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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Meng F, Uniacke-Lowe T, Lanfranchi E, Meehan G, O'Shea CA, Dennehy T, Ryan AC, Stanton C, Kelly AL. A longitudinal study of fatty acid profiles, macronutrient levels, and plasmin activity in human milk. Front Nutr 2023; 10:1172613. [PMID: 37229467 PMCID: PMC10203173 DOI: 10.3389/fnut.2023.1172613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction Human milk provides nutrients essential for infant growth and health, levels of which are dynamic during lactation. Methods In this study, changes in macronutrients, fatty acids, and plasmin activities over the first six months of lactation in term milk were studied. Results There was a significant influence of lactation stage on levels of protein and plasmin activities, but not on levels of fat and carbohydrate in term milk. Concerning fatty acids in term milk, levels of caproic acid and α-linolenic acid increased significantly (p < 0.05), whereas those of arachidonic acid and docosahexaenoic acid decreased, in the six months after birth. Significant impacts of maternal pre-pregnancy BMI and infant gender on fatty acid profiles were also found. Multivariate statistical analysis showed that protein level, plasmin activity, and several fatty acids (α-linolenic acid, lignoceric acid, and docasadienoic acid) contributed strongly to discrimination of milk from different lactational stages. Discussion The study demonstrates that not all but some fatty acids were influenced by lactation, whereas protein and protease levels showed clear decreasing trends during lactation, which may help in understanding the nutritional requirements of infants.
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Affiliation(s)
- Fanyu Meng
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | | | - Elisa Lanfranchi
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Grainne Meehan
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - Carol-Anne O'Shea
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - Theresa Dennehy
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Anthony C. Ryan
- Brookfield School of Medicine and Health, University College Cork, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome, Cork, Ireland
| | - Alan L. Kelly
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
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Warda AK, Dempsey EM, Forssten SD, Ryan CA, Cryan JF, Patterson E, O'Riordan MN, O'Shea CA, Keohane F, Meehan G, O'Connor O, Ross RP, Stanton C. Cross-sectional observational study protocol: missing microbes in infants born by caesarean section (MiMIC): antenatal antibiotics and mode of delivery. BMJ Open 2022; 12:e064398. [PMID: 36323464 PMCID: PMC9639109 DOI: 10.1136/bmjopen-2022-064398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
INTRODUCTION The intestinal microbiome in early life plays a major role in infant health and development. Factors like antibiotic exposure, breast/formula feeding and mode of delivery are known to affect the microbiome. The increasing occurrence of caesarean section (C-section) deliveries and antibiotic exposure warrants further insight into the potential missing microbes in those infants. The study objective is to study the effect of maternal antibiotic administration during pregnancy and/or C-section mode of delivery on the development of the infant's intestinal microbiome until the age of 2 years. METHODS AND ANALYSIS A single site, cross-sectional observational study of C-section and vaginally delivered infants being either exposed to maternal antibiotic treatment or not during the third trimester of pregnancy. Throughout the nine visits, stool, urine, saliva, hair, breast milk and vaginal swabs will be collected from either mother and/or infant for microbiome and metabolomic analysis. ETHICS AND DISSEMINATION The protocol was approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. The trial has been registered at ClinicalTrials.gov.The findings from this study will be disseminated in peer-reviewed journals, during scientific conferences, and directly to the study participants. Sequencing data will be deposited in public databases. TRIAL REGISTRATION NUMBER NCT04134819.
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Affiliation(s)
- Alicja K Warda
- APC Microbiome Ireland, Cork, Ireland
- Food Research Centre Moorepark, Teagasc, Moorepark, Ireland
| | - Eugene M Dempsey
- APC Microbiome Ireland, Cork, Ireland
- Cork University Maternity Hospital, Cork, Ireland
- INFANT Research Centre, University College Cork, Cork, Ireland
| | | | - C Anthony Ryan
- APC Microbiome Ireland, Cork, Ireland
- Cork University Maternity Hospital, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, Cork, Ireland
- University College Cork, Cork, Ireland
| | | | - Mairead N O'Riordan
- APC Microbiome Ireland, Cork, Ireland
- Cork University Maternity Hospital, Cork, Ireland
| | - Carol-Anne O'Shea
- APC Microbiome Ireland, Cork, Ireland
- Cork University Maternity Hospital, Cork, Ireland
| | - Finola Keohane
- APC Microbiome Ireland, Cork, Ireland
- Cork University Maternity Hospital, Cork, Ireland
| | - Grainne Meehan
- APC Microbiome Ireland, Cork, Ireland
- Cork University Maternity Hospital, Cork, Ireland
| | - Orlagh O'Connor
- APC Microbiome Ireland, Cork, Ireland
- Cork University Maternity Hospital, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, Cork, Ireland
- University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, Cork, Ireland
- Food Research Centre Moorepark, Teagasc, Moorepark, Ireland
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Ingvordsen Lindahl IE, Artegoitia VM, Downey E, O'Mahony JA, O'Shea CA, Ryan CA, Kelly AL, Bertram HC, Sundekilde UK. Quantification of Human Milk Phospholipids: the Effect of Gestational and Lactational Age on Phospholipid Composition. Nutrients 2019; 11:nu11020222. [PMID: 30678181 PMCID: PMC6412285 DOI: 10.3390/nu11020222] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/05/2019] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
Human milk (HM) provides infants with macro- and micronutrients needed for growth and development. Milk phospholipids are important sources of bioactive components, such as long-chain polyunsaturated fatty acids (LC-PUFA) and choline, crucial for neural and visual development. Milk from mothers who have delivered prematurely (<37 weeks) might not meet the nutritional requirements for optimal development and growth. Using liquid chromatography tandem-mass spectrometry, 31 phospholipid (PL) species were quantified for colostrum (<5 days postpartum), transitional (≥5 days and ≤2 weeks) and mature milk (>2 weeks and ≤15 weeks) samples from mothers who had delivered preterm (n = 57) and term infants (n = 22), respectively. Both gestational age and age postpartum affected the PL composition of HM. Significantly higher concentrations (p < 0.05) of phosphatidylcholine (PC), sphingomyelin (SM) and total PL were found in preterm milk throughout lactation, as well as significantly higher concentrations (p < 0.002) of several phosphatidylethanolamine (PE), PC and SM species. Multivariate analysis revealed that PLs containing LC-PUFA contributed highly to the differences in the PL composition of preterm and term colostrum. Differences related to gestation decreased as the milk matured. Thus, gestational age may impact the PL content of colostrum, however this effect of gestation might subside in mature milk.
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Affiliation(s)
| | | | - Eimear Downey
- School of Food and Nutritional Sciences, University College Cork, T12 YN60 Cork, Ireland.
| | - James A O'Mahony
- School of Food and Nutritional Sciences, University College Cork, T12 YN60 Cork, Ireland.
| | - Carol-Anne O'Shea
- Department of Paediatrics and Child Health, University College Cork, T12 YN60 Cork, Ireland.
| | - C Anthony Ryan
- Department of Paediatrics and Child Health, University College Cork, T12 YN60 Cork, Ireland.
| | - Alan L Kelly
- School of Food and Nutritional Sciences, University College Cork, T12 YN60 Cork, Ireland.
| | - Hanne C Bertram
- Department of Food Science, Aarhus University, 5792 Årslev, Denmark.
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Murphy K, Curley D, O'Callaghan TF, O'Shea CA, Dempsey EM, O'Toole PW, Ross RP, Ryan CA, Stanton C. The Composition of Human Milk and Infant Faecal Microbiota Over the First Three Months of Life: A Pilot Study. Sci Rep 2017; 7:40597. [PMID: 28094284 PMCID: PMC5240090 DOI: 10.1038/srep40597] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/18/2016] [Indexed: 12/26/2022] Open
Abstract
Human milk contains a diverse array of bioactives and is also a source of bacteria for the developing infant gut. The aim of this study was to characterize the bacterial communities in human milk and infant faeces over the first 3 months of life, in 10 mother-infant pairs. The presence of viable Bifidobacterium and Lactobacillus in human milk was also evaluated. MiSeq sequencing revealed a large diversity of the human milk microbiota, identifying over 207 bacterial genera in milk samples. The phyla Proteobacteria and Firmicutes and the genera Pseudomonas, Staphylococcus and Streptococcus were the predominant bacterial groups. A core of 12 genera represented 81% of the microbiota relative abundance in milk samples at week 1, 3 and 6, decreasing to 73% at week 12. Genera shared between infant faeces and human milk samples accounted for 70–88% of the total relative abundance in infant faecal samples, supporting the hypothesis of vertical transfer of bacteria from milk to the infant gut. In addition, identical strains of Bifidobacterium breve and Lactobacillus plantarum were isolated from the milk and faeces of one mother-infant pair. Vertical transfer of bacteria via breastfeeding may contribute to the initial establishment of the microbiota in the developing infant intestine.
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Affiliation(s)
- Kiera Murphy
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Co Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - David Curley
- Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - Tom F O'Callaghan
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Co Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Carol-Anne O'Shea
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - Eugene M Dempsey
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland.,College of Science, Engineering and Food Science, University College Cork, Cork, Ireland
| | - C Anthony Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - Catherine Stanton
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Co Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
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Sundekilde UK, Downey E, O'Mahony JA, O'Shea CA, Ryan CA, Kelly AL, Bertram HC. The Effect of Gestational and Lactational Age on the Human Milk Metabolome. Nutrients 2016; 8:nu8050304. [PMID: 27213440 PMCID: PMC4882716 DOI: 10.3390/nu8050304] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/28/2016] [Accepted: 05/16/2016] [Indexed: 12/30/2022] Open
Abstract
Human milk is the ideal nutrition source for healthy infants during the first six months of life and a detailed characterisation of the composition of milk from mothers that deliver prematurely (<37 weeks gestation), and of how human milk changes during lactation, would benefit our understanding of the nutritional requirements of premature infants. Individual milk samples from mothers delivering prematurely and at term were collected. The human milk metabolome, established by nuclear magnetic resonance (NMR) spectroscopy, was influenced by gestational and lactation age. Metabolite profiling identified that levels of valine, leucine, betaine, and creatinine were increased in colostrum from term mothers compared with mature milk, while those of glutamate, caprylate, and caprate were increased in mature term milk compared with colostrum. Levels of oligosaccharides, citrate, and creatinine were increased in pre-term colostrum, while those of caprylate, caprate, valine, leucine, glutamate, and pantothenate increased with time postpartum. There were differences between pre-term and full-term milk in the levels of carnitine, caprylate, caprate, pantothenate, urea, lactose, oligosaccharides, citrate, phosphocholine, choline, and formate. These findings suggest that the metabolome of pre-term milk changes within 5–7 weeks postpartum to resemble that of term milk, independent of time of gestation at pre-mature delivery.
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Affiliation(s)
| | - Eimear Downey
- School of Food and Nutritional Sciences, University College Cork, Cork T12 YN60, Ireland.
| | - James A O'Mahony
- School of Food and Nutritional Sciences, University College Cork, Cork T12 YN60, Ireland.
| | - Carol-Anne O'Shea
- Department of Paediatrics and Child Health, University College Cork, Cork T12 YN60, Ireland.
| | - C Anthony Ryan
- Department of Paediatrics and Child Health, University College Cork, Cork T12 YN60, Ireland.
| | - Alan L Kelly
- School of Food and Nutritional Sciences, University College Cork, Cork T12 YN60, Ireland.
| | - Hanne C Bertram
- Department of Food Science, Aarhus University, Årslev 5792, Denmark.
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