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Wang XH, Yang YN, Li YH, Cheng JL, Yan L, Liang Y, Zeng Q, Zhan T, Wang DW, Yu RH, Wu CM. Oral bacteriome and mycobiome of patients with idiopathic membranous nephropathy with different tongue coatings treated with a Chinese herbal formula. JOURNAL OF ETHNOPHARMACOLOGY 2024; 331:118233. [PMID: 38685365 DOI: 10.1016/j.jep.2024.118233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 02/25/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Moshen Fuyuan Formula (MSFY) is one of the representative Chinese medicine compound for Idiopathic membranous nephropathy (IMN), that originate from Fang Ji Huang Qi decoction in the Han dynasty. IMN is usually accompanied by different tongue coatings in traditional Chinese medicine (TCM), and tongue microorganisms are important factors affecting the formation of the tongue coating. Recently, oral microbiomes, including bacteria and fungi, have been identified as pivotal factors that contribute to disease development. However, the regulation of oral microbiomes by MSFY has not been defined. AIM OF THE STUDY In this work, we explore the characteristics of oral bacteria and fungi in IMN patients with different tongue coatings, and clarify the therapeutic effect of MSFY based on oral microbiome. MATERIALS AND METHODS We enrolled 24 patients with IMN, including 11 with white tongue (IMN-W) and 13 with yellow tongue (IMN-Y), and recruited an additional 10 healthy individuals. Patients with IMN were treated with the MSFY. The oral bacteriome and fungi before and after treatment were detected using full-length 16S rRNA and internal transcribed spacer gene sequencing. RESULTS The therapeutic effect of MSFY on patients with yellow tongue coating was more significant than that on patients with white tongue coating. In terms of oral bacteriome, Campylobacter bacteria were enriched in patients with yellow tongue and could be a promising biomarker for yellow coating. Enrichment of Veillonella parvula_A may partially account for the therapeutic effect of MSFY. As for oral fungi, Malassezia globosa was enhanced in patients with IMN-W and reduced in patients with IMN-Y. Notably, it was reduced by MSFY. We also found that mycobiome-bacteriome interactions were highly complex and dynamic in patients with IMN. CONCLUSION The regulation of the dynamic balance between oral fungi and bacteria by MSFY contributes to the treatment of IMN. This study determined the oral bacteriome and mycobiome of patients with IMN with different tongue coatings before and after MSFY treatment, which aids in promoting personalized treatment in clinical TCM and provides direction for investigating the mechanism of Chinese herbal medicines.
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Affiliation(s)
- Xin-Hui Wang
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Ya-Nan Yang
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Yi-Han Li
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Jia-Le Cheng
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Lei Yan
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Ying Liang
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Qin Zeng
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Tian Zhan
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Dian-Wen Wang
- Guang'anmen Hospital South Campus of China Academy of Chinese Medical Sciences, Beijing, 102611, China.
| | - Ren-Huan Yu
- Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Chong-Ming Wu
- Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China; Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin, 301617, China.
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Byndloss M, Devkota S, Duca F, Niess JH, Nieuwdorp M, Orho-Melander M, Sanz Y, Tremaroli V, Zhao L. The gut microbiota and diabetes: research, translation, and clinical applications - 2023 Diabetes, Diabetes Care, and Diabetologia Expert Forum. Diabetologia 2024:10.1007/s00125-024-06198-1. [PMID: 38910152 DOI: 10.1007/s00125-024-06198-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
This article summarises the state of the science on the role of the gut microbiota (GM) in diabetes from a recent international expert forum organised by Diabetes, Diabetes Care, and Diabetologia, which was held at the European Association for the Study of Diabetes 2023 Annual Meeting in Hamburg, Germany. Forum participants included clinicians and basic scientists who are leading investigators in the field of the intestinal microbiome and metabolism. Their conclusions were as follows: (1) the GM may be involved in the pathophysiology of type 2 diabetes, as microbially produced metabolites associate both positively and negatively with the disease, and mechanistic links of GM functions (e.g. genes for butyrate production) with glucose metabolism have recently emerged through the use of Mendelian randomisation in humans; (2) the highly individualised nature of the GM poses a major research obstacle, and large cohorts and a deep-sequencing metagenomic approach are required for robust assessments of associations and causation; (3) because single time point sampling misses intraindividual GM dynamics, future studies with repeated measures within individuals are needed; and (4) much future research will be required to determine the applicability of this expanding knowledge to diabetes diagnosis and treatment, and novel technologies and improved computational tools will be important to achieve this goal.
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Affiliation(s)
- Mariana Byndloss
- Vanderbilt University Medical Center, Nashville, TN, USA
- Howard Hughes Medical Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Suzanne Devkota
- Cedars-Sinai Medical Center, Human Microbiome Research Institute, Los Angeles, CA, USA
| | | | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Digestive Healthcare Center, Clarunis, Basel, Switzerland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
- Amsterdam Diabeter Center, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain.
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Liping Zhao
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
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3
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Wang J, He M, Yang M, Ai X. Gut microbiota as a key regulator of intestinal mucosal immunity. Life Sci 2024; 345:122612. [PMID: 38588949 DOI: 10.1016/j.lfs.2024.122612] [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: 02/04/2024] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024]
Abstract
Gut microbiota is a complex microbial community with the ability of maintaining intestinal health. Intestinal homeostasis largely depends on the mucosal immune system to defense external pathogens and promote tissue repair. In recent years, growing evidence revealed the importance of gut microbiota in shaping intestinal mucosal immunity. Therefore, according to the existing findings, this review first provided an overview of intestinal mucosal immune system before summarizing the regulatory roles of gut microbiota in intestinal innate and adaptive immunity. Specifically, this review delved into the gut microbial interactions with the cells such as intestinal epithelial cells (IECs), macrophages, dendritic cells (DCs), neutrophils, and innate lymphoid cells (ILCs) in innate immunity, and T and B lymphocytes in adaptive immunity. Furthermore, this review discussed the main effects of gut microbiota dysbiosis in intestinal diseases and offered future research prospects. The review highlighted the key regulatory roles of gut microbiota in intestinal mucosal immunity via various host-microbe interactions, providing valuable references for the development of microbial therapy in intestinal diseases.
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Affiliation(s)
- Jing Wang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China; Department of Pharmacy, North Sichuan Medical College, Nanchong 637000, China
| | - Mei He
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China; Department of Pharmacy, North Sichuan Medical College, Nanchong 637000, China
| | - Ming Yang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China; Department of Pharmacy, North Sichuan Medical College, Nanchong 637000, China.
| | - Xiaopeng Ai
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China; Department of Pharmacy, North Sichuan Medical College, Nanchong 637000, China.
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4
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Wang W, O'Driscoll M, Wang Q, Zhao S, Salje H, Yu H. Dynamics of measles immunity from birth and following vaccination. Nat Microbiol 2024:10.1038/s41564-024-01694-x. [PMID: 38740931 DOI: 10.1038/s41564-024-01694-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/03/2024] [Indexed: 05/16/2024]
Abstract
Measles remains a major threat to human health despite widespread vaccination. While we know that maternal antibodies can impair vaccine-induced immunity, the relative contributions of pre-existing immunity levels, maternal and infant characteristics on vaccine responses remain unclear, hampering evidence-based vaccination policy development. Here we combine serological data from 1,505 individuals (aged 0-12 years) in a mother-infant cohort and in a child cohort with empirical models to reconstruct antibody trajectories from birth. We show that while highly heterogeneous across a population, measles antibody evolution is strongly predictive from birth at the individual level, including following vaccination. Further, we find that caesarean section births were linked with 2.56 (95% confidence interval: 1.06-6.37) increased odds of primary vaccine failure, highlighting the long-term immunological consequences of birth route. Finally, we use our new understanding of antibody evolution to critically assess the population-level consequences of different vaccination schedules, the results of which will allow country-level evaluations of vaccine policy.
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Affiliation(s)
- Wei Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | | | - Qianli Wang
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Sihong Zhao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
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Liu Z, Zhang D, Chen S. Unveiling the gastric microbiota: implications for gastric carcinogenesis, immune responses, and clinical prospects. J Exp Clin Cancer Res 2024; 43:118. [PMID: 38641815 PMCID: PMC11027554 DOI: 10.1186/s13046-024-03034-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/29/2024] [Indexed: 04/21/2024] Open
Abstract
High-throughput sequencing has ushered in a paradigm shift in gastric microbiota, breaking the stereotype that the stomach is hostile to microorganisms beyond H. pylori. Recent attention directed toward the composition and functionality of this 'community' has shed light on its potential relevance in cancer. The microbial composition in the stomach of health displays host specificity which changes throughout a person's lifespan and is subject to both external and internal factors. Distinctive alterations in gastric microbiome signature are discernible at different stages of gastric precancerous lesions and malignancy. The robust microbes that dominate in gastric malignant tissue are intricately implicated in gastric cancer susceptibility, carcinogenesis, and the modulation of immunosurveillance and immune escape. These revelations offer fresh avenues for utilizing gastric microbiota as predictive biomarkers in clinical settings. Furthermore, inter-individual microbiota variations partially account for differential responses to cancer immunotherapy. In this review, we summarize current literature on the influence of the gastric microbiota on gastric carcinogenesis, anti-tumor immunity and immunotherapy, providing insights into potential clinical applications.
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Affiliation(s)
- Zhiyi Liu
- Department of Oncology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200092, China
| | - Dachuan Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Siyu Chen
- Department of Oncology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200092, China.
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6
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Filimonova I, Innocenti G, Vogl T. Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens. Methods Mol Biol 2024; 2717:101-122. [PMID: 37737980 DOI: 10.1007/978-1-0716-3453-0_7] [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] [Indexed: 09/23/2023]
Abstract
While thousands of food and environmental allergens have been reported, conventional methods for allergy testing typically rely on measuring immunoglobulin E (IgE) binding against panels of dozens to hundreds of antigens. Beyond IgE, also the specificity of other Ig (sub-)classes such as IgG4, has gained interest because of a potential protective role toward allergy.Phage immunoprecipitation sequencing (PhIP-Seq) allows to study hundreds of thousands of rationally selected peptide antigens and to resolve binding specificities of different Ig classes. This technology combines synthetic DNA libraries encoding antigens, with the display on the surface of T7 bacteriophages and next-generation sequencing (NGS) for quantitative readouts. Thereby binding of entire Ig repertoires can be measured to detect the exact epitopes of food allergens and to study potential cross-reactivity.In this chapter, we provide a summary of both the key experimental steps and various strategies for analyzing PhIP-Seq datasets, as well as comparing the advantages and disadvantages of this methodology for measuring antibody responses against food antigens.
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Affiliation(s)
- Ioanna Filimonova
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Gabriel Innocenti
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Thomas Vogl
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria.
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7
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Ning K, Shi C, Chi YY, Zhou YF, Zheng W, Duan Y, Tong W, Xie Q, Xiang H. Portulaca oleracea L. polysaccharide alleviates dextran sulfate sodium-induced ulcerative colitis by regulating intestinal homeostasis. Int J Biol Macromol 2024; 256:128375. [PMID: 38000581 DOI: 10.1016/j.ijbiomac.2023.128375] [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: 08/15/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/26/2023]
Abstract
Portulaca oleracea L. (purslane) is a vegetable that contains a variety of active compounds with nutritional properties and has the potential to treat ulcerative colitis (UC). However, the mechanisms underlying the effects of Portulaca oleracea L. polysaccharide (POP) in alleviating UC remain unclear. In this study, we prepared an aqueous extract of purslane and separated a fraction with molecular weight >10 kDa using membrane separation. This fraction was used to isolate POP. The effect of POP on gut microbiota and colon transcriptome in dextran sulfate sodium-induced UC model mice was evaluated. POP treatment reduced inflammation and oxidative stress imbalance in UC mice. In addition, POP improved the intestinal barrier and regulated intestinal homeostasis. Importantly, POP was found to regulate gut microbiota, maintain the levels of retinol and short-chain fatty acids in the gut, promote the proliferation and differentiation of B cells in the colon, and increase the expression of immunoglobulin A. These results provide novel insights into the role of POP in regulating intestinal homeostasis, which should guide further development of POP as a functional food.
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Affiliation(s)
- Ke Ning
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Chao Shi
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yan-Yu Chi
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yong-Fei Zhou
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Weiwei Zheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Yameng Duan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Weiwei Tong
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China
| | - Qiuhong Xie
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China; Institute of Changbai Mountain Resource and Health, Jilin University, Fusong 134504, PR China.
| | - Hongyu Xiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, PR China; Institute of Changbai Mountain Resource and Health, Jilin University, Fusong 134504, PR China.
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8
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Cormier M, Burnett E, Mo A, Notley C, Tijet N, Christie-Holmes N, Hough C, Lillicrap D. Mice possess a more limited natural antihuman factor VIII antibody repertoire than humans that is produced disproportionately by marginal zone B cells. J Thromb Haemost 2024; 22:76-89. [PMID: 37678547 PMCID: PMC10872961 DOI: 10.1016/j.jtha.2023.08.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND One-third of patients with severe hemophilia A develop neutralizing antibodies to the factor VIII (FVIII) protein in response to intravenous replacement therapy. Patients may also generate natural, nonneutralizing antibodies to FVIII before FVIII exposure. These patients are at increased risk of developing neutralizing antibodies to FVIII. However, natural anti-FVIII antibodies are also present in healthy human donors. OBJECTIVES To further characterize the natural antihuman (h) FVIII antibody repertoire in mice and humans. METHODS An in-house ELISA was developed using a purified polyclonal immunoglobulin (Ig) standard to quantify anti-hFVIII Ig in cell culture supernatant or plasma from mice (wild-type and FVIII-/-) and adult human donors. RESULTS All naïve wild-type and FVIII-/- mice, as well as healthy human donors, possess natural anti-hFVIII antibodies. Mice only have natural anti-hFVIII IgM, which is present in germ-free mice, suggesting that they are germline encoded. Although murine marginal zone B cells (MZBs) contribute 44% to all circulating natural IgM, they contribute disproportionately to the anti-hFVIII IgM repertoire (82%). This naturally occurring murine MZB-derived IgM is not B-domain specific and is reduced by intravenously administered hFVIII, suggesting that it may form immune complexes immediately upon hFVIII administration. Natural anti-hFVIII antibodies of IgG, IgM, and IgA isotypes can be detected in adult human donors. There were increased levels of B-domain-favoring anti-hFVIII IgG in 14% of healthy donors, which were markedly different from the rest of the "low-titer" population. CONCLUSIONS There is a preponderance of natural anti-hFVIII antibodies in both mice and healthy adult human donors.
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Affiliation(s)
- Matthew Cormier
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada.
| | - Erin Burnett
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Aomei Mo
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Colleen Notley
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Nathalie Tijet
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Natasha Christie-Holmes
- Emerging & Pandemic Infections Consortium, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Christine Hough
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - David Lillicrap
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada.
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Wang X, Ding C, Li HB. The crosstalk between enteric nervous system and immune system in intestinal development, homeostasis and diseases. SCIENCE CHINA. LIFE SCIENCES 2024; 67:41-50. [PMID: 37672184 DOI: 10.1007/s11427-023-2376-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/19/2023] [Indexed: 09/07/2023]
Abstract
The gut is the largest digestive and absorptive organ, which is essential for induction of mucosal and systemic immune responses, and maintenance of metabolic-immune homeostasis. The intestinal components contain the epithelium, stromal cells, immune cells, and enteric nervous system (ENS), as well as the outers, such as gut microbiota, metabolites, and nutrients. The dyshomeostasis of intestinal microenvironment induces abnormal intestinal development and functions, even colon diseases including dysplasia, inflammation and tumor. Several recent studies have identified that ENS plays a crucial role in maintaining the immune homeostasis of gastrointestinal (GI) microenvironment. The crosstalk between ENS and immune cells, mainly macrophages, T cells, and innate lymphoid cells (ILCs), has been found to exert important regulatory roles in intestinal tissue programming, homeostasis, function, and inflammation. In this review, we mainly summarize the critical roles of the interactions between ENS and immune cells in intestinal homeostasis during intestinal development and diseases progression, to provide theoretical bases and ideas for the exploration of immunotherapy for gastrointestinal diseases with the ENS as potential novel targets.
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Affiliation(s)
- Xindi Wang
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chenbo Ding
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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10
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Chen Z, Guan D, Wang Z, Li X, Dong S, Huang J, Zhou W. Microbiota in cancer: molecular mechanisms and therapeutic interventions. MedComm (Beijing) 2023; 4:e417. [PMID: 37937304 PMCID: PMC10626288 DOI: 10.1002/mco2.417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/04/2023] [Accepted: 10/12/2023] [Indexed: 11/09/2023] Open
Abstract
The diverse bacterial populations within the symbiotic microbiota play a pivotal role in both health and disease. Microbiota modulates critical aspects of tumor biology including cell proliferation, invasion, and metastasis. This regulation occurs through mechanisms like enhancing genomic damage, hindering gene repair, activating aberrant cell signaling pathways, influencing tumor cell metabolism, promoting revascularization, and remodeling the tumor immune microenvironment. These microbiota-mediated effects significantly impact overall survival and the recurrence of tumors after surgery by affecting the efficacy of chemoradiotherapy. Moreover, leveraging the microbiota for the development of biovectors, probiotics, prebiotics, and synbiotics, in addition to utilizing antibiotics, dietary adjustments, defensins, oncolytic virotherapy, and fecal microbiota transplantation, offers promising alternatives for cancer treatment. Nonetheless, due to the extensive and diverse nature of the microbiota, along with tumor heterogeneity, the molecular mechanisms underlying the role of microbiota in cancer remain a subject of intense debate. In this context, we refocus on various cancers, delving into the molecular signaling pathways associated with the microbiota and its derivatives, the reshaping of the tumor microenvironmental matrix, and the impact on tolerance to tumor treatments such as chemotherapy and radiotherapy. This exploration aims to shed light on novel perspectives and potential applications in the field.
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Affiliation(s)
- Zhou Chen
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Defeng Guan
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Zhengfeng Wang
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Xin Li
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
| | - Shi Dong
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
| | - Junjun Huang
- The First Hospital of Lanzhou UniversityLanzhouGansuChina
| | - Wence Zhou
- The First Clinical Medical CollegeLanzhou UniversityLanzhouGansuChina
- The Department of General SurgeryLanzhou University Second HospitalLanzhouGansuChina
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11
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Torres-Chávez ME, Torres-Carrillo NM, Monreal-Lugo AV, Garnés-Rancurello S, Murugesan S, Gutiérrez-Hurtado IA, Beltrán-Ramírez JR, Sandoval-Pinto E, Torres-Carrillo N. Association of intestinal dysbiosis with susceptibility to multiple sclerosis: Evidence from different population studies (Review). Biomed Rep 2023; 19:93. [PMID: 37901876 PMCID: PMC10603378 DOI: 10.3892/br.2023.1675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Understanding the relationship between microorganisms that live in our intestines and neuroinflammatory and neurodegenerative pathologies of the central nervous system (CNS) is essential, since they have been shown to have an immunomodulatory effect in neurological disorders, such as multiple sclerosis (MS). The gut microbiota can be affected by several environmental factors, including infections, physical and emotional stress and diet, the latter known as the main modulator of intestinal bacteria. An abrupt shift in the gut microbiota composition and function is known as dysbiosis, a state of local and systemic inflammation produced by pathogenic bacteria and its metabolites responsible for numerous neurological symptoms. It may also trigger neuronal damage in patients diagnosed with MS. Intestinal dysbiosis affects the permeability of the intestine, allowing chronic low-grade bacterial translocation from the intestine to the circulation, which may overstimulate immune cells and cells resident in the CNS, break immune tolerance and, in addition, alter the permeability of the blood-brain barrier (BBB). This way, toxins, inflammatory molecules and oxidative stress molecules can pass freely into the CNS and cause extensive damage to the brain. However, commensal bacteria, such as the Lactobacillus genus and Bacteroides fragilis, and their metabolites (with anti-inflammatory potential), produce neurotransmitters such as γ-aminobutyric acid, histamine, dopamine, norepinephrine, acetylcholine and serotonin, which are important for neurological regulation. In addition, reprogramming the gut microbiota of patients with MS with a healthy gut microbiota may help improve the integrity of the gut and BBB, by providing clinically protective anti-inflammatory effects and reducing the disease's degenerative progression. The present review provides valuable information about the relationship between gut microbiota and neuroinflammatory processes of the CNS. Most importantly, it highlights the importance of intestinal bacteria as an environmental factor that may mediate the clinical course of MS, or even predispose to the outbreak of this disease.
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Affiliation(s)
- María Eugenia Torres-Chávez
- Department of Microbiology and Pathology, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | - Nora Magdalena Torres-Carrillo
- Department of Microbiology and Pathology, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | - Ana Victoria Monreal-Lugo
- Department of Nutrition and Health Research Center, National Institute of Public Health, Cuernavaca, Morelos 62100, Mexico
- Department of Nutrition and Bioprogramming Coordination, Isidro Espinosa de los Reyes National Institute of Perinatology, Mexico City 11000, Mexico
| | - Sandra Garnés-Rancurello
- Department of Nutrition, Technological Institute of Higher Studies of Monterrey, Zapopan, Jalisco 45201, Mexico
| | | | - Itzae Adonai Gutiérrez-Hurtado
- Department of Molecular Biology and Genomics, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | - Jesús Raúl Beltrán-Ramírez
- Department of Information Systems, University Center of Administrative Economic Sciences, University of Guadalajara, Zapopan, Jalisco 45100, Mexico
| | - Elena Sandoval-Pinto
- Department of Cellular and Molecular Biology, University Center for Biological and Agricultural Sciences, University of Guadalajara, Zapopan, Jalisco 45200, Mexico
| | - Norma Torres-Carrillo
- Department of Microbiology and Pathology, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
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12
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Fu J, Hsiao T, Waffarn E, Meng W, Long KD, Frangaj K, Jones R, Gorur A, Shtewe A, Li M, Muntnich CB, Rogers K, Jiao W, Velasco M, Matsumoto R, Kubota M, Wells S, Danzl N, Ravella S, Iuga A, Vasilescu ER, Griesemer A, Weiner J, Farber DL, Luning Prak ET, Martinez M, Kato T, Hershberg U, Sykes M. Dynamic establishment and maintenance of the human intestinal B cell population and repertoire following transplantation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.15.23298517. [PMID: 38014202 PMCID: PMC10680888 DOI: 10.1101/2023.11.15.23298517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
It is unknown how intestinal B cell populations and B cell receptor (BCR) repertoires are established and maintained over time in humans. Following intestinal transplantation (ITx), surveillance ileal mucosal biopsies provide a unique opportunity to map the dynamic establishment of gut lymphocyte populations. Using polychromatic flow cytometry that includes HLA allele group-specific mAbs distinguishing donor from recipient cells along with high throughput BCR sequencing, we tracked the establishment of recipient B cell populations and BCR repertoire in the allograft mucosa of ITx recipients. We confirm the early presence of naïve donor B cells in the circulation and, for the first time, document the establishment of recipient B cell populations, including B resident memory cells, in the intestinal allograft mucosa. Recipient B cell repopulation of the allograft was most rapid in infant (<1 year old)-derived allografts and, unlike T cell repopulation, did not correlate with rejection rates. While recipient memory B cell populations were increased in graft mucosa compared to circulation, naïve recipient B cells remained detectable in the graft mucosa for years. Comparisons of peripheral and intra-mucosal B cell repertoires in the absence of rejection revealed increased BCR mutation rates and clonal expansion in graft mucosa compared to circulating B cells, but these parameters did not increase markedly after the first year post-transplant. Furthermore, clonal mixing between the allograft mucosa and the circulation was significantly greater in ITx recipients, even years after transplantation, than in healthy control adults. Collectively, our data demonstrate intestinal mucosal B cell repertoire establishment from a circulating pool, a process that continues for years without evidence of establishment of a stable mucosal B cell repertoire.
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Affiliation(s)
- Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Thomas Hsiao
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Elizabeth Waffarn
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine D Long
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Kristjana Frangaj
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Rebecca Jones
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Alaka Gorur
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Areen Shtewe
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Muyang Li
- Department of Pathology, Columbia University, New York, NY, USA
| | - Constanza Bay Muntnich
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Kortney Rogers
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Wenyu Jiao
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Monica Velasco
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Rei Matsumoto
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Masaru Kubota
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Steven Wells
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Nichole Danzl
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
| | - Shilpa Ravella
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Alina Iuga
- Department of Pathology, Columbia University, New York, NY, USA
| | | | - Adam Griesemer
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Joshua Weiner
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Donna L Farber
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Tomoaki Kato
- Department of Surgery, Columbia University, New York, NY, USA
| | - Uri Hershberg
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
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13
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Abdul-Kareem HH, Al-Maqtoofi MY, Burghal AA. Impact of COVID-19 vaccination on saliva immune barriers: IgA, lysozyme, and lactoferrin. Arch Virol 2023; 168:293. [PMID: 37973637 DOI: 10.1007/s00705-023-05914-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/19/2023]
Abstract
Understanding the role of salivary constituents, such as lactoferrin, lysozyme, and secretory immunoglobulin A (sIgA), in immune protection and defense mechanisms against microbial invasion and colonization of the airways is important in light of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. The salivary immune barrier in individuals affected by COVID-19 may contribute to disease prognosis. Thus, the aim of the present review is to evaluate the effect of COVID-19 vaccines on the immunological composition of saliva. IgA antibodies generated by vaccination can neutralize the virus at mucosal surfaces, whereas antimicrobial peptides, such as lysozyme and lactoferrin, have broad-spectrum antimicrobial activity. Collectively, these components contribute to the protective immune response of the oral cavity and may help minimize viral transmission as well as the severity of COVID-19. Measuring the levels of these components in the saliva of COVID-19-vaccinated individuals can help in evaluating the vaccine's ability to induce mucosal immunity, and it might also provide insights into whether saliva can be used in diagnostics or surveillance for monitoring immune responses following vaccination. This also has implications for viral transmission.
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Affiliation(s)
| | - Marwan Y Al-Maqtoofi
- Biology Department, College of Science University of Basrah, Basrah, 61001, Iraq.
| | - Ahmed A Burghal
- Biology Department, College of Science University of Basrah, Basrah, 61001, Iraq
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14
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Pichichero ME. Variability of vaccine responsiveness in early life. Cell Immunol 2023; 393-394:104777. [PMID: 37866234 DOI: 10.1016/j.cellimm.2023.104777] [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: 06/15/2023] [Revised: 09/18/2023] [Accepted: 10/14/2023] [Indexed: 10/24/2023]
Abstract
Vaccinations in early life elicit variable antibody and cellular immune responses, sometimes leaving fully vaccinated children unprotected against life-threatening infectious diseases. Specific immune cell populations and immune networks may have a critical period of development and calibration in a window of opportunity occurring during the first 100 days of early life. Among the early life determinants of vaccine responses, this review will focus on modifiable factors involving development of the infant microbiota and metabolome: antibiotic exposure, breast versus formula feeding, and Caesarian section versus vaginal delivery of newborns. How microbiota may serve as natural adjuvants for vaccine responses and how microbiota-derived metabolites influence vaccine responses are also reviewed. Early life poor vaccine responsiveness can be linked to increased infection susceptibility because both phenotypes share similar immunity dysregulation profiles. An early life pre-vaccination endotype, when interventions have the highest potential for success, should be sought that predicts vaccine response trajectories.
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Affiliation(s)
- Michael E Pichichero
- Center for Infectious Diseases and Immunology, Research Institute, Rochester General Hospital, 1425 Portland Ave, Rochester, NY 14621, USA.
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15
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Ciernikova S, Sevcikova A, Drgona L, Mego M. Modulating the gut microbiota by probiotics, prebiotics, postbiotics, and fecal microbiota transplantation: An emerging trend in cancer patient care. Biochim Biophys Acta Rev Cancer 2023; 1878:188990. [PMID: 37742728 DOI: 10.1016/j.bbcan.2023.188990] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
Treatment resistance, together with acute and late adverse effects, represents critical issues in the management of cancer patients. Promising results from preclinical and clinical research underline the emerging trend of a microbiome-based approach in oncology. Favorable bacterial species and higher gut diversity are associated with increased treatment efficacy, mainly in chemo- and immunotherapy. On the other hand, alterations in the composition and activity of gut microbial communities are linked to intestinal dysbiosis and contribute to high treatment-induced toxicity. In this Review, we provide an overview of studies concerning gut microbiota modulation in patients with solid and hematologic malignancies with a focus on probiotics, prebiotics, postbiotics, and fecal microbiota transplantation. Targeting the gut microbiome might bring clinical benefits and improve patient outcomes. However, a deeper understanding of mechanisms and large clinical trials concerning microbiome and immunological profiling is warranted to identify safe and effective ways to incorporate microbiota-based interventions in routine clinical practice.
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Affiliation(s)
- Sona Ciernikova
- Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Aneta Sevcikova
- Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lubos Drgona
- Department of Oncohematology, Comenius University and National Cancer Institute, Bratislava, Slovakia
| | - Michal Mego
- 2nd Department of Oncology, Comenius University and National Cancer Institute, Bratislava, Slovakia
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16
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Zhang S, Han Y, Schofield W, Nicosia M, Karell PE, Newhall KP, Zhou JY, Musich RJ, Pan S, Valujskikh A, Sangwan N, Dwidar M, Lu Q, Stappenbeck TS. Select symbionts drive high IgA levels in the mouse intestine. Cell Host Microbe 2023; 31:1620-1638.e7. [PMID: 37776865 DOI: 10.1016/j.chom.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/02/2023]
Abstract
Immunoglobulin A (IgA) is an important factor in maintaining homeostasis at mucosal surfaces, yet luminal IgA levels vary widely. Total IgA levels are thought to be driven by individual immune responses to specific microbes. Here, we found that the prebiotic, pectin oligosaccharide (pec-oligo), induced high IgA levels in the small intestine in a T cell-dependent manner. Surprisingly, this IgA-high phenotype was retained after cessation of pec-oligo treatment, and microbiome transmission either horizontally or vertically was sufficient to retain high IgA levels in the absence of pec-oligo. Interestingly, the bacterial taxa enriched in the overall pec-oligo bacterial community differed from IgA-coated microbes in this same community. Rather, a group of ethanol-resistant microbes, highly enriched for Lachnospiraceae bacterium A2, drove the IgA-high phenotype. These findings support a model of intestinal adaptive immunity in which a limited number of microbes can promote durable changes in IgA directed to many symbionts.
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Affiliation(s)
- Shanshan Zhang
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan 250000, P.R. China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yi Han
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Michael Nicosia
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul E Karell
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kevin P Newhall
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Julie Y Zhou
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan J Musich
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Anna Valujskikh
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mohammed Dwidar
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Qiuhe Lu
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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17
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Planchais C, Molinos-Albert LM, Rosenbaum P, Hieu T, Kanyavuz A, Clermont D, Prazuck T, Lefrou L, Dimitrov JD, Hüe S, Hocqueloux L, Mouquet H. HIV-1 treatment timing shapes the human intestinal memory B-cell repertoire to commensal bacteria. Nat Commun 2023; 14:6326. [PMID: 37816704 PMCID: PMC10564866 DOI: 10.1038/s41467-023-42027-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
HIV-1 infection causes severe alterations of gut mucosa, microbiota and immune system, which can be curbed by early antiretroviral therapy. Here, we investigate how treatment timing affects intestinal memory B-cell and plasmablast repertoires of HIV-1-infected humans. We show that only class-switched memory B cells markedly differ between subjects treated during the acute and chronic phases of infection. Intestinal memory B-cell monoclonal antibodies show more prevalent polyreactive and commensal bacteria-reactive clones in late- compared to early-treated individuals. Mirroring this, serum IgA polyreactivity and commensal-reactivity are strongly increased in late-treated individuals and correlate with intestinal permeability and systemic inflammatory markers. Polyreactive blood IgA memory B cells, many of which egressed from the gut, are also substantially enriched in late-treated individuals. Our data establish gut and systemic B-cell polyreactivity to commensal bacteria as hallmarks of chronic HIV-1 infection and suggest that initiating treatment early may limit intestinal B-cell abnormalities compromising HIV-1 humoral response.
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Affiliation(s)
- Cyril Planchais
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Luis M Molinos-Albert
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
- ISGlobal, Hospital Clínic-Universitat de Barcelona, 08036, Barcelona, Spain
| | - Pierre Rosenbaum
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Thierry Hieu
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France
| | - Alexia Kanyavuz
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006, Paris, France
| | - Dominique Clermont
- Collection of the Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Thierry Prazuck
- Service des Maladies Infectieuses et Tropicales, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Laurent Lefrou
- Service d'Hépato-Gastro-Entérologie, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006, Paris, France
| | - Sophie Hüe
- INSERM U955-Équipe 16, Université Paris-Est Créteil, Faculté de Médecine, 94000, Créteil, France
| | - Laurent Hocqueloux
- Service des Maladies Infectieuses et Tropicales, CHR d'Orléans-La Source, 45067, Orléans, France
| | - Hugo Mouquet
- Humoral Immunology Unit, Institut Pasteur, Université Paris Cité, INSERM U1222, F-75015, Paris, France.
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18
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Young GR, Nelson A, Stewart CJ, Smith DL. Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease. Curr Opin Microbiol 2023; 75:102379. [PMID: 37647765 DOI: 10.1016/j.mib.2023.102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023]
Abstract
Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.
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Affiliation(s)
- Gregory R Young
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | - Andrew Nelson
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | | | - Darren L Smith
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK.
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19
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Hissen KL, He W, Wu G, Criscitiello MF. Immunonutrition: facilitating mucosal immune response in teleost intestine with amino acids through oxidant-antioxidant balance. Front Immunol 2023; 14:1241615. [PMID: 37841275 PMCID: PMC10570457 DOI: 10.3389/fimmu.2023.1241615] [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: 06/19/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023] Open
Abstract
Comparative animal models generate fundamental scientific knowledge of immune responses. However, these studies typically are conducted in mammals because of their biochemical and physiological similarity to humans. Presently, there has been an interest in using teleost fish models to study intestinal immunology, particularly intestinal mucosa immune response. Instead of targeting the pathogen itself, a preferred approach for managing fish health is through nutrient supplementation, as it is noninvasive and less labor intensive than vaccine administrations while still modulating immune properties. Amino acids (AAs) regulate metabolic processes, oxidant-antioxidant balance, and physiological requirements to improve immune response. Thus, nutritionists can develop sustainable aquafeeds through AA supplementation to promote specific immune responses, including the intestinal mucosa immune system. We propose the use of dietary supplementation with functional AAs to improve immune response by discussing teleost fish immunology within the intestine and explore how oxidative burst is used as an immune defense mechanism. We evaluate immune components and immune responses in the intestine that use oxidant-antioxidant balance through potential selection of AAs and their metabolites to improve mucosal immune capacity and gut integrity. AAs are effective modulators of teleost gut immunity through oxidant-antioxidant balance. To incorporate nutrition as an immunoregulatory means in teleost, we must obtain more tools including genomic, proteomic, nutrition, immunology, and macrobiotic and metabonomic analyses, so that future studies can provide a more holistic understanding of the mucosal immune system in fish.
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Affiliation(s)
- Karina L. Hissen
- Comparative Immunogenetics Laboratory Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
| | - Wenliang He
- Amino Acid Laboratory, Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Guoyao Wu
- Amino Acid Laboratory, Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Michael F. Criscitiello
- Comparative Immunogenetics Laboratory Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, TX, United States
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20
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Pabst O, Nowosad CR. B cells and the intestinal microbiome in time, space and place. Semin Immunol 2023; 69:101806. [PMID: 37473559 DOI: 10.1016/j.smim.2023.101806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/08/2023] [Indexed: 07/22/2023]
Abstract
The gut immune system is shaped by the continuous interaction with the microbiota. Here we dissect temporal, spatial and contextual layers of gut B cell responses. The microbiota impacts on the selection of the developing pool of pre-immune B cells that serves as substrate for B cell activation, expansion and differentiation. However, various aspects of the gut B cell response display unique features. In particular, occurrence of somatically mutated B cells, chronic gut germinal centers in T cell-deficient settings and polyreactive binding of gut IgA to the microbiota questioned the nature and microbiota-specificity of gut germinal centers. We propose a model to reconcile these observations incorporating recent work demonstrating microbiota-specificity of gut germinal centers. We speculate that adjuvant effects of the microbiota might modify permissiveness for B cell to enter and exit gut germinal centers. We propose that separating aspects of time, space and place facilitate the occasionally puzzling discussion of gut B cell responses to the microbiota.
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Affiliation(s)
- Oliver Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany.
| | - Carla R Nowosad
- Department of Pathology, NYU Grossman School of Medicine, New York University, New York, USA; Translational Immunology Center, NYU Grossman School of Medicine, New York University, New York, USA.
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21
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Zhang Y, Shen J, Cheng W, Roy B, Zhao R, Chai T, Sheng Y, Zhang Z, Chen X, Liang W, Hu W, Liao Q, Pan S, Zhuang W, Zhang Y, Chen R, Mei J, Wei H, Fang X. Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seq. J Genet Genomics 2023; 50:688-701. [PMID: 37156441 DOI: 10.1016/j.jgg.2023.04.012] [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: 01/12/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Gut microbes exhibit complex interactions with their hosts and shape an organism's immune system throughout its lifespan. As the largest secondary lymphoid organ, the spleen has a wide range of immunological functions. To explore the role of microbiota in regulating and shaping the spleen, we employ scRNA-seq and Stereo-seq technologies based on germ-free (GF) mice to detect differences in tissue size, anatomical structure, cell types, functions, and spatial molecular characteristics. We identify 18 cell types, 9 subtypes of T cells, and 7 subtypes of B cells. Gene differential expression analysis reveals that the absence of microorganisms results in alterations in erythropoiesis within the red pulp region and congenital immune deficiency in the white pulp region. Stereo-seq results demonstrate a clear hierarchy of immune cells in the spleen, including marginal zone (MZ) macrophages, MZ B cells, follicular B cells and T cells, distributed in a well-defined pattern from outside to inside. However, this hierarchical structure is disturbed in GF mice. Ccr7 and Cxcl13 chemokines are specifically expressed in the spatial locations of T cells and B cells, respectively. We speculate that the microbiota may mediate the structural composition or partitioning of spleen immune cells by modulating the expression levels of chemokines.
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Affiliation(s)
- Yin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Juan Shen
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Wei Cheng
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bhaskar Roy
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Ruizhen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Tailiang Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yifei Sheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Zhao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xueting Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Weining Hu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qijun Liao
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Wen Zhuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yangrui Zhang
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Rouxi Chen
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Xiaodong Fang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China.
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22
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Peppas I, Ford AM, Furness CL, Greaves MF. Gut microbiome immaturity and childhood acute lymphoblastic leukaemia. Nat Rev Cancer 2023; 23:565-576. [PMID: 37280427 PMCID: PMC10243253 DOI: 10.1038/s41568-023-00584-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 06/08/2023]
Abstract
Acute lymphoblastic leukaemia (ALL) is the most common cancer of childhood. Here, we map emerging evidence suggesting that children with ALL at the time of diagnosis may have a delayed maturation of the gut microbiome compared with healthy children. This finding may be associated with early-life epidemiological factors previously identified as risk indicators for childhood ALL, including caesarean section birth, diminished breast feeding and paucity of social contacts. The consistently observed deficiency in short-chain fatty-acid-producing bacterial taxa in children with ALL has the potential to promote dysregulated immune responses and to, ultimately, increase the risk of transformation of preleukaemic clones in response to common infectious triggers. These data endorse the concept that a microbiome deficit in early life may contribute to the development of the major subtypes of childhood ALL and encourage the notion of risk-reducing microbiome-targeted intervention in the future.
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Affiliation(s)
- Ioannis Peppas
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Paediatric Oncology, The Royal Marsden Hospital Sutton, Surrey, UK
| | - Anthony M Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Caroline L Furness
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Paediatric Oncology, The Royal Marsden Hospital Sutton, Surrey, UK
| | - Mel F Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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23
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Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity 2023; 56:1393-1409.e6. [PMID: 37164015 DOI: 10.1016/j.immuni.2023.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/14/2023] [Indexed: 05/12/2023]
Abstract
Inflammatory bowel diseases (IBDs), e.g., Crohn's disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. Using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq), we identified antibodies against 344,000 antimicrobial, immune, and food antigens in 497 individuals with IBD compared with 1,326 controls. IBD was characterized by 373 differentially abundant antibody responses (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD, and 28% unique to UC. Antibody reactivities against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease, and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (area under the curve [AUC] = 0.89), and similar discrimination was achieved when using only ten antibodies (AUC = 0.87). Individuals with IBD thus show a distinct antibody repertoire against selected peptides, allowing clinical stratification and discovery of immunological targets.
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Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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24
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Kawamoto S, Uemura K, Hori N, Takayasu L, Konishi Y, Katoh K, Matsumoto T, Suzuki M, Sakai Y, Matsudaira T, Adachi T, Ohtani N, Standley DM, Suda W, Fukuda S, Hara E. Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota. Nat Cell Biol 2023; 25:865-876. [PMID: 37169880 DOI: 10.1038/s41556-023-01145-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
The elucidation of the mechanisms of ageing and the identification of methods to control it have long been anticipated. Recently, two factors associated with ageing-the accumulation of senescent cells and the change in the composition of gut microbiota-have been shown to play key roles in ageing. However, little is known about how these phenomena occur and are related during ageing. Here we show that the persistent presence of commensal bacteria gradually induces cellular senescence in gut germinal centre B cells. Importantly, this reduces both the production and diversity of immunoglobulin A (IgA) antibodies that target gut bacteria, thereby changing the composition of gut microbiota in aged mice. These results have revealed the existence of IgA-mediated crosstalk between the gut microbiota and cellular senescence and thus extend our understanding of the mechanism of gut microbiota changes with age, opening up possibilities for their control.
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Affiliation(s)
- Shimpei Kawamoto
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
| | - Ken Uemura
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Nozomi Hori
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Lena Takayasu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Konishi
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Tomonori Matsumoto
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Masae Suzuki
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yusuke Sakai
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Tatsuyuki Matsudaira
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Takahiro Adachi
- Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Naoko Ohtani
- Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Daron M Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Eiji Hara
- Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
- Immunology Frontier Research Center, Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan.
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25
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Conrey PE, Denu L, O'Boyle KC, Rozich I, Green J, Maslanka J, Lubin JB, Duranova T, Haltzman BL, Gianchetti L, Oldridge DA, De Luna N, Vella LA, Allman D, Spergel JM, Tanes C, Bittinger K, Henrickson SE, Silverman MA. IgA deficiency destabilizes homeostasis toward intestinal microbes and increases systemic immune dysregulation. Sci Immunol 2023; 8:eade2335. [PMID: 37235682 DOI: 10.1126/sciimmunol.ade2335] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
The ability of most patients with selective immunoglobulin A (IgA) deficiency (SIgAD) to remain apparently healthy has been a persistent clinical conundrum. Compensatory mechanisms, including IgM, have been proposed, yet it remains unclear how secretory IgA and IgM work together in the mucosal system and, on a larger scale, whether the systemic and mucosal anti-commensal responses are redundant or have unique features. To address this gap in knowledge, we developed an integrated host-commensal approach combining microbial flow cytometry and metagenomic sequencing (mFLOW-Seq) to comprehensively define which microbes induce mucosal and systemic antibodies. We coupled this approach with high-dimensional immune profiling to study a cohort of pediatric patients with SIgAD and household control siblings. We found that mucosal and systemic antibody networks cooperate to maintain homeostasis by targeting a common subset of commensal microbes. In IgA-deficiency, we find increased translocation of specific bacterial taxa associated with elevated levels of systemic IgG targeting fecal microbiota. Associated features of immune system dysregulation in IgA-deficient mice and humans included elevated levels of inflammatory cytokines, enhanced follicular CD4 T helper cell frequency and activation, and an altered CD8 T cell activation state. Although SIgAD is clinically defined by the absence of serum IgA, the symptomatology and immune dysregulation were concentrated in the SIgAD participants who were also fecal IgA deficient. These findings reveal that mucosal IgA deficiency leads to aberrant systemic exposures and immune responses to commensal microbes, which increase the likelihood of humoral and cellular immune dysregulation and symptomatic disease in patients with IgA deficiency.
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Affiliation(s)
- Peyton E Conrey
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lidiya Denu
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kaitlin C O'Boyle
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Isaiah Rozich
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamal Green
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeffrey Maslanka
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jean-Bernard Lubin
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Tereza Duranova
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Lauren Gianchetti
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Derek A Oldridge
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nina De Luna
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura A Vella
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan M Spergel
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyle Bittinger
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah E Henrickson
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A Silverman
- Division of Infectious Disease, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology and Immune Health (I3H), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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26
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Shen K, Din AU, Sinha B, Zhou Y, Qian F, Shen B. Translational informatics for human microbiota: data resources, models and applications. Brief Bioinform 2023; 24:7152256. [PMID: 37141135 DOI: 10.1093/bib/bbad168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.
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Affiliation(s)
- Ke Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Ahmad Ud Din
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Baivab Sinha
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Yi Zhou
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
| | - Fuliang Qian
- Center for Systems Biology, Suzhou Medical College of Soochow University, Suzhou 215123, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China
| | - Bairong Shen
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610212, China
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27
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Oh S, Seo H. Dietary intervention with functional foods modulating gut microbiota for improving the efficacy of COVID-19 vaccines. Heliyon 2023; 9:e15668. [PMID: 37124341 PMCID: PMC10121067 DOI: 10.1016/j.heliyon.2023.e15668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023] Open
Abstract
Dysbiosis of the gut microbiota with aging contributes to a reduction in important cross-feeding bacterial reactions in the gut and immunosenescence, which could contribute to a decrease in vaccine efficacy. Fever, cough, and fatigue are the main signs of coronavirus disease 2019 (COVID-19); however, some patients with COVID-19 present with gastrointestinal symptoms. COVID-19 vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the best measures to reduce SARS-CoV-2 infection rates and the severity of COVID-19. The immunogenicity of COVID-19 vaccines is influenced by the composition of the gut microbiota, and the immune response to COVID-19 vaccines decreases with age. In this review, we discuss gut microbiota dysbiosis and immunosenescence in the older adults, the role of gut microbiota in improving the efficacy of COVID-19 vaccines, and dietary interventions to improve the efficacy of COVID-19 vaccines in the older adults.
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Affiliation(s)
- Soyoung Oh
- Infectious Disease Research Center, Citizen's Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul, 04524, Republic of Korea
| | - Haesook Seo
- Infectious Disease Research Center, Citizen's Health Bureau, Seoul Metropolitan Government, 110, Sejong-daero, Jung-gu, Seoul, 04524, Republic of Korea
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28
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Doron I, Kusakabe T, Iliev ID. Immunoglobulins at the interface of the gut mycobiota and anti-fungal immunity. Semin Immunol 2023; 67:101757. [PMID: 37003056 PMCID: PMC10192079 DOI: 10.1016/j.smim.2023.101757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The dynamic and complex community of microbes that colonizes the intestines is composed of bacteria, fungi, and viruses. At the mucosal surfaces, immunoglobulins play a key role in protection against bacterial and fungal pathogens, and their toxins. Secretory immunoglobulin A (sIgA) is the most abundantly produced antibody at the mucosal surfaces, while Immunoglobulin G (IgG) isotypes play a critical role in systemic protection. IgA and IgG antibodies with reactivity to commensal fungi play an important role in shaping the mycobiota and host antifungal immunity. In this article, we review the latest evidence that establishes a connection between commensal fungi and B cell-mediated antifungal immunity as an additional layer of protection against fungal infections and inflammation.
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Affiliation(s)
- Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Takato Kusakabe
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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29
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Evaluation and deployment of isotype-specific salivary antibody assays for detecting previous SARS-CoV-2 infection in children and adults. COMMUNICATIONS MEDICINE 2023; 3:37. [PMID: 36922542 PMCID: PMC10016188 DOI: 10.1038/s43856-023-00264-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 02/17/2023] [Indexed: 03/17/2023] Open
Abstract
BACKGROUND Saliva is easily obtainable non-invasively and potentially suitable for detecting both current and previous SARS-CoV-2 infection, but there is limited evidence on the utility of salivary antibody testing for community surveillance. METHODS We established 6 ELISAs detecting IgA and IgG antibodies to whole SARS-CoV-2 spike protein, to its receptor binding domain region and to nucleocapsid protein in saliva. We evaluated diagnostic performance, and using paired saliva and serum samples, correlated mucosal and systemic antibody responses. The best-performing assays were field-tested in 20 household outbreaks. RESULTS We demonstrate in test accuracy (N = 320), spike IgG (ROC AUC: 95.0%, 92.8-97.3%) and spike IgA (ROC AUC: 89.9%, 86.5-93.2%) assays to discriminate best between pre-pandemic and post COVID-19 saliva samples. Specificity was 100% in younger age groups (0-19 years) for spike IgA and IgG. However, sensitivity was low for the best-performing assay (spike IgG: 50.6%, 39.8-61.4%). Using machine learning, diagnostic performance was improved when a combination of tests was used. As expected, salivary IgA was poorly correlated with serum, indicating an oral mucosal response whereas salivary IgG responses were predictive of those in serum. When deployed to household outbreaks, antibody responses were heterogeneous but remained a reliable indicator of recent infection. Intriguingly, unvaccinated children without confirmed infection showed evidence of exposure almost exclusively through specific IgA responses. CONCLUSIONS Through robust standardisation, evaluation and field-testing, this work provides a platform for further studies investigating SARS-CoV-2 transmission and mucosal immunity with the potential for expanding salivo-surveillance to other respiratory infections in hard-to-reach settings.
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30
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Sarden N, Yipp BG. Virus-associated fungal infections and lost immune resistance. Trends Immunol 2023; 44:305-318. [PMID: 36890064 DOI: 10.1016/j.it.2023.02.004] [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: 01/24/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/08/2023]
Abstract
Invasive fungal infections are an increasing threat to human health. Of recent concern is the emergence of influenza- or SARS-CoV-2-virus-associated invasive fungal infections. Understanding acquired susceptibilities to fungi requires consideration of the collective and newly explored roles of adaptive, innate, and natural immunity. Neutrophils are known to provide host resistance, but new concepts are emerging that implicate innate antibodies, the actions of specialized B1 B cell subsets, and B cell-neutrophil crosstalk in mediating antifungal host resistance. Based on emerging evidence, we propose that virus infections impact on neutrophil and innate B cell resistance against fungi, leading to invasive infections. These concepts provide novel approaches to developing candidate therapeutics with the aim of restoring natural and humoral immunity and boosting neutrophil resistance against fungi.
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Affiliation(s)
- Nicole Sarden
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bryan G Yipp
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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31
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Immunity orchestrates a bridge in gut-brain axis of neurodegenerative diseases. Ageing Res Rev 2023; 85:101857. [PMID: 36669690 DOI: 10.1016/j.arr.2023.101857] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
Neurodegenerative diseases, in particular for Alzheimer's disease (AD), Parkinson's disease (PD) and Multiple sclerosis (MS), are a category of diseases with progressive loss of neuronal structure or function (encompassing neuronal death) leading to neuronal dysfunction, whereas the underlying pathogenesis remains to be clarified. As the microbiological ecosystem of the intestinal microbiome serves as the second genome of the human body, it is strongly implicated as an essential element in the initiation and/or progression of neurodegenerative diseases. Nevertheless, the precise underlying principles of how the intestinal microflora impact on neurodegenerative diseases via gut-brain axis by modulating the immune function are still poorly characterized. Consequently, an overview of initiating the development of neurodegenerative diseases and the contribution of intestinal microflora on immune function is discussed in this review.
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32
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Sollid LM, Iversen R. Tango of B cells with T cells in the making of secretory antibodies to gut bacteria. Nat Rev Gastroenterol Hepatol 2023; 20:120-128. [PMID: 36056203 DOI: 10.1038/s41575-022-00674-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 02/03/2023]
Abstract
Polymeric IgA and IgM are transported across the epithelial barrier from plasma cells in the lamina propria to exert a function in the gut lumen as secretory antibodies. Many secretory antibodies are reactive with the gut bacteria, and mounting evidence suggests that these antibodies are important for the host to control gut bacterial communities. However, we have incomplete knowledge of how bacteria-reactive secretory antibodies are formed. Antibodies from gut plasma cells often show bacterial cross-species reactivity, putting the degree of specificity behind anti-bacterial antibody responses into question. Such cross-species reactive antibodies frequently recognize non-genome-encoded membrane glycan structures. On the other hand, the T cell epitopes are peptides encoded in the bacterial genomes, thereby allowing a higher degree of predictable specificity on the T cell side of anti-bacterial immune responses. In this Perspective, we argue that the production of bacteria-reactive secretory antibodies is mainly controlled by the antigen specificity of T cells, which provide help to B cells. To be able to harness this system (for instance, for manipulation with vaccines), we need to obtain insight into the bacterial epitopes recognized by T cells in addition to characterizing the reactivity of the antibodies.
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Affiliation(s)
- Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway. .,Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
| | - Rasmus Iversen
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway. .,Department of Immunology, Oslo University Hospital - Rikshospitalet, Oslo, Norway.
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Galán-Ortíz JR, Andino del Valle KA, Pérez-Rosario AA, Castañón Pereira DL, Díaz-Rivera J, Merheb-Finianos PA, Dorta-Estremera SM. B cells as modulators of HPV+ oropharyngeal cancer in a preclinical model. Front Oncol 2023; 13:1145724. [PMID: 37035195 PMCID: PMC10076859 DOI: 10.3389/fonc.2023.1145724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/28/2023] [Indexed: 04/11/2023] Open
Abstract
Among the different immune cells present within tumors, B cells also infiltrate human papillomavirus-positive (HPV+) oropharyngeal tumors. However, the role of B cells during programmed death-1 (PD-1) blockade in HPV+ oropharyngeal cancer needs to be better defined. By using the preclinical mouse model for HPV+ oropharyngeal cancer (named mEER), we characterized B cells within tumors and determined their functional role in vivo during PD-1 blockade. We determined that treatment naïve tongue-implanted tumors, which we have previously demonstrated to be sensitive to PD-1 blockade, contained high infiltration of CD8+ T cells and low infiltration of B cells whereas flank-implanted tumors, which are resistant to PD-1 blockade, contain a higher frequency of B cells compared to T cells. Moreover, B cell-deficient mice (µMt) and B cell-depleted mice showed a slower tumor growth rate compared to wild-type (WT) mice, and B cell deficiency increased CD8+ T cell infiltration in tumors. When we compared tongue tumor-bearing mice treated with anti-PD-1, we observed that tumors that responded to the therapy contained more T cells and B cells than the ones that did not respond. However, µMt mice treated with PD-1 blockade showed similar tumor growth rates to WT mice. Our data suggest that in untreated mice, B cells have a more pro-tumorigenic phenotype potentially affecting T cell infiltration in the tumors. In contrast, B cells are dispensable for PD-1 blockade efficacy. Mechanistic studies are needed to identify novel targets to promote the anti-tumorigenic function and/or suppress the immunosuppressive function of B cells in HPV+ oropharyngeal cancer.
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Affiliation(s)
- Jorge R. Galán-Ortíz
- Cancer Biology Division, Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Kamila A. Andino del Valle
- Microbiology and Medical Zoology Department, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | | | | | - Jennifer Díaz-Rivera
- Microbiology and Medical Zoology Department, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | | | - Stephanie M. Dorta-Estremera
- Cancer Biology Division, Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
- Microbiology and Medical Zoology Department, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
- *Correspondence: Stephanie M. Dorta-Estremera,
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Sayin I, Chong AS. Beyond Adaptive Alloreactivity: Contribution of Innate B Cells to Allograft Inflammation and Rejection. Transplantation 2023; 107:98-104. [PMID: 36404414 PMCID: PMC9772142 DOI: 10.1097/tp.0000000000004377] [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] [Indexed: 11/22/2022]
Abstract
Innate B cells are a heterogeneous group of cells that function in maintaining homeostatic levels of circulating natural antibodies and being the first line of defense against infections. Innate B-1 cells and marginal zone B cells may relocate to lymphoid follicles and differentiate into cytokine and antibody-secreting cells in T-independent and T-dependent manners. Although marginal zone B cells are widely described in humans, the presence of B-1 cells is more controversial. Here, we review the basic features of the innate B-cell subsets identified in mice and their equivalent in humans, as well as their potential roles in transplantation. We summarize the findings of Cascalho and colleagues on the unexpected protective role of tumor necrosis factor receptor superfamily member 13B in regulating circulating levels of protective natural immunoglobulin M, and the studies by Zorn and colleagues on the potential pathogenic role for polyreactive innate B cells infiltrating allograft explants. Finally, we discuss our studies that took a transcriptomic approach to identify innate B cells infiltrating kidney allografts with antibody-mediated rejection and to demonstrate that local antigens within the allograft together with inflammation may induce a loss of B-cell tolerance.
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Affiliation(s)
- Ismail Sayin
- Department of Surgery, The University of Chicago, Chicago, Illinois, United States
| | - Anita S. Chong
- Department of Surgery, The University of Chicago, Chicago, Illinois, United States
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Strachan E, Clemente-Casares X, Tsai S. Maternal provisions in type 1 diabetes: Evidence for both protective & pathogenic potential. Front Immunol 2023; 14:1146082. [PMID: 37033940 PMCID: PMC10073710 DOI: 10.3389/fimmu.2023.1146082] [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: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Maternal influences on the immune health and development of an infant begin in utero and continue well into the postnatal period, shaping and educating the child's maturing immune system. Two maternal provisions include early microbial colonizers to initiate microbiota establishment and the transfer of antibodies from mother to baby. Maternal antibodies are a result of a lifetime of antigenic experience, reflecting the infection history, health and environmental exposure of the mother. These same factors are strong influencers of the microbiota, inexorably linking the two. Together, these provisions help to educate the developing neonatal immune system and shape lymphocyte repertoires, establishing a role for external environmental influences even before birth. In the context of autoimmunity, the transfer of maternal autoantibodies has the potential to be harmful for the child, sometimes targeting tissues and cells with devastating consequences. Curiously, this does not seem to apply to maternal autoantibody transfer in type 1 diabetes (T1D). Moreover, despite the rising prevalence of the disease, little research has been conducted on the effects of maternal dysbiosis or antibody transfer from an affected mother to her offspring and thus their relevance to disease development in the offspring remains unclear. This review seeks to provide a thorough evaluation of the role of maternal microorganisms and antibodies within the context of T1D, exploring both their pathogenic and protective potential. Although a definitive understanding of their significance in infant T1D development remains elusive at present, we endeavor to present what has been learned with the goal of spurring further interest in this important and intriguing question.
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36
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Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 2023; 613:639-649. [PMID: 36697862 DOI: 10.1038/s41586-022-05546-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2022] [Indexed: 01/26/2023]
Abstract
Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.
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Affiliation(s)
- Katherine M Kennedy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Marcus C de Goffau
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Wellcome Sanger Institute, Cambridge, UK
| | - Maria Elisa Perez-Muñoz
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marie-Claire Arrieta
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thorsten Braun
- Department of Obstetrics and Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frederic D Bushman
- Department of Microbiology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joel Dore
- Université Paris-Saclay, INRAE, MetaGenoPolis, AgroParisTech, MICALIS, Jouy-en-Josas, France
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA
- UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephanie C Ganal-Vonarburg
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michael G Gänzle
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, MA, USA
- Department of Medicine and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL-Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Curtis Huttenhower
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liza Konnikova
- Departments of Pediatrics and Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrew J Macpherson
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ruth C Massey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover Braunschweig site, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Trevor D Lawley
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jeroen Raes
- VIB Center for Microbiology, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eran Segal
- Weizmann Institute of Science, Rehovot, Israel
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Deborah M Sloboda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, Ontario, Canada
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Harry Sokol
- Gastroenterology Department, AP-HP, Saint Antoine Hospital, Centre de Recherche Saint-Antoine, CRSA, INSERM and Sorbonne Université, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Moran Yassour
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jens Walter
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
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Strugnell RA. When secretion turns into excretion - the different roles of IgA. Front Immunol 2022; 13:1076312. [PMID: 36618388 PMCID: PMC9812643 DOI: 10.3389/fimmu.2022.1076312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
IgA deficiency is the commonest immunodeficiency affecting up to 1 in 700 individuals. The effects of IgA deficiency are difficult to see in many individuals, are mild in many fewer and severe in fewer still. While monovalent IgA is found in serum, dimeric IgA is secreted through mucosal surfaces where it helps to maintain epithelial homeostasis. Studies with knockout mice have taught us that there are subtle inflammatory consequences of removing secretory IgA (sIgA), and the best explanation for these changes can be related by the loss of the 'excretory' immune system. The excretion of antigens is a logical process in regulating the immune system, given the long half-life of complement fixing antibodies. But the function of IgA as an immune or inflammation regulator may go beyond antigen removal.
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Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals. Immunity 2022; 55:2454-2469.e6. [PMID: 36473469 DOI: 10.1016/j.immuni.2022.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/01/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
Although food-directed immunoglobulin E (IgE) has been studied in the context of allergies, the prevalence and magnitude of IgG responses against dietary antigens are incompletely characterized in the general population. Here, we measured IgG binding against food and environmental antigens obtained from allergen databases and the immune epitope database (IEDB), represented in a phage displayed library of 58,233 peptides. By profiling blood samples of a large cohort representing the average adult Israeli population (n = 1,003), we showed that many food antigens elicited systemic IgG in up to 50% of individuals. Dietary intake of specific food protein correlated with antibody binding, suggesting that diet can shape the IgG epitope repertoire. Our work documents abundant systemic IgG responses against food antigens and provides a reference map of the exact immunogenic epitopes on a population scale, laying the foundation to unravel the role of food- and environmental antigen-directed antibody binding in disease contexts.
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Immunopathophysiology of human sepsis. EBioMedicine 2022; 86:104363. [PMID: 36470832 PMCID: PMC9783164 DOI: 10.1016/j.ebiom.2022.104363] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/11/2022] [Accepted: 10/27/2022] [Indexed: 12/04/2022] Open
Abstract
Sepsis is an ill-defined syndrome yet is a leading cause of morbidity and mortality worldwide. The most recent consensus defines sepsis as life-threatening organ dysfunction caused by a dysregulated host response to infection. However, this definition belies the complexity and breadth of immune mechanisms involved in sepsis, which are characterized by simultaneous hyperinflammation and immune suppression. In this review, we describe the immunopathogenesis of sepsis and highlight some recent pathophysiological findings that have expanded our understanding of sepsis. Sepsis endotypes can be used to divide sepsis patients in different groups with distinct immune profiles and outcomes. We also summarize evidence on the role of the gut microbiome in sepsis immunity. The challenge of the coming years will be to translate our increasing knowledge about the molecular mechanisms underlying sepsis into therapies that improve relevant patient outcomes.
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40
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Mode of delivery modulates the intestinal microbiota and impacts the response to vaccination. Nat Commun 2022; 13:6638. [PMID: 36380002 PMCID: PMC9666625 DOI: 10.1038/s41467-022-34155-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The gut microbiota in early life, when critical immune maturation takes place, may influence the immunogenicity of childhood vaccinations. Here we assess the association between mode of delivery, gut microbiota development in the first year of life, and mucosal antigen-specific antibody responses against pneumococcal vaccination in 101 infants at age 12 months and against meningococcal vaccination in 66 infants at age 18 months. Birth by vaginal delivery is associated with higher antibody responses against both vaccines. Relative abundances of vaginal birth-associated Bifidobacterium and Escherichia coli in the first weeks of life are positively associated with anti-pneumococcal antibody responses, and relative abundance of E. coli in the same period is also positively associated with anti-meningococcal antibody responses. In this study, we show that mode of delivery-induced microbiota profiles of the gut are associated with subsequent antibody responses to routine childhood vaccines.
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GABA signaling enforces intestinal germinal center B cell differentiation. Proc Natl Acad Sci U S A 2022; 119:e2215921119. [PMID: 36279432 PMCID: PMC9636909 DOI: 10.1073/pnas.2215921119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent compelling results indicate possible links between neurotransmitters, intestinal mucosal IgA
+
B cell responses, and immunoglobulin A nephropathy (IgAN) pathogenesis. Here, we demonstrated that γ-amino butyric acid (GABA) transporter-2 (GAT-2) deficiency induces intestinal germinal center (GC) B cell differentiation and worsens the symptoms of IgAN in a mouse model. Mechanistically, GAT-2 deficiency enhances GC B cell differentiation through activation of GABA–mammalian target of rapamycin complex 1 (mTORC1) signaling. In addition, IgAN patients have lower GAT-2 expression but higher activation of mTORC1 in blood B cells, and both are correlated with kidney function in IgAN patients. Collectively, this study describes GABA signaling–mediated intestinal mucosal immunity as a previously unstudied pathogenesis mechanism of IgAN and challenges the current paradigms of IgAN.
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Zhang Y, Zhao J, Qin Y, Wang Y, Yu Z, Ning X, Sun S. Specific alterations of gut microbiota in patients with membranous nephropathy: A systematic review and meta-analysis. Front Physiol 2022; 13:909491. [PMID: 36388089 PMCID: PMC9664147 DOI: 10.3389/fphys.2022.909491] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/03/2022] [Indexed: 02/12/2024] Open
Abstract
Background: The pathogenesis of idiopathic membranous nephropathy (IMN) has not yet been thoroughly clarified, and gut dysbiosis may be a contributor to IMN. However, the characterization of gut microbiota in patients with IMN remains uncertain. Methods: Cochrane Library, PubMed, China National Knowledge Internet, Web of Science, and Embase were used to search for studies through 18 May 2022. A meta-analysis based on the standardized mean difference (SMD) with 95% confidence interval (CI) was conducted on the alpha diversity index. The between-group comparison of the relative abundance of gut microbiota taxa and the beta diversity were extracted and qualitatively analyzed. Results: Five studies were included involving 290 patients with IMN, 100 healthy controls (HCs), and 129 patients with diabetic kidney disease (DKD). The quantitative combination of alpha diversity indices indicated that although bacterial richness was impaired [ACE, SMD = 0.12, (-0.28, 0.52), p = 0.55, I 2 = 0%; Chao1, SMD = -0.34, (-0.62, -0.06), p < 0.05, I 2 = 36%], overall diversity was preserved [Shannon, SMD = -0.16, (-0.64, 0.31), p = 0.50, I 2 = 53%; Simpson, SMD = 0.27, (-0.08, 0.61), p = 0.13, I 2 = 0%]. The beta diversity was significantly varied compared to HCs or DKD patients. Compared to HCs, the abundance of Proteobacteria increased, while that of Firmicutes decreased at the phylum level. Furthermore, the abundance of Lachnospira were depleted, while those of Streptococcus were enriched at the genus level. Proteobacteria and Streptococcus were also increased compared to DKD patients. Conclusions: The expansion of Proteobacteria and depletion of Lachnospira may be critical features of the altered gut microbiota in patients with IMN. This condition may play an important role in the pathogenesis of IMN and could provide bacterial targets for diagnosis and therapy.
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Affiliation(s)
- Yumeng Zhang
- Department of Postgraduate Student, Xi’an Medical University, Xi’an, China
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jin Zhao
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yunlong Qin
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
- Department of Nephrology, 980th Hospital of People’s Liberation Army Joint Logistic Support Force (Bethune International Peace Hospital), Shijiazhuang, Hebei, China
| | - Yuwei Wang
- Department of Postgraduate Student, Xi’an Medical University, Xi’an, China
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Zixian Yu
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaoxuan Ning
- Department of Geriatric, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Shiren Sun
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
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Ng KW, Hobbs A, Wichmann C, Victora GD, Donaldson GP. B cell responses to the gut microbiota. Adv Immunol 2022; 155:95-131. [PMID: 36357013 DOI: 10.1016/bs.ai.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Most antibody produced by humans originates from mucosal B cell responses. The rules, mechanisms, and outcomes of this process are distinct from B cell responses to infection. Within the context of the intestine, we discuss the induction of follicular B cell responses by microbiota, the development and maintenance of mucosal antibody-secreting cells, and the unusual impacts of mucosal antibody on commensal bacteria. Much remains to be learned about the interplay between B cells and the microbiota, but past and present work hints at a complex, nuanced relationship that may be critical to the way the mammalian gut fosters a beneficial microbial ecosystem.
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Affiliation(s)
- Kevin W Ng
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States
| | - Alvaro Hobbs
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States
| | - Christopher Wichmann
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States; Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, United States; Immune Regulation Group, Department of Pediatrics, University Medical Center Rostock, Rostock, Germany
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, United States.
| | - Gregory P Donaldson
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, United States.
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44
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Prakash PK, Lakshmi A J. Effect of milk protein hydrolysate supplementation on protein energy malnutrition-induced gut dysbiosis. Food Funct 2022; 13:10305-10319. [PMID: 36125286 DOI: 10.1039/d2fo00714b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dairy proteins in the diet are beneficial for the growth of probiotics; however, what is unknown is the gut-mediated immune responses under protein energy malnutrition (PEM) and if dairy protein hydrolysates can be effective as dietary interventions. This study compares the composition of the gut microbiota of rats with moderate protein deficiency (M.PEM) and severe protein deficiency (S.PEM) induced by feeding 5% and 1% hypoprotein diets, followed by replenishment with buffalo and whey protein hydrolysates. Fecal samples were collected, and the composition of the gut bacteria was analyzed by whole genome sequencing using long-read sequencing. Gene expression studies of the immunomodulatory cytokines involved and quantification of sIgA were carried out. IL-6 and IFN-γ were downregulated by about 0.17 ± 0.06 and 0.12 ± 0.10 fold when supplemented with whey protein hydrolysate in SP-RWC rats and by about 0.02 ± 0.06 and 0.35 ± 0.12 fold when using buffalo milk hydrolysate. The percentage of Firmicutes decreased in M.PEM and S.PEM rats (33.57%, 28.83 versus 47.73% of control at 3 weeks) but increased upon protein replenishment for all three protein sources at the end of nine weeks. The percentage of Bacteroidetes increased to 31.03% in S.PEM-induced rats as against 28.17% in control rats. The relative abundance of Lactobacillus sp. decreased in M.PEM and S.PEM rats while it showed the opposite effect upon protein replenishment. Gut microbiota modulated the pathogenesis of PEM differentially based on protein intervention along with a significant increase in the relative abundance of the keystone Lactobacillus genus.
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Affiliation(s)
- Pavan Kumar Prakash
- Protein Chemistry and Technology Department, CSIR-Central Food Technological Research Institute, Mysore-570020, India. .,Department of Bioscience, Mangalore University, Mangalagangotri, Mangaluru, India
| | - Jyothi Lakshmi A
- Protein Chemistry and Technology Department, CSIR-Central Food Technological Research Institute, Mysore-570020, India.
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45
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Cerutti A, Filipska M, Fa XM, Tachó-Piñot R. Impact of the mucosal milieu on antibody responses to allergens. J Allergy Clin Immunol 2022; 150:503-512. [PMID: 36075636 DOI: 10.1016/j.jaci.2022.07.007] [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: 06/02/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
Abstract
Respiratory and digestive mucosal surfaces are continually exposed to common environmental antigens, which include potential allergens. Although innocuous in healthy individuals, allergens cause allergy in predisposed subjects and do so by triggering a pathologic TH2 cell response that induces IgE class switching and somatic hypermutation in allergen-specific B cells. The ensuing affinity maturation and plasma cell differentiation lead to the abnormal release of high-affinity IgE that binds to powerful FcεRI receptors on basophils and mast cells. When cross-linked by allergen, FcεRI-bound IgE instigates the release of prestored and de novo-induced proinflammatory mediators. Aside from causing type I hypersensitivity reactions underlying allergy, IgE affords protection against nematodes or venoms from insects and snakes, which raises questions as to the fundamental differences between protective and pathogenic IgE responses. In this review, we discuss the impact of the mucosal environment, including the epithelial and mucus barriers, on the induction of protective IgE responses against environmental antigens. We further discuss how perturbations of these barriers may contribute to the induction of pathogenic IgE production.
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Affiliation(s)
- Andrea Cerutti
- Catalan Institute for Research and Advanced Studies, Barcelona, Spain; Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona Biomedical Research Park, Barcelona, Spain; Division of Clinical Immunology, Department of Medicine, Mount Sinai School of Medicine, New York.
| | - Martyna Filipska
- Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona Biomedical Research Park, Barcelona, Spain
| | - Xavi Marcos Fa
- Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona Biomedical Research Park, Barcelona, Spain
| | - Roser Tachó-Piñot
- Lydia Becher Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
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46
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Davis EC, Castagna VP, Sela DA, Hillard MA, Lindberg S, Mantis NJ, Seppo AE, Järvinen KM. Gut microbiome and breast-feeding: Implications for early immune development. J Allergy Clin Immunol 2022; 150:523-534. [PMID: 36075638 PMCID: PMC9463492 DOI: 10.1016/j.jaci.2022.07.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022]
Abstract
Establishment of the gut microbiome during early life is a complex process with lasting implications for an individual's health. Several factors influence microbial assembly; however, breast-feeding is recognized as one of the most influential drivers of gut microbiome composition during infancy, with potential implications for function. Differences in gut microbial communities between breast-fed and formula-fed infants have been consistently observed and are hypothesized to partially mediate the relationships between breast-feeding and decreased risk for numerous communicable and noncommunicable diseases in early life. Despite decades of research on the gut microbiome of breast-fed infants, there are large scientific gaps in understanding how human milk has evolved to support microbial and immune development. This review will summarize the evidence on how breast-feeding broadly affects the composition and function of the early-life gut microbiome and discuss mechanisms by which specific human milk components shape intestinal bacterial colonization, succession, and function.
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Affiliation(s)
- Erin C Davis
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY
| | | | - David A Sela
- Department of Food Science, University of Massachusetts Amherst, Amherst, Mass; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Mass; Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, Mass
| | - Margaret A Hillard
- Department of Food Science, University of Massachusetts Amherst, Amherst, Mass; Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, Mass
| | - Samantha Lindberg
- Department of Biomedical Sciences, University of Albany, Rensselaer, NY
| | - Nicholas J Mantis
- Division of Infectious Diseases, New York State Department of Health, Albany, NY
| | - Antti E Seppo
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY
| | - Kirsi M Järvinen
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, NY; Division of Allergy, Immunology, and Rheumatology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY; Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY.
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47
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Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V. Reference-based comparison of adaptive immune receptor repertoires. CELL REPORTS METHODS 2022; 2:100269. [PMID: 36046619 PMCID: PMC9421535 DOI: 10.1016/j.crmeth.2022.100269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/01/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
B and T cell receptor (immune) repertoires can represent an individual's immune history. While current repertoire analysis methods aim to discriminate between health and disease states, they are typically based on only a limited number of parameters. Here, we introduce immuneREF: a quantitative multidimensional measure of adaptive immune repertoire (and transcriptome) similarity that allows interpretation of immune repertoire variation by relying on both repertoire features and cross-referencing of simulated and experimental datasets. To quantify immune repertoire similarity landscapes across health and disease, we applied immuneREF to >2,400 datasets from individuals with varying immune states (healthy, [autoimmune] disease, and infection). We discovered, in contrast to the current paradigm, that blood-derived immune repertoires of healthy and diseased individuals are highly similar for certain immune states, suggesting that repertoire changes to immune perturbations are less pronounced than previously thought. In conclusion, immuneREF enables the population-wide study of adaptive immune response similarity across immune states.
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Affiliation(s)
- Cédric R. Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Teresa Rubio
- Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain
| | - Longlong Wang
- BGI-Shenzhen, Shenzhen, China
- BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Philippe A. Robert
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Igor Snapkov
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | - Marieke L. Kuijjer
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sonia Tarazona
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Valencia, Spain
| | - Geir K. Sandve
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
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48
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Vujkovic-Cvijin I, Welles HC, Ha CWY, Huq L, Mistry S, Brenchley JM, Trinchieri G, Devkota S, Belkaid Y. The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces. Sci Transl Med 2022; 14:eabl3927. [PMID: 35976997 PMCID: PMC9741845 DOI: 10.1126/scitranslmed.abl3927] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Unique gut microbiota compositions have been associated with inflammatory diseases, but identifying gut bacterial functions linked to immune activation in humans remains challenging. Translocation of pathogens from mucosal surfaces into peripheral tissues can elicit immune activation, although whether and which gut commensal bacteria translocate in inflammatory diseases is difficult to assess. We report that a subset of commensal gut microbiota constituents that translocate across the gut barrier in mice and humans are associated with heightened systemic immunoglobulin G (IgG) responses. We present a modified high-throughput, culture-independent approach to quantify systemic IgG against gut commensal bacteria in human serum samples without the need for paired stool samples. Using this approach, we highlight several commensal bacterial species that elicit elevated IgG responses in patients with inflammatory bowel disease (IBD) including taxa within the clades Collinsella, Bifidobacterium, Lachnospiraceae, and Ruminococcaceae. These and other taxa identified as translocating bacteria or targets of systemic immunity in IBD concomitantly exhibited heightened transcriptional activity and growth rates in IBD patient gut microbiomes. Our approach represents a complementary tool to illuminate interactions between the host and its gut microbiota and may provide an additional method to identify microbes linked to inflammatory disease.
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Affiliation(s)
- Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Hugh C. Welles
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Connie W. Y. Ha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lutfi Huq
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Shreni Mistry
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Suzanne Devkota
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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49
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Lee H, Yoo DK, Han J, Kim KH, Noh J, Lee Y, Lee E, Kwon S, Chung J. Optimization of peripheral blood volume for in silico reconstitution of the human B cell receptor repertoire. FEBS Open Bio 2022; 12:1634-1643. [PMID: 35866358 PMCID: PMC9433817 DOI: 10.1002/2211-5463.13467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022] Open
Abstract
B cells recognize antigens via membrane‐expressed B‐cell receptors (BCR) and antibodies. Similar human BCR sequences are frequently found at a significantly higher frequency than that theoretically calculated. Patients infected with SARS‐CoV2 and HIV or with autoimmune diseases share very similar BCRs. Therefore, in silico reconstitution of BCR repertoires and identification of stereotypical BCR sequences related to human pathology have diagnostic potential. Furthermore, monitoring changes of clinically significant BCR sequences and isotype conversion has prognostic potential. For BCR repertoire analysis, peripheral blood (PB) is the most convenient source. However, the optimal human PB volume for in silico reconstitution of the BCR repertoire has not been studied in detail. Here, we sampled 5, 10, and 20 mL PB from the left arm and 40 mL PB from the right arm of two volunteers, reconstituted in silico PB BCR repertoires, and compared their composition. In both volunteers, PB sampling over 20 mL resulted in slight increases in functional unique sequences (FUSs) or almost no increase in repertoire diversity. All FUSs with a frequency above 0.08% or 0.03% in the 40 mL PB BCR repertoire were detected even in the 5 mL PB BCR repertoire from each volunteer. FUSs with a higher frequency were more likely to be found in BCR repertoires from reduced PB volume, and those coexisting in two repertoires showed a statistically significant correlation in frequency irrespective of sampled anatomical site. The correlation was more significant in higher‐frequency FUSs. These observations support the potential of BCR repertoire analysis for diagnosis.
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Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jerome Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Ki Hyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Korea.,BK21+ Creative Research Engineer Development for IT, Seoul National University, Seoul, 08826, Korea.,Bio-MAX Institute, Seoul National University, Seoul, 08826, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
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50
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Perruzza L, Strati F, Raneri M, Li H, Gargari G, Rezzonico-Jost T, Palatella M, Kwee I, Morone D, Seehusen F, Sonego P, Donati C, Franceschi P, Macpherson AJ, Guglielmetti S, Greiff V, Grassi F. Apyrase-mediated amplification of secretory IgA promotes intestinal homeostasis. Cell Rep 2022; 40:111112. [PMID: 35858559 DOI: 10.1016/j.celrep.2022.111112] [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: 01/11/2022] [Revised: 05/15/2022] [Accepted: 06/28/2022] [Indexed: 11/25/2022] Open
Abstract
Secretory immunoglobulin A (SIgA) interaction with commensal bacteria conditions microbiota composition and function. However, mechanisms regulating reciprocal control of microbiota and SIgA are not defined. Bacteria-derived adenosine triphosphate (ATP) limits T follicular helper (Tfh) cells in the Peyer's patches (PPs) via P2X7 receptor (P2X7R) and thereby SIgA generation. Here we show that hydrolysis of extracellular ATP (eATP) by apyrase results in amplification of the SIgA repertoire. The enhanced breadth of SIgA in mice colonized with apyrase-releasing Escherichia coli influences topographical distribution of bacteria and expression of genes involved in metabolic versus immune functions in the intestinal epithelium. SIgA-mediated conditioning of bacteria and enterocyte function is reflected by differences in nutrient absorption in mice colonized with apyrase-expressing bacteria. Apyrase-induced SIgA improves intestinal homeostasis and attenuates barrier impairment and susceptibility to infection by enteric pathogens in antibiotic-induced dysbiosis. Therefore, amplification of SIgA by apyrase can be leveraged to restore intestinal fitness in dysbiotic conditions.
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Affiliation(s)
- Lisa Perruzza
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Francesco Strati
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Matteo Raneri
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Hai Li
- Maurice Müller Laboratories, Department of Biomedical Research, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern 3010, Switzerland
| | - Giorgio Gargari
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan 20133, Italy
| | - Tanja Rezzonico-Jost
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Martina Palatella
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Ivo Kwee
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Diego Morone
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland
| | - Frauke Seehusen
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Paolo Sonego
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN) 38098, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN) 38098, Italy
| | - Pietro Franceschi
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (TN) 38098, Italy
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department of Biomedical Research, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern 3010, Switzerland
| | - Simone Guglielmetti
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan 20133, Italy
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo 0372, Norway
| | - Fabio Grassi
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona 6500, Switzerland.
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