Catalogue PIGMA
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.
Simple
- Date (Creation)
- 2018-01-23
- Date (Revision)
- 2021-02-25
- Identifier
- FR-330-715-368-00032-IFR_BIOINFO_BAC_TRAC2
- Identifier
- DOI:10.12770/ddce4bf7-2b71-4929-aa20-50a8fd0e706a
- Credit
- Ifremer
Author
IFREMER
-
Gourmelon Michele
Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané
,
Brest
,
France
02 98 22 45 76
Publisher
IFREMER / DYNECO/PELAGOS-LABORATOIRE D'ECOLOGIE PELAGIQUE
+33(0)2 98 22 45 98
http://www.ifremer.fr/delec/
IFREMER Centre de Brest BP70
,
PLOUZANE
,
29280
,
France
+33(0)2 98 22 43 34
+33(0)2 98 22 45 98
http://www.ifremer.fr/delec/
- GEMET - INSPIRE themes, version 1.0
-
- Habitats and biotopes
- Thèmes Sextant
-
- /Biological Environment/Bioinformatics
- Use limitation
- CC-BY (Creative Commons - Attribution)
- Access constraints
- License
- Use constraints
- License
- Metadata language
- Français
- Character set
- UTF8
- Topic category
-
- Environment
N
S
E
W
))
- Reference system identifier
- EPSG / WGS 84 (EPSG:4326) / 8.6
- Distribution format
-
-
(
)
-
(
)
- OnLine resource
- /home/ref-bioinfo/ifremer/sg2m/bactrac ( NETWORK:LINK )
- OnLine resource
-
lien de téléchargement
(
WWW:DOWNLOAD-1.0-link--download
)
Données BacTrac (lien de téléchargement)
- OnLine resource
-
DOI of the dataset
(
WWW:LINK-1.0-http--metadata-URL
)
DOI of the dataset
- Hierarchy level
- Dataset
- Statement
- 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.
- File identifier
- ddce4bf7-2b71-4929-aa20-50a8fd0e706a XML
- Metadata language
- Français
- Character set
- UTF8
- Hierarchy level
- Dataset
- Date stamp
- 2023-07-06T12:27:18.909Z
- Metadata standard name
- ISO 19115:2003/19139 - SEXTANT
- Metadata standard version
- 1.0
Point of contact
IFREMER
-
Gourmelon Michele
Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané
,
Brest
,
France
02 98 22 45 76
Overviews
Spatial extent
N
S
E
W
Provided by
Associated resources
Not available