Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys.

Toby J Wilkinson,A A Cowan,J M Moorby,Charlotte Gonot,H E Vallin,L A Onime,Linda B Oyama,C Nixey,V J Theobald,Sharon A Huws,S Bowra,D Leemans,K Waddams,S J Cameron

doi:10.3389/fmicb.2017.01089

Abstract

The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA. Sequencing data showed on a genus level, an abundance of Lactobacillus, Streptococcus, and Clostridium XI (38.2, 28.1, and 13.0% respectively) irrespective of location and age. The caeca exhibited the greatest microbiome diversity throughout the development of the turkey. PICRUSt data predicted an array of bacterial function, with most differences being apparent in the caeca of the turkeys as they matured. QPCR revealed that the caeca within 10 week old birds, contained the most Campylobacter spp. Understanding the microbial ecology of the turkey gastrointestinal tract is essential in terms of understanding production efficiency and in order to develop novel strategies for targeting Campylobacter spp.

Highlights

Poultry meat represents the main source of protein for human nutrition with consumption per capita being nearly twice that of red meat (Foley et al, 2011)
The principle coordinate analysis (PCA) plot based on OTUs showed that the microbiome of 10 week old birds was quite distinct to those of 6 and 16 week old birds irrespective of gastrointestinal tract (GI) tract location (Figure 1)
The main differences seen were that Bacteroidetes were more abundant in the caeca and firmicutes less abundant compared with other GI tract locations (Figure 2, Table 3)

Summary

Introduction

Poultry meat represents the main source of protein for human nutrition with consumption per capita being nearly twice that of red meat (Foley et al, 2011). The US consumes the most poultry meat with the European Union following closely (average 22.2 Kg/capita in 2006 for EU) (Magdelaine et al, 2008). Of this around 17% is attributable to turkey (Meleagris gallopavo) consumption, with chickens (Gallus gallus domesticus) being the main poultry consumed. The relationship between the gut microbiome of chickens, to bird health and efficient growth is well-known (Brisbin et al, 2008; Scupham et al, 2008; Yeoman et al, 2012; Danzeisen et al, 2013; Wei et al, 2013). Scupham et al (2008) showed that high density turkey production The relationship between the gut microbiome of chickens, to bird health and efficient growth is well-known (Brisbin et al, 2008; Scupham et al, 2008; Yeoman et al, 2012; Danzeisen et al, 2013; Wei et al, 2013). Scupham et al (2008) showed that high density turkey production

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