Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession

Abstract

The fine‐scale temporal dynamics of the chicken gut microbiome are unexplored, but thought to be critical for chicken health and productivity. Here, we monitored the fecal microbiome of healthy chickens on days 1–7, 10, 14, 21, 28, and 35 after hatching, and performed 16S rRNA amplicon sequencing in order to obtain a high‐resolution census of the fecal microbiome over time. In the period studied, the fecal microbiomes of the developing chickens showed a linear‐log increase in community richness and consistent shifts in community composition. Three successional stages were detected: the first stage was dominated by vertically transmitted or rapidly colonizing taxa including Streptococcus and Escherichia/Shigella; in the second stage beginning on day 4, these taxa were displaced by rapid‐growing taxa including Lachnospiraceae and Ruminococcus‐like species variants; and in the third stage, starting on day 10, slow‐growing, specialist taxa including Candidatus Arthrobacter and Romboutsia were detected. The patterns of displacement and the previously reported ecological characteristics of many of the dominant taxa observed suggest that resource competition plays an important role in regulating successional dynamics in the developing chicken gut. We propose that the boundaries between successional stages (3–4 and 14–21 days after hatching) may be optimal times for microbiome interventions.

Development of the Ileal Microbiota in Three Broiler Breeds

“…Some have found no difference in abundance at time points from 8 to 36 d.p.h while others have observed a decrease in Lactobacillaceae between 4 and 16 d.p.h (28,46). A similar pattern of succession to that described in this study has been proposed by Jurburg et al (25) after examining the fecal microbiome of chickens between 1 and 35 d.p.h although many taxa detected are associated with the caecal microbiome rather than the ileal microbiome. The first stage was dominated by rapidly-colonizing taxa such as Streptococcus and Escherichia/Shigella.…”

“…This likely explains the wide variety of results obtained by different groups when examining the intestinal microbiota in day-old chicks. In general, the initial microbiome is dominated Enterobacteriaceae or Clostridiaceae, although there are reports of high abundance other taxa such as Streptococcaceae and Enterococcaceae (3,20,24,25). At the genus level, the most commonly isolated Enterobacteriaceae are Escherichia/Shigella while Clostridiaceae are most often assigned to Clostridium sensu stricto 1.…”

“…Only two of these species, L. salivarius and L. crispatus, were present at 0 d.p.h, with four at 7 d.p.h and all seven at 21 d.p.h. Candidatus Athromitus colonizes the ileum between 7 and 14 d.p.h (20,25) and has been reported as the prominent taxa in the ileal mucus although Lactobacillus reclaims dominance at later time points (29). Other slow growing taxa such as Romboutsia, a member of Peptostreptococcaceae, begin to colonize the ileum from 10 to 21 d.p.h.…”

Application of culturomics to characterize diverse anaerobic bacteria from the gastrointestinal tract of broiler chickens in relation to environmental reservoirs

“…Thus, in our study, birds may have had more access to litter, thereby influencing the GIT bacterial community composition. Additionally, we did not isolate any Bacteroidetes spp., which may be due to the production setting and animal diets, as well as the breed and age of the birds used (Zou et al 2018;Jurburg et al 2019). If the goal is the isolation of Bacteroidetes spp.…”

“…They observed that even when birds were raised under similar conditions and on the same diet, a large degree of variation was observed within the cecal microbiota. In another study using culture-independent analysis, a succession of bacteria was observed in the fecal material of developing chicks, including a shift in the community structure from one dominated by class Alphaproteobacteria to one dominated by classes Bacteroidia and Clostridia (Jurburg et al 2019). These studies were able to ascertain limited information on activity.…”