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Mann ER, Lam YK, Uhlig HH. Short-chain fatty acids: linking diet, the microbiome and immunity. Nat Rev Immunol 2024:10.1038/s41577-024-01014-8. [PMID: 38565643 DOI: 10.1038/s41577-024-01014-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
The short-chain fatty acids (SCFAs) butyrate, propionate and acetate are microbial metabolites and their availability in the gut and other organs is determined by environmental factors, such as diet and use of antibiotics, that shape the diversity and metabolism of the microbiota. SCFAs regulate epithelial barrier function as well as mucosal and systemic immunity via evolutionary conserved processes that involve G protein-coupled receptor signalling or histone deacetylase activity. Indicatively, the anti-inflammatory role of butyrate is mediated through direct effects on the differentiation of intestinal epithelial cells, phagocytes, B cells and plasma cells, and regulatory and effector T cells. Intestinally derived SCFAs also directly and indirectly affect immunity at extra-intestinal sites, such as the liver, the lungs, the reproductive tract and the brain, and have been implicated in a range of disorders, including infections, intestinal inflammation, autoimmunity, food allergies, asthma and responses to cancer therapies. An ecological understanding of microbial communities and their interrelated metabolic states, as well as the engineering of butyrogenic bacteria may support SCFA-focused interventions for the prevention and treatment of immune-mediated diseases.
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Affiliation(s)
- Elizabeth R Mann
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Ying Ka Lam
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
- Department of Paediatrics, University of Oxford, Oxford, UK.
- Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
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2
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Wilson NG, Hernandez-Leyva A, Schwartz DJ, Bacharier LB, Kau AL. The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma. FEMS MICROBES 2024; 5:xtae010. [PMID: 38560624 PMCID: PMC10981462 DOI: 10.1093/femsmc/xtae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Asthma is a common allergic airway disease that has been associated with the development of the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from a cross-sectional cohort of 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in adults and children 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways, which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. Several differentially abundant ARGs in the asthma cohort encode resistance to macrolide antibiotics, which are often prescribed to patients with asthma. Lastly, we found that ARG and virulence factor (VF) richness in the microbiome were correlated in both cohorts. ARG and VF pairs co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are coselected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.
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Affiliation(s)
- Naomi G Wilson
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, United States
| | - Ariel Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, United States
| | - Drew J Schwartz
- Division of Infectious Diseases, Department of Pediatrics and Center for Women’s Infectious Disease Research, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, United States
| | - Leonard B Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Monroe Carell Jr Children’s Hospital at Vanderbilt University Medical Center, 2200 Children's Way, Nashville, TN 37232, United States
| | - Andrew L Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, United States
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3
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Kahhaleh FG, Barrientos G, Conrad ML. The gut-lung axis and asthma susceptibility in early life. Acta Physiol (Oxf) 2024; 240:e14092. [PMID: 38251788 DOI: 10.1111/apha.14092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/06/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024]
Abstract
Asthma is the most common chronic disease among children, with more than 300 million cases worldwide. Over the past several decades, asthma incidence has grown, and epidemiological studies identify the modernized lifestyle as playing a strong contributing role in this phenomenon. In particular, lifestyle factors that modify the maternal gut microbiome during pregnancy, or the infant microbiome in early life, can act as developmental programming events which determine health or disease susceptibility later in life. Microbial colonization of the gut begins at birth, and factors such as delivery mode, breastfeeding, diet, antibiotic use, and exposure to environmental bacteria influence the development of the infant microbiome. Colonization of the gut microbiome is crucial for proper immune system development and disruptions to this process can predispose a child to asthma development. Here, we describe the importance of early-life events for shaping immune responses along the gut-lung axis and why they may provide a window of opportunity for asthma prevention.
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Affiliation(s)
- Fariz G Kahhaleh
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gabriela Barrientos
- Laboratory of Experimental Medicine, Hospital Alemán, Buenos Aires, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires, Argentina
| | - Melanie L Conrad
- Institute of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
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4
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Kong J, Yang F, Zong Y, Wang M, Jiang S, Ma Z, Li Z, Li W, Cai Y, Zhang H, Zhao X, Wang J. Early-life antibiotic exposure promotes house dust mite-induced allergic airway inflammation by impacting gut microbiota and lung lipid metabolism. Int Immunopharmacol 2024; 128:111449. [PMID: 38199196 DOI: 10.1016/j.intimp.2023.111449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Asthma is a chronic inflammatory respiratory disease. Early-life antibiotic exposure is a unique risk factor for the incidence and severity of asthma later in life. Perturbations in microbial-metabolite-immune interaction caused by antibiotics are closely associated with the pathogenesis of allergy and asthma. We investigated the effect of early intervention with common oral antibiotics on later asthma exacerbations and found that different antibiotic exposures can amplify different types of immune responses induced by HDM. Cefixime (CFX) promoted a biased type 2 inflammation, azithromycin (AZM) enhanced Th17 immune response, and cefuroxime axetil (CFA) induced eosinophils recruitment. Moreover, early-life antibiotic exposure can have short- and long-term effects on the abundance, composition, and diversity of the gut microbiota. In the model of CFX-promoted type 2 airway inflammation, fecal metabolomics indicated abnormal lipid metabolism and T cell response. Lipidomic also suggested allergic airway inflammation amplified by CFX is closely associated with abnormal lipid metabolism in lung tissues. Moreover, abnormalities in lipid metabolism-related genes (LMRGs) were found to have cellular heterogeneity be associated with asthma severity by bioinformatics analysis.
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Affiliation(s)
- Jingwei Kong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Fan Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yuhan Zong
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Manting Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Shiyuan Jiang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zhaotian Ma
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zhuqing Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wenle Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yuyang Cai
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Huixian Zhang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoshan Zhao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China; School of Chinese Medicine, Southern Medical University, Guangzhou, China.
| | - Ji Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China.
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5
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Reuter S, Raspe J, Taube C. Microbes little helpers and suppliers for therapeutic asthma approaches. Respir Res 2024; 25:29. [PMID: 38218816 PMCID: PMC10787474 DOI: 10.1186/s12931-023-02660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 01/15/2024] Open
Abstract
Bronchial asthma is a prevalent and increasingly chronic inflammatory lung disease affecting over 300 million people globally. Initially considered an allergic disorder driven by mast cells and eosinophils, asthma is now recognized as a complex syndrome with various clinical phenotypes and immunological endotypes. These encompass type 2 inflammatory endotypes characterized by interleukin (IL)-4, IL-5, and IL-13 dominance, alongside others featuring mixed or non-eosinophilic inflammation. Therapeutic success varies significantly based on asthma phenotypes, with inhaled corticosteroids and beta-2 agonists effective for milder forms, but limited in severe cases. Novel antibody-based therapies have shown promise, primarily for severe allergic and type 2-high asthma. To address this gap, novel treatment strategies are essential for better control of asthma pathology, prevention, and exacerbation reduction. One promising approach involves stimulating endogenous anti-inflammatory responses through regulatory T cells (Tregs). Tregs play a vital role in maintaining immune homeostasis, preventing autoimmunity, and mitigating excessive inflammation after pathogenic encounters. Tregs have demonstrated their ability to control both type 2-high and type 2-low inflammation in murine models and dampen human cell-dependent allergic airway inflammation. Furthermore, microbes, typically associated with disease development, have shown immune-dampening properties that could be harnessed for therapeutic benefits. Both commensal microbiota and pathogenic microbes have demonstrated potential in bacterial-host interactions for therapeutic purposes. This review explores microbe-associated approaches as potential treatments for inflammatory diseases, shedding light on current and future therapeutics.
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Affiliation(s)
- Sebastian Reuter
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany.
| | - Jonas Raspe
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany
| | - Christian Taube
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany
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6
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Haraoui LP, Blaser MJ. The Microbiome and Infectious Diseases. Clin Infect Dis 2023; 77:S441-S446. [PMID: 38051971 DOI: 10.1093/cid/ciad577] [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: 12/07/2023] Open
Abstract
Our perception of microbes has considerably changed since the recognition of their pathogenic potential in the 19th century. The discovery of antibiotics and their subsequent widespread adoption have substantially altered the landscape of medicine, providing us with treatment options for many infectious diseases and enabling the deployment of previously risky interventions (eg, surgical procedures and chemotherapy), while also leading to the rise of AMR. The latter is commonly viewed as the predominant downside of antibiotic use. However, with the increasing recognition that all metazoan organisms rely on a community of microbes (the microbiota) for normal development and for most physiologic processes, the negative impacts of antibiotic use now extend well beyond AMR. Using the iceberg as a metaphor, we argue that the effects of antibiotics on AMR represent the tip of the iceberg, with much greater repercussions stemming from their role in the rise of so-called noncommunicable diseases (including obesity, diabetes, allergic and autoimmune diseases, neurodevelopmental disorders, and certain cancers). We highlight some of the emerging science around the intersection of the microbiome, antibiotic use, and health (including biological costs and future therapeutic avenues), and we advocate a more nuanced approach in evaluating the impacts of proposed antibiotic use, especially in the setting of preexposure and postexposure prophylaxis.
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Affiliation(s)
- Louis-Patrick Haraoui
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Centre de Recherche Charles-Le Moyne, Greenfield Park, Quebec, Canada
- Humans & the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Martin J Blaser
- Humans & the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
- Robert Wood Johnson School of Medicine, Departments of Medicine and Pathology & Laboratory Medicine, New Brunswick, New Jersey, USA
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7
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Schill EM, Joyce EL, Floyd AN, Udayan S, Rusconi B, Gaddipati S, Barrios BE, John V, Kaye ME, Kulkarni DH, Pauta JT, McDonald KG, Newberry RD. Vancomycin-induced gut microbial dysbiosis alters enteric neuron-macrophage interactions during a critical period of postnatal development. Front Immunol 2023; 14:1268909. [PMID: 37901245 PMCID: PMC10602895 DOI: 10.3389/fimmu.2023.1268909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023] Open
Abstract
Vancomycin is a broad-spectrum antibiotic widely used in cases of suspected sepsis in premature neonates. While appropriate and potentially lifesaving in this setting, early-life antibiotic exposure alters the developing microbiome and is associated with an increased risk of deadly complications, including late-onset sepsis (LOS) and necrotizing enterocolitis (NEC). Recent studies show that neonatal vancomycin treatment disrupts postnatal enteric nervous system (ENS) development in mouse pups, which is in part dependent upon neuroimmune interactions. This suggests that early-life antibiotic exposure could disrupt these interactions in the neonatal gut. Notably, a subset of tissue-resident intestinal macrophages, muscularis macrophages, has been identified as important contributors to the development of postnatal ENS. We hypothesized that vancomycin-induced neonatal dysbiosis impacts postnatal ENS development through its effects on macrophages. Using a mouse model, we found that exposure to vancomycin in the first 10 days of life, but not in adult mice, resulted in an expansion of pro-inflammatory colonic macrophages by increasing the recruitment of bone-marrow-derived macrophages. Single-cell RNA sequencing of neonatal colonic macrophages revealed that early-life vancomycin exposure was associated with an increase in immature and inflammatory macrophages, consistent with an influx of circulating monocytes differentiating into macrophages. Lineage tracing confirmed that vancomycin significantly increased the non-yolk-sac-derived macrophage population. Consistent with these results, early-life vancomycin exposure did not expand the colonic macrophage population nor decrease enteric neuron density in CCR2-deficient mice. Collectively, these findings demonstrate that early-life vancomycin exposure alters macrophage number and phenotypes in distinct ways compared with vancomycin exposure in adult mice and results in altered ENS development.
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Affiliation(s)
- Ellen Merrick Schill
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Elisabeth L. Joyce
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Alexandria N. Floyd
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Sreeram Udayan
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Brigida Rusconi
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Shreya Gaddipati
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Bibiana E. Barrios
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Vini John
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Mitchell E. Kaye
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Devesha H. Kulkarni
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Jocelyn T. Pauta
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Keely G. McDonald
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Rodney D. Newberry
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
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8
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Theodosiou AA, Jones CE, Read RC, Bogaert D. Microbiotoxicity: antibiotic usage and its unintended harm to the microbiome. Curr Opin Infect Dis 2023; 36:371-378. [PMID: 37466039 PMCID: PMC10487351 DOI: 10.1097/qco.0000000000000945] [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: 07/20/2023]
Abstract
PURPOSE OF REVIEW Antibiotic use is associated with development of antimicrobial resistance and dysregulation of the microbiome (the overall host microbial community). These changes have in turn been associated with downstream adverse health outcomes. This review analyses recent important publications in a rapidly evolving field, contextualizing the available evidence to assist clinicians weighing the potential risks of antibiotics on a patient's microbiome. RECENT FINDING Although the majority of microbiome research is observational, we highlight recent interventional studies probing the associations between antibiotic use, microbiome disruption, and ill-health. These studies include germ-free mouse models, antibiotic challenge in healthy human volunteers, and a phase III study of the world's first approved microbiome-based medicine. SUMMARY The growing body of relevant clinical and experimental evidence for antibiotic-mediated microbiome perturbation is concerning, although further causal evidence is required. Within the limits of this evidence, we propose the novel term 'microbiotoxicity' to describe the unintended harms of antibiotics on a patient's microbiome. We suggest a framework for prescribers to weigh microbiotoxic effects against the intended benefits of antibiotic use.
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Affiliation(s)
- Anastasia A. Theodosiou
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton
| | - Christine E. Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton
| | - Robert C. Read
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton
| | - Debby Bogaert
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
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9
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Vallet N, Salmona M, Malet-Villemagne J, Bredel M, Bondeelle L, Tournier S, Mercier-Delarue S, Cassonnet S, Ingram B, Peffault de Latour R, Bergeron A, Socié G, Le Goff J, Lepage P, Michonneau D. Circulating T cell profiles associate with enterotype signatures underlying hematological malignancy relapses. Cell Host Microbe 2023; 31:1386-1403.e6. [PMID: 37463582 DOI: 10.1016/j.chom.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/23/2023] [Accepted: 06/19/2023] [Indexed: 07/20/2023]
Abstract
Early administration of azithromycin after allogeneic hematopoietic stem cell transplantation was shown to increase the relapse of hematological malignancies. To determine the impact of azithromycin on the post-transplant gut ecosystem and its influence on relapse, we characterized overtime gut bacteriome, virome, and metabolome of 55 patients treated with azithromycin or a placebo. We describe four enterotypes and the network of associated bacteriophage species and metabolic pathways. One enterotype associates with sustained remission. One taxon from Bacteroides specifically associates with relapse, while two from Bacteroides and Prevotella correlate with complete remission. These taxa are associated with lipid, pentose, and branched-chain amino acid metabolic pathways and several bacteriophage species. Enterotypes and taxa associate with exhausted T cells and the functional status of circulating immune cells. These results illustrate how an antibiotic influences a complex network of gut bacteria, viruses, and metabolites and may promote cancer relapse through modifications of immune cells.
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Affiliation(s)
- Nicolas Vallet
- Université de Paris Cité, INSERM U976, 75010 Paris, France
| | - Maud Salmona
- Université de Paris Cité, INSERM U976, 75010 Paris, France; Virology Department, AP-HP, Saint-Louis Hospital, 75010 Paris, France
| | - Jeanne Malet-Villemagne
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - Maxime Bredel
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - Louise Bondeelle
- Pneumology Unit, AP-HP, Saint-Louis Hospital, 75010 Paris, France
| | - Simon Tournier
- Core Facilities, Saint-Louis Research Institute, Université de Paris Cité, UAR 2030/US 53, 75010 Paris, France
| | | | - Stéphane Cassonnet
- Service de Biostatistique et Information Médicale, AP-HP, Saint-Louis Hospital, 75010 Paris, France
| | | | - Régis Peffault de Latour
- Hematology Transplantation, AP-HP, Saint-Louis Hospital, 1 avenue Claude Vellefaux, 75010 Paris, France; Cryostem Consortium, 13382 Marseille, France
| | - Anne Bergeron
- Pneumology Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Gérard Socié
- Université de Paris Cité, INSERM U976, 75010 Paris, France; Hematology Transplantation, AP-HP, Saint-Louis Hospital, 1 avenue Claude Vellefaux, 75010 Paris, France
| | - Jérome Le Goff
- Université de Paris Cité, INSERM U976, 75010 Paris, France; Virology Department, AP-HP, Saint-Louis Hospital, 75010 Paris, France
| | - Patricia Lepage
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - David Michonneau
- Université de Paris Cité, INSERM U976, 75010 Paris, France; Hematology Transplantation, AP-HP, Saint-Louis Hospital, 1 avenue Claude Vellefaux, 75010 Paris, France.
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10
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Peppas I, Ford AM, Furness CL, Greaves MF. Gut microbiome immaturity and childhood acute lymphoblastic leukaemia. Nat Rev Cancer 2023; 23:565-576. [PMID: 37280427 PMCID: PMC10243253 DOI: 10.1038/s41568-023-00584-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 06/08/2023]
Abstract
Acute lymphoblastic leukaemia (ALL) is the most common cancer of childhood. Here, we map emerging evidence suggesting that children with ALL at the time of diagnosis may have a delayed maturation of the gut microbiome compared with healthy children. This finding may be associated with early-life epidemiological factors previously identified as risk indicators for childhood ALL, including caesarean section birth, diminished breast feeding and paucity of social contacts. The consistently observed deficiency in short-chain fatty-acid-producing bacterial taxa in children with ALL has the potential to promote dysregulated immune responses and to, ultimately, increase the risk of transformation of preleukaemic clones in response to common infectious triggers. These data endorse the concept that a microbiome deficit in early life may contribute to the development of the major subtypes of childhood ALL and encourage the notion of risk-reducing microbiome-targeted intervention in the future.
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Affiliation(s)
- Ioannis Peppas
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Paediatric Oncology, The Royal Marsden Hospital Sutton, Surrey, UK
| | - Anthony M Ford
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Caroline L Furness
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Paediatric Oncology, The Royal Marsden Hospital Sutton, Surrey, UK
| | - Mel F Greaves
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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11
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Borbet TC, Pawline MB, Li J, Ho ML, Yin YS, Zhang X, Novikova E, Jackson K, Mullins BJ, Ruiz VE, Hines MJ, Zhang XS, Müller A, Koralov SB, Blaser MJ. Disruption of the early-life microbiota alters Peyer's patch development and germinal center formation in gastrointestinal-associated lymphoid tissue. iScience 2023; 26:106810. [PMID: 37235047 PMCID: PMC10206152 DOI: 10.1016/j.isci.2023.106810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/17/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
During postnatal development, both the maturing microbiome and the host immune system are susceptible to environmental perturbations such as antibiotic use. The impact of timing in which antibiotic exposure occurs was investigated by treating mice from days 5-9 with amoxicillin or azithromycin, two of the most commonly prescribed medications in children. Both early-life antibiotic regimens disrupted Peyer's patch development and immune cell abundance, with a sustained decrease in germinal center formation and diminished intestinal immunoglobulin A (IgA) production. These effects were less pronounced in adult mice. Through comparative analysis of microbial taxa, Bifidobacterium longum abundance was found to be associated with germinal center frequency. When re-introduced to antibiotic-exposed mice, B. longum partially rescued the immunological deficits. These findings suggest that early-life antibiotic use affects the development of intestinal IgA-producing B cell functions and that probiotic strains could be used to restore normal development after antibiotic exposure.
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Affiliation(s)
- Timothy C. Borbet
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Miranda B. Pawline
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Jackie Li
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Melody L. Ho
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Yue Sandra Yin
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ 08854, USA
| | - Xiaozhou Zhang
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Ekaterina Novikova
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Katelyn Jackson
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Briana J. Mullins
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Victoria E. Ruiz
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Marcus J. Hines
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Xue-Song Zhang
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ 08854, USA
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Sergei B. Koralov
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Martin J. Blaser
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ 08854, USA
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12
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Luchen CC, Chibuye M, Spijker R, Simuyandi M, Chisenga C, Bosomprah S, Chilengi R, Schultsz C, Mende DR, Harris VC. Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review. PLoS Med 2023; 20:e1004235. [PMID: 37368871 PMCID: PMC10298773 DOI: 10.1371/journal.pmed.1004235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/13/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Inappropriate antimicrobial usage is a key driver of antimicrobial resistance (AMR). Low- and middle-income countries (LMICs) are disproportionately burdened by AMR and young children are especially vulnerable to infections with AMR-bearing pathogens. The impact of antibiotics on the microbiome, selection, persistence, and horizontal spread of AMR genes is insufficiently characterized and understood in children in LMICs. This systematic review aims to collate and evaluate the available literature describing the impact of antibiotics on the infant gut microbiome and resistome in LMICs. METHODS AND FINDINGS In this systematic review, we searched the online databases MEDLINE (1946 to 28 January 2023), EMBASE (1947 to 28 January 2023), SCOPUS (1945 to 29 January 2023), WHO Global Index Medicus (searched up to 29 January 2023), and SciELO (searched up to 29 January 2023). A total of 4,369 articles were retrieved across the databases. Duplicates were removed resulting in 2,748 unique articles. Screening by title and abstract excluded 2,666 articles, 92 articles were assessed based on the full text, and 10 studies met the eligibility criteria that included human studies conducted in LMICs among children below the age of 2 that reported gut microbiome composition and/or resistome composition (AMR genes) following antibiotic usage. The included studies were all randomized control trials (RCTs) and were assessed for risk of bias using the Cochrane risk-of-bias for randomized studies tool. Overall, antibiotics reduced gut microbiome diversity and increased antibiotic-specific resistance gene abundance in antibiotic treatment groups as compared to the placebo. The most widely tested antibiotic was azithromycin that decreased the diversity of the gut microbiome and significantly increased macrolide resistance as early as 5 days posttreatment. A major limitation of this study was paucity of available studies that cover this subject area. Specifically, the range of antibiotics assessed did not include the most commonly used antibiotics in LMIC populations. CONCLUSION In this study, we observed that antibiotics significantly reduce the diversity and alter the composition of the infant gut microbiome in LMICs, while concomitantly selecting for resistance genes whose persistence can last for months following treatment. Considerable heterogeneity in study methodology, timing and duration of sampling, and sequencing methodology in currently available research limit insights into antibiotic impacts on the microbiome and resistome in children in LMICs. More research is urgently needed to fill this gap in order to better understand whether antibiotic-driven reductions in microbiome diversity and selection of AMR genes place LMIC children at risk for adverse health outcomes, including infections with AMR-bearing pathogens.
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Affiliation(s)
- Charlie C. Luchen
- Amsterdam UMC, location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Amsterdam Institute of Infection and Immunity, Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Mwelwa Chibuye
- Amsterdam UMC, location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Amsterdam Institute of Infection and Immunity, Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Rene Spijker
- Amsterdam UMC, location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | - Michelo Simuyandi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Caroline Chisenga
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Samuel Bosomprah
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Department of Biostatistics, School of Public Health, University of Ghana, Accra, Ghana
| | - Roma Chilengi
- Research Division, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia
- Republic of Zambia State House, Lusaka, Zambia
| | - Constance Schultsz
- Amsterdam UMC, location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
- Amsterdam Institute of Infection and Immunity, Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology, Amsterdam, the Netherlands
| | - Daniel R. Mende
- Amsterdam Institute of Infection and Immunity, Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Medical Microbiology, Amsterdam, the Netherlands
| | - Vanessa C. Harris
- Amsterdam UMC, location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
- Amsterdam Institute of Infection and Immunity, Infectious Diseases, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Internal Medicine, Division of Infectious Diseases, Amsterdam, the Netherlands
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13
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Campbell C, Kandalgaonkar MR, Golonka RM, Yeoh BS, Vijay-Kumar M, Saha P. Crosstalk between Gut Microbiota and Host Immunity: Impact on Inflammation and Immunotherapy. Biomedicines 2023; 11:biomedicines11020294. [PMID: 36830830 PMCID: PMC9953403 DOI: 10.3390/biomedicines11020294] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Gut microbes and their metabolites are actively involved in the development and regulation of host immunity, which can influence disease susceptibility. Herein, we review the most recent research advancements in the gut microbiota-immune axis. We discuss in detail how the gut microbiota is a tipping point for neonatal immune development as indicated by newly uncovered phenomenon, such as maternal imprinting, in utero intestinal metabolome, and weaning reaction. We describe how the gut microbiota shapes both innate and adaptive immunity with emphasis on the metabolites short-chain fatty acids and secondary bile acids. We also comprehensively delineate how disruption in the microbiota-immune axis results in immune-mediated diseases, such as gastrointestinal infections, inflammatory bowel diseases, cardiometabolic disorders (e.g., cardiovascular diseases, diabetes, and hypertension), autoimmunity (e.g., rheumatoid arthritis), hypersensitivity (e.g., asthma and allergies), psychological disorders (e.g., anxiety), and cancer (e.g., colorectal and hepatic). We further encompass the role of fecal microbiota transplantation, probiotics, prebiotics, and dietary polyphenols in reshaping the gut microbiota and their therapeutic potential. Continuing, we examine how the gut microbiota modulates immune therapies, including immune checkpoint inhibitors, JAK inhibitors, and anti-TNF therapies. We lastly mention the current challenges in metagenomics, germ-free models, and microbiota recapitulation to a achieve fundamental understanding for how gut microbiota regulates immunity. Altogether, this review proposes improving immunotherapy efficacy from the perspective of microbiome-targeted interventions.
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Affiliation(s)
- Connor Campbell
- Department of Physiology & Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Mrunmayee R. Kandalgaonkar
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Rachel M. Golonka
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Beng San Yeoh
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Matam Vijay-Kumar
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Piu Saha
- Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
- Correspondence:
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Wilson NG, Hernandez-Leyva A, Schwartz DJ, Bacharier LB, Kau AL. The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522677. [PMID: 36711684 PMCID: PMC9882014 DOI: 10.1101/2023.01.03.522677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Asthma is a common allergic airway disease that develops in association with the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in children and adults 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. One differentially abundant ARG was a macrolide resistance marker, ermF, which significantly co-occurred with the Bacteroides fragilis toxin, suggesting a possible relationship between enterotoxigenic B. fragilis, antibiotic resistance, and asthma. Lastly, we found multiple virulence factor (VF) and ARG pairs that co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are co-selected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.
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Affiliation(s)
- Naomi G. Wilson
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ariel Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Drew J. Schwartz
- Division of Infectious Diseases, Department of Pediatrics and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Leonard B. Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Monroe Carell Jr Children’s Hospital at Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew L. Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
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