Data from: 16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife ...

• Main Authors: Galan, Maxime, Razzauti, Maria, Bard, Emilie, Bernard, Maria, Brouat, Carine, Charbonnel, Nathalie, Dehne-Garcia, Alexandre, Loiseau, Anne, Tatard, Caroline, Tamisier, Lucie, Vayssier-Taussat, Muriel, Vignes, Hélène, Cosson, Jean-François
• Format: Dataset
• Language: English
• Published: Dryad 2017
• Subjects: Bartonella; Mastomys erythroleucus; HTS; Mycoplasma; MiSeq; Orientia; Mus musculus domesticus; Next-generation sequencing; Borrelia; 16S rRNA amplicon sequencing; Rodents; West Africa; Metagenomics; Disease monitoring; Streptobacillus; Rattus rattus; Mastomys natalensis; Rickettsia; Ehrlichia
• Online Access: https://dx.doi.org/10.5061/dryad.m3p7d; https://datadryad.org/stash/dataset/doi:10.5061/dryad.m3p7d

The human impact on natural habitats is increasing the complexity of human-wildlife interactions and leading to the emergence of infectious diseases worldwide. Highly successful synanthropic wildlife species, such as rodents, will undoubtedly play an increasingly important role in transmitting zoonotic diseases. We investigated the potential for recent developments in 16S rRNA amplicon sequencing to facilitate the multiplexing of the large numbers of samples needed to improve our understanding of the risk of zoonotic disease transmission posed by urban rodents in West Africa. In addition to listing pathogenic bacteria in wild populations, as in other high-throughput sequencing (HTS) studies, our approach can estimate essential parameters for studies of zoonotic risk, such as prevalence and patterns of coinfection within individual hosts. However, the estimation of these parameters requires cleaning of the raw data to mitigate the biases generated by HTS methods. We present here an extensive review of these ... : Informations concerning the samples and positive and negative controls multiplexed in the two MiSeq runsThis XLSX file contains the run names, the sample IDs, the sample types, the PCR IDs, the PCR replicate numbers, the localities, the rodent species and the fastq file names for each of the 1560 PCR products multiplexed in the two Illumina MiSeq runs.Table_of_the_samples_and_fastq_informaions.xlsxMiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 1 to 4)This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & ...