Here we tested the application of shotgun metagenomics on airfilter samples from poultry houses or from artificial mock communities. Both types of samples were spiked with different quantities of two Campylobacter jejuni isolate to study the usefulness of the specific DNA extraction protocol as well as sequence depth needed to detect these species in a complex background.
These analyses were performed as part of the European Joint Project - AIRSAMPLE (https://onehealthejp.eu/jrp-air-sample/). AIR-SAMPLE aims to develop and validate air sampling as a low-cost and multi-purpose alternative to fecal droppings or boot swab for surveillance, monitoring and eradication of Campylobacter in confined and biosecured broiler production.
The 16 samples deposited here are 8 mock community samples (ZymoBIOMICS Microbial Community Standard II (Log Distribution)) and 8 airfilter samples from two poultry houses from the same farm.
More...Here we tested the application of shotgun metagenomics on airfilter samples from poultry houses or from artificial mock communities. Both types of samples were spiked with different quantities of two Campylobacter jejuni isolate to study the usefulness of the specific DNA extraction protocol as well as sequence depth needed to detect these species in a complex background.
These analyses were performed as part of the European Joint Project - AIRSAMPLE (https://onehealthejp.eu/jrp-air-sample/). AIR-SAMPLE aims to develop and validate air sampling as a low-cost and multi-purpose alternative to fecal droppings or boot swab for surveillance, monitoring and eradication of Campylobacter in confined and biosecured broiler production.
The 16 samples deposited here are 8 mock community samples (ZymoBIOMICS Microbial Community Standard II (Log Distribution)) and 8 airfilter samples from two poultry houses from the same farm. Four of the mock community samples were spiked with the C. jejuni isolate CCUG11284T and four of the poultry farm samples were spiked with C. jejuni 927. Both spikes were applied in different concentrations. For the exact genome assemblies go to project accession number: PRJEB43619
Less...| Accession | PRJEB44024 |
| Type | Umbrella project |
| Submission | Registration date: 18-May-2021
NORWEGIAN VETERINARY INSTITUTE |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| Nucleotide (total) | 174 |
| WGS master | 3 |
| SRA Experiments | 18 |
| Protein Sequences | 5588 |
| Other datasets |
| BioSample | 21 |
| Assembly | 3 |
This project encompasses the following 3 sub-projects:
| Project Type | Number of Projects |
Genome sequencingHighest level of assembly : Contigs |
1
|
BioProject
accession | Assembly
level | Name | Title |
|---|
| PRJEB43619 | Contigs | Campylobacter jejuni genome assemblies used for mapping experiments with metagenomics shotgun data | Genome assemblies of Campylobacter jejuni isolates (NORWEGIAN VETERINARY INSTITUTE) |
|
| Other | 2 |
BioProject
accession | Name | Title |
|---|
| PRJEB43621 | Campylobacter jejuni shotgun sequencing data used for spike in experiments | Campylobacter jejuni Illumina sequence data (NORWEGIAN VETERINARY INSTITUTE) | | PRJEB43623 | Detection of Campylobacter in air samples from poultry houses using shot-gun metagenomics | Metagenomic shotgun data from poultry houses and mock communties (NORWEGIAN VETERINARY INSTITUTE) |
|