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Masi AC, Beck LC, Perry JD, Granger CL, Hiorns A, Young GR, Bode L, Embleton ND, Berrington JE, Stewart CJ. Human milk microbiota, oligosaccharide profiles, and infant gut microbiome in preterm infants diagnosed with necrotizing enterocolitis. Cell Rep Med 2024; 5:101708. [PMID: 39216480 DOI: 10.1016/j.xcrm.2024.101708] [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: 04/10/2024] [Revised: 06/25/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Necrotizing enterocolitis (NEC) is a severe intestinal disease of very preterm infants with mother's own milk (MOM) providing protection, but the contribution of the MOM microbiota to NEC risk has not been explored. Here, we analyze MOM of 110 preterm infants (48 NEC, 62 control) in a cross-sectional study. Breast milk contains viable bacteria, but there is no significant difference in MOM microbiota between NEC and controls. Integrative analysis between MOM microbiota, human milk oligosaccharides (HMOs), and the infant gut microbiota shows positive correlations only between Acinetobacter in the infant gut and Acinetobacter and Staphylococcus in MOM. This study suggests that NEC protection from MOM is not modulated through the MOM microbiota. Thus, "'restoring" the MOM microbiota in donor human milk is unlikely to reduce NEC, and emphasis should instead focus on increasing fresh maternal human milk intake and researching different therapies for NEC prevention.
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Affiliation(s)
- Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lauren C Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - John D Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Claire L Granger
- Newcastle Neonatal Service, Newcastle Hospitals NHS Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Alice Hiorns
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gregory R Young
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lars Bode
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California San Diego, La Jolla, CA 92093, USA; The Human Milk Institute (HMI), University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Newcastle Hospitals NHS Trust, Newcastle upon Tyne NE1 4LP, UK; Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Janet E Berrington
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; Newcastle Neonatal Service, Newcastle Hospitals NHS Trust, Newcastle upon Tyne NE1 4LP, UK.
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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2
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Koerner R, Bendixen MM, Monk A, Lamberti MF, Lorca GL, Neu J, Parker LA. A Scoping Review of the Oral Microbiome in Preterm Infants. Am J Perinatol 2024; 41:e2990-e3002. [PMID: 37907200 PMCID: PMC11058105 DOI: 10.1055/s-0043-1776344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The purpose of this scoping review was to examine the oral microbiome composition in preterm infants, sampling and collection methods, as well as exposures associated with oral microbiome composition and health implications. We conducted a scoping review of the literature using the Arskey and O'Malley framework. We identified a total of 13 articles which met our inclusion criteria and purpose of this scoping review. Articles included in this review compared the oral microbiome in preterm infants to term infants, examined alterations to the oral microbiome over time, compared the oral microbiome to different body site microbiomes, and explored associations with clinically relevant covariates and outcomes. Exposures associated with the diversity and composition of the oral microbiome in preterm infants included delivery mode, oral feeding, oropharyngeal care, skin-to-skin care, and antibiotics. Day of life and birth weight were also associated with oral microbiome composition. The oral microbiome may be associated with the composition of the tracheal and gut microbiomes, likely due to their proximity. Alpha and beta diversity findings varied across studies as well as the relative abundance of taxa. This is likely due to the different sampling techniques and timing of collection, as well as the wide range of infant clinical characteristics. Multiple factors may influence the composition of the oral microbiome in preterm infants. However, given the heterogeneity of sampling techniques and results within this review, the evidence is not conclusive on the development as well as short- and long-term implications of the oral microbiome in preterm infants and needs to be explored in future research studies. KEY POINTS: · Day of life is a critical factor in oral microbiome development in preterm infants.. · The oral microbiome may be associated with tracheal and gut microbiome colonization.. · Future research should examine sampling methodology for examining the oral microbiome.. · Future research should explore associations with the oral microbiome and adverse health outcomes..
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Affiliation(s)
- Rebecca Koerner
- Department of Biobehavioral Nursing Science, College of Nursing, University of Florida, Gainesville, Florida
| | - Marion M. Bendixen
- Department of Family, Community and Health System Science, University of Florida, Gainesville, Florida
| | - Angela Monk
- Department of Biobehavioral Nursing Science, College of Nursing, University of Florida, Gainesville, Florida
| | - Monica F.T. Lamberti
- Department of Microbiology and Cell Science University of Florida, Microbiology and Cell Science, Gainesville, Florida
| | - Graciela L. Lorca
- Department of Microbiology and Cell Science University of Florida, Microbiology and Cell Science, Gainesville, Florida
| | - Josef Neu
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida
| | - Leslie A. Parker
- Department of Biobehavioral Nursing Science, College of Nursing, University of Florida, Gainesville, Florida
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3
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Colombo SFG, Nava C, Castoldi F, Fabiano V, Meneghin F, Lista G, Cavigioli F. Preterm Infants' Airway Microbiome: A Scoping Review of the Current Evidence. Nutrients 2024; 16:465. [PMID: 38398790 PMCID: PMC10891673 DOI: 10.3390/nu16040465] [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: 12/08/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
The aim of this scoping review was to investigate and synthesize existing evidence on the airway microbiome of preterm infants to outline the prognostic and therapeutic significance of these microbiomes within the preterm population and identify gaps in current knowledge, proposing avenues for future research. We performed a scoping review of the literature following the Arskey and O'Malley framework. In accordance with our inclusion criteria and the intended purpose of this scoping review, we identified a total of 21 articles. The investigation of the airway microbiome in preterm infants has revealed new insights into its unique characteristics, highlighting distinct dynamics when compared to term infants. Perinatal factors, such as the mode of delivery, chorioamnionitis, the respiratory support, and antibiotic treatment, could impact the composition of the airway microbiome. The 'gut-lung axis', examining the link between the lung and gut microbiome as well as modifications in respiratory microbiome across different sites and over time, has also been explored. Furthermore, correlations between the airway microbiome and adverse outcomes, such as bronchopulmonary dysplasia (BPD), have been established. Additional research in neonatal care is essential to understand the early colonization of infants' airways and explore methods for its optimization. The critical opportunity to shape long-term health through microbiome-mediated effects likely lies within the neonatal period.
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Affiliation(s)
- Sofia Fatima Giuseppina Colombo
- Department of Pediatrics, Buzzi Children’s Hospital, 20154 Milan, Italy; (S.F.G.C.); (C.N.)
- Division of Neonatology, Buzzi Children’s Hospital, 20154 Milan, Italy; (F.C.); (F.M.); (G.L.)
| | - Chiara Nava
- Department of Pediatrics, Buzzi Children’s Hospital, 20154 Milan, Italy; (S.F.G.C.); (C.N.)
- Division of Neonatology, Buzzi Children’s Hospital, 20154 Milan, Italy; (F.C.); (F.M.); (G.L.)
| | - Francesca Castoldi
- Division of Neonatology, Buzzi Children’s Hospital, 20154 Milan, Italy; (F.C.); (F.M.); (G.L.)
| | - Valentina Fabiano
- Department of Pediatrics, Buzzi Children’s Hospital, 20154 Milan, Italy; (S.F.G.C.); (C.N.)
| | - Fabio Meneghin
- Division of Neonatology, Buzzi Children’s Hospital, 20154 Milan, Italy; (F.C.); (F.M.); (G.L.)
| | - Gianluca Lista
- Division of Neonatology, Buzzi Children’s Hospital, 20154 Milan, Italy; (F.C.); (F.M.); (G.L.)
| | - Francesco Cavigioli
- Division of Neonatology, Buzzi Children’s Hospital, 20154 Milan, Italy; (F.C.); (F.M.); (G.L.)
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Vanzele PAR, Sparvoli LG, de Camargo PP, Tragante CR, Beozzo GPNS, Krebs VLJ, Cortez RV, Taddei CR. Establishment of oral microbiome in very low birth weight infants during the first weeks of life and the impact of oral diet implementation. PLoS One 2023; 18:e0295962. [PMID: 38100452 PMCID: PMC10723731 DOI: 10.1371/journal.pone.0295962] [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: 08/30/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023] Open
Abstract
Very low birth weight (VLBW) infants, mostly preterm, have many barriers to feeding directly from the mother's breast, and need to be fed alternatively. Feeding is a major influencer in oral microbial colonization, and this colonization in early life is crucial for the promotion of human health. Therefore, this research aimed to observe the establishment of oral microbiome in VLBW infants during their first month of life through hospitalization, and to verify the impact caused by the implementation of oral diet on the colonization of these newborns. We included 23 newborns followed during hospitalization and analyzed saliva samples collected weekly, using 16S rRNA gene sequencing. We observed a significant decrease in richness and diversity and an increase in dominance over time (q-value < 0.05). The oral microbiome is highly dynamic during the first weeks of life, and beta diversity suggests a microbial succession in early life. The introduction of oral diet does not change the community structure, but affects the abundance, especially of Streptococcus. Our results indicate that although time is related to significant changes in the oral microbial profile, oral feeding benefits genera that will remain colonizers throughout the host's life.
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Affiliation(s)
- Pedro A. R. Vanzele
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Luiz Gustavo Sparvoli
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Patricia P. de Camargo
- Neonatal Intensive Care Center, Children’s Institute, Hospital das Clínicas, São Paulo Medical School, University of São Paulo, São Paulo, SP, Brazil
| | - Carla R. Tragante
- Neonatal Intensive Care Center, Children’s Institute, Hospital das Clínicas, São Paulo Medical School, University of São Paulo, São Paulo, SP, Brazil
| | - Glenda P. N. S. Beozzo
- Neonatal Intensive Care Center, Children’s Institute, Hospital das Clínicas, São Paulo Medical School, University of São Paulo, São Paulo, SP, Brazil
| | - Vera L. J. Krebs
- Neonatal Intensive Care Center, Children’s Institute, Hospital das Clínicas, São Paulo Medical School, University of São Paulo, São Paulo, SP, Brazil
| | - Ramon V. Cortez
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Carla R. Taddei
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- School of Arts, Sciences and Humanity, University of São Paulo, São Paulo, SP, Brazil
- Division of Clinical Laboratory, University Hospital ‐ University of São Paulo, São Paulo, SP, Brazil
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5
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Yew WC, Young GR, Nelson A, Cheung W, Stewart CJ, Bridge SH, Granger C, Berrington JE, Embleton ND, Smith DL. The core phageome and its interrelationship with preterm human milk lipids. Cell Rep 2023; 42:113373. [PMID: 37967008 DOI: 10.1016/j.celrep.2023.113373] [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: 03/24/2023] [Revised: 08/09/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023] Open
Abstract
Phages and lipids in human milk (HM) may benefit preterm infant health by preventing gastrointestinal pathobiont overgrowth and microbiome modulation. Lipid association may promote vertical transmission of phages to the infant. Despite this, interrelationships between lipids and phages are poorly characterized in preterm HM. Shotgun metagenomics and untargeted lipidomics of phage and lipid profiles from 99 preterm HM samples reveals that phages are abundant and prevalent from the first week and throughout the first 100 days of lactation. Phage-host richness of preterm HM increases longitudinally. Core phage communities characterized by Staphylococcus- and Propionibacterium-infecting phages are significantly correlated with long-chain fatty acid abundances over lactational age. We report here a phage-lipid interaction in preterm HM, highlighting the potential importance of phage carriage in preterm HM. These results reveal possible strategies for phage carriage in HM and their importance in early-life microbiota development.
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Affiliation(s)
- Wen C Yew
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Gregory R Young
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - William Cheung
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Simon H Bridge
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Claire Granger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Neonatal Medicine, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Janet E Berrington
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Neonatal Medicine, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Nicholas D Embleton
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK; Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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6
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Young GR, Nelson A, Stewart CJ, Smith DL. Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease. Curr Opin Microbiol 2023; 75:102379. [PMID: 37647765 DOI: 10.1016/j.mib.2023.102379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/30/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023]
Abstract
Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.
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Affiliation(s)
- Gregory R Young
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | - Andrew Nelson
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK
| | | | - Darren L Smith
- Applied Sciences, Health and Life Sciences, Northumbria University, Newcastle, UK.
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7
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Healy D, Wang S, Grimaud G, Warda AK, Ross P, Stanton C, Dempsey EM. Longitudinal observational study protocol - Preterm Infants: Microbiome Establishment, Neuro-CrossTalk and Origins (PIMENTO). BMJ Open 2023; 13:e075060. [PMID: 37748849 PMCID: PMC10533688 DOI: 10.1136/bmjopen-2023-075060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/17/2023] [Indexed: 09/27/2023] Open
Abstract
INTRODUCTION Very preterm infants are at risk of abnormal microbiome colonisation in the first weeks to months of life. Several important associated factors have been identified including gestational age, mode of delivery, antibiotic exposure and feeding. Preterm infants are at risk of a number of pathologies for which the microbiome may play a central role, including necrotising enterocolitis and sepsis. The objective of this study is to determine detailed microbiome changes that occur around implementation of different management practices including empiric antibiotic use, advancement of feeds and administration of probiotics during admission to the neonatal intensive care unit. METHODS AND ANALYSIS A single-site, longitudinal observational study of infants born less than 32 weeks gestation, including collection of maternal samples around delivery and breastmilk and infant samples from admission through discharge from the neonatal unit. ETHICS AND DISSEMINATION The protocol was approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals.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 NCT05803577.
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Affiliation(s)
- David Healy
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | - Shuo Wang
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Alicja Katarzyna Warda
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre Moorepark, Moorepark, Ireland
| | - Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre Moorepark, Moorepark, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre Moorepark, Moorepark, Ireland
| | - Eugene M Dempsey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- INFANT Research Centre, University College Cork, Cork, Ireland
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8
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Selway CA, Collins CT, Makrides M, Sullivan TR, Weyrich LS. Variable preterm oral microbiome stabilizes and reflects a full-term infant profile within three months. Pediatr Res 2023:10.1038/s41390-023-02517-1. [PMID: 36859444 DOI: 10.1038/s41390-023-02517-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 03/03/2023]
Abstract
BACKGROUND Preterm infants suffer higher morbidity and mortality rates compared to full-term infants, but little is known about how changes to oral and respiratory tract microbiota may impact disease development. METHODS Here, very preterm neonates (n = 50) were selected to study oral and respiratory microbiota development during the first few months post-birth, where 26 individuals were diagnosed with BPD and/or sepsis. These infants were compared to 14 healthy full-term infants and 16 adults. Microbiota diversity, composition, and species abundances were calculated from 16S ribosomal RNA gene sequences in buccal swabs and tracheal aspirates at two time points (within a week and 1-3 months post-birth). RESULTS Collection time point was the biggest factor to significantly influence the preterm oral microbial diversity and composition. In addition, BPD and sepsis were linked to distinct preterm oral microbiota diversity and composition, and opportunistic pathogens previously associated with these diseases were identified in the initial sample for both healthy preterm neonates and those with the disease. Compared to the full-term infant and adult dataset, preterm infant diversity and composition was initially significantly different, but resembled full-term infant diversity and composition over time. CONCLUSION Overall, consequences of microbiota development need further examination in preterm infant infections and later development. IMPACT Non-gut microbiota research on preterm infants is limited. At one week post-birth, preterm infants harbor distinct oral microbiota that are not shared with full-term children or adults, eventually becoming similar to full-term infants at 36 weeks postmenstrual age. DNA from potential opportunistic pathogens was observed in the mouth and lungs of preterm infants within a week of birth, and microbes associated with BPD were identified in the lungs. Oral microbiota in preterm infants over the first 2-3 months is unique and may be connected to short- and long-term health outcomes in these children.
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Affiliation(s)
- Caitlin A Selway
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
| | - Carmel T Collins
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Adelaide Medical School, Discipline of Paediatrics, The University of Adelaide, Adelaide, SA, Australia
| | - Maria Makrides
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Adelaide Medical School, Discipline of Paediatrics, The University of Adelaide, Adelaide, SA, Australia
| | - Thomas R Sullivan
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- School of Public Health, The University of Adelaide, Adelaide, SA, Australia
| | - Laura S Weyrich
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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9
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Khan A, Mi H, Gao F, Hu Q, Gu X, Ma F, Qu L, Li S, Dai Y, Hao H. Dynamic changes of the gut microbial colonization in preterm infants with different time points after birth. Front Microbiol 2023; 14:1078426. [PMID: 36876108 PMCID: PMC9983350 DOI: 10.3389/fmicb.2023.1078426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/12/2023] [Indexed: 02/19/2023] Open
Abstract
Risks associated with preterm birth are unevenly distributed across all gestations. At earlier gestational ages, complications such as necrotizing enterocolitis (NEC) and late-onset sepsis (LOS) conditions are significantly more common and are associated with a shift in the composition of the gut microbiome. Conventional bacterial culture techniques demonstrate that the colonization of the gut microbiota of preterm infants differs significantly from that of healthy-term infants. The current study aimed to investigate the impact of preterm infancy on the dynamic changes of fecal microbiota in preterm infants at different time points (1, 7, 14, 21, 28, and 42 days) after birth. We selected 12 preterm infants hospitalized in the Sixth Affiliated Hospital of Sun Yat-sen University from January 2017 to December 2017. A total of 130 fecal specimens from preterm infants were analyzed using 16S rRNA gene sequencing. We found that the colonization process of fecal microbiota in preterm infants is highly dynamic at different time points after birth, i.e., Exiguobacterium, Acinetobacter, and Citrobacter showed a declining abundance pattern with the advancement of age, while the bacterial groups of Enterococcus (Klebsiella and Escherichia coli) gradually grew and became the main microbiota during the development of fecal microbiota in preterm infants at the age of 42 days. Furthermore, the colonization of intestinal Bifidobacteria in preterm infants was relatively late and did not rapidly become the predominant microbiota. Moreover, the results also showed the presence of Chryseobacterium bacterial group, whose colonization was different in different time point groups. Conclusively, our findings deepen our comprehension and offer new perspectives on targeting particular bacteria in the treatment of preterm infants at different time points after birth.
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Affiliation(s)
- Adnan Khan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hongying Mi
- Department of Pediatric, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Fei Gao
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Qi Hu
- NEOMICS Institute, Shenzhen, China
| | - Xia Gu
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fei Ma
- Department of Pediatrics, Zhuhai Women and Children's Hospital, Zhuhai, China
| | - LiuHong Qu
- Department of Neonatology, The Maternal and Child Health Care Hospital of HuaDu District, Guangzhou, China
| | - Sitao Li
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yiheng Dai
- Department of Neonatology, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Hu Hao
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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10
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Romo JA, Arsenault AB, Laforce-Nesbitt SS, Bliss JM, Kumamoto CA. Minimal Effects of Medium-Chain Triglyceride Supplementation on the Intestinal Microbiome Composition of Premature Infants: A Single-Center Pilot Study. Nutrients 2022; 14:2159. [PMID: 35631300 PMCID: PMC9145469 DOI: 10.3390/nu14102159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/04/2022] Open
Abstract
Compared to term infants, the microbiota of preterm infants is less diverse and often enriched for potential pathogens (e.g., members of the family Enterobacteriaceae). Additionally, antibiotics are frequently given to preterm infants, further destabilizing the microbiota and increasing the risk of fungal infections. In a previous communication, our group showed that supplementation of the premature infant diet with medium-chain triglyceride (MCT) oil reduced the fungal burden of Candida spp. in the gastrointestinal tract. The objective of this study was to determine whether MCT supplementation impacts the bacterial component of the microbiome. Pre-term infants (n = 17) receiving enteral feedings of either infant formula (n = 12) or human milk (n = 5) were randomized to MCT supplementation (n = 9) or no supplementation (n = 8). Fecal samples were taken at randomization and prior to MCT supplementation (Week 0), on days 5-7 (Week 1) and day 21 (Week 3). After DNA extraction from samples, the QIIME2 pipeline was utilized to measure community diversity and composition (genera and phyla). Our findings show that MCT supplementation did not significantly alter microbiota diversity or composition in the gastrointestinal tract. Importantly, there were no significant changes in the family Enterobacteriaceae, suggesting that MCT supplementation did not enrich for potential pathogens. MCT holds promise as a therapeutic intervention for reducing fungal colonization without significant impact on the bacterial composition of the host gastrointestinal tract.
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Affiliation(s)
- Jesús A. Romo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA;
| | - Amanda B. Arsenault
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA; (A.B.A.); (S.S.L.-N.); (J.M.B.)
- Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Sonia S. Laforce-Nesbitt
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA; (A.B.A.); (S.S.L.-N.); (J.M.B.)
- Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Joseph M. Bliss
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA; (A.B.A.); (S.S.L.-N.); (J.M.B.)
- Warren Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Carol A. Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA;
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11
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Healy DB, Ryan CA, Ross RP, Stanton C, Dempsey EM. Clinical implications of preterm infant gut microbiome development. Nat Microbiol 2022; 7:22-33. [PMID: 34949830 DOI: 10.1038/s41564-021-01025-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 11/12/2021] [Indexed: 12/12/2022]
Abstract
Perturbations to the infant gut microbiome during the first weeks to months of life affect growth, development and health. In particular, assembly of an altered intestinal microbiota during infant development results in an increased risk of immune and metabolic diseases that can persist into childhood and potentially into adulthood. Most research into gut microbiome development has focused on full-term babies, but health-related outcomes are also important for preterm babies. The systemic physiological immaturity of very preterm gestation babies (born earlier than 32 weeks gestation) results in numerous other microbiome-organ interactions, the mechanisms of which have yet to be fully elucidated or in some cases even considered. In this Perspective, we compare assembly of the intestinal microbiome in preterm and term infants. We focus in particular on the clinical implications of preterm infant gut microbiome composition and discuss the prospects for microbiome diagnostics and interventions to improve the health of preterm babies.
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Affiliation(s)
- David B Healy
- APC Microbiome Ireland, University College Cork, Cork, Ireland. .,Department of Paediatrics and Child Health, University College Cork, Cork, Ireland.
| | - C Anthony Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Eugene M Dempsey
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Paediatrics and Child Health, University College Cork, Cork, Ireland.,INFANT Research Centre, Cork University Hospital, Cork, Ireland
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12
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Young GR, Yew WC, Nelson A, Bridge SH, Berrington JE, Embleton ND, Smith DL. Optimisation and Application of a Novel Method to Identify Bacteriophages in Maternal Milk and Infant Stool Identifies Host-Phage Communities Within Preterm Infant Gut. Front Pediatr 2022; 10:856520. [PMID: 35558373 PMCID: PMC9087270 DOI: 10.3389/fped.2022.856520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Human milk oligosaccharides, proteins, such as lactoferrin, and bacteria represent just some of the bioactive components of mother's breast milk (BM). Bacteriophages (viruses that infect bacteria) are an often-overlooked component of BM that can cause major changes in microbial composition and metabolism. BM bacteriophage composition has been explored in term and healthy infants, suggesting vertical transmission of bacteriophages occurs between mothers and their infants. Several important differences between term and very preterm infants (<30 weeks gestational age) may limit this phenomenon in the latter. To better understand the link between BM bacteriophages and gut microbiomes of very preterm infants in health and disease, standardised protocols are required for isolation and characterisation from BM. In this study, we use isolated nucleic acid content, bacteriophage richness and Shannon diversity to validate several parameters applicable during bacteriophage isolation from precious BM samples. Parameters validated include sample volume required; centrifugal sedimentation of microbes; hydrolysis of milk samples with digestive enzymes; induction of temperate bacteriophages and concentration/purification of isolated bacteriophage particles in donor milk (DM). Our optimised method enables characterisation of bacteriophages from as little as 0.1 mL BM. We identify viral families that were exclusively identified with the inclusion of induction of temperate bacteriophages (Inoviridae) and hydrolysis of milk lipid processes (Iridoviridae and Baculoviridae). Once applied to a small clinical cohort we demonstrate the vertical transmission of bacteriophages from mothers BM to the gut of very preterm infants at the species level. This optimised method will enable future research characterising the bacteriophage composition of BM in very preterm infants to determine their clinical relevance in the development of a healthy preterm infant gut microbiome.
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Affiliation(s)
- Gregory R Young
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.,Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Wen C Yew
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Simon H Bridge
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Janet E Berrington
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Newcastle upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Nicholas D Embleton
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Darren L Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.,Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, United Kingdom
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13
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Cortez RV, Fernandes A, Sparvoli LG, Padilha M, Feferbaum R, Neto CM, Taddei CR. Impact of Oropharyngeal Administration of Colostrum in Preterm Newborns' Oral Microbiome. Nutrients 2021; 13:nu13124224. [PMID: 34959775 PMCID: PMC8703686 DOI: 10.3390/nu13124224] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 01/04/2023] Open
Abstract
The initial colonization of the human microbiota is of paramount importance. In this context, the oropharyngeal administration of colostrum is a safe, viable, and well-tolerated practice even by the smallest preterm infants. Therefore, this study evaluated the effects of oropharyngeal administration of colostrum on the establishment of preterm infants' oral microbiota. A longitudinal observational study was carried out with 20 premature neonates, divided into two groups: one receiving the protocol (Oropharyngeal Administration of Colostrum; OAC) and the other one receiving Standard Caare (SC). Saliva samples were collected from the newborns weekly during the study period (from the day of birth until the 21st day of life) for analysis of oral microbiota through 16S rRNA gene sequencing. We observed that the colonization of the oral microbiota of preterm newborns preseanted a higher relative abundance of Staphylococcus on the 7th day of life, mainly in the OAC group. Additionally, an increased abundance of Bifidobacterium and Bacteroides was observed in the OAC group at the first week of life. Regarding alpha and beta diversity, time was a key factor in the oral modulation of both groups, showing how dynamic this environment is in early life.
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Affiliation(s)
- Ramon V. Cortez
- Department of Clinical Analysis and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (R.V.C.); (L.G.S.)
| | - Andrea Fernandes
- Human Milk Bank, Hospital Maternidade Leonor Mendes de Barros, São Paulo 03015-000, Brazil; (A.F.); (C.M.N.)
| | - Luiz Gustavo Sparvoli
- Department of Clinical Analysis and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (R.V.C.); (L.G.S.)
| | - Marina Padilha
- Department of Social and Applied Nutrition, Federal University of Rio de Janeiro, Rio de Janeiro 21941-590, Brazil;
| | - Rubens Feferbaum
- Children’s Institute, University of São Paulo, Rua Tremembé, São Paulo 01256-010, Brazil;
| | - Corintio Mariani Neto
- Human Milk Bank, Hospital Maternidade Leonor Mendes de Barros, São Paulo 03015-000, Brazil; (A.F.); (C.M.N.)
| | - Carla R. Taddei
- Department of Clinical Analysis and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (R.V.C.); (L.G.S.)
- School of Arts, Sciences and Humanity, University of São Paulo, São Paulo 03828-000, Brazil
- Correspondence:
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14
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Risk Factors for Gut Dysbiosis in Early Life. Microorganisms 2021; 9:microorganisms9102066. [PMID: 34683389 PMCID: PMC8541535 DOI: 10.3390/microorganisms9102066] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 12/22/2022] Open
Abstract
Dysbiosis refers to a reduction in microbial diversity, combined with a loss of beneficial taxa, and an increase in pathogenic microorganisms. Dysbiosis of the intestinal microbiota can have a substantial effect on the nervous and immune systems, contributing to the onset of several inflammatory diseases. Epidemiological studies provided insight in how changes in the living environment have contributed to an overall loss of diversity and key taxa in the gut microbiome, coinciding with increased reports of atopy and allergic diseases. The gut microbiome begins development at birth, with major transition periods occurring around the commencement of breastfeeding, and the introduction of solid foods. As such, the development of the gut microbiome remains highly plastic and easily influenced by environmental factors until around three years of age. Developing a diverse and rich gut microbiome during this sensitive period is crucial to setting up a stable gut microbiome into adulthood and to prevent gut dysbiosis. Currently, the delivery route, antibiotic exposure, and diet are the best studied drivers of gut microbiome development, as well as risk factors of gut dysbiosis during infancy. This review focuses on recent evidence regarding key environmental factors that contribute to promoting gut dysbiosis.
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15
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Composition of the microbial communities at different body sites in women with preterm birth and their newborns. MEDICINE IN MICROECOLOGY 2021. [DOI: 10.1016/j.medmic.2021.100046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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16
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Sun T, Yu H, Fu J. Respiratory Tract Microecology and Bronchopulmonary Dysplasia in Preterm Infants. Front Pediatr 2021; 9:762545. [PMID: 34966701 PMCID: PMC8711720 DOI: 10.3389/fped.2021.762545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/22/2021] [Indexed: 12/23/2022] Open
Abstract
Bronchopulmonary dysplasia (BPD) is a severe respiratory complication in preterm infants. Although the etiology and pathogenesis of BPD are complex and remain to be clarified, recent studies have reported a certain correlation between the microecological environment of the respiratory tract and BPD. Changes in respiratory tract microecology, such as abnormal microbial diversity and altered evolutional patterns, are observed prior to the development of BPD in premature infants. Therefore, research on the colonization and evolution of neonatal respiratory tract microecology and its relationship with BPD is expected to provide new ideas for its prevention and treatment. In this paper, we review microecological changes in the respiratory tract and the mechanisms by which they can lead to BPD in preterm infants.
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Affiliation(s)
- Tong Sun
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Haiyang Yu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jianhua Fu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
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