Patterned progression of bacterial populations in the premature infant gut - PubMed (original) (raw)

Observational Study

. 2014 Aug 26;111(34):12522-7.

doi: 10.1073/pnas.1409497111. Epub 2014 Aug 11.

Barbara B Warner 2, Yanjiao Zhou 3, George M Weinstock 3, Erica Sodergren 3, Carla M Hall-Moore 2, Harold J Stevens 2, William E Bennett Jr 2, Nurmohammad Shaikh 2, Laura A Linneman 2, Julie A Hoffmann 2, Aaron Hamvas 2, Elena Deych 1, Berkley A Shands 1, William D Shannon 4, Phillip I Tarr 5

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Observational Study

Patterned progression of bacterial populations in the premature infant gut

Patricio S La Rosa et al. Proc Natl Acad Sci U S A. 2014.

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Abstract

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.

Keywords: mixed model regression analysis; necrotizing enterocolitis; nonmetric multidimensional scaling; prematurity.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

Bacterial taxa composition at class level as function of day of life of a single subject. These samples are from subject 32 who was born after 29 wk gestation. Each bar represents the bacterial proportions within single samples. From left to right, bars correspond to stools obtained on days of life 3, 4, 6, 8, 9, 10, 12, 14, 14, 16, 17, 19, 25, and 39, respectively. The predominant classes are Bacilli (dark blue), Gammaproteobacteria (red), and Clostridia (green). Eleven additional classes (light blue) were also present, mostly in stools obtained on days of life 3 and 4.

Fig. 2.

Fig. 2.

Percent bacterial class abundance. Proportion of each bacterial class is represented in y axes in each graph. The x axes represent samples obtained at various postconceptional ages (weeks). The columns represent class proportions, as indicated. (A–C) All infants in cohort (n = 58 subjects). (D–F) Infants in <26 wk gestational age subcohort (_n_ = 15 subjects). (_G–I_) Infants in 26–28 wk gestational age subcohort (_n_ = 20 subjects). (_J–L_) Infants in >28 wk gestational age subcohort (n = 23 subjects). To reduce the effect of random fluctuations in the data (noise), the lines were produced by fitting a cubic smooth spline (thick black line) to the data with 95% confidence bands (thinner lines) generated using a nonparametric bootstrap method.

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