Data from: Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations

ABSTRACT
Understanding the driving forces that control vole population dynamics requires identifying bacterial parasites hosted by the voles and describing their dynamics at the community level. To this end, we used high-throughput DNA sequencing to identify bacterial parasites in cyclic populations of montane water voles that exhibited a population outbreak and decline in 2014-2018. An unexpectedly large number of 155 Operational Taxonomic Units (OTUs) representing at least 13 genera in 11 families was detected. Individual bacterial richness was higher during declines, and vole body condition was lower. Richness as estimated by Chao2 at the local population scale did not exhibit clear seasonal or cycle phase-related patterns, but at the vole meta-population scale, exhibited seasonal and phase-related patterns. Moreover, bacterial OTUs that were detected in the low density phase were geographically widespread and detected earlier in the outbreak; some were associated with each other. Our results demonstrate the complexity of bacterial community patterns with regard to host density variations, and indicate that investigations about how parasites interact with host populations must be conducted at several temporal and spatial scales: multiple times per year over multiple years, and at both local and long-distance dispersal scales for the host(s) under consideration.

FILE DESCRIPTION:

Trapping, physical, and demographic data for the 1376 Arvicola terrestris included in sequencing runs 1 to 8

This XLSX file contains the following information concerning the 1376 animals included in the eight sequencing runs: location, session numbering, animal_id,         trap_name, capture_date, species, sex (1=male, 2=female), weight (g), length_body (mm),  length_tail (mm, testes (0=abdominal, 1=scrotal), testes_length (mm), testes_width (mm), nipples (0=small, 1=lactating), vagina (0=not perforate, 1=perforate), pub_symph (0=closed, 1=open), uterus_scars (#), embryos(#), lens_weight (g), lens_weight2 (g) and sequencing labels

File name: Animal_details.xlsx

Information concerning the Arvicola terrestris samples and the positive and negative controls multiplexed in the 16Sv4 MiSeq sequencing runs 1 to 8

This XLSX file contains the Run IDs, Sample IDs, Sample types, Dates & Site names, DNA extraction kit, PCR IDs, PCR replicate numbers, numbers of reads before and after filtering and the fastq file names for the 6615 PCR products multiplexed in the eight different Illumina MiSeq runs.

File name: Sample_and_sequencing_informations.xlsx

MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run1)

This ZIP file contains the Run1 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1570 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.

File name: MiSeq_Reads_16S_Arvicola_terrestris_Run1.zip

MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run2)

This ZIP file contains the Run2 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1668 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.

File name: MiSeq_Reads_16S_Arvicola_terrestris_Run2.zip

MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run3)

This ZIP file contains the Run3 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1646 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.

File name: MiSeq_Reads_16S_Arvicola_terrestris_Run3.zip

MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run4)

This ZIP file contains the Run4 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1712 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.

File name: MiSeq_Reads_16S_Arvicola_terrestris_Run4.zip

MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run5)

This ZIP file contains the Run5 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1680 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.

File name: MiSeq_Reads_16S_Arvicola_terrestris_Run5.zip

MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run6)

This ZIP file contains the Run6 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1704 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.

File name: MiSeq_Reads_16S_Arvicola_terrestris_Run6.zip

MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run7)

This ZIP file contains the Run7 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1620 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.

File name: MiSeq_Reads_16S_Arvicola_terrestris_Run7.zip

MiSeq raw sequences of the 16Sv4 rRNA gene from Arvicola terrestris samples (Run8)

This ZIP file contains the Run8 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Arvicola terrestris sample using the MiSeq platform. The 1630 multiplexed PCR products were indexed using both forward and reverse indices. The list of the multiplexed samples and positive & negative controls are provided in the following XLSX file titled: Sample_and_sequencing_informations.xlsx.

File name: MiSeq_Reads_16S_Arvicola_terrestris_Run8.zip

Raw abundance table of the 16v4 rRNA gene from Arvicola terrestris samples before data filtering (Run1 to 8)

This CSV file contains the number of reads for each distinct variant (OTU) and each of the 6615 PCR products, including the Arvicola terrestris samples and the controls, sequenced in the MiSeq runs 1 to 8 before the data filtering.

File name: Read_abundance_table_before_filtering.csv

Abundance table of the 16v4 rRNA gene from Arvicola terrestris samples after data filtering (Run1 to 8)

This CSV file contains the number of reads for each distinct variant (OTU) and each Arvicola terrestris sample sequenced in the MiSeq runs 1 to 8 after the data filtering.

File name: Read_abundance_table_after_filtering.csv