Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants
Abstract Background The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African Ame...
Saved in:
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | Microbiome |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s40168-024-01999-3 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832585580707315712 |
|---|---|
| author | Alain J. Benitez Ceylan Tanes Elliot S. Friedman Joseph P. Zackular Eileen Ford Jeffrey S. Gerber Patricia A. DeRusso Andrea Kelly Hongzhe Li Michal A. Elovitz Gary D. Wu Babette Zemel Kyle Bittinger |
| author_facet | Alain J. Benitez Ceylan Tanes Elliot S. Friedman Joseph P. Zackular Eileen Ford Jeffrey S. Gerber Patricia A. DeRusso Andrea Kelly Hongzhe Li Michal A. Elovitz Gary D. Wu Babette Zemel Kyle Bittinger |
| author_sort | Alain J. Benitez |
| collection | DOAJ |
| description | Abstract Background The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry. Results Stool samples were collected at ages 4, 12, and 24 months for antibiotic-exposed (n = 170) and unexposed (n = 153) participants. A short-term substudy (n = 39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2 weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition. Conclusions Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age. |
| format | Article |
| id | doaj-art-9b9864d9bbf2404895294c575653104a |
| institution | Kabale University |
| issn | 2049-2618 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj-art-9b9864d9bbf2404895294c575653104a2025-01-26T12:43:08ZengBMCMicrobiome2049-26182025-01-0113111110.1186/s40168-024-01999-3Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infantsAlain J. Benitez0Ceylan Tanes1Elliot S. Friedman2Joseph P. Zackular3Eileen Ford4Jeffrey S. Gerber5Patricia A. DeRusso6Andrea Kelly7Hongzhe Li8Michal A. Elovitz9Gary D. Wu10Babette Zemel11Kyle Bittinger12Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of PhiladelphiaDivision of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of PhiladelphiaDivision of Gastroenterology and Hepatology, The University of Pennsylvania Perelman School of MedicineDepartment of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, and The University of Pennsylvania Perelman School of MedicineDivision of Endocrinology and Diabetes, The Children’s Hospital of PhiladelphiaDepartment of Pediatrics, The University of Pennsylvania Perelman School of MedicineDivision of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of PhiladelphiaDepartment of Pediatrics, The University of Pennsylvania Perelman School of MedicineDepartment of Biostatistics, Informatics, and Epidemiology, The University of Pennsylvania Perelman School of MedicineWomen’s Biomedical Research Institute, Icahn School of MedicineDivision of Gastroenterology and Hepatology, The University of Pennsylvania Perelman School of MedicineDivision of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of PhiladelphiaDivision of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of PhiladelphiaAbstract Background The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry. Results Stool samples were collected at ages 4, 12, and 24 months for antibiotic-exposed (n = 170) and unexposed (n = 153) participants. A short-term substudy (n = 39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2 weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition. Conclusions Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.https://doi.org/10.1186/s40168-024-01999-3Infant gut microbiotaAntibioticsAmoxicillinBifidobacteriumMetagenomicsBile acid |
| spellingShingle | Alain J. Benitez Ceylan Tanes Elliot S. Friedman Joseph P. Zackular Eileen Ford Jeffrey S. Gerber Patricia A. DeRusso Andrea Kelly Hongzhe Li Michal A. Elovitz Gary D. Wu Babette Zemel Kyle Bittinger Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants Microbiome Infant gut microbiota Antibiotics Amoxicillin Bifidobacterium Metagenomics Bile acid |
| title | Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants |
| title_full | Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants |
| title_fullStr | Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants |
| title_full_unstemmed | Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants |
| title_short | Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants |
| title_sort | antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants |
| topic | Infant gut microbiota Antibiotics Amoxicillin Bifidobacterium Metagenomics Bile acid |
| url | https://doi.org/10.1186/s40168-024-01999-3 |
| work_keys_str_mv | AT alainjbenitez antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT ceylantanes antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT elliotsfriedman antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT josephpzackular antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT eileenford antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT jeffreysgerber antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT patriciaaderusso antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT andreakelly antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT hongzheli antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT michalaelovitz antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT garydwu antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT babettezemel antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants AT kylebittinger antibioticexposureisassociatedwithminimalgutmicrobiomeperturbationsinhealthyterminfants |