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Patangia DV, Grimaud G, O'Shea CA, Ryan CA, Dempsey E, Stanton C, Ross RP. Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome. MICROBIOME 2024; 12:19. [PMID: 38310316 PMCID: PMC10837951 DOI: 10.1186/s40168-023-01732-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/24/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied. METHODS Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort's first week of life. RESULTS Newborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs). CONCLUSION These data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures-leading to what can be an extensive and diverse resistome. Video Abstract.
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Affiliation(s)
- Dhrati V Patangia
- School of Microbiology, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Ghjuvan Grimaud
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | | | - C A Ryan
- APC Microbiome Ireland, Cork, Ireland
| | - Eugene Dempsey
- APC Microbiome Ireland, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- Infant Research Centre, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy Co., Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland.
- APC Microbiome Ireland, Cork, Ireland.
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Tejesvi MV, Turunen J, Salmi S, Reunanen J, Paalanne N, Tapiainen T. Delivery Mode and Perinatal Antibiotics Influence the Infant Gut Bacteriome and Mycobiome: A Network Analysis. J Fungi (Basel) 2023; 9:718. [PMID: 37504707 PMCID: PMC10381809 DOI: 10.3390/jof9070718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023] Open
Abstract
Both exposure to antibiotics at birth and delivery via Caesarean section influence the gut bacteriome's development in infants. Using 16S rRNA and internal transcribed spacer sequencing on the Ion Torrent platform, we employed network analysis to investigate the bacterial and fungal interkingdom relationships in the gut microbiome from birth to age 18 months in a prospective cohort study of 140 infants. The gut microbiome at ages six and 18 months revealed distinctive microbial interactions, including both positive and negative associations between bacterial and fungal genera in the gut ecosystem. Perinatal factors, delivery mode and intrapartum antibiotic exposure affected the associations between bacterial and fungal species. In infants exposed and unexposed to perinatal antibiotics, the gut microbiome formed distinct networks for the bacteriome and mycobiome. The fungi Saccharomyces, Trichosporon, Pezoloma, Cystofilobasidium, Rigidoporus and Fomitopsis were strongly associated with exposure to antibiotics at birth. Hyaloscypha, Trichosporon, Fomitopsis and Vishniacozyma were strongly associated with the control group that was not exposed to antibiotics. Five distinct networks were formed according to delivery mode. The present study confirms that bacteria and fungi clearly interact in the infant gut ecosystem. Furthermore, perinatal factors appear to influence the relationships between bacteria and fungi in the developing gut microbiome.
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Affiliation(s)
- Mysore V Tejesvi
- Research Unit of Clinical Medicine, University of Oulu, 90014 Oulu, Finland
- Ecology and Genetics, Faculty of Science, University of Oulu, 90014 Oulu, Finland
| | - Jenni Turunen
- Research Unit of Clinical Medicine, University of Oulu, 90014 Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
| | - Sonja Salmi
- Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, 90014 Oulu, Finland
- Disease Networks Research Unit, University of Oulu, 90014 Oulu, Finland
| | - Justus Reunanen
- Biocenter Oulu, University of Oulu, 90014 Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, 90014 Oulu, Finland
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, 90014 Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, 90014 Oulu, Finland
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine, University of Oulu, 90014 Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, 90014 Oulu, Finland
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Robertson RC, Edens TJ, Carr L, Mutasa K, Gough EK, Evans C, Geum HM, Baharmand I, Gill SK, Ntozini R, Smith LE, Chasekwa B, Majo FD, Tavengwa NV, Mutasa B, Francis F, Tome J, Stoltzfus RJ, Humphrey JH, Prendergast AJ, Manges AR. The gut microbiome and early-life growth in a population with high prevalence of stunting. Nat Commun 2023; 14:654. [PMID: 36788215 PMCID: PMC9929340 DOI: 10.1038/s41467-023-36135-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/12/2023] [Indexed: 02/16/2023] Open
Abstract
Stunting affects one-in-five children globally and is associated with greater infectious morbidity, mortality and neurodevelopmental deficits. Recent evidence suggests that the early-life gut microbiome affects child growth through immune, metabolic and endocrine pathways. Using whole metagenomic sequencing, we map the assembly of the gut microbiome in 335 children from rural Zimbabwe from 1-18 months of age who were enrolled in the Sanitation, Hygiene, Infant Nutrition Efficacy Trial (SHINE; NCT01824940), a randomized trial of improved water, sanitation and hygiene (WASH) and infant and young child feeding (IYCF). Here, we show that the early-life gut microbiome undergoes programmed assembly that is unresponsive to the randomized interventions intended to improve linear growth. However, maternal HIV infection is associated with over-diversification and over-maturity of the early-life gut microbiome in their uninfected children, in addition to reduced abundance of Bifidobacterium species. Using machine learning models (XGBoost), we show that taxonomic microbiome features are poorly predictive of child growth, however functional metagenomic features, particularly B-vitamin and nucleotide biosynthesis pathways, moderately predict both attained linear and ponderal growth and growth velocity. New approaches targeting the gut microbiome in early childhood may complement efforts to combat child undernutrition.
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Affiliation(s)
- Ruairi C Robertson
- Blizard Institute, Queen Mary University of London, London, UK
- Microenvironment & Immunity Unit, INSERM U1224, Institut Pasteur, 75015, Paris, France
| | | | - Lynnea Carr
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Kuda Mutasa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Ethan K Gough
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ceri Evans
- Blizard Institute, Queen Mary University of London, London, UK
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Hyun Min Geum
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Iman Baharmand
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Sandeep K Gill
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Robert Ntozini
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Laura E Smith
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Department of Public and Ecosystem Health, Cornell University, Ithaca, NY, USA
| | - Bernard Chasekwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Florence D Majo
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Naume V Tavengwa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Batsirai Mutasa
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Freddy Francis
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Joice Tome
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | | | - Jean H Humphrey
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew J Prendergast
- Blizard Institute, Queen Mary University of London, London, UK
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Amee R Manges
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada.
- British Columbia Centre for Disease Control, Vancouver, BC, Canada.
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Hamidou Soumana I, Ryu MH, Leitao Filho FS, Yang J, Orach J, Nislow C, Leung JM, Rider CF, Carlsten C. Exposure to diesel exhaust alters the functional metagenomic composition of the airway microbiome in former smokers. ENVIRONMENTAL RESEARCH 2023; 216:114826. [PMID: 36403657 DOI: 10.1016/j.envres.2022.114826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/01/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The lung microbiome plays a crucial role in airway homeostasis, yet we know little about the effects of exposures such as air pollution therein. We conducted a controlled human exposure study to assess the impact of diesel exhaust (DE) on the human airway microbiome. Twenty-four participants (former smokers with mild to moderate COPD (N = 9), healthy former smokers (N = 7), and control healthy never smokers (N = 8)) were exposed to DE (300 μg/m3 PM2.5) and filtered air (FA) for 2 h in a randomized order, separated by a 4-week washout. Endobronchial brushing samples were collected 24 h post-exposure and sequenced for the 16S microbiome, which was analyzed using QIIME2 and PICRUSt2 to examine diversity and metabolic functions, respectively. DE exposure altered airway microbiome metabolic functions in spite of statistically stable microbiome diversity. Affected functions included increases in: superpathway of purine deoxyribonucleosides degradation (pathway differential abundance 743.9, CI 95% 201.2 to 1286.6), thiazole biosynthesis I (668.5, CI 95% 139.9 to 1197.06), and L-lysine biosynthesis II (666.5, CI 95% 73.3 to 1257.7). There was an exposure-by-age effect, such that menaquinone biosynthesis superpathways were the most enriched function in the microbiome of participants aged >60, irrespective of smoking or health status. Moreover, exposure-by-phenotype analysis showed metabolic alterations in former smokers after DE exposure. These observations suggest that DE exposure induced substantial changes in the metabolic functions of the airway microbiome despite the absence of diversity changes.
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Affiliation(s)
- Illiassou Hamidou Soumana
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Min Hyung Ryu
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Julia Yang
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Juma Orach
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Janice M Leung
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Christopher Francis Rider
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Christopher Carlsten
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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Díaz-Rodríguez K, Pacheco-Aranibar J, Manrique-Sam C, Ita-Balta Y, del Carpio-Toia AM, López-Casaperalta P, Chocano-Rosas T, Fernandez-F F, Villanueva-Salas J, Bernabe-Ortiz JC. Intestinal Microbiota in Children with Anemia in Southern Peru through Next-Generation Sequencing Technology. CHILDREN (BASEL, SWITZERLAND) 2022; 9:1615. [PMID: 36360343 PMCID: PMC9688611 DOI: 10.3390/children9111615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 08/30/2023]
Abstract
Knowledge of the sequencing of the 16S rRNA gene constitutes a true revolution in understanding the composition of the intestinal microbiota and its implication in health states. This study details microbial composition through next-generation sequencing (NGS) technology in children with anemia. Anemia is the most frequent hematological disorder that affects human beings. In Peru, it is one of the conditions that presents the most significant concern due to the adverse effects that cause it, such as delayed growth and psychomotor development, in addition to a deficiency in cognitive development.
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Affiliation(s)
- Karla Díaz-Rodríguez
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Jani Pacheco-Aranibar
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Deparment of Biology, Universidad Nacional de San Agustín, Santa Catalina Nro. 117, Arequipa 04001, Peru
- Department of Molecular Biology, Instituto de Biotecnología del ADN Uchumayo, Arequipa 04401, Peru
| | - Cecilia Manrique-Sam
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Yuma Ita-Balta
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Agueda Muñoz del Carpio-Toia
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Patricia López-Casaperalta
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Teresa Chocano-Rosas
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Fernando Fernandez-F
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Jose Villanueva-Salas
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
| | - Julio Cesar Bernabe-Ortiz
- Post-Graduate School, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
- Deparment of Biology, Universidad Nacional de San Agustín, Santa Catalina Nro. 117, Arequipa 04001, Peru
- Department of Molecular Biology, Instituto de Biotecnología del ADN Uchumayo, Arequipa 04401, Peru
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n, Umacollo, Arequipa 04013, Peru
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Miniello VL, Verga MC, Miniello A, Di Mauro C, Diaferio L, Francavilla R. Complementary Feeding and Iron Status: " The Unbearable Lightness of Being" Infants. Nutrients 2021; 13:4201. [PMID: 34959753 PMCID: PMC8707490 DOI: 10.3390/nu13124201] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022] Open
Abstract
The complementary feeding (CF) period that takes place between 6 and 24 months of age is of key importance for nutritional and developmental reasons during the transition from exclusively feeding on milk to family meals. In 2021, a multidisciplinary panel of experts from four Italian scientific pediatric societies elaborated a consensus document on CF, focusing in particular on healthy term infants. The aim was to provide healthcare providers with useful guidelines for clinical practice. Complementary feeding is also the time window when iron deficiency (ID) and iron deficiency anemia (IDA) are most prevalent. Thus, it is appropriate to address the problem of iron deficiency through nutritional interventions. Adequate iron intake during the first two years is critical since rapid growth in that period increases iron requirements per kilogram more than at any other developmental stage. Complementary foods should be introduced at around six months of age, taking into account infant iron status.
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Affiliation(s)
- Vito Leonardo Miniello
- Nutrition Unit, Department of Pediatrics, “Giovanni XXIII” Children Hospital, “Aldo Moro” University of Bari, 70126 Bari, Italy
| | | | - Andrea Miniello
- Department of Allergology and Immunology, “Aldo Moro” University of Bari, 70124 Bari, Italy;
| | - Cristina Di Mauro
- Regional Centre of Pharmacovigilance Campania, Department of Experimental Medicine, University “Luigi Vanvitelli”, 80138 Naples, Italy;
| | | | - Ruggiero Francavilla
- Gastroenterology Unit, Department of Pediatrics, “Giovanni XXIII” Children Hospital, “Aldo Moro” University of Bari, 70126 Bari, Italy;
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Lorenzo AJ. Vesicoureteral Reflux, Renal Scars, and Urinary Tract Infections in Children: A New Way to Think About an Old Problem. Eur Urol 2021; 81:155-156. [PMID: 34635343 DOI: 10.1016/j.eururo.2021.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Armando J Lorenzo
- Department of Surgery, University of Toronto, Division of Urology, Hospital for Sick Children, Toronto, Canada.
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