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Stinson LF, Ma J, Lai CT, Rea A, Perrella SL, Geddes DT. Milk microbiome transplantation: recolonizing donor milk with mother's own milk microbiota. Appl Microbiol Biotechnol 2024; 108:74. [PMID: 38194146 PMCID: PMC10776751 DOI: 10.1007/s00253-023-12965-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/29/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024]
Abstract
Donor human milk (DHM) provides myriad nutritional and immunological benefits for preterm and low birthweight infants. However, pasteurization leaves DHM devoid of potentially beneficial milk microbiota. In the present study, we performed milk microbiome transplantation from freshly collected mother's own milk (MOM) into pasteurized DHM. Small volumes of MOM (5%, 10%, or 30% v/v) were inoculated into pasteurized DHM and incubated at 37 °C for up to 8 h. Further, we compared microbiome recolonization in UV-C-treated and Holder-pasteurized DHM, as UV-C treatment has been shown to conserve important biochemical components of DHM that are lost during Holder pasteurization. Bacterial culture and viability-coupled metataxonomic sequencing were employed to assess the effectiveness of milk microbiome transplantation. Growth of transplanted MOM bacteria occurred rapidly in recolonized DHM samples; however, a greater level of growth was observed in Holder-pasteurized DHM compared to UV-C-treated DHM, potentially due to the conserved antimicrobial properties in UV-C-treated DHM. Viability-coupled metataxonomic analysis demonstrated similarity between recolonized DHM samples and fresh MOM samples, suggesting that the milk microbiome can be successfully transplanted into pasteurized DHM. These results highlight the potential of MOM microbiota transplantation to restore the microbial composition of UV-C-treated and Holder-pasteurized DHM and enhance the nutritional and immunological benefits of DHM for preterm and vulnerable infants. KEY POINTS: • Mother's own milk microbiome can be successfully transplanted into donor human milk. • Recolonization is equally successful in UV-C-treated and Holder-pasteurized milk. • Recolonization time should be restricted due to rapid bacterial growth.
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Affiliation(s)
- Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Australia.
| | - Jie Ma
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Ching Tat Lai
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Alethea Rea
- Mathematics and Statistics, Murdoch University, Perth, Australia
| | - Sharon L Perrella
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
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2
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Waller ME, Eichhorn CJ, Gutierrez A, Baatz JE, Wagner CL, Chetta KE, Engevik MA. Analyzing the Responses of Enteric Bacteria to Neonatal Intensive Care Supplements. Int J Microbiol 2024; 2024:3840327. [PMID: 39220439 PMCID: PMC11364479 DOI: 10.1155/2024/3840327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
In the neonatal intensive care unit, adequate nutrition requires various enteral products, including human milk and formula. Human milk is typically fortified to meet increased calorie goals, and infants commonly receive vitamin mixes, iron supplements, and less frequently, thickening agents. We examined the growth of 16 commensal microbes and 10 pathobionts found in the premature infant gut and found that formula, freshly pasteurized milk, and donated banked milk generally increased bacterial growth. Fortification of human milk significantly elevated the growth of all microbes. Supplementation with thickeners or NaCl in general did not stimulate additional growth. Vitamin mix promoted the growth of several commensals, while iron promoted growth of pathobionts. These data indicate that pathobionts in the preterm gut have significant growth advantage with preterm formula, fortified donor milk, and supplemented iron and suggest that the choice of milk and supplements may impact the infant gut microbiota.
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Affiliation(s)
- Megan E. Waller
- Department of Regenerative Medicine and Cell BiologyMedical University of South Carolina, Charleston, USA
| | - Caroline J. Eichhorn
- Department of Regenerative Medicine and Cell BiologyMedical University of South Carolina, Charleston, USA
| | - Alyssa Gutierrez
- Department of Regenerative Medicine and Cell BiologyMedical University of South Carolina, Charleston, USA
| | - John E. Baatz
- Department of PediatricsC.P. Darby Children's Research InstituteMedical University of South Carolina, Charleston, USA
- Department of PediatricsDivision of Neonatal-Perinatal MedicineMedical University of South CarolinaShawn Jenkins Children's Hospital, 10 McClennan Banks Drive, MSC 915, Charleston, SC 29425, USA
| | - Carol L. Wagner
- Department of PediatricsC.P. Darby Children's Research InstituteMedical University of South Carolina, Charleston, USA
- Department of PediatricsDivision of Neonatal-Perinatal MedicineMedical University of South CarolinaShawn Jenkins Children's Hospital, 10 McClennan Banks Drive, MSC 915, Charleston, SC 29425, USA
| | - Katherine E. Chetta
- Department of PediatricsC.P. Darby Children's Research InstituteMedical University of South Carolina, Charleston, USA
- Department of PediatricsDivision of Neonatal-Perinatal MedicineMedical University of South CarolinaShawn Jenkins Children's Hospital, 10 McClennan Banks Drive, MSC 915, Charleston, SC 29425, USA
| | - Melinda A. Engevik
- Department of Regenerative Medicine and Cell BiologyMedical University of South Carolina, Charleston, USA
- Department of Microbiology and ImmunologyMedical University of South Carolina, Charleston, USA
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3
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Hick E, Suárez M, Rey A, Mantecón L, Fernández N, Solís G, Gueimonde M, Arboleya S. Personalized Nutrition with Banked Human Milk for Early Gut Microbiota Development: In Pursuit of the Perfect Match. Nutrients 2024; 16:1976. [PMID: 38999725 PMCID: PMC11243202 DOI: 10.3390/nu16131976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
The correct initial colonization and establishment of the gut microbiota during the early stages of life is a key step, with long-lasting consequences throughout the entire lifespan of the individual. This process is affected by several perinatal factors; among them, feeding mode is known to have a critical role. Breastfeeding is the optimal nutrition for neonates; however, it is not always possible, especially in cases of prematurity or early pathology. In such cases, most commonly babies are fed with infant formulas in spite of the official nutritional and health international organizations' recommendation on the use of donated human milk through milk banks for these cases. However, donated human milk still does not totally match maternal milk in terms of infant growth and gut microbiota development. The present review summarizes the practices of milk banks and hospitals regarding donated human milk, its safety and quality, and the health outcomes in infants fed with donated human milk. Additionally, we explore different alternatives to customize pasteurized donated human milk with the aim of finding the perfect match between each baby and banked milk for promoting the establishment of a beneficial gut microbiota from the early stages of life.
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Affiliation(s)
- Emilia Hick
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain
| | - Marta Suárez
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Alejandra Rey
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain
| | - Laura Mantecón
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Nuria Fernández
- Pediatrics Service, University Hospital of Cabueñes (CAB-SESPA), 33394 Gijón, Spain
| | - Gonzalo Solís
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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4
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Valentino V, Magliulo R, Farsi D, Cotter PD, O'Sullivan O, Ercolini D, De Filippis F. Fermented foods, their microbiome and its potential in boosting human health. Microb Biotechnol 2024; 17:e14428. [PMID: 38393607 PMCID: PMC10886436 DOI: 10.1111/1751-7915.14428] [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: 11/29/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Fermented foods (FFs) are part of the cultural heritage of several populations, and their production dates back 8000 years. Over the last ~150 years, the microbial consortia of many of the most widespread FFs have been characterised, leading in some instances to the standardisation of their production. Nevertheless, limited knowledge exists about the microbial communities of local and traditional FFs and their possible effects on human health. Recent findings suggest they might be a valuable source of novel probiotic strains, enriched in nutrients and highly sustainable for the environment. Despite the increasing number of observational studies and randomised controlled trials, it still remains unclear whether and how regular FF consumption is linked with health outcomes and enrichment of the gut microbiome in health-associated species. This review aims to sum up the knowledge about traditional FFs and their associated microbiomes, outlining the role of fermentation with respect to boosting nutritional profiles and attempting to establish a link between FF consumption and health-beneficial outcomes.
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Affiliation(s)
- Vincenzo Valentino
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
| | - Raffaele Magliulo
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- NBFC‐National Biodiversity Future CenterPalermoItaly
| | - Dominic Farsi
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
| | - Paul D. Cotter
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
- APC Microbiome IrelandNational University of IrelandCorkIreland
- VistaMilk, FermoyCorkIreland
| | - Orla O'Sullivan
- Department of Food BiosciencesTeagasc Food Research CentreMooreparkFermoyIreland
- APC Microbiome IrelandNational University of IrelandCorkIreland
- VistaMilk, FermoyCorkIreland
| | - Danilo Ercolini
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- Task Force on Microbiome StudiesUniversity of Naples Federico IIPorticiItaly
| | - Francesca De Filippis
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
- NBFC‐National Biodiversity Future CenterPalermoItaly
- Task Force on Microbiome StudiesUniversity of Naples Federico IIPorticiItaly
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5
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Catassi G, Aloi M, Giorgio V, Gasbarrini A, Cammarota G, Ianiro G. The Role of Diet and Nutritional Interventions for the Infant Gut Microbiome. Nutrients 2024; 16:400. [PMID: 38337684 PMCID: PMC10857663 DOI: 10.3390/nu16030400] [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: 12/14/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
The infant gut microbiome plays a key role in the healthy development of the human organism and appears to be influenced by dietary practices through multiple pathways. First, maternal diet during pregnancy and infant nutrition significantly influence the infant gut microbiota. Moreover, breastfeeding fosters the proliferation of beneficial bacteria, while formula feeding increases microbial diversity. The timing of introducing solid foods also influences gut microbiota composition. In preterm infants the gut microbiota development is influenced by multiple factors, including the time since birth and the intake of breast milk, and interventions such as probiotics and prebiotics supplementation show promising results in reducing morbidity and mortality in this population. These findings underscore the need for future research to understand the long-term health impacts of these interventions and for further strategies to enrich the gut microbiome of formula-fed and preterm infants.
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Affiliation(s)
- Giulia Catassi
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Umberto I Hospital, 00161 Rome, Italy;
| | - Marina Aloi
- Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Umberto I Hospital, 00161 Rome, Italy;
| | - Valentina Giorgio
- Department of Woman and Child Health and Public Health, UOC Pediatria, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy;
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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6
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Chieu RV, Hamilton K, Ryan PM, Copeland J, Wang PW, Retnakaran R, Guttman DS, Parkinson J, Hamilton JK. The impact of gestational diabetes on functional capacity of the infant gut microbiome is modest and transient. Gut Microbes 2024; 16:2356277. [PMID: 38798005 PMCID: PMC11135868 DOI: 10.1080/19490976.2024.2356277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Gestational diabetes mellitus (GDM) is a metabolic complication that manifests as hyperglycemia during the later stages of pregnancy. In high resource settings, careful management of GDM limits risk to the pregnancy, and hyperglycemia typically resolves after birth. At the same time, previous studies have revealed that the gut microbiome of infants born to mothers who experienced GDM exhibit reduced diversity and reduction in the abundance of several key taxa, including Lactobacillus. What is not known is what the functional consequences of these changes might be. In this case control study, we applied 16S rRNA sequence surveys and metatranscriptomics to profile the gut microbiome of 30 twelve-month-old infants - 16 from mothers with GDM, 14 from mothers without - to examine the impact of GDM during pregnancy. Relative to the mode of delivery and sex of the infant, maternal GDM status had a limited impact on the structure and function of the developing microbiome. While GDM samples were associated with a decrease in alpha diversity, we observed no effect on beta diversity and no differentially abundant taxa. Further, while the mode of delivery and sex of infant affected the expression of multiple bacterial pathways, much of the impact of GDM status on the function of the infant microbiome appears to be lost by twelve months of age. These data may indicate that, while mode of delivery appears to impact function and diversity for longer than anticipated, GDM may not have persistent effects on the function nor composition of the infant gut microbiome.
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Affiliation(s)
- Ryan V. Chieu
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Katharine Hamilton
- Division of Endocrinology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Paul M. Ryan
- Division of Endocrinology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Julia Copeland
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Ravi Retnakaran
- Leadership Sinai Centre for Diabetes, Mount Sinai Hospital, Toronto, ON, Canada
| | - David S. Guttman
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, Canada
| | - John Parkinson
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Jill K. Hamilton
- Division of Endocrinology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
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7
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Eckermann HA, Meijer J, Cooijmans K, Lahti L, de Weerth C. Daily skin-to-skin contact alters microbiota development in healthy full-term infants. Gut Microbes 2024; 16:2295403. [PMID: 38197254 PMCID: PMC10793693 DOI: 10.1080/19490976.2023.2295403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/12/2023] [Indexed: 01/11/2024] Open
Abstract
The gut microbiota is vital for human body development and function. Its development in early life is influenced by various environmental factors. In this randomized controlled trial, the gut microbiota was obtained as a secondary outcome measure in a study on the effects of one hour of daily skin-to-skin contact (SSC) for five weeks in healthy full-term infants. Specifically, we studied the effects on alpha/beta diversity, volatility, microbiota maturation, and bacterial and gut-brain-axis-related functional abundances in microbiota assessed thrice in the first year. Pregnant Dutch women (n = 116) were randomly assigned to the SSC or care-as-usual groups. The SSC group participants engaged in one hour of daily SSC from birth to five weeks of age. Stool samples were collected at two, five, and 52 weeks and the V4 region was sequenced. We observed significant differences in the microbiota composition, bacterial abundances, and predicted functional pathways between the groups. The SSC group exhibited lower microbiota volatility during early infancy. Microbiota maturation was slower in the SSC group during the first year and our results suggested that breastfeeding duration may have partially mediated this relation. Our findings provide evidence that postpartum SSC may influence microbiota development. Replication is necessary to validate and generalize these results. Future studies should include direct stress measurements and extend microbiota sampling beyond the first year to investigate stress as a mechanism and research SSC's impact on long-term microbiota maturation trajectories.
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Affiliation(s)
- Henrik Andreas Eckermann
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
| | - Jennifer Meijer
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
| | - Kelly Cooijmans
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
- Behavioural Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Carolina de Weerth
- Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands
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8
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Greenfield KG, Harlow OS, Witt LT, Dziekan EM, Tamar CR, Meier J, Brumbaugh JE, Levy ER, Knoop KA. Neonatal intestinal colonization of Streptococcus agalactiae and the multiple modes of protection limiting translocation. Gut Microbes 2024; 16:2379862. [PMID: 39042143 PMCID: PMC11268251 DOI: 10.1080/19490976.2024.2379862] [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: 09/28/2023] [Accepted: 07/10/2024] [Indexed: 07/24/2024] Open
Abstract
Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a predominant pathogen of neonatal sepsis, commonly associated with early-onset neonatal sepsis. GBS has also been associated with cases of late-onset sepsis potentially originating from the intestine. Previous findings have shown GBS can colonize the infant intestinal tract as part of the neonatal microbiota. To better understand GBS colonization dynamics in the neonatal intestine, we collected stool and milk samples from prematurely born neonates for identification of potential pathogens in the neonatal intestinal microbiota. GBS was present in approximately 10% of the cohort, and this colonization was not associated with maternal GBS status, delivery route, or gestational weight. Interestingly, we observed the relative abundance of GBS in the infant stool negatively correlated with maternal IgA concentration in matched maternal milk samples. Using a preclinical murine model of GBS infection, we report that both vertical transmission and direct oral introduction resulted in intestinal colonization of GBS; however, translocation beyond the intestine was limited. Finally, vaccination of dams prior to breeding induced strong immunoglobulin responses, including IgA responses, which were associated with reduced mortality and GBS intestinal colonization. Taken together, we show that maternal IgA may contribute to infant immunity by limiting the colonization of GBS in the intestine.
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Affiliation(s)
| | | | - Lila T Witt
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Jane E Brumbaugh
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Emily R Levy
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kathryn A Knoop
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
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Tan A, Murugapiran S, Mikalauskas A, Koble J, Kennedy D, Hyde F, Ruotti V, Law E, Jensen J, Schroth GP, Macklaim JM, Kuersten S, LeFrançois B, Gohl DM. Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes. BMC Microbiol 2023; 23:299. [PMID: 37864136 PMCID: PMC10588151 DOI: 10.1186/s12866-023-03037-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
The microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. Gene expression measurements can provide insights into microbiome composition and function. However, efficient and unbiased removal of microbial ribosomal RNA (rRNA) presents a barrier to acquiring metatranscriptomic data. Here we describe a probe set that achieves efficient enzymatic rRNA removal of complex human-associated microbial communities. We demonstrate that the custom probe set can be further refined through an iterative design process to efficiently deplete rRNA from a range of human microbiome samples. Using synthetic nucleic acid spike-ins, we show that the rRNA depletion process does not introduce substantial quantitative error in gene expression profiles. Successful rRNA depletion allows for efficient characterization of taxonomic and functional profiles, including during the development of the human gut microbiome. The pan-human microbiome enzymatic rRNA depletion probes described here provide a powerful tool for studying the transcriptional dynamics and function of the human microbiome.
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Affiliation(s)
- Asako Tan
- Illumina, Inc, Madison, WI, 53719, USA
| | | | | | - Jeff Koble
- Illumina, Inc, San Diego, CA, 92122, USA
| | | | - Fred Hyde
- Illumina, Inc, Madison, WI, 53719, USA
| | | | - Emily Law
- Diversigen, Inc, New Brighton, MN, 55112, USA
| | | | | | | | | | | | - Daryl M Gohl
- Diversigen, Inc, New Brighton, MN, 55112, USA.
- University of Minnesota Genomics Center, Minneapolis, MN, 55455, USA.
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, 55455, USA.
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10
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Chen X, Shi Y. Determinants of microbial colonization in the premature gut. Mol Med 2023; 29:90. [PMID: 37407941 DOI: 10.1186/s10020-023-00689-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Abnormal microbial colonization in the gut at an early stage of life affects growth, development, and health, resulting in short- and long-term adverse effects. Microbial colonization patterns of preterm infants differ from those of full-term infants in that preterm babies and their mothers have more complicated prenatal and postnatal medical conditions. Maternal complications, antibiotic exposure, delivery mode, feeding type, and the use of probiotics may significantly shape the gut microbiota of preterm infants at an early stage of life; however, these influences subside with age. Although some factors and processes are difficult to intervene in or avoid, understanding the potential factors and determinants will help in developing timely strategies for a healthy gut microbiota in preterm infants. This review discusses potential determinants of gut microbial colonization in preterm infants and their underlying mechanisms.
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Affiliation(s)
- Xiaoyu Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110000, China
| | - Yongyan Shi
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110000, China.
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11
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Guo S, Huang K, Liu R, Sun J, Yin C. Regulation of Gut Microbiota through Breast Milk Feeding Benefits Language and Cognitive Development of Preterm Toddlers. Microorganisms 2023; 11:microorganisms11040866. [PMID: 37110289 PMCID: PMC10146954 DOI: 10.3390/microorganisms11040866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Feeding practice is essential to growth and development of preterm toddlers. However, the relationship of feeding mode with gut microbiota and neurodevelopment outcomes of preterm toddlers has not been characterized fully. We conducted this cohort study to assess neurodevelopment outcomes and gut microbiota community structures of preterm toddlers who received either breast milk, formula or mixed feeding. Fifty-five preterm toddlers born <37 weeks and 24 term toddlers were recruited in the study. Bayley III mental and physical index scores were measured among preterm toddlers at 12 ± 2 and 18 ± 2 months corrected age (CA). Gut microbiome composition was analyzed by 16S rRNA gene sequencing in fecal samples collected from all participants at 12 months, 16 months and 20 months after birth. We found exclusive breast milk feeding for over three months in the first six months after birth was associated with significant increase in language composite score at 12 months CA (86 (79,97) vs. 77 (71.75,79), p = 0.008) and both language (106.05 ± 14.68 vs. 90.58 ± 12.25, p = 0.000) and cognitive composite score at 18 months CA (107.17 ± 10.85 vs. 99.00 ± 9.24, p = 0.007). The alpha diversity, beta diversity and composition of gut microbiota from those breastfed preterm toddlers not only resembled healthy term toddlers but also followed similar structure of preterm toddlers with enhanced language and cognitive performance. Our results suggest exclusive breast milk feeding for over three months in preterm toddlers leads to optimal cognitive and language development and well-balanced microbiota.
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A Scoping Review of Neonatal Opioid Withdrawal and the Infant Gut Microbiome: Does Human Milk Optimize Infant Outcomes? Adv Neonatal Care 2023; 23:237-245. [PMID: 36867674 DOI: 10.1097/anc.0000000000001056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
BACKGROUND While a growing body of literature has established the role of human milk as a mechanism of protection in the formation of the infant gut microbiome, it remains unclear the extent to which this association exists for infants with neonatal opioid withdrawal syndrome. PURPOSE The purpose of this scoping review was to describe the current state of the literature regarding the influence of human milk on infant gut microbiota in infants with neonatal opioid withdrawal syndrome. DATA SOURCES CINAHL, PubMed, and Scopus databases were searched for original studies published from January 2009 through February 2022. Additionally, unpublished studies across relevant trial registries, conference proceedings, websites, and organizations were reviewed for possible inclusion. A total of 1610 articles met selection criteria through database and register searches and 20 through manual reference searches. STUDY SELECTION Inclusion criteria were primary research studies, written in English, published between 2009 and 2022, including a sample of infants with neonatal opioid withdrawal syndrome/neonatal abstinence syndrome, and focusing on the relationship between the receipt of human milk and the infant gut microbiome. DATA EXTRACTION Two authors independently conducted title/abstract and full-text review until there was consensus of study selection. RESULTS No studies satisfied the inclusion criteria, which resulted in an empty review. IMPLICATIONS FOR PRACTICE AND RESEARCH Findings from this study document the paucity of data exploring the associations between human milk, the infant gut microbiome, and subsequent neonatal opioid withdrawal syndrome. Further, these results highlight the timely importance of prioritizing this area of scientific inquiry.
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13
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The conundrum of breast cancer and microbiome - A comprehensive review of the current evidence. Cancer Treat Rev 2022; 111:102470. [DOI: 10.1016/j.ctrv.2022.102470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
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Kumbhare SV, Jones WD, Fast S, Bonner C, Jong G', Van Domselaar G, Graham M, Narvey M, Azad MB. Source of human milk (mother or donor) is more important than fortifier type (human or bovine) in shaping the preterm infant microbiome. Cell Rep Med 2022; 3:100712. [PMID: 36029771 PMCID: PMC9512671 DOI: 10.1016/j.xcrm.2022.100712] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/13/2022] [Accepted: 07/14/2022] [Indexed: 12/20/2022]
Abstract
Milk fortifiers help meet the nutritional needs of preterm infants receiving their mother's own milk (MOM) or donor human milk. We conducted a randomized clinical trial (NCT03214822) in 30 very low birth weight premature neonates comparing bovine-derived human milk fortifier (BHMF) versus human-derived fortifier (H2MF). We found that fortifier type does not affect the overall microbiome, although H2MF infants were less often colonized by an unclassified member of Clostridiales Family XI. Secondary analyses show that MOM intake is strongly associated with weight gain and microbiota composition, including Bifidobacterium, Veillonella, and Propionibacterium enrichment. Finally, we show that while oxidative stress (urinary F2-isoprostanes) is not affected by fortifier type or MOM intake, fecal calprotectin is higher in H2MF infants and lower in those consuming more MOM. Overall, the source of human milk (mother versus donor) appears more important than the type of milk fortifier (human versus bovine) in shaping preterm infant gut microbiota.
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Affiliation(s)
- Shreyas V Kumbhare
- Manitoba Interdisciplinary Lactation Centre (MILC), Winnipeg, MB, Canada; Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - William-Diehl Jones
- Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB, Canada; Faculty of Health Disciplines, Athabasca University, Athabasca, AB, Canada
| | - Sharla Fast
- Department of Nutrition and Food Services, Health Sciences Centre, Winnipeg, MB, Canada
| | - Christine Bonner
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Geert 't Jong
- Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Morag Graham
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Michael Narvey
- Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Meghan B Azad
- Manitoba Interdisciplinary Lactation Centre (MILC), Winnipeg, MB, Canada; Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB, Canada; Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada.
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15
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Nasogastric enteral feeding tubes modulate preterm colonization in early life. Pediatr Res 2022; 92:838-847. [PMID: 34845351 DOI: 10.1038/s41390-021-01852-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/04/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Preterm infants are generally fed through nasogastric enteral feeding tubes (NEFTs). The aim of this work was to evaluate the role of NEFTs in the initial colonization of the preterm gut and its evolution within the first 2 weeks after birth. METHODS For this purpose, fecal and NEFT-derived samples from 30 preterm infants hospitalized in a neonatal intensive care unit (NICU) were collected from birth to the second week of life. Samples were cultivated in ten culture media, including three for the isolation of antibiotic-resistant microorganisms. RESULTS Isolates (561) were identified by 16S ribosomal RNA gene sequencing. Although the first NEFTs inserted into the neonates after birth were rarely colonized, analysis of NEFTs and fecal samples over time revealed a significant increase in bacterial abundance, diversity, and detection frequency. Results showed a parallel colonization between time-matched NEFTs and fecal samples, suggesting an ongoing bidirectional transfer of bacteria from the neonatal gut to the NEFTs and vice versa. CONCLUSIONS In short-term hospitalization, length is by far the determinant factor for the early colonization of preterm infants. As NEFT populations reflect the bacterial populations that are colonizing the preterm in a precise moment, their knowledge could be useful to prevent the dissemination of antibiotic-resistant strains. IMPACT The hospital environment modulates preterm colonization immediately after birth. The colonization of preterm feces and NEFTs occurs in parallel. There is an ongoing bidirectional transfer of microorganisms from the neonatal gut to the NEFTs and vice versa. Bacterial communities inside NEFTs could act as reservoirs of antibiotic resistance genes. NEFT populations reflect the bacteria that are colonizing the preterm at a precise moment.
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16
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Subramanian S, Geng H, Du C, Chou PM, Bu HF, Wang X, Swaminathan S, Tan SC, Ridlon JM, De Plaen IG, Tan XD. Feeding mode influences dynamic gut microbiota signatures and affects susceptibility to anti-CD3 mAb-induced intestinal injury in neonatal mice. Am J Physiol Gastrointest Liver Physiol 2022; 323:G205-G218. [PMID: 35819158 PMCID: PMC9394775 DOI: 10.1152/ajpgi.00337.2021] [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: 11/29/2021] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 01/31/2023]
Abstract
Feeding modes influence the gut microbiome, immune system, and intestinal barrier homeostasis in neonates; how feeding modes impact susceptibility to neonatal gastrointestinal (GI) diseases is still uncertain. Here, we investigated the impact of dam feeding (DF) and formula feeding (FF) on features of the gut microbiome and physiological inflammation during the first 2 days of postnatal development and on the susceptibility to intestinal injury related to the inflammatory state in neonatal mouse pups. 16S rRNA sequencing data revealed microbiome changes, lower α-diversity, and a distinct pattern of β-diversity including expansion of f_Enterobacteriaceae and f_Enterococcaceae in the ileum of FF pups compared with DF pups by postnatal day (P)2. Together with gut dysbiosis, the FF cohort also had greater ileal mucosa physiological inflammatory activity compared with DF pups by P2 but maintained normal histological features. Interestingly, FF but not DF mouse pups developed necrotizing enterocolitis (NEC)-like intestinal injury within 24 h after anti-CD3 mAb treatment, suggesting that FF influences the susceptibility to intestinal injury in neonates. We further found that NEC-like incidence in anti-CD3 mAb-treated FF neonatal pups was attenuated by antibiotic treatment. Collectively, our data suggest that FF predisposes mouse pups to anti-CD3 mAb-induced intestinal injury due to abnormal f_Enterobacteriaceae and f_Enterococcaceae colonization. These findings advance our understanding of FF-associated microbial colonization and intestinal inflammation, which may help inform the development of new therapeutic approaches to GI diseases like NEC in infants.NEW & NOTEWORTHY This report shows that a feeding mode profoundly affects gut colonization in neonatal mice. Furthermore, our results demonstrate that formula feeding predisposes mouse pups to anti-CD3 mAb-induced necrotizing enterocolitis (NEC)-like intestinal injury upon inadequate microbial colonization. The study suggests the role of the combined presence of formula feeding-associated dysbiosis and mucosal inflammation in the pathogenesis of NEC and provides a new mouse model to study this disease.
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Affiliation(s)
- Saravanan Subramanian
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Center for Intestinal and Liver Inflammation Research, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Hua Geng
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Center for Intestinal and Liver Inflammation Research, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Chao Du
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Center for Intestinal and Liver Inflammation Research, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Pauline M Chou
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Heng-Fu Bu
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Center for Intestinal and Liver Inflammation Research, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Xiao Wang
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Center for Intestinal and Liver Inflammation Research, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Suchitra Swaminathan
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Stephanie C Tan
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Center for Intestinal and Liver Inflammation Research, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois
| | - Isabelle G De Plaen
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Division of Neonatology, Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Xiao-Di Tan
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Center for Intestinal and Liver Inflammation Research, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Department of Research and Development, Jesse Brown Department of Veterans Affairs Medical Center, Chicago, Illinois
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17
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Asbury MR, Shama S, Sa JY, Bando N, Butcher J, Comelli EM, Copeland JK, Forte V, Kiss A, Sherman PM, Stintzi A, Taibi A, Tomlinson C, Unger S, Wang PW, O'Connor DL. Human milk nutrient fortifiers alter the developing gastrointestinal microbiota of very-low-birth-weight infants. Cell Host Microbe 2022; 30:1328-1339.e5. [PMID: 35987195 DOI: 10.1016/j.chom.2022.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]
Abstract
Nutrient fortifiers are added to human milk to support the development of very-low-birth-weight infants. Currently, bovine-milk-based fortifiers (BMBFs) are predominantly administered, with increasing interest in adopting human-milk-based fortifiers (HMBFs). Although beneficial for growth, their effects on the gastrointestinal microbiota are unclear. This triple-blind, randomized clinical trial (NCT02137473) tested how nutrient-enriching human milk with HMBF versus BMBF affects the gastrointestinal microbiota of infants born < 1,250 g during hospitalization. HMBF-fed infants (n = 63, n = 269 stools) showed lower microbial diversity, altered microbial community structure, and changes in predicted microbial functions compared with BMBF-fed infants (n = 56, n = 239 stools). HMBF-fed infants had higher relative and normalized abundances of unclassified Enterobacteriaceae and lower abundances of Clostridium sensu stricto. Post hoc analyses identified dose-dependent relationships between individual feed components (volumes of mother's milk, donor milk, and fortifiers) and the microbiota. These results highlight how nutrient fortifiers impact the microbiota of very-low-birth-weight infants during a critical developmental window.
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Affiliation(s)
- Michelle R Asbury
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Translational Medicine Program, SickKids Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sara Shama
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Translational Medicine Program, SickKids Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jong Yup Sa
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Translational Medicine Program, SickKids Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nicole Bando
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Translational Medicine Program, SickKids Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - James Butcher
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa ON, K1H 8M5, Canada
| | - Elena M Comelli
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Joannah and Brian Lawson Centre for Child Nutrition, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Victoria Forte
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Translational Medicine Program, SickKids Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Alex Kiss
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada; Evaluative and Clinical Sciences, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | - Philip M Sherman
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Cell Biology Program, SickKids Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Gastroenterology, Hepatology, and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1X3, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Ottawa Institute of Systems Biology, University of Ottawa, Ottawa ON, K1H 8M5, Canada
| | - Amel Taibi
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Christopher Tomlinson
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Translational Medicine Program, SickKids Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Joannah and Brian Lawson Centre for Child Nutrition, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Neonatology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Sharon Unger
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Neonatology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, Sinai Health, Toronto, ON M5G 1X5, Canada; Rogers Hixon Ontario Human Milk Bank, Toronto, ON M5G 1X5, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Deborah L O'Connor
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada; Translational Medicine Program, SickKids Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Joannah and Brian Lawson Centre for Child Nutrition, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pediatrics, Sinai Health, Toronto, ON M5G 1X5, Canada; Rogers Hixon Ontario Human Milk Bank, Toronto, ON M5G 1X5, Canada.
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18
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Dimitrakopoulou EI, Pouliakis A, Falaina V, Xanthos T, Zoumpoulakis P, Tsiaka T, Sokou R, Iliodromiti Z, Boutsikou T, Iacovidou N. The Metagenomic and Metabolomic Profile of the Infantile Gut: Can They Be “Predicted” by the Feed Type? CHILDREN 2022; 9:children9020154. [PMID: 35204875 PMCID: PMC8870590 DOI: 10.3390/children9020154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 11/20/2022]
Abstract
Purpose: The composition and the metabolic activity of the gut microbiota of breastfed and formula-fed infants has been the focus of several studies over the last two decades. Gene sequencing techniques and metabolomics in biological samples have led to expansion of our knowledge in this field. A more thorough comprehension of the metabolic role of the intestinal microbiota could assist and expedite the development of optimal feeding strategies. The aim of this systematic review is to present available data regarding the effect of the feed type on the infantile intestinal microbiota (microbial composition and metabolites) by DNA-sequencing and metabolome analysis of neonatal stool. Methods: A systematic search of the literature in PubMed was attempted to establish relevant studies. Randomized controlled trials studying the diversity and composition of gut microbiota and metabolites of infants that received different types of feed were included. The study subjects were infants/neonates born at term or preterm receiving either breast, donor, or formula milk. Formula could be either classic or fortified with probiotics, prebiotics, or both. The included trials compared the differences on metagenomics and metabolomics of infantile stool, aiming at investigating the beneficial effects of fortification of formula with synbiotics. Results: Out of 1452 papers identified by the initial search, seven were selected for inclusion, following screening for eligibility. Eligibility was determined by closer examination for relevance of the title, abstract, and subsequent full text. The results of these studies mostly support that the feed type modulates the microbiome composition. In terms of the alpha-diversity, no significant difference exists between the feeding groups, whereas significant differences were noted with regards to beta-diversity in breastfed and formula-fed infants. As for the microbial composition, the studies revealed different populations in the formula-fed group compared to the breastfed group at the phylum and genus level. Bifidobacteria supplementation of infant formula did not seem to change the proportions of Bifidobacterial sequences during the first year of life. Another finding according to the studies is that the pH of fecal samples in breastfed as well as prebiotic-supplemented formula-fed infants. was significantly lower than that of formula-fed infants. Infant milk formula with a mixture of prebiotics (GOS/FOS oligosaccharides) was shown to be capable of selectively stimulating the growth of Bifidobacteria with analogous changes in fecal pH and short-chain fatty acid content in fully formula-fed infants. Conclusions: Overall, there is evidence to support that feed type modulates the infants’ microbiome constitution. The impact of feeding on term and preterm microbiota could have potential benefits on intestinal functionality, immune system, and metabolism, and probably pursuing the host for life.
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Affiliation(s)
- Eftychia Ioanna Dimitrakopoulou
- Department of Neonatology, National and Kapodistrian University of Athens, 157 72 Athens, Greece; (R.S.); (Z.I.); (T.B.); (N.I.)
- Correspondence:
| | - Abraham Pouliakis
- 2nd Department of Pathology, National and Kapodistrian University of Athens, 124 62 Athens, Greece;
| | - Vasiliki Falaina
- Neonatal Intensive Care Unit, General Hospital of Nikaia, Piraeus “Agios Panteleimon”, 184 54 Piraeus, Greece;
| | - Theodoros Xanthos
- Department of Medicine, European University Cyprus, Nicosia 2404, Cyprus;
| | - Panagiotis Zoumpoulakis
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece; (P.Z.); (T.T.)
- Department of Food Science and Technology, University of West Attica, 122 43 Egaleo, Greece
| | - Thalia Tsiaka
- Institute of Chemical Biology, National Hellenic Research Foundation, 116 35 Athens, Greece; (P.Z.); (T.T.)
- Department of Food Science and Technology, University of West Attica, 122 43 Egaleo, Greece
| | - Rozeta Sokou
- Department of Neonatology, National and Kapodistrian University of Athens, 157 72 Athens, Greece; (R.S.); (Z.I.); (T.B.); (N.I.)
| | - Zoi Iliodromiti
- Department of Neonatology, National and Kapodistrian University of Athens, 157 72 Athens, Greece; (R.S.); (Z.I.); (T.B.); (N.I.)
| | - Theodora Boutsikou
- Department of Neonatology, National and Kapodistrian University of Athens, 157 72 Athens, Greece; (R.S.); (Z.I.); (T.B.); (N.I.)
| | - Nicoletta Iacovidou
- Department of Neonatology, National and Kapodistrian University of Athens, 157 72 Athens, Greece; (R.S.); (Z.I.); (T.B.); (N.I.)
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19
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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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20
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From Mum to Bum: An Observational Study Protocol to Follow Digestion of Human Milk Oligosaccharides and Glycoproteins from Mother to Preterm Infant. Nutrients 2021; 13:nu13103430. [PMID: 34684428 PMCID: PMC8538091 DOI: 10.3390/nu13103430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 11/21/2022] Open
Abstract
The nutritional requirements of preterm infants are challenging to meet in neonatal care, yet crucial for their growth, development and health. Aberrant maturation of the gastrointestinal tract and the microbiota could affect the digestion of human milk and its nutritional value considerably. Therefore, the main objective of the proposed research is to investigate how the intestinal microbiota of preterm and full-term infants differ in their ability to extract energy and nutrients from oligosaccharides and glycoproteins in human milk. This pilot study will be an observational, single-center study performed at the Neonatal Intensive Care Unit at Isala Women and Children’s Hospital (Zwolle, The Netherlands). A cohort of thirty mother–infant pairs (preterm ≤30 weeks of gestation, n = 15; full-term 37–42 weeks of gestation, n = 15) will be followed during the first six postnatal weeks with follow-up at three- and six-months postnatal age. We will collect human milk of all mothers, gastric aspirates of preterm infants and fecal samples of all infants. A combination of 16S rRNA amplicon sequencing, proteomics, peptidomics, carbohydrate analysis and calorimetric measurements will be performed. The role of the microbiota in infant growth and development is often overlooked yet offers opportunities to advance neonatal care. The ‘From Mum to Bum’ study is the first study in which the effect of a preterm gut microbiota composition on its metabolic capacity and subsequent infant growth and development is investigated. By collecting human milk of all mothers, gastric aspirates of preterm infants and fecal samples of all infants at each timepoint, we can follow digestion of human milk from the breast of the mother throughout the gastrointestinal tract of the infant, or ‘From Mum to Bum’.
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21
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Chen J, Li H, Hird SM, Chen MH, Xu W, Maas K, Cong X. Sex Differences in Gut Microbial Development of Preterm Infant Twins in Early Life: A Longitudinal Analysis. Front Cell Infect Microbiol 2021; 11:671074. [PMID: 34458157 PMCID: PMC8387566 DOI: 10.3389/fcimb.2021.671074] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/23/2021] [Indexed: 12/12/2022] Open
Abstract
Infant gut microbiota plays a vital role in immune response, mediates neurobehavioral development and health maintenance. Studies of twins’ gut microbiota found that gut microbiota composition and diversity tend to be mature and stable with increasing postnatal age (PNA). Preterm infant gut microbiome shifts dramatically when they were staying in the neonatal intensive care unit (NICU). Compositions and shifting characteristics of gut microbiota among neonatal preterm twins and triplets during their early life are still unknown, which impedes a better understanding of the mechanism underpinning neurobehavioral development and precise intervention/health of preterm neonates. This longitudinal cohort study used a twins/triplets design to investigate the interaction of genetic (e.g., male vs. female) and environmental factors influencing the development of the gut microbiome in early life. We included 39 preterm infants, 12 were Female twins/triplets (Female T/T) including 3 twins pairs and 2 triplets, 12 were male twins (Male T) including 6 twins pairs, and 15 were mixed-sex twins/triplets (Mix T/T) including 6 twins pairs and 1 triplet (8 females and 7 males) during the first four weeks of NICU stay. Weekly gut microbiota patterns between females and males were compared by linear discriminant analysis (LDA) effect size (LEfSe). Metagenomics function of gut microbiota was predicted by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Weekly function (KEGG pathways) differences between females and males were detected by using Statistical Analysis of Metagenomic Profiles (STAMP). Results found that female pairs and male pairs were significantly different in gut microbiome diversity, compositions, and predicted metabolic profiles, importantly, females and males were also significantly dissimilar within their co-twin/triplet pairs of the mixed-sex group, infants of co-twins/triplets shared more similar features than un-related infants from different twins’ pair. Future research developing personalized interventions for vulnerable high-risk infants should consider sex, and the interaction of sex and environmental factors.
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Affiliation(s)
- Jie Chen
- School of Nursing, University of Connecticut, Storrs, CT, United States
| | - Hongfei Li
- Department of Statistics, University of Connecticut, Storrs, CT, United States
| | - Sarah M Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Ming-Hui Chen
- Department of Statistics, University of Connecticut, Storrs, CT, United States
| | - Wanli Xu
- School of Nursing, University of Connecticut, Storrs, CT, United States
| | - Kendra Maas
- Microbial Analysis, Resources, and Services (MARS), University of Connecticut, Storrs, CT, United States
| | - Xiaomei Cong
- School of Nursing, University of Connecticut, Storrs, CT, United States.,Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States
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22
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Yang Z, Xu F, Li H, He Y. Beyond samples: A metric revealing more connections of gut microbiota between individuals. Comput Struct Biotechnol J 2021; 19:3930-3937. [PMID: 34377361 PMCID: PMC8319210 DOI: 10.1016/j.csbj.2021.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/03/2021] [Accepted: 07/07/2021] [Indexed: 10/31/2022] Open
Abstract
Studies of gut microbiota explore their complicated connections between individuals of different characteristics by applying different metrics to abundance data obtained from fecal samples. Although classic metrics are capable to quantify differences between samples, the microbiome of fecal sample is not a good surrogate for the gut microbiome of individuals because the microbial populations of the distal colon does not adequately represent that of the entire gastrointestinal tract. To overcome the deficiency of classic metrics in which the differences can be measured between the samples analyzed, but not the corresponding populations, we propose a metric for representing composition differences in the gut microbiota of individuals. Our investigation shows this metric outperforms traditional measures for multiple scenarios. For gut microbiota in diverse geographic populations, this metric presents more explainable data variance than others, not only in regular variance analysis but also in principle component analysis and partition analysis of biologic characteristics. With time-series data, the metric further presents a strong correlation with the time interval of serial sampling. Our findings suggest that the metric is robust and powerfully detects the intrinsic variations in gut microbiota. The metric holds promise for revealing more relations between gut microbiota and human health.
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Affiliation(s)
- Zhen Yang
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Feng Xu
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hongdou Li
- Obstetrics Gynecology Hospital, The Institute of Reproduction and Developmental Biology, Fudan University, Shanghai, China
| | - Yungang He
- Shanghai Fifth People's Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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23
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Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization. Biomolecules 2021; 11:biom11070999. [PMID: 34356622 PMCID: PMC8301799 DOI: 10.3390/biom11070999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/16/2022] Open
Abstract
Background: The human intestinal microbiome plays a central role in overall health status, especially in early life stages. 16S rRNA amplicon sequencing is used to profile its taxonomic composition; however, multiomic approaches have been proposed as the most accurate methods for study of the complexity of the gut microbiota. In this study, we propose an optimized method for bacterial diversity analysis that we validated and complemented with metabolomics by analyzing fecal samples. Methods: Forty-eight different analytical combinations regarding (1) 16S rRNA variable region sequencing, (2) a feature selection approach, and (3) taxonomy assignment methods were tested. A total of 18 infant fecal samples grouped depending on the type of feeding were analyzed by the proposed 16S rRNA workflow and by metabolomic analysis. Results: The results showed that the sole use of V4 region sequencing with ASV identification and VSEARCH for taxonomy assignment produced the most accurate results. The application of this workflow showed clear differences between fecal samples according to the type of feeding, which correlated with changes in the fecal metabolic profile. Conclusion: A multiomic approach using real fecal samples from 18 infants with different types of feeding demonstrated the effectiveness of the proposed 16S rRNA-amplicon sequencing workflow.
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Chang HY, Chiang Chiau JS, Ho YH, Chang JH, Tsai KN, Liu CY, Hsu CH, Lin CY, Ko MHJ, Lee HC. Impact of Early Empiric Antibiotic Regimens on the Gut Microbiota in Very Low Birth Weight Preterm Infants: An Observational Study. Front Pediatr 2021; 9:651713. [PMID: 34136438 PMCID: PMC8200535 DOI: 10.3389/fped.2021.651713] [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: 01/10/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
Frequent use of antibiotics in preterm infants disturbs their gut microbial balance. In this preliminary observational study, we investigated the effect of different antibiotic regimens, administered during the first week of life, on microbial composition and diversity in very low birth weight (VLBW) preterm infants. We performed fecal sampling of breastfed VLBW infants on days 7, 14, and 30. After excluding stool samples from infants who received probiotics or who were administered antibiotics beyond the age of 7 days, we compared gut microbiota profiles between infants receiving a combination of ampicillin and gentamicin for 3 days (AG group, n = 10) and those receiving a combination of ampicillin and cefotaxime for 7 days (AC group, n = 14) using 16S ribosomal DNA community profiling. We also assessed the changes over time in each group. Compared to the AG group, Enterococcus species were significantly more abundant in the AC group (P = 0.002), especially in 7-day samples (12.3 vs. 0.6%, respectively, P = 0.032). No difference was observed at phylum and genus level over time within each group. Species richness in the AC group decreased significantly in the 14-day (P = 0.038) and 30-day (P = 0.03) samples compared to that in the 7-day sample. The same was observed for microbial evenness; in contrast, no significant difference in Shannon index and beta-diversity was detected between the two groups. Controlling for relevant confounding variables did not change the results. In conclusion, different antibiotic regimens affect the early development of gut microbiota in VLBW preterm infants. Prolonged use of ampicillin and cefotaxime might result in overabundance of Enterococcus. However, given that no significant differences were observed in 1-month samples, bacterial genera appear to continue colonizing the gastrointestinal tract despite previous exposure to antibiotics. The clinical relevance of these findings should be elucidated by further studies.
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Affiliation(s)
- Hung-Yang Chang
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | | | - Yu-Hsuan Ho
- Life Science, Delta Research Center, Delta Electronics Incorporation, Taipei, Taiwan
| | - Jui-Hsing Chang
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Kun-Nan Tsai
- Life Science, Delta Research Center, Delta Electronics Incorporation, Taipei, Taiwan
| | - Chia-Yen Liu
- Life Science, Delta Research Center, Delta Electronics Incorporation, Taipei, Taiwan
| | - Chyong-Hsin Hsu
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Chia-Ying Lin
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Mary Hsin-Ju Ko
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Hung-Chang Lee
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
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Fragkou PC, Karaviti D, Zemlin M, Skevaki C. Impact of Early Life Nutrition on Children's Immune System and Noncommunicable Diseases Through Its Effects on the Bacterial Microbiome, Virome and Mycobiome. Front Immunol 2021; 12:644269. [PMID: 33815397 PMCID: PMC8012492 DOI: 10.3389/fimmu.2021.644269] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
The first 1000 days of life, including the intrauterine period, are regarded as a fundamental stepping stone for the development of a human. Unequivocally, nutrition during this period plays a key role on the proper development of a child, both directly through the intake of essential nutrients and indirectly by affecting the composition of the gut microbiota. The gut microbiota, including bacteria, viruses, fungi, protists and other microorganisms, is a highly modifiable and adaptive system that is influenced by diet, lifestyle, medicinal products and the environment. Reversely, it affects the immune system in multiple complex ways. Many noncommunicable diseases (NCDs) associated with dysbiosis are "programmed" during childhood. Nutrition is a potent determinant of the children's microbiota composition and maturation and, therefore, a strong determinant of the NCDs' programming. In this review we explore the interplay between nutrition during the first 1000 days of life, the gut microbiota, virome and mycobiome composition and the development of NCDs.
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Affiliation(s)
- Paraskevi C. Fragkou
- 4 Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Dareilena Karaviti
- 2 Department of Pediatrics, P. & A. Kyriakou Children’s Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Michael Zemlin
- Neonatal Intensive Care Unit, Department of Pediatrics and Neonatology, Saarland University Medical Center, Homburg, Germany
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
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Chong CYL, Vatanen T, Alexander T, Bloomfield FH, O'Sullivan JM. Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial. Front Cell Infect Microbiol 2021; 11:595323. [PMID: 33732655 PMCID: PMC7958882 DOI: 10.3389/fcimb.2021.595323] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/20/2021] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota of preterm infants is affected by perinatal factors and, in turn, may impact upon infant health. In this study, we collected fecal samples at Day-10 (D10) and 4-months corrected-age (4M) from 227 moderate–late preterm (MLPT) babies enrolled in a randomized controlled trial of nutritional management. A total of 320 samples underwent 16S amplicon sequencing, and shotgun metagenomic sequencing was performed on 94 samples from the 4M time point. The microbiome of babies whose families lived in lower socioeconomic status (SES) areas exhibited a significantly higher microbial alpha diversity at D10 (Wilcoxon test, p = 0.021), greater abundance of Bifidobacterium (linear model, q = 0.020) at D10 and Megasphaera (q = 0.031) at 4M. Hospital of birth explained 5.2% of the observed variance in 4M samples (PERMANOVA, p = 0.038), with Staphylococcus aureus more abundant in fecal samples from babies born in Middlemore hospital (linear model, q = 0.016). Maternal antibiotic (Wilcoxon test, p = 0.013) and probiotic (p = 0.04) usage within the four-week period before sample collection was associated with a reduction in the alpha diversity of D10 samples. Infant probiotic intake explained 2.1% (PERMANOVA, p = 0.021) of the variance in the D10 microbial profile with increased Lactobacillus (linear model, q = 1.1 × 10−10) levels. At 4M, the microbiome of infants who were breastmilk fed had reduced alpha diversity when compared to non-breastmilk fed infants (Wilcoxon test, p < 0.05). Although causality cannot be inferred within our study, we conclude that in MLPT babies, maternal socioeconomic factors, as well as the perinatal medical environment and nutrition impact on the development of the newborn microbiome.
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Affiliation(s)
| | - Tommi Vatanen
- Liggins Institute, The University of Auckland, Auckland, New Zealand.,Infectious Disease & Microbiome Program, The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Tanith Alexander
- Liggins Institute, The University of Auckland, Auckland, New Zealand.,Neonatal Unit, Kidz First, Middlemore Hospital, Auckland, New Zealand
| | | | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand.,The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
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