Abstract
Studies investigating the role that complex microbiotas associated with animals and humans play in health and wellbeing have been greatly facilitated by advances in DNA sequencing technology. Due to the still relatively high sequencing costs and the expense of establishing and running animal trials and collecting clinical samples, most of the studies reported in the literature are limited to a single trial and relatively small numbers of samples. Results from different laboratories, investigating similar trials and samples, have often produced quite different pictures of microbiota composition. This study investigated batch to batch variations in chicken cecal microbiota across three similar trials, represented by individually analysed samples from 207 birds. Very different microbiota profiles were found across the three flocks. The flocks also differed in the efficiency of nutrient use as indicated by feed conversion ratios. In addition, large variations in the microbiota of birds within a single trial were noted. It is postulated that the large variability in microbiota composition is due, at least in part, to the lack of colonisation of the chicks by maternally derived bacteria. The high hygiene levels maintained in modern commercial hatcheries, although effective in reducing the burden of specific diseases, may have the undesirable effect of causing highly variable bacterial colonization of the gut. Studies in humans and other animals have previously demonstrated large variations in microbiota composition when comparing individuals from different populations and from different environments but this study shows that even under carefully controlled conditions large variations in microbiota composition still occur.
Highlights
A range of studies have investigated the structure of the microbiome in the gut of broiler chickens
The 16S-based methods have used a number of different approaches including terminal restriction fragment length polymorphism analysis [4], temporal temperature gradient gel electrophoresis [5], denaturing gradient gel electrophoresis (DGGE) [6], low throughput clone analysis [7] or multivariate curve resolution [8]
Since Feed Conversion Ratio (FCR) is calculated as the ratio of consumed feed and gained weight, flocks with the lowest FCR values, that need lowest amount of food per kg of weight, are regarded as the best performing
Summary
A range of studies have investigated the structure of the microbiome in the gut of broiler chickens. Inter-study comparisons are complicated by the different ways that results have been reported, with some papers detailing populations down to the class and genus level whereas other studies demonstrate similarities or differences, for example in DGGE gel profiles, without any detailed quantitative taxonomic information. Compounding these difficulties are different approaches to sample analysis with some studies looking at results from individual birds and others using pooled samples [10]. Further complicating any cross-study analysis is the wide variation in experimental or field conditions investigated with variation across the birds (source, breed, age, sex, history), feed, environmental conditions, and different treatments investigated
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