We then focus our attention on the well-defined layers of large nocturnal migrants that form in the early evening, usually at heights of 200-500 m above ground. We present evidence from both radar and trap data that these nocturnal layers are composed mainly of noctuid moths, with species such as Noctua pronuba, Autographa gamma, Agrotis exclamationis, A. segetum, Xestia c-nigrum and Phlogophora meticulosa predominating.
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Affiliation(s)
- C R Wood
- Department of Meteorology, University of Reading, Reading, UK.
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