High through put 16S rRNA gene-based pyrosequencing analysis of the fecal microbiota of high FCR and low FCR broiler growers

Abstract

The performance of birds appears to vary among the flock of growing broilers which may in part be due to variation in their gut microbiota. In the view of poultry industry, it is desirable to minimise such variation. We investigated metagenomic profile of fecal bacteria in birds with high and low feed conversion ratio (FCR) to identify microbial community linked to low and high FCR by employing high throughput pyrosequencing of 16S rRNA genomic targets. Therefore feeding trial was investigated in order to identify fecal bacteria consistently linked with better feed conversion ratio in bird performance as measured by body weight gain. High-throughput 16S rRNA gene based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. The fecal microbial community of birds was predominated by Proteobacteria (48.04 % in high FCR and 49.98 % in low FCR), Firmicutes (26.17 % in high FCR and 36.23 % in low FCR), Bacteroidetes (18.62 % in high FCR and 11.66 % in low FCR), as well as unclassified bacteria (15.77 % in high FCR and 14.29 % in low FCR), suggesting that a large portion of fecal microbiota is novel and could be involved in currently unknown functions. The most prevalent bacterial classes in high FCR and low FCR were Gammaproteobacteria, Clostridia and Bacteroidia. However in low FCR birds Phascolarctobacterium, Faecalibacterium and Clostridium predominated among the Clostridia. In FCR comparison of fecal bacteria, about 36 genera were differentially abundant between high and low FCR birds. This information could be used to formulate effective strategies to improve feed efficiency and feed formulation for optimal gut health.

Taxons of Chicken Cecum Microbiom Are Abundant, and Influenced by the Combined Feed Composition and Decreased Metabolizable Energy

“…Our results confirmed the data of several authors who have demonstrated by NGS sequencing predominance of phylum Firmicutes [19,21] and genera Clostridium and Bacteroides bacteria [23] in broiler cecum. At the same time, our results are contrary to other reports which indicated the dominance of the phylum Proteobacteria representatives [22]. Probably, some variations in the analysis of poultry cecum microflora by NGS sequencing may be due to the differences in the study 16S rRNA gene region and instrument base, and to other factors such as climatic conditions, sanitary hygienic environment, diet, use of antibiotics, poultry age and cross [19,21].…”

“…Despite the widespread use of these methods to study of numbers and taxonomic diversity of microbes in the human intestine [17,18], there are only a few reports on poultry. In particular, they relate to the GIT microbiome state in poultry infected by pathogenic bacteria Campylobacter jejuni [19,20] due to the effects of coccidiostats [21] and in relation to the productivity [22,23].…”

Phylogenetic and Functional Alterations in Bacterial Community Compositions in Broiler Ceca as a Result of Mannan Oligosaccharide Supplementation

“…The development and diversity of the bacterial intestinal microbiota in poultry have been well documented (24)(25)(26)(27)(28). In the present study, 454 sequencing was successfully used to compare the gut microbiota development during a total grow-out period in broilers fed either a control or MOS-supplemented diet.…”

“…Bacteroidetes species are common bacteria in the gut, involved in many important metabolic activities, including the fermentation of carbohydrates, the utilization of nitrogenous substances, the biotransformation of bile acids, and the prevention of pathogen colonization (25,37,38). Numerous efforts, especially dietary intervention and litter management, have been attempted to consistently modulate the microbiome to enhance feed conversion and gut health (9,23,26,29). What we have observed here is a concordant effect of MOS supplementation on microbial modulation across two individual trials with birds raised in different sheds, using birds from the same hatchery but different crops.…”

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

“…Feed efficiency is a complex trait because it is influenced not only by the host genetics and physiological state but also by the intestinal microbiota, which would affect the nutrient digestion and energy absorption of the host. Singh et al 25 investigated the difference in microbial communities between good and poor feed efficiency broilers using fecal samples; Acinetobacter, Anaerosporobacter and Arcobacter were dominant in the poor efficiency group, whereas Escherichia/Shigella, Faecalibacterium and Helicobacter were dominant in the better efficiency group. However, the abundances of Lactobacillus and Bacteroides were similar in both groups.…”