Label Rouge broiler carcass microbiota
The dataset provides information on the bacterial composition of 465 Label Rouge broiler carcasses collected in a French slaughterhouse between september 2023 and february 2024. Carcasses were cuted in halves and 16S rRNA metabarcoding sequencing was performed before ("J0") and after 7 days of storage at 4°C ("J7") (on the two half of the same carcasse). Carcass rinses were pooled in groups of three to create one sample, resulting in a total of 310 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 fre-range chicken meat.   Raw Sequencing Data The 310 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.  Sample accession numbers for the 16S rRNA sequencing, including forward (R1) and reverse (R2) reads, range from: - Before storage: J0_177_libLAG5511_R1  to J0_336_libLAG5670_R2 - After storage: J7_177_libLAG5671_R1 to J7_336_libLAG3507_R2  The sequence names correspond to the raw sequence names assigned by Eurofins.   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 S3 and S4, respectively in https://doi.org/10.57745/NA1UY3.  Metadata Details The metadata includes: - Analysis number and month - Slaughter rapidity (slaughter rate), which corresponds to the number of chickens processed per hour, and the time of slaughter - Slaughter batches (FSB = first slaughter batch, LSB = later slaughter batch) - The storage condition (J0 = D0 and J7 = D7) - Type of chickens (Label Rouge chickens)
The dataset provides information on the bacterial composition of 465 Label Rouge broiler carcasses collected in a French slaughterhouse between september 2023 and february 2024. Carcasses were cuted in halves and 16S rRNA metabarcoding sequencing was performed before ("J0") and after 7 days of storage at 4°C ("J7") (on the two half of the same carcasse). Carcass rinses were pooled in groups of three to create one sample, resulting in a total of 310 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 fre-range chicken meat.   Raw Sequencing Data The 310 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.  Sample accession numbers for the 16S rRNA sequencing, including forward (R1) and reverse (R2) reads, range from: - Before storage: J0_177_libLAG5511_R1  to J0_336_libLAG5670_R2 - After storage: J7_177_libLAG5671_R1 to J7_336_libLAG3507_R2  The sequence names correspond to the raw sequence names assigned by Eurofins.   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 S3 and S4, respectively in https://doi.org/10.57745/NA1UY3.  Metadata Details The metadata includes: - Analysis number and month - Slaughter rapidity (slaughter rate), which corresponds to the number of chickens processed per hour, and the time of slaughter - Slaughter batches (FSB = first slaughter batch, LSB = later slaughter batch) - The storage condition (J0 = D0 and J7 = D7) - Type of chickens (Label Rouge chickens)