RT Journal
A1 Olm, Matthew R
A1 Brown, Christopher T
A1 Brooks, Brandon
A1 Firek, Brian
A1 Baker, Robyn
A1 Burstein, David
A1 Soenjoyo, Karina
A1 Thomas, Brian C
A1 Morowitz, Michael
A1 Banfield, Jillian
T1 Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates
JF Genome Research 
JO Genome Research 
YR 2017 
FD January 10 
DO 10.1101/gr.213256.116 
SP gr.213256.116 
UL http://genome.cshlp.org/content/early/2017/01/10/gr.213256.116.abstract 
AB 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 sub-populations, one of which appeared in the gut after one week 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.