Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants View Full Text


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Article Info

DATE

2016-06-03

AUTHORS

Tali Raveh-Sadka, Brian Firek, Itai Sharon, Robyn Baker, Christopher T Brown, Brian C Thomas, Michael J Morowitz, Jillian F Banfield

ABSTRACT

The potentially critical stage of initial gut colonization in premature infants occurs in the hospital environment, where infants are exposed to a variety of hospital-associated bacteria. Because few studies of microbial communities are strain-resolved, we know little about the extent to which specific strains persist in the hospital environment and disperse among infants. To study this, we compared 304 near-complete genomes reconstructed from fecal samples of 21 infants hospitalized in the same intensive care unit in two cohorts, over 3 years apart. The genomes represent 159 distinct bacterial strains, only 14 of which occurred in multiple infants. Enterococcus faecalis and Staphylococcus epidermidis, common infant gut colonists, exhibit diversity comparable to that of reference strains, inline with introduction of strains from infant-specific sources rather than a hospital strain pool. Unlike other infants, a pair of sibling infants shared multiple strains, even after extensive antibiotic administration, suggesting overlapping strain-sources and/or genetic selection drive microbiota similarities. Interestingly, however, five strains were detected in infants hospitalized three years apart. Three of these were also detected in multiple infants in the same year. This finding of a few widely dispersed and persistent bacterial colonizers despite overall low potential for strain dispersal among infants has implications for understanding and directing healthy colonization. More... »

PAGES

2817-2830

References to SciGraph publications

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  • 2009-08-21. Community-wide analysis of microbial genome sequence signatures in GENOME BIOLOGY
  • 2004-06-16. Early Intestinal Bacterial Colonization and Necrotizing Enterocolitis in Premature Infants: The Putative Role of Clostridium in PEDIATRIC RESEARCH
  • 2013-12-17. Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life in MICROBIOME
  • 2013-04-16. Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants in MICROBIOME
  • 2009-04-16. 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2014-12-31. Temporal dynamics of the very premature infant gut dominant microbiota in BMC MICROBIOLOGY
  • 2014-04-17. Identification of Mutations in Laboratory-Evolved Microbes from Next-Generation Sequencing Data Using breseq in ENGINEERING AND ANALYZING MULTICELLULAR SYSTEMS
  • 2010-03-08. Prodigal: prokaryotic gene recognition and translation initiation site identification in BMC BIOINFORMATICS
  • 2007-02-26. Minimus: a fast, lightweight genome assembler in BMC BIOINFORMATICS
  • 2014-01-28. Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants in MICROBIOME
  • 2014-10-13. Development of the preterm infant gut microbiome: a research priority in MICROBIOME
  • 2012-03-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ismej.2016.83

    DOI

    http://dx.doi.org/10.1038/ismej.2016.83

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1008606938

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27258951


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