Beyond Bacteria: A Study of the Enteric Microbial Consortium in Extremely Low Birth Weight Infants

Abstract

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.

The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing

“…Nevertheless, Jacquot et al 17 have shown that bacterial diversity increases more slowly in extremely preterm (GA < 28 wk) than in moderately preterm infants (GA ⩾ 28 wk), 17 supported by the increase of Shannon diversity index with increasing corrected GA seen in our study. Additionally, many studies have concluded that preterm infants have generally low bacterial diversity, 8,10,15 which can be seen by us in ELBW infants as well.…”

“…[6][7][8] Increasing number of studies using 16S rRNA gene specific sequencing are in general confirming but on the other hand expanding the previous knowledge. [9][10][11][12][13][14] We aimed to broaden the understanding of the composition of gut microbiota in preterm infants by describing the profile of gut microbiota in 50 extremely low birth weight (ELBW; birth weight [BW] <1200 g) neonates, all requiring treatment in 3rd level neonatal intensive care unit (NICU) and The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing …”

Patterned progression of bacterial populations in the premature infant gut

“…Studies of gut bacteria in preterm infants have been limited in subject and/or sample numbers (24,28,29), have used cross-sectional comparisons (30), or did not stratify extensively by gestational age at birth or age postconception (30)(31)(32)(33)(34)(35)(36). Our intensive and extensive dataset suggests that limited sampling in premature neonates is problematic because of very frequent alterations in population structure.…”

Fungal Diversity in Gut Microbiota in Patients with Cancer

“…Culture dependent methods to extract DNA from purported samples and subsequent analysis by techniques such as polymerase chain reaction (PCR), cloning, sequencing and next generation sequencing have been used to identify and explore human gut mycobiome, these approaches are unique to identify fastidious fungi that cannot be identified by traditional culture methods (Hamad et al, 2012, Ott et al, 2008, Scanlan and Marchesi, 2008, LaTuga et al, 2011. Our study aims to investigate the fungal components in patients with various cancer types from the gut of infected patients and healthy individuals using conventional clone sequencing technology.…”

“…were previously detected in the gastrointestinal tract of patients and healthy individuals whereas, Asperg-illus and Pencillium spp. are ubiquitous fungi and have worldwide distribution (Hamad et al, 2012, LaTuga et al, 2011, Ott et al, 2008, Scanlan and Marchesi, 2008. Other fungal variety of species were accounted for the isolates, but of no signific-ant numbers, reports by others have isolated many fungal pathogens other than Candida spp.…”