Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity

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.

Lactic Acid Bacteria – A Promising Tool for Controlling Chicken Campylobacter Infection

“…The author hypothesized that these six taxa might be involved in the maintenance of the resilience within the microbial community ( Patuzzi et al, 2021 ). This is in line with the theory put forward by Duquenoy et al Increased abundance of Faecalibacterium prausnitzii , which has a documented anti-inflammatory effect, would improve the ability of Campylobacter -colonized chickens to control inflammation caused by this microorganism ( Duquenoy et al, 2020 ). Therefore, the importance of Faecalibacterium for chicken intestinal health remains to be determined.…”

“…Stabilization of the microbial diversity occurs after 10–20days post-hatch. The diagram is based on the information provided by ( Oakley et al, 2014a ; Thibodeau et al, 2015 ; Connerton et al, 2018 ; Richards et al, 2019 ; Duquenoy et al, 2020 ). The distribution of the most common and abundant bacterial taxa (phylum, order, and family) in the ceca of the chickens is presented.…”

“…The presence of C. jejuni in the chicken gastrointestinal tract was also associated with a diminution of the relative abundance of Mollicutes and Anaeroplasmateles ( Thibodeau et al, 2015 ). In recently conducted studies, a high level of Campylobacter has been also linked to a higher abundance of Faecalibacterium ( Duquenoy et al, 2020 ). The positive interaction of these species has not yet been fully explained.…”

Microbiota of Chicken Breast and Thigh Fillets Stored under Different Refrigeration Temperatures Assessed by Next-Generation Sequencing

“…To date, various studies have employed NGS to investigate the chicken microbiome. However, these studies have mainly focused on the chicken gastrointestinal tract [ 25 , 26 , 27 , 28 , 29 ], chicken carcasses at various stages throughout processing line [ 30 , 31 , 32 , 33 , 34 ], and fresh chicken cuts [ 35 , 36 , 37 , 38 ]. To our knowledge, limited studies have investigated the overall microbial profile on chicken broiler meat or cuts stored under chilled conditions by amplicon sequencing [ 34 , 39 , 40 , 41 , 42 ].…”

Are there consistent effects of gut microbiota composition on performance, productivity and condition in poultry?

“…In our survey, 23 of the 33 reviewed correlational studies also considered the effect of alpha diversity in poultry. However, the positive association with performance was shown only in a single study ( Lv et al, 2021 ), and the negative relationship in 3 studies ( Konsak et al, 2013 ; Duquenoy et al, 2020 ; Zhang et al, 2022a ). Others reported sampling site-dependent or not significant associations of alpha diversity with performance.…”