Application of methods for identifying broiler chicken gut bacterial species linked with increased energy metabolism

Abstract

A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds.

FIG. 1.

nMDS ordination of gut microbial communities identified by gut section and diet. (A) Gut microbial communities from the duodenum (triangles), jejunum (inverted triangles), ileum (circles), and ceca (squares) from all birds (n = 48) regardless of diet. (B) Same nMDS as in panel A. However, samples are identified by both gut section and diet. Gut microbial communities from the four gut sections of birds on the barley control diet are identified as duodenum (gray triangles), jejunum (inverted gray triangles), ileum (gray circles), and ceca (gray squares), while those of birds on the barley diet supplemented with enzyme are identified as duodenum (black triangles), jejunum (black inverted triangles), ileum (black circles), and ceca (black squares). The ordination is based on Bray-Curtis similarities calculated from fourth-root transformed OTU abundances (147 OTUs).

FIG. 2.

nMDS ordination of gut microbial communities from the ileum of birds fed either a barley control diet (filled circles) or barley diet supplemented with enzyme (open squares) showing the extent to which the overall community pattern generated from the full set of 91 OTUs (A) is reproducible by a smaller subset of 17 OTUs (B) identified by the BVSTEP procedure. The matching coefficient (ρ) to panel A is shown in panel B. The subset of 17 OTUs identified consisted of OTUs 70, 96, 148, 182, 184, 190, 214, 224, 286, 288, 290, 300, 480, 522, 580, 590, and 880.

FIG. 3.

nMDS ordination of gut microbial communities from the ceca of birds fed either a barley control diet (filled circles) or a barley diet supplemented with enzyme (open squares) showing the extent to which the overall community pattern identified from the full set of 111 species (A) is reproducible by a smaller subset of 29 species (B) identified by the BVSTEP procedure. The matching coefficient (ρ) to panel A is shown in panel B. The subset of 29 OTUs identified were OTUs 70, 92, 94, 96, 146, 158, 184, 188, 198, 212, 214, 216, 222, 286, 290, 300, 486, 488, 490, 496, 526, 528, 530, 536, 538, 546, 548, 580, and 590.

FIG. 4.

PCO ordination of ileal microbial communities from birds fed either a barley control diet (filled circles) or a barley diet supplemented with enzyme (open squares). Overlaid onto the PCO are vectors of the subset of 17 OTUs identified by the BVSTEP procedure, indicating the association of OTUs with particular diets.

FIG. 5.

PCO ordination of cecal microbial communities from birds fed either a barley control diet (filled circles) or a barley diet supplemented with enzyme (open squares). Overlaid onto the PCO are vectors of the subset of 29 OTUs identified by the BVSTEP procedure, indicating an association of OTUs with particular diets.

FIG. 6.

CAP of diet-associated gut microbial communities related to AME. CAP-versus-AME biplots for the ileum (A) and the ceca (B) are shown. CAP analysis was based on Bray-Curtis similarities calculated from fourth-root transformed species abundances. “m” achieves the maximum proportion of correct allocations (% of trace [G]) of samples to diet. Symbols: open squares, birds on the barley-plus-enzyme diet; filled circles, birds on the barley-only control diet.