Human metagenome of extremely low birth weight infants
Human metagenome of extremely low birth weight infants
Extremely low birth weight (ELBW) infants have high morbidity and mortality, frequently due to invasive infections from Bacteria, fungi, and viruses.  The microbial communities present in their gastrointestinal tracts may serve as a reservoir for invasive infections, but yet the whole developing microbial consortium in the preterm infant remains poorly characterized.  Deep pyrosequencing was employed to map a detailed molecular blueprint  of primary microbial colonization among 11 ELBW infants.  We examined the gut-associated microbiome in the first month of life, including Bacteria,  Eukaryotes, viruses, and other pathogenic groups in premature infants.  Enterobacteriales, Pseudomonas, Staphylococcus., and Enterococcus were most abundant taxa within a moderately diverse bacterial community (mean Shannon-Weaver Index of 2.22 + 0.85), with relatively static intra-individual diversity  over time.  Candida sp. and Clavispora sp. dominated among the fungi, but sequences originating from a wide range of environmental molds were also observed.   Fifty seven percent of the samples analyzed for   Eukaryote ribosomal sequences contained sequences for the parasitic organism Trichinella.  16S rDNA sequences for the roundworm symbiont Xenorhabdus accompanied these sequences in the infant with the greatest proportion of Trichinella sequences.  To supplement the ribosomal sequence data, shotgun sequencing was performed on multiple displacement amplified genomic  DNA from two infants.  Virulence-associated genes and genes for carbohydrate, amino acid, and nucleic acid metabolism were enriched in a relatively simplified metagenome compared to adults. The metagenome also revealed sequences for gram positive and gram negative bacteriophages as well as human adenovirus C.  Together these data reveal previously unappreciated eukaryotic and viral microbial diversity underlying a developing enteric microbiota in the ELBW infant that is dominated by a reservoir of pathogenic bacteria.