Three broiler feeding trials were investigated in order to identify gut bacteria consistently linked with improvements in bird performance as measured by feed efficiency. Trials were done in various geographic locations and varied in diet composition, broiler breed, and bird age. Gut microbial communities were investigated using microbial profiling. Eight common performance-linked operational taxonomic units (OTUs) were identified within both the ilea (180, 492, and 564-566) and ceca (140-142, 218-220, 284-286, 312, and 482) across trials. OTU 564-566 was associated with lower performance, while OTUs 140-142, 482, and 492 were associated with improved performance. Targeted cloning and sequencing of these eight OTUs revealed that they represented 26 bacterial species or phylotypes which clustered phylogenetically into seven groups related to Lactobacillus spp., Ruminococcaceae, Clostridiales, Gammaproteobacteria, Bacteroidales, Clostridiales/Lachnospiraceae, and unclassified bacteria/clostridia. Where bacteria were identifiable to the phylum level, they belonged predominantly to the Firmicutes, with Bacteroidetes and Proteobacteria also identified. Some of the potential performance-related phylotypes showed high sequence identity with classified bacteria (Lactobacillus salivarius, Lactobacillus aviarius, Lactobacillus crispatus, Faecalibacterium prausnitzii, Escherichia coli, Gallibacterium anatis, Clostridium lactatifermentans, Ruminococcus torques, Bacteroides vulgatus, and Alistipes finegoldii). The 16S rRNA gene sequence information generated will allow quantitative assays to be developed which will enable elucidations of which of these phylotypes are truly performance related. This information could be used to monitor strategies to improve feed efficiency and feed formulation for optimal gut health.Because feed constitutes approximately 70% of the cost of raising broiler chickens (1), the most common measures of bird performance have been linked to weight gain and feed efficiency. Broiler performance is closely linked to the genetics, diet, age, and rearing environment of the bird (1,23,32,54). Genetic selection has largely driven the vast improvements observed in weight gain and feed efficiency in meat chickens over the last 50 years, although a small proportion of these improvements have been attributed to nutrition and other management practices (32). The genetic changes associated with improved weight gain and feed efficiency have also resulted in changes to the gut physiology and gut microbial community composition of birds (44). Diet, age, and environmental factors have also been reported to influence the gut microbiota (43,71,72). Therefore, there appears to be a clear link between bird performance and gut microbiota composition.In medicine, much interest has already focused on the influence of the gut microbiota in human health (35,78) and energy metabolism (73,74,83).

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.

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The effects of avilamycin, zinc bacitracin, and flavophospholipol on broiler gut microbial community colonization and bird performance in the first 17 days posthatch were investigated. Significant differences in gut microbiota associated with gut section, dietary treatment, and age were identified by terminal restriction fragment length polymorphism (T-RFLP), although no performance-related differences between dietary treatments were detected. Similar age-related shifts in the gut microbiota were identified regardless of diet but varied between the ilea and ceca. Interbird variabilities in ileal bacterial communities were reduced (3 to 7 days posthatch) in chicks fed with feed containing antimicrobial agents. Avilamycin and flavophospholipol had the most consistent effect on gut microbial communities. Operational taxonomic units (OTU) linked to changes in gut microbiota in birds on antimicrobial-supplemented diets were characterized and identified. Some OTUs could be identified to the species level; however, the majority could be only tentatively classified to the genus, family, order, or domain level.

A chicken growth study was conducted to determine if litter type influenced gut microbiota and performance in broilers. Seven bedding materials were investigated and included soft and hardwood sawdust, softwood shavings, shredded paper, chopped straw, rice hulls, and reused softwood shavings. Microbial profiling was done to investigate changes in cecal bacterial communities associated with litter material and age. Cecal microbiota were investigated at 14 and 28 d of age (n = 12 birds/litter material). At both ages, the cecal microbiota of chickens raised on reused litter was significantly (P < 0.05) different from that of chickens raised on any of the other litter materials, except softwood shavings at d 28. Cecal microbiota was also significantly different between birds raised on shredded paper and rice hulls at both ages. Age had a significant influence on cecal microbiota composition regardless of litter material. Similarity in cecal microbial communities among birds raised on the same litter treatment was greater at 28 d of age (29 to 40%) than at 14 d of age (25 to 32%). Bird performance on the different litter materials was measured by feed conversion ratio, live weight, and feed intake. Significant (P < 0.05) differences were detected in live weight at 14 d of age and feed intake at 14 and 28 d of age among birds (n = 160/treatment) raised on some of the different litter materials. However, no significant (P > 0.05) differences were observed in feed conversion ratio among birds raised on any of the 7 different litter materials at either 14 or 28 d of age. The type of litter material can influence colonization and development of cecal microbiota in chickens. Litter-induced changes in the gut microbiota may be partially responsible for some of the significant differences observed in early rates of growth; therefore, litter choice may have an important role in poultry gut health particularly in the absence of in-feed antibiotics.