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Abstract
There is growing interest in exploring the chickens' intestinal microbiota and understanding its interactions with the host. The objective is to optimize this parameter in order to increase the productivity of farm animals. With the goal to isolate candidate probiotic strains, specific culturomic methods were used in our study to culture commensal bacteria from 7-days old chicks raised in two farms presenting long history of high performance. A total of 347 isolates were cultured, corresponding to at least 64 species. Among the isolates affiliated to the Firmicutes, 26 had less than 97% identity of their partial 16S sequence with that of the closest described species, while one presented less than 93% identity, thus revealing a significant potential for new species in this ecosystem. In parallel, and in order to better understand the differences between the microbiota of high-performing and low-performing animals, caecal contents of animals collected from these two farms and from a third farm with long history of low performance were collected and sequenced. This compositional analysis revealed an enrichment of Faecalibacterium-and Campylobacter-related sequences in lower-performing animals whereas there was a higher abundance of enterobacteria-related sequences in high-performing animals. We then investigated antibiosis activity against C. jejuni ATCC 700819 and C. jejuni field isolate as a first phenotypic trait to select probiotic candidates. Antibiosis was found to be limited to a few strains, including several lactic acid bacteria, a strain of Bacillus horneckiae and a strain of Escherichia coli. The antagonist activity depended on test conditions that mimicked the evolution of the intestinal environment of the chicken during its lifetime, i.e. temperature (37°C or 42°C) and oxygen levels (aerobic or anaerobic conditions). This should be taken into account according to the stage of development of the animal at which administration of the active strain is envisaged.
Highlights
Among other food-producing animals markets, the huge, constantly increasing chicken meat market represents a major economical stake, with approx. 25 billion of live animals representing 122 million tons of meat output in 2017, and a 21.3 million tons increase in world poultry meat production between 2010 and 2017
The 16S rRNA gene-repertoire was analysed for ten caecal contents collected from high- (Farms 1 and 2) or low- (Farm 3) performing farms
Sequences affiliated to the phylum Bacteroidetes represented 0.1% to 35.1% of the 16S rRNA gene repertoire for caeca collected from Farm #1, and less than 1% for caeca collected from Farm #2 and Farm #3, respectively (S1 Fig)
Summary
Among other food-producing animals markets, the huge, constantly increasing chicken meat market represents a major economical stake, with approx. 25 billion of live animals representing 122 million tons (carcass weight equivalent) of meat output in 2017, and a 21.3 million tons increase in world poultry meat production between 2010 and 2017 (http://www.fao.org/ faostat). The use of antibiotics as growth-promoting agents are being banned in certain regions to prevent selection of antibiotic resistant bacteria [4] This antibiotic ban stressed the need for alternative means of improving critical parameters such as resistance of poultry to infections and feed efficiency, which represents the amount of feed required (in kg) to produce 1 kg of poultry meat. In this context, the chicken gastrointestinal microbiota has emerged as an important parameter that should be taken into account to increase animals’ performances. An important criterion in the selection of these candidate strains is their ability to confer resistance to infection by pathogenic microorganisms and/or colonization by zoonotic commensals, which can be due to different mechanisms including the production of antagonistic compounds [16] or
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