Prematurity is the leading cause of neonatal deaths and long-term infant disability, with the rate of preterm births continuing to rise. Despite improved medical and respiratory management, the mortality rate for the most premature infants remains high. Extremely low birth weight infants are at increased risk for complications such as sepsis, meningitis, necrotizing enterocolitis and poor growth- problems, all associated with high risk for neurodevelopmental impairment, and all of which may be impacted by the microbial communities in their gut. Among premature infants, frequently used treatments, such as antibiotics and histamine-2 blockers are associated with an increased risk of necrotizing enterocolitis and may exert their influence via alternations in gut microbiota.
This paper uses molecular methods to resolve the microbial constituents of the gut-associated microbiome in premature babies. The study highlights unprecedented early fungal diversity, evidence of roundworms, human and bacterial viruses, and a bacterial community harboring many potential pathogens.
Beyond Bacteria: A Study of the Enteric Microbial Consortium in Extremely Low Birth Weight Infants. (2011) PLoS ONE 6(12): e27858
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 the gastrointestinal tracts of preterm infants may serve as a reservoir for invasive organisms and remain poorly characterized. We used deep pyrosequencing to examine the gut-associated microbiome of 11 ELBW infants in the first postnatal month, with a first time determination of the eukaryote microbiota such as fungi and nematodes, including bacteria and viruses that have not been previously described. Among the fungi observed, Candida sp. and Clavispora sp. dominated the sequences, but a range of environmental molds were also observed. Surprisingly, seventy-one percent of the infant fecal samples tested contained ribosomal sequences corresponding to the parasitic organism Trichinella. Ribosomal DNA sequences for the roundworm symbiont Xenorhabdus accompanied these sequences in the infant with the greatest proportion of Trichinella sequences. When examining ribosomal DNA sequences in aggregate, Enterobacteriales, Pseudomonas, Staphylococcus, and Enterococcus were the most abundant bacterial taxa in a low diversity bacterial community (mean Shannon-Weaver Index of 1.02±0.69), with relatively little change within individual infants through time. To supplement the ribosomal sequence data, shotgun sequencing was performed on DNA from multiple displacement amplification (MDA) of total fecal genomic DNA from two infants. In addition to the organisms mentioned previously, the metagenome also revealed sequences for gram positive and gram negative bacteriophages, as well as human adenovirus C. Together, these data reveal surprising eukaryotic and viral microbial diversity in ELBW enteric microbiota dominated bytypes of bacteria known to cause invasive disease in these infants.