EVALUATING THE GASTROINTESTINAL MICROBIOTA OF HOSPITALIZED NEONATES USING CULTUROMICS AND METAGENOMICS
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Authors
Oladipo, Jummy
Date
Type
thesis
Language
eng
Keyword
Newborn , Culturomics , Metagenomics , Neonate , Microbial communities , Gut microbiome , Gastrointestinal microbiome , Bacteria isolation , Mass spectrometry , 16S rRNA
Alternative Title
Abstract
Background: The developing gastrointestinal microbiota (GIM) of neonates plays an important role in long and short-term health. ‘Culturomics’, the use of specialized media in conjunction with metagenomics has the potential of providing further insight into the isolation and identification of bacterial populations in the GIM that so far have been overlooked for their health benefits. This study aims to better characterize the GIM of neonates in the NICU through high-throughput culturing methods and metagenomics. We hypothesize that by enriching bacteria found in neonatal stools, our team will identify previously unappreciated fastidious anaerobes in the neonatal GIM. Methods: Using a culturomics approach, we isolated bacterial species from the stools of low birth weight (LBW) and normal birth weight (NBW) (n=10) neonates in the NICU who were unexposed to probiotics or antibiotics. Stool was cultured either immediately on 8 different selective and differential media or preincubated in blood culture bottles with or without sheep blood and rumen fluid supplementation before culturing on selective and differential agar. Bacteria were identified using MALDI-TOF mass spectrometry and/or 16S Sanger sequencing (V3-V4) hypervariable regions). Results: Culturomics allowed for the isolation of 33 species of bacteria from the neonatal stool within the 5 families identified through 16S Next-generation Sequencing (NGS); Enterobacteriaceae, Staphylococcaceae, Enterococcaceae, Bacteroidaceae, and Streptococcaceae. Enrichment allowed for the isolation of 11 bacterial species not previously identified in the unenriched conditions including S. haemolyticus, S. parasanguinis. V. rogosae, and R. solanacearum and resulted in more fastidious anaerobes being recovered. Conclusions: Future studies investigating neonatal GIM should utilize both culturomic and metagenomic approaches. These studies will increase our understanding of the membership of the neonatal GIM and provide insight into the role of fastidious bacteria in the neonatal GIM and neonatal health.
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ProQuest PhD and Master's Theses International Dissemination Agreement
Intellectual Property Guidelines at Queen's University
Copying and Preserving Your Thesis
This publication is made available by the authority of the copyright owner solely for the purpose of private study and research and may not be copied or reproduced except as permitted by the copyright laws without written authority from the copyright owner.