16S metabarcoding data of seabird droppings, poultry droppings and litters, sewage treatment plant water and cattle and pig feces and manure samples

This dataset provides an overview of the diversity of bacterial communities present in faeces and effluents of different origins and particularly in the droppings of wild birds in France. The aim is to develop new molecular markers associated with these different origins/hosts to identify the origin of faecal contamination in the environment. The new high-throughput sequencing technologies (NGS) offer new methods for analysing microbial diversity, including the 16S metabarcoding approach. This tool has been selected in the framework of the BacTrac project (Fecal bacteria, Microbial Source Tracking markers , 2016-2020) to develop new "Microbial Source Tracking" (MST) toolboxes for microbial source markers. A sampling of faeces (including in particular wild bird droppings) and effluents of different origins (sources of pollution) was carried out in France (mainly in Brittany), and total DNAs were extracted. The bacterial diversity of these samples was investigated by targeting the hypervariable V3-V4 region of the gene coding for 16S rRNA, the taxonomic reference marker for the identification of bacteria, whether culturable or not. The sequencing data (Illumina MiSeq) were analysed with bioinformatics tools (mainly SAMBA, a pipeline developed at Sebimer, Ifremer) using the resources of Ifremer's Datarmor calculator. These bioinformatics analyses coupled with biostatistical analyses made it possible to extract ASVs specific to a series of sources. An alignment of the sequences obtained with a database created in the laboratory allows the definition of specific primers that can be used in qPCR for a routine investigation of targeted pollution sources.