Patterned progression of bacterial populations in the premature infant gut

Patricio S. La Rosa, Barbara B. Warner, Yanjiao Zhou, George M. Weinstock, Erica Sodergren, Carla M. Hall-Moore, Harold J. Stevens, William E. Bennett, Nurmohammad Shaikh, Laura A. Linneman, Julie A. Hoffmann, Aaron Hamvas, Elena Deych, Berkley A. Shands, William D. Shannon*, Phillip I. Tarr

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

388 Scopus citations


In the weeks after birth, the gut acquires a nascent microbiome, and starts its transition to bacterial population equilibrium. This early-in-life microbial population quite likely influences later-in-life host biology. However, we know little about the governance of community development: does the gut serve as a passive incubator where the first organisms randomly encountered gain entry and predominate, or is there an orderly progression of members joining the community of bacteria? We used fine interval enumeration of microbes in stools from multiple subjects to answer this question. We demonstrate via 16S rRNA gene pyrosequencing of 922 specimens from 58 subjects that the gut microbiota of premature infants residing in a tightly controlled microbial environment progresses through a choreographed succession of bacterial classes from Bacilli to Gammaproteobacteria to Clostridia, interrupted by abrupt population changes. As infants approach 33-36 wk postconceptional age (corresponding to the third to the twelfth weeks of life depending on gestational age at birth), the gut is well colonized by anaerobes. Antibiotics, vaginal vs. Caesarian birth, diet, and age of the infants when sampled influence the pace, but not the sequence, of progression. Our results suggest that in infants in a microbiologically constrained ecosphere of a neonatal intensive care unit, gut bacterial communities have an overall nonrandom assembly that is punctuated by microbial population abruptions. The possibility that the pace of this assembly depends more on host biology (chiefly gestational age at birth) than identifiable exogenous factors warrants further consideration.

Original languageEnglish (US)
Pages (from-to)12522-12527
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number34
StatePublished - Aug 26 2014


  • Mixed model regression analysis
  • Necrotizing enterocolitis
  • Nonmetric multidimensional scaling
  • Prematurity

ASJC Scopus subject areas

  • General


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