Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

Abstract

The intestinal microbiome is a critical determinant of human health. Alterations in its composition have been correlated with chronic disorders, such as obesity and inflammatory bowel disease in adults, and may be associated with neonatal necrotizing enterocolitis in premature infants. Increasing evidence suggests that strain-level genomic variation may underpin distinct ecological trajectories within mixed populations, yet there have been few strain-resolved analyses of genotype–phenotype connections in the context of the human ecosystem. Here, we document strain-level genomic divergence during the first 3 wk of life within the fecal microbiota of an infant born at 28-wk gestation. We observed three compositional phases during colonization, and reconstructed and intensively curated population genomic datasets from the third phase. The relative abundance of two Citrobacter strains sharing ~99% nucleotide identity changed significantly over time within a community dominated by a nearly clonal Serratia population and harboring a lower abundance Enterococcus population and multiple plasmids and bacteriophage. Modeling of Citrobacter strain abundance suggests differences in growth rates and host colonization patterns. We identified genotypic variation potentially responsible for divergent strain ecologies, including hotspots of sequence variation in regulatory genes and intergenic regions, and in genes involved in transport, flagellar biosynthesis, substrate metabolism, and host colonization, as well as differences in the complements of these genes. Our results demonstrate that a community genomic approach can elucidate gut microbial colonization at the resolution required to discern medically relevant strain and species population dynamics, and hence improve our ability to diagnose and treat microbial community-mediated disorders.

Host genetic and environmental effects on mouse intestinal microbiota

“…In some cases, extensive genetic coevolution between the animal host and microbes has resulted in obligate, highly specific, nutritional symbioses involving one or a few vertically transmitted microbial species, such as the endosymbionts of some hydrothermal vent invertebrates and those of plant sap-feeding insects (Moran, 2007;Dubilier et al, 2008). Even for more complex animal gut microbial communities, acquired and maintained dynamically after hatching or birth, there are likely host-microbe specificity determinants, as revealed by natural colonization and experimental microbiota transplantation across host species (Rawls et al, 2004;Rawls et al, 2006;Palmer et al, 2007;Morowitz et al, 2011). Distinct community structure and composition characterizes different vertebrate and invertebrate species in their natural environments, global microbiota and interspecies relatedness, reflecting host phylogeny and incorporating elements of developmental and nutritional specialization (Ley et al, 2008a, b;Ochman et al, 2010;Yidirim et al, 2010).…”

An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

“…The 16S rRNA gene was amplified from metagenomic DNAs extracted with different methodologies following optimized PCR conditions [24]. The resulting amplicons were analyzed using agarose gel electrophoresis and quantified with Qubit® dsDNA HS Assay Kit.…”

“…The 16S rRNA gene sequences generated and used in the current study were submitted as a NCBI Bioproject (Accession ID: PRJNA295000). Subsequently, Quantitative Insights Into Microbial Ecology (QIIME) pipeline was implemented for pyrosequencing data analysis [24], along with 16S rRNA gene sequence data obtained from the Human Microbiome Project (HMP) [25]. Variability analysis of 16S rRNA gene sequences was performed using QIIME statistical tools [24], [25], [26].…”

Impact of Early-Life Microbiota on the Development of Infants

“…Полученные результаты позволили расценивать отсутствие выделения с калом Propionibacterium у детей первой недели жизни как фактор, предрасполагающий к развитию НЭК [34].…”