Conventional broiler carcass microbiota
The dataset provides information on the bacterial diversity of 480 conventional broiler carcasses collected in a French slaughterhouse between 2022 and 2023. It includes 16S rRNA metabarcoding data from the broiler carcass rinses, both before and after 7 days of storage at 4°C. To minimize high individual variability, the carcass rinses were pooled in groups of three to create one sample, resulting in a total of 320 sequenced samples. However, due to poor library quality, two samples were removed, leaving a total 318 sequenced samples. Amplicons from the region V3-V4 of 16S rRNA were sequenced with Illumina MiSeq technology. The aim of collecting these carcass microbial diversity data was to characterize bacterial species that are positively or negatively correlated with Campylobacter on chicken meat.   Raw Sequencing Data The 320 samples were sequenced by amplifying the V3-V4 region of the 16S rRNA and deposited in the ANR-21-CE21-0008 (ESCAPE) project in the INRAE Institutional Data Repository under this DOI: https://doi.org/10.57745/WUII9H with the name “16S RNA metabarcoding dataset from microbiota of conventional broiler carcass rinses“. Sample accession numbers for the 16S rRNA sequencing, including forward (R1) and reverse (R2) reads, range from: - Before storage: J017_lib692622_cleaned_R1 to J0176_lib692782_cleaned_R2 - After storage: J717_lib692783_cleaned_R1 to J7176_lib692988_cleaned_R2  The sequence names correspond to the raw sequence names assigned by Eurofins. "Lib" corresponds to libraries, and "cleaned" indicates that the libraries and sequences were cleaned before being deposited. Additionally, J0 or J7 in the sample names correspond to D0 and D7, respectively.  Analyzed Data The sequencing data analyzed before and after storage, including tables for ASV abundance, ASV taxonomic assignment, and sample metadata, are available in Tables S03 and S04, respectively.  Metadata Details The metadata includes: - Analysis number and date - Slaughter rapidity (slaughter rate), which corresponds to the number of chickens processed per hour - Breeder's name in acronym for anonymity - Weight of each carcass - Type of chickens (STANDARD for conventional and NA for unspecified, but all are conventional carcasses)  Additional Quantifications In parallel, we quantified Campylobacter and Total M=Viable Count (TVC) on agar plates before and after storage. Concentrations were determined using NF EN ISO 7218 norm. The CFU.ml corresponds to the CFU.ml of carcass rinses. These data are represented in Table S02.  Supplementary Tables All supplementary tables (Tables S01, S02, S03, and S04) are available and can be downloaded under this DOI: https://doi.org/10.57745/ETSMIM.
The dataset provides information on the bacterial diversity of 480 conventional broiler carcasses collected in a French slaughterhouse between 2022 and 2023. It includes 16S rRNA metabarcoding data from the broiler carcass rinses, both before and after 7 days of storage at 4°C. To minimize high individual variability, the carcass rinses were pooled in groups of three to create one sample, resulting in a total of 320 sequenced samples. However, due to poor library quality, two samples were removed, leaving a total 318 sequenced samples. Amplicons from the region V3-V4 of 16S rRNA were sequenced with Illumina MiSeq technology. The aim of collecting these carcass microbial diversity data was to characterize bacterial species that are positively or negatively correlated with Campylobacter on chicken meat.   Raw Sequencing Data The 320 samples were sequenced by amplifying the V3-V4 region of the 16S rRNA and deposited in the ANR-21-CE21-0008 (ESCAPE) project in the INRAE Institutional Data Repository under this DOI: https://doi.org/10.57745/WUII9H with the name “16S RNA metabarcoding dataset from microbiota of conventional broiler carcass rinses“. Sample accession numbers for the 16S rRNA sequencing, including forward (R1) and reverse (R2) reads, range from: - Before storage: J017_lib692622_cleaned_R1 to J0176_lib692782_cleaned_R2 - After storage: J717_lib692783_cleaned_R1 to J7176_lib692988_cleaned_R2  The sequence names correspond to the raw sequence names assigned by Eurofins. "Lib" corresponds to libraries, and "cleaned" indicates that the libraries and sequences were cleaned before being deposited. Additionally, J0 or J7 in the sample names correspond to D0 and D7, respectively.  Analyzed Data The sequencing data analyzed before and after storage, including tables for ASV abundance, ASV taxonomic assignment, and sample metadata, are available in Tables S03 and S04, respectively.  Metadata Details The metadata includes: - Analysis number and date - Slaughter rapidity (slaughter rate), which corresponds to the number of chickens processed per hour - Breeder's name in acronym for anonymity - Weight of each carcass - Type of chickens (STANDARD for conventional and NA for unspecified, but all are conventional carcasses)  Additional Quantifications In parallel, we quantified Campylobacter and Total M=Viable Count (TVC) on agar plates before and after storage. Concentrations were determined using NF EN ISO 7218 norm. The CFU.ml corresponds to the CFU.ml of carcass rinses. These data are represented in Table S02.  Supplementary Tables All supplementary tables (Tables S01, S02, S03, and S04) are available and can be downloaded under this DOI: https://doi.org/10.57745/ETSMIM.