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Feng Y, Pulendran B. Antibiotics, microbiota and the calibration of infant vaccine responses. Nat Immunol 2025:10.1038/s41590-025-02169-9. [PMID: 40389563 DOI: 10.1038/s41590-025-02169-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2025]
Affiliation(s)
- Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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Ryan FJ, Clarke M, Lynn MA, Benson SC, McAlister S, Giles LC, Choo JM, Rossouw C, Ng YY, Semchenko EA, Richard A, Leong LEX, Taylor SL, Blake SJ, Mugabushaka JI, Walker M, Wesselingh SL, Licciardi PV, Seib KL, Tumes DJ, Richmond P, Rogers GB, Marshall HS, Lynn DJ. Bifidobacteria support optimal infant vaccine responses. Nature 2025; 641:456-464. [PMID: 40175554 PMCID: PMC12058517 DOI: 10.1038/s41586-025-08796-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/17/2025] [Indexed: 04/04/2025]
Abstract
Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses1-4; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.
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Affiliation(s)
- Feargal J Ryan
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Michelle Clarke
- Women's and Children's Health Network, North Adelaide, South Australia, Australia
- Adelaide Medical School and The Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Vaccinology and Immunology Research Trials Unit, Women's and Children's Health Network, Adelaide, South Australia, Australia
| | - Miriam A Lynn
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Saoirse C Benson
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Sonia McAlister
- Wesfarmers Centre for Vaccines and Infectious Diseases, The Kids Institute, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Lynne C Giles
- School of Public Health, The University of Adelaide, Adelaide, South Australia, Australia
| | - Jocelyn M Choo
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Charné Rossouw
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Yan Yung Ng
- Vaccine Immunology, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Evgeny A Semchenko
- Institute for Biomedicine and Glycomics, Griffith University, Southport, Queensland, Australia
| | - Alyson Richard
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Lex E X Leong
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Steven L Taylor
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Stephen J Blake
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Joyce I Mugabushaka
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Mary Walker
- Women's and Children's Health Network, North Adelaide, South Australia, Australia
| | - Steve L Wesselingh
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Paul V Licciardi
- Vaccine Immunology, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Kate L Seib
- Institute for Biomedicine and Glycomics, Griffith University, Southport, Queensland, Australia
| | - Damon J Tumes
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia, Australia
| | - Peter Richmond
- Wesfarmers Centre for Vaccines and Infectious Diseases, The Kids Institute, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
- Department of Immunology and General Paediatrics, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Geraint B Rogers
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Helen S Marshall
- Women's and Children's Health Network, North Adelaide, South Australia, Australia
- Adelaide Medical School and The Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Vaccinology and Immunology Research Trials Unit, Women's and Children's Health Network, Adelaide, South Australia, Australia
| | - David J Lynn
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia.
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Martino D, Schultz N, Kaur R, van Haren SD, Kresoje N, Hoch A, Diray-Arce J, Su JL, Levy O, Pichichero M. Respiratory infection- and asthma-prone, low vaccine responder children demonstrate distinct mononuclear cell DNA methylation pathways. Clin Epigenetics 2024; 16:85. [PMID: 38961479 PMCID: PMC11223352 DOI: 10.1186/s13148-024-01703-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Infants with frequent viral and bacterial respiratory infections exhibit compromised immunity to routine immunizations. They are also more likely to develop chronic respiratory diseases in later childhood. This study investigated the feasibility of epigenetic profiling to reveal endotype-specific molecular pathways with potential for early identification and immuno-modulation. Peripheral blood mononuclear cells from respiratory infection allergy/asthma-prone (IAP) infants and non-infection allergy/asthma prone (NIAP) were retrospectively selected for genome-wide DNA methylation and single nucleotide polymorphism analysis. The IAP infants were enriched for the low vaccine responsiveness (LVR) phenotype (Fisher's exact p-value = 0.02). RESULTS An endotype signature of 813 differentially methylated regions (DMRs) comprising 238 lead CpG associations (FDR < 0.05) emerged, implicating pathways related to asthma, mucin production, antigen presentation and inflammasome activation. Allelic variation explained only a minor portion of this signature. Stimulation of mononuclear cells with monophosphoryl lipid A (MPL), a TLR agonist, partially reversed this signature at a subset of CpGs, suggesting the potential for epigenetic remodeling. CONCLUSIONS This proof-of-concept study establishes a foundation for precision endotyping of IAP children and highlights the potential for immune modulation strategies using adjuvants for future investigation.
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Affiliation(s)
- David Martino
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
| | - Nikki Schultz
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Ravinder Kaur
- Centre for Infectious Disease and Vaccine Immunology, Research Institute, Rochester General Hospital, 1425 Portland Avenue, Rochester, NY, 14621, USA
| | - Simon D van Haren
- Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave, BCH 3104, Boston, MA, 02115, USA
| | - Nina Kresoje
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Annmarie Hoch
- Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave, BCH 3104, Boston, MA, 02115, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave, BCH 3104, Boston, MA, 02115, USA
| | - Jessica Lasky Su
- Channing Division of Network Medicine and Harvard Medical School, Boston, MA, 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Department of Pediatrics, Boston Children's Hospital, 300 Longwood Ave, BCH 3104, Boston, MA, 02115, USA
- Channing Division of Network Medicine and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Michael Pichichero
- Centre for Infectious Disease and Vaccine Immunology, Research Institute, Rochester General Hospital, 1425 Portland Avenue, Rochester, NY, 14621, USA
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