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Embleton ND, Sproat T, Uthaya S, Young GR, Garg S, Vasu V, Masi AC, Beck L, Modi N, Stewart CJ, Berrington JE. Effect of an Exclusive Human Milk Diet on the Gut Microbiome in Preterm Infants: A Randomized Clinical Trial. JAMA Netw Open 2023; 6:e231165. [PMID: 36857051 PMCID: PMC9978942 DOI: 10.1001/jamanetworkopen.2023.1165] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
IMPORTANCE The effect of using an exclusive human milk diet compared with one that uses bovine products in preterm infants is uncertain, but some studies demonstrate lower rates of key neonatal morbidities. A potential mediating pathway is the gut microbiome. OBJECTIVE To determine the effect of an exclusive human milk diet on gut bacterial richness, diversity, and proportions of specific taxa in preterm infants from enrollment to 34 weeks' postmenstrual age. DESIGN, SETTING, AND PARTICIPANTS In this randomized clinical trial conducted at 4 neonatal intensive care units in the United Kingdom from 2017 to 2020, microbiome analyses were blind to group. Infants less than 30 weeks' gestation who had only received own mother's milk were recruited before 72 hours of age. Statistical analysis was performed from July 2019 to September 2021. INTERVENTIONS Exclusive human milk diet using pasteurized human milk for any shortfall in mother's own milk supply and human milk-derived fortifiers (intervention) compared with bovine formula and bovine-derived fortifier (control) until 34 weeks' postmenstrual age. Fortifier commenced less than 48 hours of tolerating 150 mL/kg per day. MAIN OUTCOMES AND MEASURES Gut microbiome profile including alpha and beta diversity, and presence of specific bacterial taxa. RESULTS Of 126 preterm infants enrolled in the study, 63 were randomized to control (median [IQR] gestation: 27.0 weeks [26.0-28.1 weeks]; median [IQR] birthweight: 910 g [704-1054 g]; 32 [51%] male) and 63 were randomized to intervention (median [IQR] gestation: 27.1 weeks [25.7-28.1 weeks]; median [IQR] birthweight: 930 g [733-1095 g]; 38 [60%] male); 472 stool samples from 116 infants were analyzed. There were no differences in bacterial richness or Shannon diversity over time, or at 34 weeks between trial groups. The exclusive human milk diet group had reduced relative abundance of Lactobacillus after adjustment for confounders (coefficient estimate, 0.056; P = .03), but not after false discovery rate adjustment. There were no differences in time to full feeds, necrotizing enterocolitis, or other key neonatal morbidities. CONCLUSIONS AND RELEVANCE In this randomized clinical trial in preterm infants using human milk-derived formula and/or fortifier to enable an exclusive human milk diet, there were no effects on overall measures of gut bacterial diversity but there were effects on specific bacterial taxa previously associated with human milk receipt. These findings suggest that the clinical impact of human milk-derived products is not modulated via microbiomic mechanisms. TRIAL REGISTRATION ISRCTN trial registry identifier: ISRCTN16799022.
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Affiliation(s)
- Nicholas D. Embleton
- Newcastle Hospitals NHS Trust, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Thomas Sproat
- Newcastle Hospitals NHS Trust, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sabita Uthaya
- Section of Neonatal Medicine, School of Public Health, Imperial College London, London, United Kingdom
- Chelsea and Westminster Hospital, NHS Foundation Trust, London, United Kingdom
| | | | - Shalabh Garg
- James Cook University Hospital, Middlesbrough, United Kingdom
| | - Vimal Vasu
- William Harvey Hospital, Ashford, Kent, United Kingdom
| | - Andrea C. Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lauren Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Neena Modi
- Section of Neonatal Medicine, School of Public Health, Imperial College London, London, United Kingdom
- Chelsea and Westminster Hospital, NHS Foundation Trust, London, United Kingdom
| | - Christopher J. Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Janet E. Berrington
- Newcastle Hospitals NHS Trust, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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Beck LC, Masi AC, Young GR, Vatanen T, Lamb CA, Smith R, Coxhead J, Butler A, Marsland BJ, Embleton ND, Berrington JE, Stewart CJ. Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants. Nat Microbiol 2022; 7:1525-1535. [PMID: 36163498 PMCID: PMC9519454 DOI: 10.1038/s41564-022-01213-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/25/2022] [Indexed: 12/23/2022]
Abstract
The development of the gut microbiome from birth plays important roles in short- and long-term health, but factors influencing preterm gut microbiome development are poorly understood. In the present study, we use metagenomic sequencing to analyse 1,431 longitudinal stool samples from 123 very preterm infants (<32 weeks' gestation) who did not develop intestinal disease or sepsis over a study period of 10 years. During the study period, one cohort had no probiotic exposure whereas two cohorts were given different probiotic products: Infloran (Bifidobacterium bifidum and Lactobacillus acidophilus) or Labinic (B. bifidum, B. longum subsp. infantis and L. acidophilus). Mothers' own milk, breast milk fortifier, antibiotics and probiotics were significantly associated with the gut microbiome, with probiotics being the most significant factor. Probiotics drove microbiome transition into different preterm gut community types (PGCTs), each enriched in a different Bifidobacterium sp. and significantly associated with increased postnatal age. Functional analyses identified stool metabolites associated with PGCTs and, in preterm-derived organoids, sterile faecal supernatants impacted intestinal, organoid monolayer, gene expression in a PGCT-specific manner. The present study identifies specific influencers of gut microbiome development in very preterm infants, some of which overlap with those impacting term infants. The results highlight the importance of strain-specific differences in probiotic products and their impact on host interactions in the preterm gut.
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Affiliation(s)
- Lauren C Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK
| | - Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK
| | - Gregory R Young
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle, UK
| | - Tommi Vatanen
- Liggins Institute, University of Auckland, Auckland, New Zealand
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Rachel Smith
- Bioscience Institute, Newcastle University, Newcastle, UK
| | | | - Alana Butler
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Benjamin J Marsland
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Newcastle Hospitals NHS Trust, Newcastle, UK
- Population Health Sciences Institute, Newcastle University, Newcastle, UK
| | - Janet E Berrington
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK.
- Newcastle Neonatal Service, Newcastle Hospitals NHS Trust, Newcastle, UK.
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Abstract
The developing gut microbiome in infancy plays a key role in shaping the host immune system and metabolic state, and human milk is the main factor influencing its composition. Human milk does not only serve to feed the baby, but also to help the new-born adapt to its new environment and microbial exposures. Human milk protects the infant by providing multiple bioactive molecules, including human milk oligosaccharides (HMOs), which are the third most abundant solid component after lipids and lactose. The infant is unable to digest HMOs, so they reach the small and large intestines intact where they have many roles, including acting as prebiotics. Bifidobacterium spp. are the main, but not the only, commensals equipped with genes for HMO degradation. In this review we will outline the HMOs structures and functions, list the genes needed for their digestion, and describe the main strategies adopted by bacteria for their utilization.
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Affiliation(s)
- Andrea C Masi
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, 3rd Floor Leech Building, Newcastle NE2 4HH, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, 3rd Floor Leech Building, Newcastle NE2 4HH, UK
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Masi AC, Fofanova TY, Lamb CA, Auchtung JM, Britton RA, Estes MK, Ramani S, Cockell SJ, Coxhead J, Embleton ND, Berrington JE, Petrosino JF, Stewart CJ. Distinct gene expression profiles between human preterm-derived and adult-derived intestinal organoids exposed to Enterococcus faecalis: a pilot study. Gut 2021; 71:gutjnl-2021-326552. [PMID: 34921063 PMCID: PMC9231289 DOI: 10.1136/gutjnl-2021-326552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tatiana Y Fofanova
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Christopher A Lamb
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jennifer M Auchtung
- Nebraska Food for Health Center and Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Simon J Cockell
- Bioinformatics Support Unit, Newcastle University, Newcastle Upon Tyne, UK
| | - Jonathan Coxhead
- Bioscience Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Janet E Berrington
- Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Joseph F Petrosino
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, The Baylor College of Medicine, Houston, Texas, USA
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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Masi AC, Embleton ND, Lamb CA, Young G, Granger CL, Najera J, Smith DP, Hoffman KL, Petrosino JF, Bode L, Berrington JE, Stewart CJ. Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis. Gut 2021; 70:2273-2282. [PMID: 33328245 PMCID: PMC9231288 DOI: 10.1136/gutjnl-2020-322771] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Necrotising enterocolitis (NEC) is a devastating intestinal disease primarily affecting preterm infants. The underlying mechanisms are poorly understood: mother's own breast milk (MOM) is protective, possibly relating to human milk oligosaccharide (HMO) and infant gut microbiome interplay. We investigated the interaction between HMO profiles and infant gut microbiome development and its association with NEC. DESIGN We performed HMO profiling of MOM in a large cohort of infants with NEC (n=33) with matched controls (n=37). In a subset of 48 infants (14 with NEC), we also performed longitudinal metagenomic sequencing of infant stool (n=644). RESULTS Concentration of a single HMO, disialyllacto-N-tetraose (DSLNT), was significantly lower in MOM received by infants with NEC compared with controls. A MOM threshold level of 241 nmol/mL had a sensitivity and specificity of 0.9 for NEC. Metagenomic sequencing before NEC onset showed significantly lower relative abundance of Bifidobacterium longum and higher relative abundance of Enterobacter cloacae in infants with NEC. Longitudinal development of the microbiome was also impacted by low MOM DSLNT associated with reduced transition into preterm gut community types dominated by Bifidobacterium spp and typically observed in older infants. Random forest analysis combining HMO and metagenome data before disease accurately classified 87.5% of infants as healthy or having NEC. CONCLUSION These results demonstrate the importance of HMOs and gut microbiome in preterm infant health and disease. The findings offer potential targets for biomarker development, disease risk stratification and novel avenues for supplements that may prevent life-threatening disease.
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Affiliation(s)
- Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK,Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK,Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gregory Young
- School of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Claire L Granger
- Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Julia Najera
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, California, USA
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, California, USA
| | - Janet E Berrington
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK .,Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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Beck LC, Granger CL, Masi AC, Stewart CJ. Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside. Expert Rev Proteomics 2021; 18:247-259. [PMID: 33896313 DOI: 10.1080/14789450.2021.1922278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: At birth, the gastrointestinal (GI) tract is colonized by a complex community of microorganisms, forming the basis of the gut microbiome. The gut microbiome plays a fundamental role in host health, disorders of which can lead to an array of GI diseases, both short and long term. Pediatric GI diseases are responsible for significant morbidity and mortality, but many remain poorly understood. Recent advancements in high-throughput technologies have enabled deeper profiling of GI morbidities. Technologies, such as metagenomics, transcriptomics, proteomics and metabolomics, have already been used to identify associations with specific pathologies, and highlight an exciting area of research. However, since these diseases are often complex and multifactorial by nature, reliance on a single experimental approach may not capture the true biological complexity. Therefore, multi-omics aims to integrate singular omic data to further enhance our understanding of disease.Areas covered: This review will discuss and provide an overview of the main omic technologies that are used to study complex GI pathologies in early life.Expert opinion: Multi-omic technologies can help to unravel the complexities of several diseases during early life, aiding in biomarker discovery and enabling the development of novel therapeutics and augment predictive models.
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Affiliation(s)
- Lauren C Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Claire L Granger
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.,Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
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Masi AC, Oppong YEA, Haugk B, Lamb CA, Sharp L, Shaw JM, Stewart CJ, Oppong KW. Endoscopic ultrasound (EUS)-guided fine needle biopsy (FNB) formalin fixed paraffin-embedded (FFPE) pancreatic tissue samples are a potential resource for microbiota analysis. Gut 2021; 70:999-1001. [PMID: 32816963 DOI: 10.1136/gutjnl-2020-322457] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Andrea C Masi
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Yaa E A Oppong
- Department of Infection Biology, Faculty of Infectious and Tropical Medicine, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Beate Haugk
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Linda Sharp
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - James M Shaw
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Kofi W Oppong
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK .,HPB Unit and Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
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Masi AC, Koo S, Lamb CA, Hull MA, Sharp L, Nelson A, Hampton JS, Rees CJ, Stewart CJ. Using faecal immunochemical test (FIT) undertaken in a national screening programme for large-scale gut microbiota analysis. Gut 2021; 70:429-431. [PMID: 32430347 DOI: 10.1136/gutjnl-2020-321594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/01/2020] [Indexed: 12/08/2022]
Affiliation(s)
- Andrea C Masi
- Gastroenterology, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Sara Koo
- Gastroenterology, South Tyneside General Hospital, South Shields, UK.,Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.,Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Mark A Hull
- Leeds Institute of Biomedical & Clinical Sciences, St James's University Hospital, Leeds, UK
| | - Linda Sharp
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - James S Hampton
- Gastroenterology, South Tyneside General Hospital, South Shields, UK.,Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Colin J Rees
- Gastroenterology, South Tyneside General Hospital, South Shields, UK .,Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
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Abstract
Late-onset sepsis (LOS) and necrotising enterocolitis (NEC) account for the highest number of deaths in premature infants and often cause severe morbidity in survivors. NEC is an inflammatory mediated condition, but its pathophysiology remains poorly understood. There is increasing evidence that in LOS the causative organism most often translocates from the gut. No causative microorganism has been consistently associated with either LOS or NEC, but an aberrant gut microbiome development could play a pivotal role. A low bacterial diversity and a delay in anaerobic bacteria colonization may predispose preterm infants to disease development. Conversely, a predominance of Bifidobacterium species and breast milk feeding might help to prevent disease onset. With numerous studies reporting conflicting results, further research is needed to better understand the role of microorganisms and type of feeding in the health status of preterm infants.
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Affiliation(s)
- Andrea C Masi
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
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