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Du X, Li H, Zhao H, Cui S, Sun X, Tan X. Causal relationship between gut microbiota and ankylosing spondylitis and potential mediating role of inflammatory cytokines: A mendelian randomization study. PLoS One 2024; 19:e0306792. [PMID: 39083521 PMCID: PMC11290680 DOI: 10.1371/journal.pone.0306792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024] Open
Abstract
Associations between gut microbiota and ankylosing spondylitis have been discovered in previous studies, but whether these associations reflect a causal relationship remains inconclusive. Aiming to reveal the bidirectional causal associations between gut microbiota and ankylosing spondylitis, we utilized publicly available genome wide association study summary data for 211 gut microbiota (GM) taxa and ankylosing spondylitis (AS) to conduct two sample mendelian randomization analyses. Mediation analysis was performed to explore mediating inflammatory cytokines. We found that genetically predicted higher abundance of Lactobacillaceae family, Rikenellaceae family and Howardella genus had suggestive associations with decreased risk of ankylosing spondylitis while genetic proxied higher abundance of Actinobacteria class and Ruminococcaceae_NK4A214_group genus was associated with increased risk of ankylosing spondylitis. IL23 and IFN-γ were potential mediating cytokines for GM dysbiosis, especially for Actinobacteria class, leading to AS. Our study provided a new exploration direction for the treatment of AS. Lactobacillaceae family, Rikenellaceae family, Howardella genus, Actinobacteria class and Ruminococcaceae_NK4A214_group genus are expected to become new therapeutic targets and monitoring indicators for AS.
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Affiliation(s)
- Xinyu Du
- Orthopedics and Traumatology Department of Integrated Traditional Chinese and Western Medicine, Tianjin Hospital, Tianjin, China
| | - Haibo Li
- Orthopedics and Traumatology Department of Integrated Traditional Chinese and Western Medicine, Tianjin Hospital, Tianjin, China
| | - Hongzhou Zhao
- Orthopedics and Traumatology Department of Integrated Traditional Chinese and Western Medicine, Tianjin Hospital, Tianjin, China
| | - Shuangshuang Cui
- Orthopedics Institute, Tianjin Hospital, Tianjin University, Tianjin, China
| | - Xiaozhuo Sun
- Preventive Treatment of Disease Department, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaochan Tan
- Acupuncture Department, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, China
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Chen X, Bi W, Ruan X, Jin L, Zhang N. Genome Sequencing Analysis of a Rare Case of Blood Infection Caused by Flavonifractor plautii. AMERICAN JOURNAL OF CASE REPORTS 2024; 25:e943920. [PMID: 38881048 PMCID: PMC11196211 DOI: 10.12659/ajcr.943920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/27/2024] [Accepted: 04/15/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Flavonifractor plautii belongs to the clostridium family, which can lead to local infections as well as the bloodstream infections. Flavonifractor plautii caused infection is rarely few in the clinic. To understand better Flavonifractor plautii, we investigated the drug sensitivity and perform genome sequencing of Flavonifractor plautii isolated from blood samples in China and explored the drug resistance and pathogenic mechanism of the bacteria. CASE REPORT The Epsilometer test method was used to detect the sensitivity of flavonoid bacteria to antimicrobial agents. PacBio sequencing technology was employed to sequence the whole genome of Flavonifractor plautii, and gene prediction and functional annotation were also analyzed. Flavonifractor plautii displayed sensitivity to most drugs but resistance to fluoroquinolones and tetracycline, potentially mediated by tet (W/N/W). The total genome size of Flavonifractor plautii was 4,573,303 bp, and the GC content was 59.78%. Genome prediction identified 4,506 open reading frames, including 9 ribosomal RNAs and 66 transfer RNAs. It was detected that the main virulence factor-coding genes of the bacteria were the capsule, polar flagella and FbpABC, which may be associated with bacterial movement, adhesion, and biofilm formation. CONCLUSIONS The results of whole-genome sequencing could provide relevant information about the drug resistance mechanism and pathogenic mechanism of bacteria and offer a basis for clinical diagnosis and treatment.
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Affiliation(s)
- Xingying Chen
- Department of Clinical Laboratory, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, Zhejiang, PR China
| | - Wei Bi
- Department of Clinical Laboratory, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, Zhejiang, PR China
| | - Xinyi Ruan
- College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, PR China
| | - Limin Jin
- Department of Clinical Laboratory, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, Zhejiang, PR China
| | - Nenghua Zhang
- Department of Clinical Laboratory, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, Zhejiang, PR China
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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4
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Tang J, Mo S, Fan L, Fu S, Liu X. Causal association of gut microbiota on spondyloarthritis and its subtypes: a Mendelian randomization analysis. Front Immunol 2024; 15:1284466. [PMID: 38390322 PMCID: PMC10883304 DOI: 10.3389/fimmu.2024.1284466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Background Despite establishing an association between gut microbiota and spondyloarthritis (SpA) subtypes, the causal relationship between them remains unclear. Methods Gut microbiota data were obtained from the MiBioGen collaboration, and SpA genome-wide association study (GWAS) summary data were obtained from the FinnGen collaboration. We conducted a two-sample Mendelian randomization (MR) analysis using the inverse-variance-weighted method supplemented with four additional MR methods (MR-Egger, weighted median, simple mode, and weighted mode). Pleiotropy and heterogeneity were also assessed. Reverse MR analysis was used to detect reverse causal relationships. Results We identified 23 causal links between specific gut microbiota taxa and SpA levels. Of these, 22 displayed nominal causal associations, and only one demonstrated a robust causal connection. Actinobacteria id.419 increased the risk of ankylosing spondylitis (AS) (odds ratio (OR) = 1.86 (95% confidence interval (CI): 1.29-2.69); p = 8.63E-04). The family Rikenellaceae id.967 was associated with a reduced risk of both AS (OR = 0.66 (95% CI: 0.47-0.93); p = 1.81E-02) and psoriatic arthritis (OR = 0.70 (95% CI: 0.50-0.97); p = 3.00E-02). Bacillales id.1674 increased the risk of AS (OR = 1.23 (95% CI: 1.00-1.51); p = 4.94E-02) and decreased the risk of enteropathic arthritis (OR = 0.56 (95% CI: 0.35-0.88); p = 1.14E-02). Directional pleiotropy, or heterogeneity, was not observed. No reverse causal associations were observed between the diseases and the gut microbiota. Conclusion Our MR analysis suggested a genetic-level causal relationship between specific gut microbiota and SpA, providing insights into the underlying mechanisms behind SpA development mediated by gut microbiota.
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Affiliation(s)
- Jun Tang
- Experimental Teaching Management Center, Chongqing Medical University, Chongqing, China
| | - Shiyan Mo
- Department of Rheumatology and Immunology, Hainan Hospital of Chinese People's Liberation Army of China (PLA) General Hospital, Sanya, Hainan, China
| | - Lina Fan
- Department of Rheumatology and Immunology, Hainan Hospital of Chinese People's Liberation Army of China (PLA) General Hospital, Sanya, Hainan, China
| | - Shihui Fu
- Department of Cardiovascular, Hainan Hospital of Chinese People’s Liberation Army of China (PLA) General Hospital, Sanya, Hainan, China
| | - Xiaofei Liu
- Department of Rheumatology and Immunology, Hainan Hospital of Chinese People's Liberation Army of China (PLA) General Hospital, Sanya, Hainan, China
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Thompson KN, Bonham KS, Ilott NE, Britton GJ, Colmenero P, Bullers SJ, McIver LJ, Ma S, Nguyen LH, Filer A, Brough I, Pearson C, Moussa C, Kumar V, Lam LH, Jackson MA, Pawluk A, Kiriakidis S, Taylor PC, Wedderburn LR, Marsden B, Young SP, Littman DR, Faith JJ, Pratt AG, Bowness P, Raza K, Powrie F, Huttenhower C. Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes. Sci Transl Med 2023; 15:eabn4722. [PMID: 37494472 DOI: 10.1126/scitranslmed.abn4722] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
Musculoskeletal diseases affect up to 20% of adults worldwide. The gut microbiome has been implicated in inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects inflammatory arthritis. To characterize the community structure and associated functional processes driving gut microbial involvement in arthritis, the Inflammatory Arthritis Microbiome Consortium investigated 440 stool shotgun metagenomes comprising 221 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, or psoriatic arthritis and 219 healthy controls and individuals with joint pain without an underlying inflammatory cause. Diagnosis explained about 2% of gut taxonomic variability, which is comparable in magnitude to inflammatory bowel disease. We identified several candidate microbes with differential carriage patterns in patients with elevated blood markers for inflammation. Our results confirm and extend previous findings of increased carriage of typically oral and inflammatory taxa and decreased abundance and prevalence of typical gut clades, indicating that distal inflammatory conditions, as well as local conditions, correspond to alterations to the gut microbial composition. We identified several differentially encoded pathways in the gut microbiome of patients with inflammatory arthritis, including changes in vitamin B salvage and biosynthesis and enrichment of iron sequestration. Although several of these changes characteristic of inflammation could have causal roles, we hypothesize that they are mainly positive feedback responses to changes in host physiology and immune homeostasis. By connecting taxonomic alternations to functional alterations, this work expands our understanding of the shifts in the gut ecosystem that occur in response to systemic inflammation during arthritis.
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Affiliation(s)
- Kelsey N Thompson
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kevin S Bonham
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicholas E Ilott
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Graham J Britton
- Marc and Jennifer Lipschultz Precision Immunology Institute and Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paula Colmenero
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Samuel J Bullers
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Lauren J McIver
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Siyuan Ma
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Long H Nguyen
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Andrew Filer
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research and Research Into Inflammatory Arthritis Centre Versus Arthritis, University of Birmingham, Chesterfield S41 7TD, UK
| | - India Brough
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Claire Pearson
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Caroline Moussa
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Vinod Kumar
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Lilian H Lam
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Matthew A Jackson
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - April Pawluk
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Serafim Kiriakidis
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Peter C Taylor
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Lucy R Wedderburn
- Centre for Adolescent Rheumatology Versus Arthritis, University College London, UCLH, and GOSH, Chesterfield S41 7TD, UK
- NIHR Great Ormond Street Biomedical Research Centre, University College London, London WC1N 1EH, UK
- UCL GOS Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Brian Marsden
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Stephen P Young
- Department of Rheumatology, Sandwell & West Birmingham NHS Trust, West Bromwich B71 4HJ, UK
| | - Dan R Littman
- Howard Hughes Medical Institute and the Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Jeremiah J Faith
- Marc and Jennifer Lipschultz Precision Immunology Institute and Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arthur G Pratt
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Research into Inflammatory Arthritis Centre Versus Arthritis, Newcastle Birmingham, Glasgow, and Oxford, Chesterfield S41 7TD, UK
- Department of Rheumatology, Musculoskeletal Services Directorate, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Paul Bowness
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Karim Raza
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Queen Elizabeth Hospital, Birmingham B15 2TT, UK
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research and Research Into Inflammatory Arthritis Centre Versus Arthritis, University of Birmingham, Chesterfield S41 7TD, UK
- Department of Rheumatology, Sandwell & West Birmingham NHS Trust, West Bromwich B71 4HJ, UK
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedic, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford OX3 7FY, UK
| | - Curtis Huttenhower
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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Li C, Zhang Y, Yan Q, Guo R, Chen C, Li S, Zhang Y, Meng J, Ma J, You W, Wu Z, Sun W. Alterations in the gut virome in patients with ankylosing spondylitis. Front Immunol 2023; 14:1154380. [PMID: 37063855 PMCID: PMC10098016 DOI: 10.3389/fimmu.2023.1154380] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
IntroductionAnkylosing spondylitis (AS), a chronic autoimmune disease, has been linked to the gut bacteriome.MethodsTo investigate the characteristics of the gut virome in AS, we profiled the gut viral community of 193 AS patients and 59 healthy subjects based on a metagenome-wide analysis of fecal metagenomes from two publicly available datasets.ResultsAS patients revealed a significant decrease in gut viral richness and a considerable alteration of the overall viral structure. At the family level, AS patients had an increased abundance of Gratiaviridae and Quimbyviridae and a decreased abundance of Drexlerviridae and Schitoviridae. We identified 1,004 differentially abundant viral operational taxonomic units (vOTUs) between patients and controls, including a higher proportion of AS-enriched Myoviridae viruses and control-enriched Siphoviridae viruses. Moreover, the AS-enriched vOTUs were more likely to infect bacteria such as Flavonifractor, Achromobacter, and Eggerthellaceae, whereas the control-enriched vOTUs were more likely to be Blautia, Ruminococcus, Collinsella, Prevotella, and Faecalibacterium bacteriophages. Additionally, some viral functional orthologs differed significantly in frequency between the AS-enriched and control-enriched vOTUs, suggesting the functional role of these AS-associated viruses. Moreover, we trained classification models based on gut viral signatures to discriminate AS patients from healthy controls, with an optimal area under the receiver operator characteristic curve (AUC) up to 0.936, suggesting the clinical potential of the gut virome for diagnosing AS.DiscussionThis work provides novel insight into the AS gut virome, and the findings may guide future mechanistic and therapeutic studies for other autoimmune diseases.
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Affiliation(s)
- Chen Li
- Department of Rheumatology, Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yan Zhang
- Department of Traditional Chinese Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Changming Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | | | - Yue Zhang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | | | - Jie Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wei You
- Beijing Key Laboratory of Acupuncture Neuromodulation, Department of Acupuncture and Moxibustion, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Zhisong Wu
- Department of Intensive Care Medicine, Dongfang Hospital Beijing University of Chinese Medicine, Beijing, China
| | - Wen Sun
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- Key Laboratory of Health Cultivation of the Ministry of Education, Beijing University of Chinese Medicine, Beijing, China
- Beijing Key Laboratory of Health Cultivation, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Wen Sun,
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7
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Wang L, Wei Z, Pan F, Song C, Peng L, Yang Y, Huang F. Case report: Fecal microbiota transplantation in refractory ankylosing spondylitis. Front Immunol 2023; 14:1093233. [PMID: 36911747 PMCID: PMC9996308 DOI: 10.3389/fimmu.2023.1093233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Ankylosing spondylitis (AS) is the prototype of a group of systemic inflammatory diseases referred to as spondyloarthritis. Comorbid inflammatory bowel disease and changed gut microbiota in AS have attracted attention to the influence of gut-joint axis and encouraged treating AS by targeting gut microbiota. Here we first reported a patient with refractory AS and comorbid ulcerative colitis (UC) who underwent three fecal microbiota transplantations (FMTs). Inadequate response to conventional treatments including tumor necrosis factor inhibitors impelled FMT as alternative therapy. Notable improvements in AS and UC accompanied with changed fecal microbiota were recorded at 1 week post-FMT1. Further recovery was found after the other two FMTs, and a roughly stable status was maintained in the follow-up period. More studies are needed to validate the effectiveness of FMT in AS and its mechanisms.
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Affiliation(s)
- Lei Wang
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhimin Wei
- Health Service Department of the Guard Bureau of the General Office of the Central Committee of the Communist Party of China, Beijing, China
| | - Fei Pan
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Chuan Song
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Lihua Peng
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yunsheng Yang
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Feng Huang
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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8
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Zhang H, Wei Y, Jia H, Chen D, Tang X, Wang J, Chen M, Guo Y. Immune activation of characteristic gut mycobiota Kazachstania pintolopesii on IL-23/IL-17R signaling in ankylosing spondylitis. Front Cell Infect Microbiol 2022; 12:1035366. [PMID: 36605130 PMCID: PMC9808786 DOI: 10.3389/fcimb.2022.1035366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
It is very important to understand the communication and interaction mechanisms between the host and its resident microorganisms on host physiology and for precise diagnosis and treatment. Although intestinal fungi and bacteria dysbiosis is increasingly linked to ankylosing spondylitis (AS), their mechanisms of action have been rarely illustrated. In this paper, fecal samples from 10 AS monkeys and 10 healthy controls were collected to systematically characterize the gut mycobiota and microbiota in AS monkeys by 16S rRNA and ITS2 DNA sequencing. Our results showed the gut fungi of Kazachstania pintolopesii, Saccharomycetaceae, Kazachstania, and Saccharomyceteles. Saccharomycetes were specially enriched in AS, and the microbiota of AS monkeys was characterized by an increased abundance of Clostridia, Clostridiales, Ruminococcaceae, and Prevotella 2, using Line Discriminant Analysis Effect Size. Compared to healthy controls, decreased ITS2/16S biodiversity ratios and altered bacterial-fungal interkingdom networks were observed in AS monkeys. Oral administration of K. pintolopesii activates IL-17RA pathway and induce inflammatory reaction in the colonic tissue of C57BL/6 mice, as well as multiple AS phenotypes, including fungal and bacterial dysbiosis, immune responses of NK cells, platelets, T cells, leukocytes, B-cell activation, rheumatoid arthritis, and inflammatory bowel disease. We also found the secreted products of K. pintolopesii could activate the IL-17RA pathway, which induces PANoptosis in macrophage RAW264.7 cells. Much worse, the PANoptosis products could promote the proliferation and morphological changes of K. pintolopesii, which resulted in much more K. pintolopesii and a severe inflammatory reaction. Interestingly, the inflammatory factor TNF-α can promote the morphological transformation of Candida albicans and K. pintolopesii, which is worthy of further study. The characteristic fungi in all these findings implied that fungal and bacterial dysbiosis have a close link to AS and that their communication and interaction indeed play an important role in autoimmune responses, and K. pintolopesii could be a potential marker microorganism in AS, although its specific mechanism is not fully elucidated.
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Affiliation(s)
- Haiting Zhang
- Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China,*Correspondence: Haiting Zhang, ; Meili Chen, ; Yinrui Guo,
| | - Yu Wei
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Huanhuan Jia
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, China
| | - Diling Chen
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Xiaocui Tang
- Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Jian Wang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Meili Chen
- Guangdong Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, China,*Correspondence: Haiting Zhang, ; Meili Chen, ; Yinrui Guo,
| | - Yinrui Guo
- Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, Zhuhai, Guangdong, China,*Correspondence: Haiting Zhang, ; Meili Chen, ; Yinrui Guo,
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9
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Wilton A, Glezos CM, Pananwala H, Lim HK. Periprosthetic Hip Joint Infection with Flavonifractor plautii: A Literature Review and Case Report. Hip Pelvis 2022; 34:255-261. [PMID: 36601614 PMCID: PMC9763828 DOI: 10.5371/hp.2022.34.4.255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 12/14/2022] Open
Abstract
The purpose of this case report and review of the literature is to provide documentation on periprosthetic hip joint infection with Flavonifractor plautii (formerly known as Eubacterium plautii), a strictly anaerobic bacterium, and to report on a successful pathway for management including staged surgical revisions and extended antibiotic therapy. A systematic review of the literature was conducted, which identified this case as only the fifth documented case of human infection with this organism; as a result, conduct of further research is warranted, based on the paucity of reports in the literature addressing anaerobic periprosthetic joint infection.
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Affiliation(s)
- Alexander Wilton
- Department of Orthopaedics, Ryde Hospital, Eastwood, NSW, Australia
| | - Constantine Michael Glezos
- Department of Orthopaedics, Ryde Hospital, Eastwood, NSW, Australia.,Department of Orthopaedics, Sydney Adventist Hospital, Wahroonga, NSW, Australia
| | | | - Han Kiong Lim
- Department of Orthopaedics, Ryde Hospital, Eastwood, NSW, Australia
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10
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Song ZY, Yuan D, Zhang SX. Role of the microbiome and its metabolites in ankylosing spondylitis. Front Immunol 2022; 13:1010572. [PMID: 36311749 PMCID: PMC9608452 DOI: 10.3389/fimmu.2022.1010572] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
Ankylosing spondylitis (AS), a chronic condition that commonly influences the spine and sacroiliac joints, usually progresses to stiffness and progressive functional limitation. Its fundamental etiology and pathogenesis are likely multifactorial and remain elusive. As environmental factors, gut microbiota performs critical functions in the pathogenesis of AS through various mechanisms, including interacting with genes, enhancing intestinal permeability, activating the gut mucosa immune system, and affecting the intestinal microbiota metabolites. This review provides an overview of recent advances in investigating gut microbiota in AS pathogenesis and discusses potential methods for future therapeutic intervention.
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Affiliation(s)
- Zi-Yi Song
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
- Shanxi Provincial Key Laboratory of Rheumatism Immune Microecology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Duo Yuan
- Department of Gynecology and Obstetrics, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Sheng-Xiao Zhang
- Department of Rheumatology, The Second Hospital of Shanxi Medical University, Taiyuan, China
- Key Laboratory of Cellular Physiology at Shanxi Medical University, Ministry of Education, Taiyuan, China
- Shanxi Provincial Key Laboratory of Rheumatism Immune Microecology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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11
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Comparative genomics reveals the evolution of antimicrobial resistance in Bacteroides nordii. Microb Pathog 2022; 173:105811. [PMID: 36183960 DOI: 10.1016/j.micpath.2022.105811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022]
Abstract
Bacteroides nordii, is an understudied member of the pathogenic B. fragilis group which comprises several multidrug-resistant (MDR) strains. Thus, it is of great interest to study the genome biology of Bacteroides nordii. However, no detailed study is available that characterized B. nordii at the genetic level and explored its role as a potential pathogen. We isolated an MDR strain viz., B. nordii PGMM4098 from the pus sample and subjected it to whole genome sequencing using Illumina technology. The draft genome was de-novo assembled and annotated, followed by comprehensive comparative genomics analyses using the publicly available genome dataset of B. nordii. The pan-genome analysis revealed the open nature of B. nordii, indicating the continuous accumulation of novel genes in non-core components leading to the emergence of new strains of this species. The thirteen antimicrobial resistance (AMR) genes identified in the genomes of all B. nordii strains were part of the non-core component of the pan-genome. Of these, four AMR genes, nimE, aadS, mef(En2), and ermB/F/G were found to be acquired via the process of horizontal gene transfer (HGT) from anaerobic Bacteroidetes. Importantly, the nimE gene conferring metronidazole resistance was found to be present only in B. nordii PGMM4098, which harbors five other AMR genes encoded in its genome. Of these, nimE (metronidazole resistance), ermB/F/G (macrolide-lincosamide-streptogramin B resistance), and cfxA2/A3 (class A β-lactam resistance) genes were further validated using targeted polymerase chain reaction assay. Notably, these three genes were also found to be under the operation of positive selective pressure suggesting the diversification of these genes, which might lead to the emergence of new MDR strains of B. nordii in the near future. Our study reported and characterized the genome of the first MDR strain of B. nordii and revealed the AMR evolution in this species using a comprehensive comparative genomics approach.
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12
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Gill T, Stauffer P, Asquith M, Laderas T, Martin TM, Davin S, Schleisman M, Ramirez C, Ogle K, Lindquist I, Nguyen J, Planck SR, Shaut C, Diamond S, Rosenbaum JT, Karstens L. Axial spondyloarthritis patients have altered mucosal IgA response to oral and fecal microbiota. Front Immunol 2022; 13:965634. [PMID: 36248884 PMCID: PMC9556278 DOI: 10.3389/fimmu.2022.965634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Axial spondyloarthritis (axSpA) is an inflammatory arthritis involving the spine and the sacroiliac joint with extra-articular manifestations in the eye, gut, and skin. The intestinal microbiota has been implicated as a central environmental component in the pathogenesis of various types of spondyloarthritis including axSpA. Additionally, alterations in the oral microbiota have been shown in various rheumatological conditions, such as rheumatoid arthritis (RA). Therefore, the aim of this study was to investigate whether axSpA patients have an altered immunoglobulin A (IgA) response in the gut and oral microbial communities. We performed 16S rRNA gene (16S) sequencing on IgA positive (IgA+) and IgA negative (IgA-) fractions (IgA-SEQ) from feces (n=17 axSpA; n=14 healthy) and saliva (n=14 axSpA; n=12 healthy), as well as on IgA-unsorted fecal and salivary samples. PICRUSt2 was used to predict microbial metabolic potential in axSpA patients and healthy controls (HCs). IgA-SEQ analyses revealed enrichment of several microbes in the fecal (Akkermansia, Ruminococcaceae, Lachnospira) and salivary (Prevotellaceae, Actinobacillus) microbiome in axSpA patients as compared with HCs. Fecal microbiome from axSpA patients showed a tendency towards increased alpha diversity in IgA+ fraction and decreased diversity in IgA- fraction in comparison with HCs, while the salivary microbiome exhibits a significant decrease in alpha diversity in both IgA+ and IgA- fractions. Increased IgA coating of Clostridiales Family XIII in feces correlated with disease severity. Inferred metagenomic analysis suggests perturbation of metabolites and metabolic pathways for inflammation (oxidative stress, amino acid degradation) and metabolism (propanoate and butanoate) in axSpA patients. Analyses of fecal and salivary microbes from axSpA patients reveal distinct populations of immunoreactive microbes compared to HCs using the IgA-SEQ approach. These bacteria were not identified by comparing their relative abundance alone. Predictive metagenomic analysis revealed perturbation of metabolites/metabolic pathways in axSpA patients. Future studies on these immunoreactive microbes may lead to better understanding of the functional role of IgA in maintaining microbial structure and human health.
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Affiliation(s)
- Tejpal Gill
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Tejpal Gill,
| | - Patrick Stauffer
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Mark Asquith
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Ted Laderas
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
| | - Tammy M. Martin
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, United States
| | - Sean Davin
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Matthew Schleisman
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Claire Ramirez
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Kimberly Ogle
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Ingrid Lindquist
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
- Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Justine Nguyen
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
| | - Stephen R. Planck
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Carley Shaut
- Laboratory of Immunogenetics, Oregon Health & Science University, Portland, OR, United States
| | - Sarah Diamond
- Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - James T. Rosenbaum
- Division of Arthritis and Rheumatic Diseases, Department of Medicine, Oregon Health & Science University, Portland, OR, United States
- Casey Eye Institute/Department of Ophthalmology, School of Medicine, Oregon Health & Science University, Portland, OR, United States
- Department of Cell Biology, Oregon Health & Science University, Portland, OR, United States
- Legacy Devers Eye Institute, Portland, OR, United States
| | - Lisa Karstens
- Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
- Division of Urogynecology, Department of Obstetrics and Gynecology Oregon Health & Science University, Portland, OR, United States
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13
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Cui Y, Zhang L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Roles of intestinal Parabacteroides in human health and diseases. FEMS Microbiol Lett 2022; 369:6659190. [PMID: 35945336 DOI: 10.1093/femsle/fnac072] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The stability of gut microbiota is essential for the host health. Parabacteroides spp., core members of the human gut microbiota, have average abundance of 1.27% in the human of 12 populations. Parabacteroides has been recently reported to have a close relationship with host health (E.g., metabolic syndrome, inflammatory bowel disease and obesity). Parabacteroides have the physiological characteristics of carbohydrate metabolism and secreting SCFAs. However, antimicrobial resistance of Parabacteroides to antibiotic (such as clindamycin, moxifloxacin and cefoxitin) should not be ignored. In this review, we primarily focused on Parabacteroides distasoniss, Parabacteroides goldsteinii, Parabacteroides johnsonii and Parabacteroides merdae and discussed their relationships with host disease, diet and the prevention or induction of diseases. P. distasonis and P. goldsteinii may be viewed as the potential next generation probiotics (NGP) candidate due to their protective effects on inflammation and obesity in mice. We also discussed the potential therapeutic application of Parabacteroides spp. in maintaining host-intestine homeostasis.
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Affiliation(s)
- Yanlong Cui
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Leshan Zhang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Wang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yanglei Yi
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuanyuan Shan
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Bianfang Liu
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuan Zhou
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Lü
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
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14
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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: 241] [Impact Index Per Article: 120.5] [Reference Citation Analysis] [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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15
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Liao HT, Tsai CY, Lai CC, Hsieh SC, Sun YS, Li KJ, Shen CY, Wu CH, Lu CH, Kuo YM, Li TH, Chou CT, Yu CL. The Potential Role of Genetics, Environmental Factors, and Gut Dysbiosis in the Aberrant Non-Coding RNA Expression to Mediate Inflammation and Osteoclastogenic/Osteogenic Differentiation in Ankylosing Spondylitis. Front Cell Dev Biol 2022; 9:748063. [PMID: 35127698 PMCID: PMC8811359 DOI: 10.3389/fcell.2021.748063] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/09/2021] [Indexed: 12/17/2022] Open
Abstract
Ankylosing spondylitis (AS) or radiographic axial spondyloarthritis is a chronic immune-mediated rheumatic disorder characterized by the inflammation in the axial skeleton, peripheral joints, and soft tissues (enthesis, fascia, and ligament). In addition, the extra-skeletal complications including anterior uveitis, interstitial lung diseases and aortitis are found. The pathogenesis of AS implicates an intricate interaction among HLA (HLA-B27) and non-HLA loci [endoplasmic reticulum aminopeptidase 1 (ERAP1), and interleukin-23 receptor (IL23R), gut dysbiosis, immune plasticity, and numerous environmental factors (infections, heavy metals, stress, cigarette smoking, etc.) The latter multiple non-genetic factors may exert a powerful stress on epigenetic regulations. These epigenetic regulations of gene expression contain DNA methylation/demethylation, histone modifications and aberrant non-coding RNAs (ncRNAs) expression, leading to inflammation and immune dysfunctions. In the present review, we shall discuss these contributory factors that are involved in AS pathogenesis, especially the aberrant ncRNA expression and its effects on the proinflammatory cytokine productions (TNF-α, IL-17 and IL-23), T cell skewing to Th1/Th17, and osteoclastogenic/osteogenic differentiation. Finally, some potential investigatory approaches are raised for solving the puzzles in AS pathogenesis.
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Affiliation(s)
- Hsien-Tzung Liao
- Division of Allergy, Immunology and Rheumatology, Taipei Veterans General Hospital, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Chang-Youh Tsai
- Division of Allergy, Immunology and Rheumatology, Taipei Veterans General Hospital, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
- *Correspondence: Chang-Youh Tsai, ; Chia-Li Yu,
| | - Chien-Chih Lai
- Division of Allergy, Immunology and Rheumatology, Taipei Veterans General Hospital, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Song-Chou Hsieh
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Syuan Sun
- Division of Allergy, Immunology and Rheumatology, Taipei Veterans General Hospital, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Ko-Jen Li
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chieh-Yu Shen
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Cheng-Han Wu
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Cheng-Hsun Lu
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Min Kuo
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tzu-Hao Li
- Division of Allergy, Immunology and Rheumatology, Taipei, Taiwan
- Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Chung-Tei Chou
- Division of Allergy, Immunology and Rheumatology, Taipei Veterans General Hospital, National Yang-Ming Chiao-Tung University, Taipei, Taiwan
| | - Chia-Li Yu
- Division of Rheumatology, Immunology and Allergy, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- *Correspondence: Chang-Youh Tsai, ; Chia-Li Yu,
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16
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Ezeji JC, Sarikonda DK, Hopperton A, Erkkila HL, Cohen DE, Martinez SP, Cominelli F, Kuwahara T, Dichosa AEK, Good CE, Jacobs MR, Khoretonenko M, Veloo A, Rodriguez-Palacios A. Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. Gut Microbes 2022; 13:1922241. [PMID: 34196581 PMCID: PMC8253142 DOI: 10.1080/19490976.2021.1922241] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health.
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Affiliation(s)
- Jessica C. Ezeji
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daven K. Sarikonda
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Austin Hopperton
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Hailey L. Erkkila
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daniel E. Cohen
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | - Fabio Cominelli
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA,Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, United States
| | - Tomomi Kuwahara
- Department of Microbiology, Faculty of Medicine, Kagawa University, Miki, Kagawa, Japan
| | - Armand E. K. Dichosa
- B-10 Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Caryn E. Good
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Michael R. Jacobs
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | | | - Alida Veloo
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Rodriguez-Palacios
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, United States,University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA,CONTACT Alexander Rodriguez-Palacios Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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17
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Wang L, Wang Y, Zhang P, Song C, Pan F, Li G, Peng L, Yang Y, Wei Z, Huang F. Gut microbiota changes in patients with spondyloarthritis: A systematic review. Semin Arthritis Rheum 2021; 52:151925. [PMID: 34844732 DOI: 10.1016/j.semarthrit.2021.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Gut microbiota has been proposed as a pivotal role in the progression of Spondyloarthritis (SpA), however diverse results remain to be synthesized. We performed a systematic review to collect evidence on the characteristic of the gut microbiota in patients with SpA, as compared to controls. METHODS We systematically searched MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, and Cochrane Central Register of Controlled Trials databases, through June 1, 2021 for studies that compared gut microbiota of cases with SpA versus healthy controls. RESULTS Of 3756 records identified, 28 studies from 23 articles were included in the analysis. Results of β-diversity showed SpA patients hold a significantly different microbial composition compared with controls. Several taxa-level differences of gut microbiota between SpA (and its subtypes) cases and controls were identified. Fourteen studies including only patients with ankylosing spondylitis (AS) reported increased amounts of Actinobacteria, Dialister, Streptococcus, and Clostridium bolteae, and decreased amounts of Bacteroidales and Parasutterella in AS cases versus controls in ≥ 3 studies. Dialister invisus was increased in axial-SpA cases versus controls in 3 studies. Bacteroides fragilis was increased in enthesitis-related arthritis (ERA) cases versus controls in 2 studies. For all SpA studies, Proteobacteria, Enterobacteriaceae, and Bacteroidaceae were increased, whereas Bacteroidetes, Bacteroidales, and Akkermansia were decreased in cases versus controls in ≥ 3 studies. Over 40% of the studies showed comparable data of both sex and age between cases and controls. CONCLUSION The microbial characteristics of SpA summarized in the systematic review laid the groundwork for evidence-based microbial treatment. The microbial variance among subtypes of SpA remains to be explored. Further studies are needed to elucidate how the altered microbiota participate in the pathogenesis of SpA.
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Affiliation(s)
- Lei Wang
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Yiwen Wang
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Pei Zhang
- School of Medicine, Nankai University, Tianjin, China
| | - Chuan Song
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China
| | - Fei Pan
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Gang Li
- Health Service Department of the Guard Bureau of the Joint Staff Department, Beijing, China
| | - Lihua Peng
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yunsheng Yang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhimin Wei
- Health Service Department of the Guard Bureau of the Joint Staff Department, Beijing, China.
| | - Feng Huang
- Department of Rheumatology and Immunology, The First Medical Center, Chinese PLA General Hospital, Beijing, China.
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Harkins P, Burke E, Swales C, Silman A. 'All disease begins in the gut'-the role of the intestinal microbiome in ankylosing spondylitis. Rheumatol Adv Pract 2021; 5:rkab063. [PMID: 34557624 PMCID: PMC8452999 DOI: 10.1093/rap/rkab063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Ankylosing spondylitis is a chronic, debilitating arthritis with a predilection for the axial skeleton. It has a strong genetic predisposition, but the precise pathogenetic mechanisms involved in its development have not yet been fully elucidated. This has implications both for early diagnosis and for effective management. Recently, alterations in the intestinal microbiome have been implicated in disease pathogenesis. In this review, we summarize studies assessing the intestinal microbiome in AS pathogenesis, in addition to synthesizing the literature exploring the postulated mechanisms by which it exerts it pathogenic potential. Finally, we review studies analysing manipulation of the microbiome as a potential therapeutic avenue in AS management.
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Affiliation(s)
- Patricia Harkins
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Eoghan Burke
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Catherine Swales
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Alan Silman
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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Berlinberg AJ, Regner EH, Stahly A, Brar A, Reisz JA, Gerich ME, Fennimore BP, Scott FI, Freeman AE, Kuhn KA. Multi 'Omics Analysis of Intestinal Tissue in Ankylosing Spondylitis Identifies Alterations in the Tryptophan Metabolism Pathway. Front Immunol 2021; 12:587119. [PMID: 33746944 PMCID: PMC7966505 DOI: 10.3389/fimmu.2021.587119] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/08/2021] [Indexed: 12/20/2022] Open
Abstract
Intestinal microbial dysbiosis, intestinal inflammation, and Th17 immunity are all linked to the pathophysiology of spondyloarthritis (SpA); however, the mechanisms linking them remain unknown. One potential hypothesis suggests that the dysbiotic gut microbiome as a whole produces metabolites that influence human immune cells. To identify potential disease-relevant, microbiome-produced metabolites, we performed metabolomics screening and shotgun metagenomics on paired colon biopsies and fecal samples, respectively, from subjects with axial SpA (axSpA, N=21), Crohn's disease (CD, N=27), and Crohn's-axSpA overlap (CD-axSpA, N=12), as well as controls (HC, N=24). Using LC-MS based metabolomics of 4 non-inflamed pinch biopsies of the distal colon from subjects, we identified significant alterations in tryptophan pathway metabolites, including an expansion of indole-3-acetate (IAA) in axSpA and CD-axSpA compared to HC and CD and indole-3-acetaldehyde (I3Ald) in axSpA and CD-axSpA but not CD compared to HC, suggesting possible specificity to the development of axSpA. We then performed shotgun metagenomics of fecal samples to characterize gut microbial dysbiosis across these disease states. In spite of no significant differences in alpha-diversity among the 4 groups, our results confirmed differences in gene abundances of numerous enzymes involved in tryptophan metabolism. Specifically, gene abundance of indolepyruvate decarboxylase, which generates IAA and I3Ald, was significantly elevated in individuals with axSpA while gene abundances in HC demonstrated a propensity towards tryptophan synthesis. Such genetic changes were not observed in CD, again suggesting disease specificity for axSpA. Given the emerging role of tryptophan and its metabolites in immune function, altogether these data indicate that tryptophan metabolism into I3Ald and then IAA is one mechanism by which the gut microbiome potentially influences the development of axSpA.
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Affiliation(s)
- Adam J. Berlinberg
- Division of Rheumatology, Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Emilie H. Regner
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Andrew Stahly
- Division of Rheumatology, Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Ana Brar
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, United States
| | - Mark E. Gerich
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Blair P. Fennimore
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Frank I. Scott
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Alison E. Freeman
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Kristine A. Kuhn
- Division of Rheumatology, Department of Medicine, University of Colorado, Aurora, CO, United States
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