Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

Abstract

The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity.

Active Surveillance Cultures and Targeted Decolonization Are Associated with Reduced Methicillin-Susceptible <b><i>Staphylococcus aureus</i></b> Infections in VLBW Infants

“…Although no topical side effects were observed, the broad antimicrobial activity of octenidin and mupirocin used in our studies might alter the microbiome towards a more harmful bacterial composition. The skin of premature infants appears to be colonized with identical bacterial strains within the first month of life, showing a close relationship of the oral, skin, and gut microbiome [21]. Hence, the impact of decolonization strategies on the skin microbiome of premature neonates is unknown but could potentially lead to dysbiosis.…”

The infantile cutaneous microbiome: A review

“…There are scarce data on the composition of the neonatal microbiome, as well as its relationship to common neonatal skin conditions. Existing studies are limited by small sample size and lack of controls . Herein, we summarize the existing literature on the infantile cutaneous microbiome, its relation to normal skin barrier development, and its contribution to three common skin conditions: AD, seborrheic dermatitis (SD), and erythema toxicum neonatorum (ETN).…”

A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges

“…The in-situ replication rate was inferred based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication using iRep (Brown et al, 2016). The presence of TsSOB in the two un-binned sponge samples as well as in the seawater sample was determined by calculate_breadth.py, a python script which calculates the breadth and coverage of the genome according to the mapped reads from each of the metagenomic samples (Olm et al, 2017).…”