1
|
Bank NC, Singh V, McCourt B, Burberry A, Roberts KD, Grubb B, Rodriguez-Palacios A. Antigenic operon fragmentation and diversification mechanism in Bacteroidota impacts gut metagenomics and pathobionts in Crohn's disease microlesions. Gut Microbes 2024; 16:2350150. [PMID: 38841888 PMCID: PMC11164228 DOI: 10.1080/19490976.2024.2350150] [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] [Received: 09/20/2023] [Accepted: 04/26/2024] [Indexed: 06/07/2024] Open
Abstract
Comensal Bacteroidota (Bacteroidota) and Enterobacteriacea are often linked to gut inflammation. However, the causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism in Bacteroidota remain unclear. By using the classical lipopolysaccharide/O-antigen 'rfb operon' in Enterobacteriaceae as a surface antigen model (5-rfb-gene-cluster rfbABCDX), and a recent rfbA-typing strategy for strain classification, we characterized the integrity and conservancy of the entire rfb operon in Bacteroidota. Through exploratory analysis of complete genomes and metagenomes, we discovered that most Bacteroidota have the rfb operon fragmented into nonrandom patterns of gene-singlets and doublets/triplets, termed 'rfb-gene-clusters', or rfb-'minioperons' if predicted as transcriptional. To reflect global operon integrity, contiguity, duplication, and fragmentation principles, we propose a six-category (infra/supra-numerary) cataloging system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly Bacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in gut-wall specific micro-niches or micropathologies. Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota have fewer KEGG-pathways despite large genomes. DNA insertions, overrepresenting DNA-exchange-avid (Bacteroides) species, impact our interpretation of functional metagenomics data by inflating by inflating gene-based pathway inference and by overestimating 'extra-species' abundance. Of disease relevance, Bacteroidota species isolated from cavitating/cavernous fistulous tract (CavFT) microlesions in Crohn's Disease have supra-numerary fragmented operons, stimulate TNF-alpha from macrophages with low potency, and do not induce hyperacute peritonitis in mice compared to CavFT Enterobacteriaceae. The impact of 'foreign-DNA' insertions on pro-inflammatory operons, metagenomics, and commensalism/opportunism requires further studies to elucidate their potential for novel diagnostics and therapeutics, and to elucidate the role of co-existing pathobionts in Crohn's disease microlesions.
Collapse
Affiliation(s)
- Nicholas C. Bank
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Vaidhvi Singh
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Blake McCourt
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Aaron Burberry
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kyle D. Roberts
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, USA
| | - Brandon Grubb
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
2
|
Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [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] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
Collapse
Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | |
Collapse
|
3
|
Donaldson GP, Reis GL, Saad M, Mamede I, Chen G, DelGaudio NL, Zhang D, Aydin B, Harrer CE, Castro TB, Grivennikov S, Reis BS, Stadtmueller BM, Victora GD, Mucida D. Suppression of epithelial proliferation and tumorigenesis by immunoglobulin A. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561290. [PMID: 37873082 PMCID: PMC10592636 DOI: 10.1101/2023.10.06.561290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Immunoglobulin A (IgA) is the most abundant antibody isotype produced across mammals and plays a specialized role in mucosal homeostasis 1 . Constantly secreted into the lumen of the intestine, IgA binds commensal microbiota to regulate their colonization and function 2,3 , with unclear implications for health. IgA deficiency is common in humans but is difficult to study due to its complex etiology and comorbidities 4-8 . Using genetically and environmentally controlled mice, here we show that IgA-deficient animals have a baseline alteration in the colon epithelium that increases susceptibility to multiple models of colorectal cancer. Transcriptome, imaging, and flow cytometry-based analyses revealed that, in the absence of IgA, colonic epithelial cells induce antibacterial factors and accelerate cell cycling in response to the microbiota. Oral treatment with IgA was sufficient to suppress aberrant epithelial proliferation independently of bacterial binding, suggesting that IgA provides a feedback signal to epithelial cells in parallel with its known roles in microbiome shaping. In a primary colonic organoid culture system, IgA directly suppresses epithelial growth. Conversely, the susceptibility of IgA-deficient mice to colorectal cancer was reversed by Notch inhibition to suppress the absorptive colonocyte developmental program, or by inhibition of the cytokine MIF, the receptor for which was upregulated in stem cells of IgA-deficient animals. These studies demonstrate a homeostatic function for IgA in tempering physiological epithelial responses to microbiota to maintain mucosal health.
Collapse
|
4
|
Hockenberry A, Slack E, Stadtmueller BM. License to Clump: Secretory IgA Structure-Function Relationships Across Scales. Annu Rev Microbiol 2023; 77:645-668. [PMID: 37713459 DOI: 10.1146/annurev-micro-032521-041803] [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] [Indexed: 09/17/2023]
Abstract
Secretory antibodies are the only component of our adaptive immune system capable of attacking mucosal pathogens topologically outside of our bodies. All secretory antibody classes are (a) relatively resistant to harsh proteolytic environments and (b) polymeric. Recent elucidation of the structure of secretory IgA (SIgA) has begun to shed light on SIgA functions at the nanoscale. We can now begin to unravel the structure-function relationships of these molecules, for example, by understanding how the bent conformation of SIgA enables robust cross-linking between adjacent growing bacteria. Many mysteries remain, such as the structural basis of protease resistance and the role of noncanonical bacteria-IgA interactions. In this review, we explore the structure-function relationships of IgA from the nano- to the metascale, with a strong focus on how the seemingly banal "license to clump" can have potent effects on bacterial physiology and colonization.
Collapse
Affiliation(s)
- Alyson Hockenberry
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
- Department of Environmental Systems Science (D-USYS), ETH Zürich, Zürich, Switzerland;
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland;
- Botnar Research Centre for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Beth M Stadtmueller
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA;
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois, Urbana, Illinois, USA
| |
Collapse
|
5
|
Hockenberry A, Radiom M, Arnoldini M, Turgay Y, Dunne M, Adamcik J, Stadtmueller B, Mezzenga R, Ackermann M, Slack E. Nanoscale clustering by O-antigen-Secretory Immunoglobulin-A binding limits outer membrane diffusion by encaging individual Salmonella cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548943. [PMID: 37503073 PMCID: PMC10369997 DOI: 10.1101/2023.07.13.548943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Secreted immunoglobulins, predominantly SIgA, influence the colonization and pathogenicity of mucosal bacteria. While part of this effect can be explained by SIgA-mediated bacterial aggregation, we have an incomplete picture of how SIgA binding influences cells independently of aggregation. Here we show that akin to microscale crosslinking of cells, SIgA targeting the Salmonella Typhimurium O-antigen extensively crosslinks the O-antigens on the surface of individual bacterial cells at the nanoscale. This crosslinking results in an essentially immobilized bacterial outer membrane. Membrane immobilization, combined with Bam-complex mediated outer membrane protein insertion results in biased inheritance of IgA-bound O-antigen, concentrating SIgA-bound O-antigen at the oldest poles during cell growth. By combining empirical measurements and simulations, we show that this SIgA-driven biased inheritance increases the rate at which phase-varied daughter cells become IgA-free: a process that can accelerate IgA escape via phase-variation of O-antigen structure. Our results show that O-antigen-crosslinking by SIgA impacts workings of the bacterial outer membrane, helping to mechanistically explain how SIgA may exert aggregation-independent effects on individual microbes colonizing the mucosae.
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Interrogation of the mammalian gut-brain axis using LC-MS/MS-based targeted metabolomics with in vitro bacterial and organoid cultures and in vivo gnotobiotic mouse models. Nat Protoc 2023; 18:490-529. [PMID: 36352124 DOI: 10.1038/s41596-022-00767-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 07/26/2022] [Indexed: 11/11/2022]
Abstract
Interest in the communication between the gastrointestinal tract and central nervous system, known as the gut-brain axis, has prompted the development of quantitative analytical platforms to analyze microbe- and host-derived signals. This protocol enables investigations into connections between microbial colonization and intestinal and brain neurotransmitters and contains strategies for the comprehensive evaluation of metabolites in in vitro (organoids) and in vivo mouse model systems. Here we present an optimized workflow that includes procedures for preparing these gut-brain axis model systems: (stage 1) growth of microbes in defined media; (stage 2) microinjection of intestinal organoids; and (stage 3) generation of animal models including germ-free (no microbes), specific-pathogen-free (complete gut microbiota) and specific-pathogen-free re-conventionalized (germ-free mice associated with a complete gut microbiota from a specific-pathogen-free mouse), and Bifidobacterium dentium and Bacteroides ovatus mono-associated mice (germ-free mice colonized with a single gut microbe). We describe targeted liquid chromatography-tandem mass spectrometry-based metabolomics methods for analyzing microbially derived short-chain fatty acids and neurotransmitters from these samples. Unlike other protocols that commonly examine only stool samples, this protocol includes bacterial cultures, organoid cultures and in vivo samples, in addition to monitoring the metabolite content of stool samples. The incorporation of three experimental models (microbes, organoids and animals) enhances the impact of this protocol. The protocol requires 3 weeks of murine colonization with microbes and ~1-2 weeks for liquid chromatography-tandem mass spectrometry-based instrumental and quantitative analysis, and sample post-processing and normalization.
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Yang C, Chen-Liaw A, Spindler MP, Tortorella D, Moran TM, Cerutti A, Faith JJ. Immunoglobulin A antibody composition is sculpted to bind the self gut microbiome. Sci Immunol 2022; 7:eabg3208. [PMID: 35857580 PMCID: PMC9421563 DOI: 10.1126/sciimmunol.abg3208] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Despite being the most abundantly secreted immunoglobulin isotype, the pattern of reactivity of immunoglobulin A (IgA) antibodies toward each individual's own gut commensal bacteria still remains elusive. By colonizing germ-free mice with defined commensal bacteria, we found that the binding specificity of bulk fecal and serum IgA toward resident gut bacteria resolves well at the species level and has modest strain-level specificity. IgA hybridomas generated from lamina propria B cells of gnotobiotic mice showed that most IgA clones recognized a single bacterial species, whereas a small portion displayed cross-reactivity. Orally administered hybridoma-produced IgAs still retained bacterial antigen binding capability, implying the potential for a new class of therapeutic antibodies. Species-specific IgAs had a range of strain specificities. Given the distinctive bacterial species and strain composition found in each individual's gut, our findings suggest the IgA antibody repertoire is shaped uniquely to bind "self" gut bacteria.
Collapse
Affiliation(s)
- Chao Yang
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alice Chen-Liaw
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew P. Spindler
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Domenico Tortorella
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas M. Moran
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Therapeutic Antibody Development, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Cerutti
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona 08003, Spain
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
10
|
Saini A, Dalal P, Sharma D. Deciphering the Interdependent Labyrinth between Gut Microbiota and the Immune System. Lett Appl Microbiol 2022; 75:1122-1135. [PMID: 35730958 DOI: 10.1111/lam.13775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/18/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022]
Abstract
The human gut microbiome interacts with each other and the host, which has significant effects on health and disease development. Intestinal homeostasis and inflammation are maintained by the dynamic interactions between gut microbiota and the innate and adaptive immune systems. Numerous metabolic products produced by the gut microbiota play a role in mediating cross-talk between gut epithelial and immune cells. In the event of an imbalance between the immune system and microbiota, the body becomes susceptible to infections, and homeostasis is compromised. This review mainly focuses on the interplay between microbes and the immune system, such as, T-cell and B-cell mediated adaptive responses to microbiota and signaling pathways for effective communication between the two. We have also highlighted the role of microbes in the activation of the immune response, the development of memory cells, and how the immune system determines the diversity of human gut microbiota. The review also explains the relationship of commensal microbiota and their relation in the production of immunoglobulins.
Collapse
Affiliation(s)
- Anamika Saini
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab, -140306, India.,Amity Institute of Biotechnology, Amity University Jaipur, Rajasthan, 302006
| | - Priyanka Dalal
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab, -140306, India
| | - Deepika Sharma
- Institute of Nano Science and Technology, Knowledge City, Sector 81, Mohali, Punjab, -140306, India
| |
Collapse
|
11
|
Making Sense of Quorum Sensing at the Intestinal Mucosal Interface. Cells 2022; 11:cells11111734. [PMID: 35681429 PMCID: PMC9179481 DOI: 10.3390/cells11111734] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome can produce metabolic products that exert diverse activities, including effects on the host. Short chain fatty acids and amino acid derivatives have been the focus of many studies, but given the high microbial density in the gastrointestinal tract, other bacterial products such as those released as part of quorum sensing are likely to play an important role for health and disease. In this review, we provide of an overview on quorum sensing (QS) in the gastrointestinal tract and summarise what is known regarding the role of QS molecules such as auto-inducing peptides (AIP) and acyl-homoserine lactones (AHL) from commensal, probiotic, and pathogenic bacteria in intestinal health and disease. QS regulates the expression of numerous genes including biofilm formation, bacteriocin and toxin secretion, and metabolism. QS has also been shown to play an important role in the bacteria–host interaction. We conclude that the mechanisms of action of QS at the intestinal neuro–immune interface need to be further investigated.
Collapse
|
12
|
Sánchez Montalvo A, Gohy S, Rombaux P, Pilette C, Hox V. The Role of IgA in Chronic Upper Airway Disease: Friend or Foe? FRONTIERS IN ALLERGY 2022; 3:852546. [PMID: 35386640 PMCID: PMC8974816 DOI: 10.3389/falgy.2022.852546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/10/2022] [Indexed: 01/28/2023] Open
Abstract
Chronic upper airway inflammation is amongst the most prevalent chronic disease entities in the Western world with prevalence around 30% (rhinitis) and 11% (rhinosinusitis). Chronic rhinitis and rhinosinusitis may severely impair the quality of life, leading to a significant socio-economic burden. It becomes more and more clear that the respiratory mucosa which forms a physiological as well as chemical barrier for inhaled particles, plays a key role in maintaining homeostasis and driving disease. In a healthy state, the mucosal immune system provides protection against pathogens as well as maintains a tolerance toward non-harmful commensal microbes and benign environmental substances such as allergens. One of the most important players of the mucosal immune system is immunoglobulin (Ig) A, which is well-studied in gut research where it has emerged as a key factor in creating tolerance to potential food allergens and maintaining a healthy microbiome. Although, it is very likely that IgA plays a similar role at the level of the respiratory epithelium, very little research has been performed on the role of this protein in the airways, especially in chronic upper airway diseases. This review summarizes what is known about IgA in upper airway homeostasis, as well as in rhinitis and rhinosinusitis, including current and possible new treatments that may interfere with the IgA system. By doing so, we identify unmet needs in exploring the different roles of IgA in the upper airways required to find new biomarkers or therapeutic options for treating chronic rhinitis and rhinosinusitis.
Collapse
Affiliation(s)
- Alba Sánchez Montalvo
- Pole of Pneumology, ENT and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
- Allergy and Clinical Immunology Research Group, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Sophie Gohy
- Pole of Pneumology, ENT and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
- Department of Pulmonology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
- Cystic Fibrosis Reference Center, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Philippe Rombaux
- Department of Otorhinolaryngology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Charles Pilette
- Pole of Pneumology, ENT and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
- Department of Pulmonology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Valérie Hox
- Pole of Pneumology, ENT and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain (UCLouvain), Brussels, Belgium
- Department of Otorhinolaryngology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
- *Correspondence: Valérie Hox
| |
Collapse
|
13
|
Affiliation(s)
- Oliver Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany.
| | - Ana Izcue
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
14
|
The impact of the Th17:Treg axis on the IgA-Biome across the glycemic spectrum. PLoS One 2021; 16:e0258812. [PMID: 34669745 PMCID: PMC8528330 DOI: 10.1371/journal.pone.0258812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
Secretory IgA (SIgA) is released into mucosal surfaces where its function extends beyond that of host defense to include the shaping of resident microbial communities by mediating exclusion/inclusion of respective microbes and regulating bacterial gene expression. In this capacity, SIgA acts as the fulcrum on which host immunity and the health of the microbiota are balanced. We recently completed an analysis of the gut and salivary IgA-Biomes (16S rDNA sequencing of SIgA-coated/uncoated bacteria) in Mexican-American adults that identified IgA-Biome differences across the glycemic spectrum. As Th17:Treg ratio imbalances are associated with gut microbiome dysbiosis and chronic inflammatory conditions such as type 2 diabetes, the present study extends our prior work by examining the impact of Th17:Treg ratios (pro-inflammatory:anti-inflammatory T-cell ratios) and the SIgA response (Th17:Treg-SIgA axis) in shaping microbial communities. Examining the impact of Th17:Treg ratios (determined by epigenetic qPCR lymphocyte subset quantification) on the IgA-Biome across diabetes phenotypes identified a proportional relationship between Th17:Treg ratios and alpha diversity in the stool IgA-Biome of those with dysglycemia, significant changes in community composition of the stool and salivary microbiomes across glycemic profiles, and genera preferentially abundant by T-cell inflammatory phenotype. This is the first study to associate epigenetically quantified Th17:Treg ratios with both the larger and SIgA-fractionated microbiome, assess these associations in the context of a chronic inflammatory disease, and offers a novel frame through which to evaluate mucosal microbiomes in the context of host responses and inflammation.
Collapse
|
15
|
Parallelism of intestinal secretory IgA shapes functional microbial fitness. Nature 2021; 598:657-661. [PMID: 34646015 DOI: 10.1038/s41586-021-03973-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022]
Abstract
Dimeric IgA secreted across mucous membranes in response to nonpathogenic taxa of the microbiota accounts for most antibody production in mammals. Diverse binding specificities can be detected within the polyclonal mucosal IgA antibody response1-10, but limited monoclonal hybridomas have been studied to relate antigen specificity or polyreactive binding to functional effects on microbial physiology in vivo11-17. Here we use recombinant dimeric monoclonal IgAs (mIgAs) to finely map the intestinal plasma cell response to microbial colonization with a single microorganism in mice. We identify a range of antigen-specific mIgA molecules targeting defined surface and nonsurface membrane antigens. Secretion of individual dimeric mIgAs targeting different antigens in vivo showed distinct alterations in the function and metabolism of intestinal bacteria, largely through specific binding. Even in cases in which the same microbial antigen is targeted, microbial metabolic alterations differed depending on IgA epitope specificity. By contrast, bacterial surface coating generally reduced motility and limited bile acid toxicity. The overall intestinal IgA response to a single microbe therefore contains parallel components with distinct effects on microbial carbon-source uptake, bacteriophage susceptibility, motility and membrane integrity.
Collapse
|
16
|
Abstract
Immunoglobulin A (IgA) is the most abundant antibody at mucosal surfaces and has been the subject of many investigations involving microbiota research in the last decade. Although the classic functions of IgA include neutralization of harmful toxins, more recent investigations have highlighted an important role for IgA in regulating the composition and function of the commensal microbiota. Multiple reviews have comprehensively covered the literature that describes recent, novel mechanisms of action of IgA and development of the IgA response within the intestine. Here we focus on how the interaction between IgA and the microbiota promotes homeostasis with the host to prevent disease.
Collapse
Affiliation(s)
- Allison M Weis
- Department of Pathology, University of Utah School of Medicine, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA
| | - June L Round
- Department of Pathology, University of Utah School of Medicine, Division of Microbiology and Immunology, Salt Lake City, UT 84112, USA.
| |
Collapse
|
17
|
Abstract
IgA mediates microbial homeostasis at the intestinal mucosa. Within the gut, IgA acts in a context-dependent manner to both prevent and promote bacterial colonization and to influence bacterial gene expression, thus providing exquisite control of the microbiota. IgA-microbiota interactions are highly diverse across individuals and populations, yet the factors driving this variation remain poorly understood. In this Review, we summarize evidence for the host, bacterial and environmental factors that influence IgA-microbiota interactions. Recent advances have helped to clarify the antigenic specificity and immune selection of intestinal IgA and have highlighted the importance of microbial glycan recognition. Furthermore, emerging evidence suggests that diet and nutrition play an important role in shaping IgA recognition of the microbiota. IgA-microbiota interactions are disrupted during both overnutrition and undernutrition and may be altered dynamically in response to diet, with potential implications for host health. We situate this research in the context of outstanding questions and future directions in order to better understand the fascinating paradigm of IgA-microbiota homeostasis.
Collapse
|
18
|
Hsieh SA, Donermeyer DL, Horvath SC, Allen PM. Phase-variable bacteria simultaneously express multiple capsules. MICROBIOLOGY-SGM 2021; 167. [PMID: 34224345 PMCID: PMC8489884 DOI: 10.1099/mic.0.001066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Capsular polysaccharides (CPSs) protect bacteria from host and environmental factors. Many bacteria can express different CPSs and these CPSs are phase variable. For example, Bacteroides thetaiotaomicron (B. theta) is a prominent member of the human gut microbiome and expresses eight different capsular polysaccharides. Bacteria, including B. theta, have been shown to change their CPSs to adapt to various niches such as immune, bacteriophage, and antibiotic perturbations. However, there are limited tools to study CPSs and fundamental questions regarding phase variance, including if gut bacteria can express more than one capsule at the same time, remain unanswered. To better understand the roles of different CPSs, we generated a B. theta CPS1-specific antibody and a flow cytometry assay to detect CPS expression in individual bacteria in the gut microbiota. Using these novel tools, we report for the first time that bacteria can simultaneously express multiple CPSs. We also observed that nutrients such as glucose and salts had no effect on CPS expression. The ability to express multiple CPSs at the same time may provide bacteria with an adaptive advantage to thrive amid changing host and environmental conditions, especially in the intestine.
Collapse
Affiliation(s)
- Samantha A Hsieh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David L Donermeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephen C Horvath
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paul M Allen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
19
|
Patnode ML, Guruge JL, Castillo JJ, Couture GA, Lombard V, Terrapon N, Henrissat B, Lebrilla CB, Gordon JI. Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles. Cell Host Microbe 2021; 29:664-673.e5. [PMID: 33571448 DOI: 10.1016/j.chom.2021.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/07/2020] [Accepted: 01/18/2021] [Indexed: 01/26/2023]
Abstract
Greater understanding of the spatial relationships between members of the human gut microbiota and available nutrients is needed to gain deeper insights about community dynamics and expressed functions. Therefore, we generated a panel of artificial food particles with each type composed of microscopic paramagnetic beads coated with a fluorescent barcode and one of 60 different dietary or host glycan preparations. Analysis of 160 Bacteroides and Parabacteroides strains disclosed diverse strain-specific and glycan-specific binding phenotypes. We identified carbohydrate structures that correlated with binding by specific bacterial strains in vitro and noted strain-specific differences in the catabolism of glycans that mediate adhesion. Mixed in vitro cultures revealed that these adhesion phenotypes are maintained in more complex communities. Additionally, orally administering glycan beads to gnotobiotic mice confirmed specificity in glycan binding. This approach should facilitate analyses of how strains occupying the same physical niche interact, and it should advance the development of synbiotics, more nutritious foods, and microbiota-based diagnostics.
Collapse
Affiliation(s)
- Michael L Patnode
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Janaki L Guruge
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Garret A Couture
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR7257 Centre National de la Recherche Scientifique and Aix-Marseille Université, USC1408 Institut National de la Recherche Agronomique, 13288 Marseille cedex 9, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
20
|
Kabbert J, Benckert J, Rollenske T, Hitch TCA, Clavel T, Cerovic V, Wardemann H, Pabst O. High microbiota reactivity of adult human intestinal IgA requires somatic mutations. J Exp Med 2021; 217:151927. [PMID: 32640466 PMCID: PMC7526496 DOI: 10.1084/jem.20200275] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/25/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
The gut is home to the body’s largest population of plasma cells. In healthy individuals, IgA is the dominating isotype, whereas patients with inflammatory bowel disease also produce high concentrations of IgG. In the gut lumen, secretory IgA binds pathogens and toxins but also the microbiota. However, the antigen specificity of IgA and IgG for the microbiota and underlying mechanisms of antibody binding to bacteria are largely unknown. Here we show that microbiota binding is a defining property of human intestinal antibodies in both healthy and inflamed gut. Some bacterial taxa were commonly targeted by different monoclonal antibodies, whereas others selectively bound single antibodies. Interestingly, individual human monoclonal antibodies from both healthy and inflamed intestines bound phylogenetically unrelated bacterial species. This microbiota cross-species reactivity did not correlate with antibody polyreactivity but was crucially dependent on the accumulation of somatic mutations. Therefore, our data suggest that a system of affinity-matured, microbiota cross-species–reactive IgA is a common aspect of SIgA–microbiota interactions in the gut.
Collapse
Affiliation(s)
- Johanna Kabbert
- Institute of Molecular Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Julia Benckert
- Max Planck Research Group Molecular Immunology, Max Planck Institute for Infection Biology, Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tim Rollenske
- B Cell Immunology, German Cancer Research Centre, Heidelberg, Germany
| | - Thomas C A Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Vuk Cerovic
- Institute of Molecular Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Hedda Wardemann
- B Cell Immunology, German Cancer Research Centre, Heidelberg, Germany
| | - Oliver Pabst
- Institute of Molecular Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| |
Collapse
|
21
|
Pietrzak B, Tomela K, Olejnik-Schmidt A, Mackiewicz A, Schmidt M. Secretory IgA in Intestinal Mucosal Secretions as an Adaptive Barrier against Microbial Cells. Int J Mol Sci 2020; 21:ijms21239254. [PMID: 33291586 PMCID: PMC7731431 DOI: 10.3390/ijms21239254] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Secretory IgA (SIgA) is the dominant antibody class in mucosal secretions. The majority of plasma cells producing IgA are located within mucosal membranes lining the intestines. SIgA protects against the adhesion of pathogens and their penetration into the intestinal barrier. Moreover, SIgA regulates gut microbiota composition and provides intestinal homeostasis. In this review, we present mechanisms of SIgA generation: T cell-dependent and -independent; in different non-organized and organized lymphoid structures in intestinal lamina propria (i.e., Peyer’s patches and isolated lymphoid follicles). We also summarize recent advances in understanding of SIgA functions in intestinal mucosal secretions with focus on its role in regulating gut microbiota composition and generation of tolerogenic responses toward its members.
Collapse
Affiliation(s)
- Bernadeta Pietrzak
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-627 Poznań, Poland;
- Correspondence: (B.P.); (M.S.)
| | - Katarzyna Tomela
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznań, Poland; (K.T.); (A.M.)
| | - Agnieszka Olejnik-Schmidt
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-627 Poznań, Poland;
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznań, Poland; (K.T.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznań, Poland
| | - Marcin Schmidt
- Department of Food Biotechnology and Microbiology, Poznan University of Life Sciences, 48 Wojska Polskiego, 60-627 Poznań, Poland;
- Correspondence: (B.P.); (M.S.)
| |
Collapse
|
22
|
Commensal Bacteria Modulate Immunoglobulin A Binding in Response to Host Nutrition. Cell Host Microbe 2020; 27:909-921.e5. [PMID: 32289261 DOI: 10.1016/j.chom.2020.03.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 01/29/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022]
Abstract
Immunoglobulin (Ig) A controls host-microbial homeostasis in the gut. IgA recognition of beneficial bacteria is decreased in acutely undernourished children, but the factors driving these changes in IgA targeting are unknown. Child undernutrition is a global health challenge that is exacerbated by poor sanitation and intestinal inflammation. To understand how nutrition impacts immune-microbe interactions, we used a mouse model of undernutrition with or without fecal-oral exposure and assessed IgA-bacterial targeting from weaning to adulthood. In contrast to healthy control mice, undernourished mice fail to develop IgA recognition of intestinal Lactobacillus. Glycan-mediated interactions between Lactobacillus and host antibodies are lost in undernourished mice due to rapid bacterial adaptation. Lactobacillus adaptations occur in direct response to nutritional pressure, independently of host IgA, and are associated with reduced mucosal colonization and with bacterial mutations in carbohydrate processing genes. Together these data indicate that diet-driven bacterial adaptations shape IgA recognition in the gut.
Collapse
|
23
|
Rollenske T, Macpherson AJ. Anti-commensal Ig-from enormous diversity to clear function. Mucosal Immunol 2020; 13:1-2. [PMID: 31719642 DOI: 10.1038/s41385-019-0223-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Tim Rollenske
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories (Department of Biomedical Research), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland.
| |
Collapse
|
24
|
Janzon A, Goodrich JK, Koren O, Waters JL, Ley RE. Interactions between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut. mSystems 2019; 4:e00612-19. [PMID: 31771976 PMCID: PMC6880043 DOI: 10.1128/msystems.00612-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Interactions between the gut microbiome and immunoglobulin A (IgA) in the gut during infancy are important for future health. IgM and IgG are also present in the gut; however, their interactions with the microbiome in the developing infant remain to be characterized. Using stool samples sampled 15 times in infancy from 32 healthy subjects at 4 locations in 3 countries, we characterized patterns of microbiome development in relation to fecal levels of IgA, IgG, and IgM. For 8 infants from a single location, we used fluorescence-activated cell sorting of microbial cells from stool by Ig-coating status over 18 months. We used 16S rRNA gene profiling on full and sorted microbiomes to assess patterns of antibody coating in relation to age and other factors. All antibodies decreased in concentration with age but were augmented by breastmilk feeding regardless of infant age. Levels of IgA correlated with relative abundances of operational taxonomic units (OTUs) belonging to the Bifidobacteria and Enterobacteriaceae, which dominated the early microbiome, and IgG levels correlated with Haemophilus The diversity of Ig-coated microbiota was influenced by breastfeeding and age. IgA and IgM coated the same microbiota, which reflected the overall diversity of the microbiome, while IgG targeted a different subset. Blautia generally evaded antibody coating, while members of the Bifidobacteria and Enterobacteriaceae were high in IgA/M. IgA/M displayed similar dynamics, generally coating the microbiome proportionally, and were influenced by breastfeeding status. IgG only coated a small fraction of the commensal microbiota and differed from the proportion targeted by IgA and IgM.IMPORTANCE Antibodies are secreted into the gut and attach to roughly half of the trillions of bacterial cells present. When babies are born, the breastmilk supplies these antibodies until the baby's own immune system takes over this task after a few weeks. The vast majority of these antibodies are IgA, but two other types, IgG and IgM, are also present in the gut. Here, we ask if these three different antibody types target different types of bacteria in the infant gut as the infant develops from birth to 18 months old and how patterns of antibody coating of bacteria change with age. In this study of healthy infant samples over time, we found that IgA and IgM coat the same bacteria, which are generally representative of the diversity present, with a few exceptions that were more or less antibody coated than expected. IgG coated a separate suite of bacteria. These results provide a better understanding of how these antibodies interact with the developing infant gut microbiome.
Collapse
Affiliation(s)
- Anders Janzon
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Julia K Goodrich
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Omry Koren
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
25
|
Joglekar P, Ding H, Canales-Herrerias P, Pasricha PJ, Sonnenburg JL, Peterson DA. Intestinal IgA Regulates Expression of a Fructan Polysaccharide Utilization Locus in Colonizing Gut Commensal Bacteroides thetaiotaomicron. mBio 2019; 10:e02324-19. [PMID: 31690674 PMCID: PMC6831775 DOI: 10.1128/mbio.02324-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022] Open
Abstract
Gut-derived immunoglobulin A (IgA) is the most abundant antibody secreted in the gut that shapes gut microbiota composition and functionality. However, most of the microbial antigens targeted by gut IgA remain unknown, and the functional effects of IgA targeting these antigens are currently understudied. This study provides a framework for identifying and characterizing gut microbiota antigens targeted by gut IgA. We developed a small intestinal ex vivo culture assay to harvest lamina propria IgA from gnotobiotic mice, with the aim of identifying antigenic targets in a model human gut commensal, Bacteroides thetaiotaomicron VPI-5482. Colonization by B. thetaiotaomicron induced a microbe-specific IgA response that was reactive against diverse antigens, including capsular polysaccharides, lipopolysaccharides, and proteins. IgA against microbial protein antigens targeted membrane and secreted proteins with diverse functionalities, including an IgA specific against proteins of the polysaccharide utilization locus (PUL) that are necessary for utilization of fructan, which is an important dietary polysaccharide. Further analyses demonstrated that the presence of dietary fructan increased the production of fructan PUL-specific IgA, which then downregulated the expression of fructan PUL in B. thetaiotaomicron, both in vivo and in vitro Since the expression of fructan PUL has been associated with the ability of B. thetaiotaomicron to colonize the gut in the presence of dietary fructans, our work suggests a novel role for gut IgA in regulating microbial colonization by modulating their metabolism.IMPORTANCE Given the significant impact that gut microbes have on our health, it is essential to identify key host and environmental factors that shape this diverse community. While many studies have highlighted the impact of diet on gut microbiota, little is known about how the host regulates this critical diet-microbiota interaction. In our present study, we discovered that gut IgA targeted a protein complex involved in the utilization of an important dietary polysaccharide: fructan. While the presence of dietary fructans was previously thought to allow unrestricted growth of fructan-utilizing bacteria, our work shows that gut IgA, by targeting proteins responsible for fructan utilization, provides the host with tools that can restrict the microbial utilization of such polysaccharides, thereby controlling their growth.
Collapse
Affiliation(s)
- Payal Joglekar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hua Ding
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Pablo Canales-Herrerias
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Pankaj Jay Pasricha
- Center for Neurogastroenterology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Daniel A Peterson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
26
|
Pathogen Colonization Resistance in the Gut and Its Manipulation for Improved Health. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1300-1310. [PMID: 31100210 DOI: 10.1016/j.ajpath.2019.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/15/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
Mammals have coevolved with a large community of symbiotic, commensal, and some potentially pathogenic microbes. The trillions of bacteria and hundreds of species in our guts form a relatively stable community that resists invasion by outsiders, including pathogens. This powerful protective force is referred to as colonization resistance. We discuss the variety of proposed or demonstrated mechanisms that can mediate colonization resistance and some potential ways to manipulate them for improved human health. Instances in which certain bacterial pathogens can overcome colonization resistance are also discussed.
Collapse
|
27
|
IgA Responses to Microbiota. Immunity 2019; 49:211-224. [PMID: 30134201 DOI: 10.1016/j.immuni.2018.08.011] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/03/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
Various immune mechanisms are deployed in the mucosa to confront the immense diversity of resident bacteria. A substantial fraction of the commensal microbiota is coated with immunoglobulin A (IgA) antibodies, and recent findings have established the identities of these bacteria under homeostatic and disease conditions. Here we review the current understanding of IgA biology, and present a framework wherein two distinct types of humoral immunity coexist in the gastrointestinal mucosa. Homeostatic IgA responses employ a polyreactive repertoire to bind a broad but taxonomically distinct subset of microbiota. In contrast, mucosal pathogens and vaccines elicit high-affinity, T cell-dependent antibody responses. This model raises fundamental questions including how polyreactive IgA specificities are generated, how these antibodies exert effector functions, and how they exist together with other immune responses during homeostasis and disease.
Collapse
|
28
|
Di Lorenzo F, De Castro C, Silipo A, Molinaro A. Lipopolysaccharide structures of Gram-negative populations in the gut microbiota and effects on host interactions. FEMS Microbiol Rev 2019; 43:257-272. [DOI: 10.1093/femsre/fuz002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/11/2019] [Indexed: 12/15/2022] Open
Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126 Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, via Cinthia 4, 80126 Naples, Italy
| | - Cristina De Castro
- Task Force on Microbiome Studies, University of Naples Federico II, via Cinthia 4, 80126 Naples, Italy
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126 Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, via Cinthia 4, 80126 Naples, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126 Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, via Cinthia 4, 80126 Naples, Italy
| |
Collapse
|
29
|
Vitetta L, Vitetta G, Hall S. Immunological Tolerance and Function: Associations Between Intestinal Bacteria, Probiotics, Prebiotics, and Phages. Front Immunol 2018; 9:2240. [PMID: 30356736 PMCID: PMC6189397 DOI: 10.3389/fimmu.2018.02240] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/10/2018] [Indexed: 12/12/2022] Open
Abstract
Post-birth there is a bacterial assault on all mucosal surfaces. The intestinal microbiome is an important participant in health and disease. The pattern of composition and concentration of the intestinal microbiome varies greatly. Therefore, achieving immunological tolerance in the first 3-4 years of life is critical for maintaining health throughout a lifetime. Probiotic bacteria are organisms that afford beneficial health effects to the host and in certain instances may protect against the development of disease. The potential benefits of modifying the composition of the intestinal microbial cohort for therapeutic benefit is evident in the use in high risks groups such as premature infants, children receiving antibiotics, rotavirus infections in non-vaccinated children and traveler's diarrhea in adults. Probiotics and prebiotics are postulated to have immunomodulating capabilities by influencing the intestinal microbial cohort and dampening the activity of pathobiont intestinal microbes, such as Klebsiella pneumonia and Clostridia perfringens. Lactobacilli and Bifidobacteria are examples of probiotics found in the large intestine and so far, the benefits afforded to probiotics have varied in efficacy. Most likely the efficacy of probiotic bacteria has a multifactorial dependency, namely on a number of factors that include agents used, the dose, the pattern of dosing, and the characteristics of the host and the underlying luminal microbial environment and the activity of bacteriophages. Bacteriophages, are small viruses that infect and lyse intestinal bacteria. As such it can be posited that these viruses display an effective local protective control mechanism for the intestinal barrier against commensal pathobionts that indirectly may assist the host in controlling bacterial concentrations in the gut. A co-operative activity may be envisaged between the intestinal epithelia, mucosal immunity and the activity of bacteriophages to eliminate pathobiots, highlighting the potential role of bacteriophages in assisting with maintaining intestinal homeostasis. Hence bacteriophage local control of inflammation and immune responses may be an additional immunological defense mechanism that exploits bacteriophage-mucin glycoprotein interactions that controls bacterial diversity and abundance in the mucin layers of the gut. Moreover, and importantly the efficacy of probiotics may be dependent on the symbiotic incorporation of prebiotics, and the abundance and diversity of the intestinal microbiome encountered. The virome may be an important factor that determines the efficacy of some probiotic formulations.
Collapse
Affiliation(s)
- Luis Vitetta
- Discipline of Pharmacology, Faculty of Medicine and Health, School of Medicine, The University of Sydney, Camperdown, NSW, Australia
- Medlab Clinical Ltd., Sydney, NSW, Australia
| | | | - Sean Hall
- Medlab Clinical Ltd., Sydney, NSW, Australia
| |
Collapse
|
30
|
Macpherson AJ, Ganal-Vonarburg SC. IgA-about the unexpected. J Exp Med 2018; 215:1965-1966. [PMID: 30045944 PMCID: PMC6080912 DOI: 10.1084/jem.20181153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this issue of JEM, Nakajima et al. (https://doi.org/10.1084/jem.20180427) demonstrate that glycan-dependent, epitope-independent IgA coating of intestinal bacteria alters bacterial gene expression and metabolism. This conferred coated bacteria with fitness within the mucus niche and contributed to intestinal homeostasis through cross-phylum interactions.
Collapse
Affiliation(s)
- Andrew J Macpherson
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Stephanie C Ganal-Vonarburg
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, Bern, Switzerland
| |
Collapse
|
31
|
Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species. ISME JOURNAL 2018; 12:2919-2928. [PMID: 30065309 DOI: 10.1038/s41396-018-0244-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/31/2018] [Accepted: 07/06/2018] [Indexed: 12/30/2022]
Abstract
The ability to antagonize competing strains and species is often important for bacterial fitness in microbial communities. The extent to which intra-species antagonism drives phenotypic diversity of bacterial species is rarely examined in a comprehensive manner at both the genetic and phenotypic levels. Here we show that for nine abundant human gut Bacteroides species examined, there are only a few LPS glycan genetic types. We show that for a given Bacteroides species, there is a predominant lipopolysaccharide (LPS) glycan locus present in the majority of strains. However, other strains have replacements of glycosyltransferase-encoding genes, in most cases, adjacent to a membrane attack/perforin (MACPF) domain-encoding gene not present in the predominant type. We show that the MACPF genes present in LPS glycan biosynthesis loci of four Bacteroides species encode antimicrobial proteins and in Bacteroides vulgatus and Bacteroides dorei, we show the MACPF toxin targets the LPS of strains with the predominant LPS glycan locus. By a combination of gene deletion and replacement, we converted a MACPF toxin-producing strain into a sensitive strain. Genetic diversity of LPS glycan biosynthesis regions in Bacteroides is similar to phage serotype conversion whereby the receptor is altered to render the strain immune to infection/toxicity, and is a rare example in bacteria of toxin immunity conferred to the toxin-producing strain by replacement of genetic material to modify the receptor rather than by a cognate immunity protein.
Collapse
|
32
|
Zhang Y, Kim TJ, Wroblewska JA, Tesic V, Upadhyay V, Weichselbaum RR, Tumanov AV, Tang H, Guo X, Tang H, Fu YX. Type 3 innate lymphoid cell-derived lymphotoxin prevents microbiota-dependent inflammation. Cell Mol Immunol 2018; 15:697-709. [PMID: 28579615 PMCID: PMC6123485 DOI: 10.1038/cmi.2017.25] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/25/2022] Open
Abstract
Splenomegaly is a well-known phenomenon typically associated with inflammation. However, the underlying cause of this phenotype has not been well characterized. Furthermore, the splenomegaly phenotype seen in lymphotoxin (LT) signaling-deficient mice is characterized by increased numbers of splenocytes and splenic neutrophils. Splenomegaly, as well as the related phenotype of increased lymphocyte counts in non-lymphoid tissues, is thought to result from the absence of secondary lymphoid tissues in LT-deficient mice. We now present evidence that mice deficient in LTα1β2 or LTβR develop splenomegaly and increased numbers of lymphocytes in non-lymphoid tissues in a microbiota-dependent manner. Antibiotic administration to LTα1β2- or LTβR-deficient mice reduces splenomegaly. Furthermore, re-derived germ-free Ltbr-/- mice do not exhibit splenomegaly or increased inflammation in non-lymphoid tissues compared to specific pathogen-free Ltbr-/- mice. By using various LTβ- and LTβR-conditional knockout mice, we demonstrate that retinoic acid-related orphan receptor γT-positive type 3 innate lymphoid cells provide the required active LT signaling to prevent the development of splenomegaly. Thus, this study demonstrates the importance of LT-mediated immune responses for the prevention of splenomegaly and systemic inflammation induced by microbiota.
Collapse
MESH Headings
- Animals
- Immunity, Innate
- Inflammation/genetics
- Inflammation/immunology
- Inflammation/pathology
- Lymphocytes/immunology
- Lymphocytes/pathology
- Lymphotoxin alpha1, beta2 Heterotrimer/genetics
- Lymphotoxin alpha1, beta2 Heterotrimer/immunology
- Lymphotoxin beta Receptor/genetics
- Lymphotoxin beta Receptor/immunology
- Mice
- Mice, Knockout
- Microbiota/immunology
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
Collapse
Affiliation(s)
- Yuan Zhang
- Department of Pathology, University of Chicago, 60637, Chicago, USA, IL
| | - Tae-Jin Kim
- Department of Pathology, University of Chicago, 60637, Chicago, USA, IL
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, 02841, Seoul, Korea
| | - Joanna A Wroblewska
- Committee on Immunology, Department of Pathology, University of Chicago, 60637, Chicago, IL, USA
| | - Vera Tesic
- Department of Pathology, University of Chicago, 60637, Chicago, USA, IL
| | - Vaibhav Upadhyay
- Committee on Immunology, Department of Pathology, University of Chicago, 60637, Chicago, IL, USA
| | - Ralph R Weichselbaum
- Department of Radiation and Cellular Oncology and The Ludwig Center for Metastasis Research, University of Chicago, 60637, Chicago, IL, USA
| | - Alexei V Tumanov
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center San Antonio, 78229, San Antonio, TX, USA
| | - Hong Tang
- Chinese Academy of Sciences Key Laboratory for Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Xiaohuan Guo
- Institute of Immunology, Tsinghua University School of Medicine, 100084, Beijing, China
| | - Haidong Tang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yang-Xin Fu
- Department of Pathology, University of Chicago, 60637, Chicago, USA, IL.
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
33
|
Abstract
Lipopolysaccharide (LPS), a cell-associated glycolipid that makes up the outer leaflet of the outer membrane of Gram-negative bacteria, is a canonical mediator of microbe-host interactions. The most prevalent Gram-negative gut bacterial taxon, Bacteroides, makes up around 50% of the cells in a typical Western gut; these cells harbor ~300 mg of LPS, making it one of the highest-abundance molecules in the intestine. As a starting point for understanding the biological function of Bacteroides LPS, we have identified genes in Bacteroides thetaiotaomicron VPI 5482 involved in the biosynthesis of its lipid A core and glycan, generated mutants that elaborate altered forms of LPS, and used matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry to interrogate the molecular features of these variants. We demonstrate, inter alia, that the glycan does not appear to have a repeating unit, and so this strain produces lipooligosaccharide (LOS) rather than LPS. This result contrasts with Bacteroides vulgatus ATCC 8482, which by SDS-PAGE analysis appears to produce LPS with a repeating unit. Additionally, our identification of the B. thetaiotaomicron LOS oligosaccharide gene cluster allowed us to identify similar clusters in other Bacteroides species. Our work lays the foundation for developing a structure-function relationship for Bacteroides LPS/LOS in the context of host colonization. Much is known about the bacterial species and genes that make up the human microbiome, but remarkably little is known about the molecular mechanisms through which the microbiota influences host biology. A well-known mechanism by which bacteria influence the host centers around lipopolysaccharide (LPS), a component of the Gram-negative bacterial outer membrane. Pathogen-derived LPS is a potent ligand for host receptor Toll-like receptor 4, which plays an important role in sensing bacteria as part of the innate immune response. Puzzlingly, the most common genus of human gut bacteria, Bacteroides, produces LPS but does not elicit a potent proinflammatory response. Previous work showing that Bacteroides LPS differs structurally from pathogen-derived LPS suggested the outlines of an explanation. Here, we take the next step, elucidating the biosynthetic pathway for Bacteroides LPS and generating mutants in the process that will be of great use in understanding how this molecule modulates the host immune response.
Collapse
|
34
|
White EC, Houlden A, Bancroft AJ, Hayes KS, Goldrick M, Grencis RK, Roberts IS. Manipulation of host and parasite microbiotas: Survival strategies during chronic nematode infection. SCIENCE ADVANCES 2018; 4:eaap7399. [PMID: 29546242 PMCID: PMC5851687 DOI: 10.1126/sciadv.aap7399] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/05/2018] [Indexed: 06/08/2023]
Abstract
Intestinal dwelling parasites have evolved closely with the complex intestinal microbiota of their host, but the significance of the host microbiota for metazoan pathogens and the role of their own intestinal microbiota are still not fully known. We have found that the parasitic nematode Trichuris muris acquired a distinct intestinal microbiota from its host, which was required for nematode fitness. Infection of germ-free mice and mice monocolonized with Bacteroides thetaiotaomicron demonstrated that successful T. muris infections require a host microbiota. Following infection, T. muris-induced alterations in the host intestinal microbiota inhibited subsequent rounds of infection, controlling parasite numbers within the host intestine. This dual strategy could promote the long-term survival of the parasite within the intestinal niche necessary for successful chronic nematode infection.
Collapse
Affiliation(s)
- Emily C. White
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Ashley Houlden
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Allison J. Bancroft
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Kelly S. Hayes
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Marie Goldrick
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Richard K. Grencis
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| | - Ian S. Roberts
- School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PT, UK
| |
Collapse
|
35
|
Macpherson AJ, Yilmaz B, Limenitakis JP, Ganal-Vonarburg SC. IgA Function in Relation to the Intestinal Microbiota. Annu Rev Immunol 2018; 36:359-381. [PMID: 29400985 DOI: 10.1146/annurev-immunol-042617-053238] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
IgA is the dominant immunoglobulin isotype produced in mammals, largely secreted across the intestinal mucosal surface. Although induction of IgA has been a hallmark feature of microbiota colonization following colonization in germ-free animals, until recently appreciation of the function of IgA in host-microbial mutualism has depended mainly on indirect evidence of alterations in microbiota composition or penetration of microbes in the absence of somatic mutations in IgA (or compensatory IgM). Highly parallel sequencing techniques that enable high-resolution analysis of either microbial consortia or IgA sequence diversity are now giving us new perspectives on selective targeting of microbial taxa and the trajectory of IgA diversification according to induction mechanisms, between different individuals and over time. The prospects are to link the range of diversified IgA clonotypes to specific antigenic functions in modulating the microbiota composition, position and metabolism to ensure host mutualism.
Collapse
Affiliation(s)
- Andrew J Macpherson
- Maurice Müller Laboratories (Department of Biomedical Research), University of Bern, 3008 Bern, Switzerland.,University Clinic of Visceral Surgery and Medicine, Inselspital, 3010 Bern, Switzerland;
| | - Bahtiyar Yilmaz
- Maurice Müller Laboratories (Department of Biomedical Research), University of Bern, 3008 Bern, Switzerland.,University Clinic of Visceral Surgery and Medicine, Inselspital, 3010 Bern, Switzerland;
| | - Julien P Limenitakis
- Maurice Müller Laboratories (Department of Biomedical Research), University of Bern, 3008 Bern, Switzerland.,University Clinic of Visceral Surgery and Medicine, Inselspital, 3010 Bern, Switzerland;
| | - Stephanie C Ganal-Vonarburg
- Maurice Müller Laboratories (Department of Biomedical Research), University of Bern, 3008 Bern, Switzerland.,University Clinic of Visceral Surgery and Medicine, Inselspital, 3010 Bern, Switzerland;
| |
Collapse
|
36
|
Roughgarden J, Gilbert SF, Rosenberg E, Zilber-Rosenberg I, Lloyd EA. Holobionts as Units of Selection and a Model of Their Population Dynamics and Evolution. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s13752-017-0287-1] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
37
|
Bunker JJ, Erickson SA, Flynn TM, Henry C, Koval JC, Meisel M, Jabri B, Antonopoulos DA, Wilson PC, Bendelac A. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science 2017; 358:science.aan6619. [PMID: 28971969 DOI: 10.1126/science.aan6619] [Citation(s) in RCA: 297] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 12/11/2022]
Abstract
Large quantities of immunoglobulin A (IgA) are constitutively secreted by intestinal plasma cells to coat and contain the commensal microbiota, yet the specificity of these antibodies remains elusive. Here we profiled the reactivities of single murine IgA plasma cells by cloning and characterizing large numbers of monoclonal antibodies. IgAs were not specific to individual bacterial taxa but rather polyreactive, with broad reactivity to a diverse, but defined, subset of microbiota. These antibodies arose at low frequencies among naïve B cells and were selected into the IgA repertoire upon recirculation in Peyer's patches. This selection process occurred independent of microbiota or dietary antigens. Furthermore, although some IgAs acquired somatic mutations, these did not substantially influence their reactivity. These findings reveal an endogenous mechanism driving homeostatic production of polyreactive IgAs with innate specificity to microbiota.
Collapse
Affiliation(s)
- Jeffrey J Bunker
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Steven A Erickson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Carole Henry
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jason C Koval
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Marlies Meisel
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Bana Jabri
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Dionysios A Antonopoulos
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA. .,Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
38
|
Repression of Salmonella Host Cell Invasion by Aromatic Small Molecules from the Human Fecal Metabolome. Appl Environ Microbiol 2017; 83:AEM.01148-17. [PMID: 28754707 DOI: 10.1128/aem.01148-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/18/2017] [Indexed: 02/07/2023] Open
Abstract
The human microbiome is a collection of microorganisms that inhabit every surface of the body that is exposed to the environment, generally coexisting peacefully with their host. These microbes have important functions, such as producing vitamins, aiding in maturation of the immune system, and protecting against pathogens. We have previously shown that a small-molecule extract from the human fecal microbiome has a strong repressive effect on Salmonella enterica serovar Typhimurium host cell invasion by modulating the expression of genes involved in this process. Here, we describe the characterization of this biological activity. Using a series of purification methods, we obtained fractions with biological activity and characterized them by mass spectrometry. These experiments revealed an abundance of aromatic compounds in the bioactive fraction. Selected compounds were obtained from commercial sources and tested with respect to their ability to repress the expression of hilA, the gene encoding the master regulator of invasion genes in Salmonella We found that the aromatic compound 3,4-dimethylbenzoic acid acts as a strong inhibitor of hilA expression and of invasion of cultured host cells by Salmonella Future studies should reveal the molecular details of this phenomenon, such as the signaling cascades involved in sensing this bioactive molecule.IMPORTANCE Microbes constantly sense and adapt to their environment. Often, this is achieved through the production and sensing of small extracellular molecules. The human body is colonized by complex communities of microbes, and, given their biological and chemical diversity, these ecosystems represent a platform where the production and sensing of molecules occur. In previous work, we showed that small molecules produced by microbes from the human gut can significantly impair the virulence of the enteric pathogen Salmonella enterica Here, we describe a specific compound from the human gut that produces this same effect. The results from this work not only shed light on an important biological phenomenon occurring in our bodies but also may represent an opportunity to develop drugs that can target these small-molecule interactions to protect us from enteric infections and other diseases.
Collapse
|
39
|
Evolutionary and ecological forces that shape the bacterial communities of the human gut. Mucosal Immunol 2017; 10:567-579. [PMID: 28145439 PMCID: PMC5700752 DOI: 10.1038/mi.2016.138] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/20/2016] [Indexed: 02/04/2023]
Abstract
Since microbes were first described in the mid-1600s, we have come to appreciate that they live all around and within us with both beneficial and detrimental effects on nearly every aspect of our lives. The human gastrointestinal tract is inhabited by a dynamic community of trillions of bacteria that constantly interact with each other and their human host. The acquisition of these bacteria is not stochastic but determined by circumstance (environment), host rules (genetics, immune state, mucus, etc), and dynamic self-selection among microbes to form stable, resilient communities that are in balance with the host. In this review, we will discuss how these factors lead to formation of the gut bacterial community and influence its interactions with the host. We will also address how gut bacteria contribute to disease and how they could potentially be targeted to prevent and treat a variety of human ailments.
Collapse
|
40
|
Berbers RM, Nierkens S, van Laar JM, Bogaert D, Leavis HL. Microbial Dysbiosis in Common Variable Immune Deficiencies: Evidence, Causes, and Consequences. Trends Immunol 2017; 38:206-216. [DOI: 10.1016/j.it.2016.11.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/29/2016] [Accepted: 11/30/2016] [Indexed: 12/19/2022]
|
41
|
Vo Ngoc DTL, Krist L, van Overveld FJ, Rijkers GT. The long and winding road to IgA deficiency: causes and consequences. Expert Rev Clin Immunol 2016; 13:371-382. [PMID: 27776452 DOI: 10.1080/1744666x.2017.1248410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The most common humoral immunodeficiency is IgA deficiency. One of the first papers addressing the cellular and molecular mechanisms underlying IgA deficiency indicated that immature IgA-positive B-lymphocytes are present in these patients. This suggests that the genetic background for IgA is still intact and that class switching can take place. At this moment, it cannot be ruled out that genetic as well as environmental factors are involved. Areas covered: A clinical presentation, the biological functions of IgA, and the management of IgA deficiency are reviewed. In some IgA deficient patients, a relationship with a loss-of-function mutation in the TACI (transmembrane activator and calcium-modulating cyclophilin ligand interaction) gene has been found. Many other genes also have been associated. Gut microbiota are an important environmental trigger for IgA synthesis. Expert commentary: Expression of IgA deficiency is due to both genetic and environmental factors and a role for gut microbiota cannot be excluded.
Collapse
Affiliation(s)
- D T Laura Vo Ngoc
- a Department of Science , University College Roosevelt , Middelburg , The Netherlands
| | - Lizette Krist
- a Department of Science , University College Roosevelt , Middelburg , The Netherlands
| | - Frans J van Overveld
- a Department of Science , University College Roosevelt , Middelburg , The Netherlands
| | - Ger T Rijkers
- a Department of Science , University College Roosevelt , Middelburg , The Netherlands
| |
Collapse
|
42
|
Pabst O, Cerovic V, Hornef M. Secretory IgA in the Coordination of Establishment and Maintenance of the Microbiota. Trends Immunol 2016; 37:287-296. [PMID: 27066758 DOI: 10.1016/j.it.2016.03.002] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 02/06/2023]
Abstract
Starting at birth, the intestinal microbiota changes dramatically from a highly individual collection of microorganisms, dominated by comparably few species, to a mature, competitive, and diverse microbial community. Microbial colonization triggers and accompanies the maturation of the mucosal immune system and ultimately results in a mutually beneficial host-microbe interrelation in the healthy host. Here, we discuss the role of secretory immunoglobulin A (SIgA) during the establishment of the infant microbiota and life-long host-microbial homeostasis. We critically review the published literature on how SIgA affects the enteric microbiota and highlight the accessibility of the infant microbiota to therapeutic intervention.
Collapse
Affiliation(s)
- Oliver Pabst
- Institute of Molecular Medicine, RWTH University, 52074 Aachen, Germany.
| | - Vuk Cerovic
- Institute of Molecular Medicine, RWTH University, 52074 Aachen, Germany
| | - Mathias Hornef
- Institute of Medical Microbiology, RWTH University, 52074 Aachen, Germany
| |
Collapse
|
43
|
Secretory IgA in complex with Lactobacillus rhamnosus potentiates mucosal dendritic cell-mediated Treg cell differentiation via TLR regulatory proteins, RALDH2 and secretion of IL-10 and TGF-β. Cell Mol Immunol 2016; 14:546-556. [PMID: 26972771 DOI: 10.1038/cmi.2015.110] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 12/16/2022] Open
Abstract
The importance of secretory IgA in controlling the microbiota is well known, yet how the antibody affects the perception of the commensals by the local immune system is still poorly defined. We have previously shown that the transport of secretory IgA in complex with bacteria across intestinal microfold cells results in an association with dendritic cells in Peyer's patches. However, the consequences of such an interaction on dendritic cell conditioning have not been elucidated. In this study, we analyzed the impact of the commensal Lactobacillus rhamnosus, alone or associated with secretory IgA, on the responsiveness of dendritic cells freshly recovered from mouse Peyer's patches, mesenteric lymph nodes, and spleen. Lactobacillus rhamnosus-conditioned mucosal dendritic cells are characterized by increased expression of Toll-like receptor regulatory proteins [including single immunoglobulin interleukin-1 receptor-related molecule, suppressor of cytokine signaling 1, and Toll-interacting molecule] and retinaldehyde dehydrogenase 2, low surface expression of co-stimulatory markers, high anti- versus pro-inflammatory cytokine production ratios, and induction of T regulatory cells with suppressive function. Association with secretory IgA enhanced the anti-inflammatory/regulatory Lactobacillus rhamnosus-induced conditioning of mucosal dendritic cells, particularly in Peyer's patches. At the systemic level, activation of splenic dendritic cells exposed to Lactobacillus rhamnosus was partially dampened upon association with secretory IgA. These data suggest that secretory IgA, through coating of commensal bacteria, contributes to the conditioning of mucosal dendritic cells toward tolerogenic profiles essential for the maintenance of intestinal homeostasis.
Collapse
|
44
|
Abstract
Animals assemble and maintain a diverse but host-specific gut microbial community. In addition to characteristic microbial compositions along the longitudinal axis of the intestines, discrete bacterial communities form in microhabitats, such as the gut lumen, colonic mucus layers and colonic crypts. In this Review, we examine how the spatial distribution of symbiotic bacteria among physical niches in the gut affects the development and maintenance of a resilient microbial ecosystem. We consider novel hypotheses for how nutrient selection, immune activation and other mechanisms control the biogeography of bacteria in the gut, and we discuss the relevance of this spatial heterogeneity to health and disease.
Collapse
|
45
|
The bilateral responsiveness between intestinal microbes and IgA. Trends Immunol 2015; 36:460-70. [PMID: 26169256 DOI: 10.1016/j.it.2015.06.006] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/01/2015] [Accepted: 06/19/2015] [Indexed: 12/30/2022]
Abstract
The immune system has developed strategies to maintain a homeostatic relationship with the resident microbiota. IgA is central in holding this relationship, as the most dominant immunoglobulin isotype at the mucosal surface of the intestine. Recent studies report a role for IgA in shaping the composition of the intestinal microbiota and exploit strategies to characterise IgA-binding bacteria for their inflammatory potential. We review these findings here, and place them in context of the current understanding of the range of microorganisms that contribute to the IgA repertoire and the pathways that determine the quality of the IgA response. We examine why only certain intestinal microbes are coated with IgA, and discuss how understanding the determinants of this specific responsiveness may provide insight into diseases associated with dysbiosis.
Collapse
|