https://doi.org/10.5061/dryad.v6wwpzh5d

Description of the data and file structure

This OTUs table and fastq sequences underlie the main results of the study "Evidences that host genetic background more than the environment shapes the microbiota of the snail Bulinus truncatus, an intermediate host of Schistosoma species.".

In this study, our aim was to characterise and compare the bacterial communities found in B. truncatus snails and in the aquatic environment at 9 ecologically contrasted.  The field work was conducted in February 2022 and we focused on 9 natural sites from Northern Senegal that differ in terms of habitats. At each of these sites, we sampled the water-sediment interface and all B. truncatus snails found. We also filtered comercial spring water at each site to have a field negative control. We caracterised the microbiota using v3-v4 16s rDNA metabarcoding a MiSeq amplicons sequencing approach. 

Those approaches led to the processing of 198 bacterial 16S metabarcoding libraries including the DNA extracts of the 124 snails, 70 eDNA replicates consisting in 54 eDNA samples (each extraction triplicate was amplified in duplicate) and 16 technical field negative controls (each control was amplified in duplicate), and 4 negative PCR controls (milliρ water).

Files and variables

File: raw_edna.tar

Description: fastq sequences coming from the 16s rDNA sequencing of environmental samples (54 samples + 16 field negative controls)

File: raw_bulinus_truncatus.tar

Description: fastq sequences coming from the 16s rDNA sequencing of Bulinus truncatus snails

File: controls.tar

Description: fastq sequences coming from the 16s rDNA sequencing of the PCR negative controls (water)

Naming convention for FASTQ files

The FASTQ files follow an extended Illumina naming structure that encodes sample type, site, replicate information, and sequencing metadata.

General structure:

[SampleCode]_[InternalID]_L001_R[ReadNumber]_001.fastq.gz

Where:

• SampleCode = descriptive identifier indicating sample type and origin
  • S1-1 = snail sample 1 from site 1
  • C-S1-1 = field eDNA control 1 from site 1
  • S1-1-1 = eDNA sample 1, subsample 1 from site 1
  • neg-9D-pl3 = PCR negative control (plate 3)
• InternalID = sequencing facility internal sample ID (e.g., S1, S101, S103, S194)
• L001 = sequencing lane
• R1 / R2 = forward and reverse reads
• 001 = file index (always 001)

Examples

• S1-1_S1_L001_R1_001.fastq.gz → snail sample 1 from site 1, forward read
• C-S1-1_S101_L001_R1_001.fastq.gz → field eDNA control 1 from site 1, forward read
• S1-1-1_S103_L001_R1_001.fastq.gz → eDNA sample 1, subsample 1 from site 1, forward read
• neg-9D-pl3_S194_L001_R1_001.fastq.gz → PCR negative control (plate 3), forward read

All reverse reads follow the same structure with R2.

All FASTQ files contained in the .tar archives follow this naming convention.

File: Suppl_table_2.csv

Description: file containing the individual snail shell size (length and width). 

Variables:

• sample_id : unique snail identifier
• shell_length : shell length (mm)
• shell_width : shell width (mm)

Delimiter: ;

Decimal notation: ,

File: suppl_table_4.csv

Description: asv table containing all samples, prior to any cleaning step.

Variables:

• asv : ASV identifier
• sample_id : sample name
• sample_type : sample type (eDNA control, negative control, eDNA, snail)
• count : read count

Delimiter: ;

File: suppl_table_5.csv

Description: table showing all ASVs present in the negative controls, with taxonomy details.

Variables:

• asv_id
• sample_id
• count
• taxonomy

Delimiter: ;

File: suppl_table_6.csv

Description: table showing the read counts per sample during cleaning steps.

Variables:

• sample_id
• Read count after preprocessing
• Read count after removing mitochondria reads
• Read count after removing chloroplast reads
• Read count after removing kingdom = NA reads
• Read count after removing phylum = NA reads
• Read count after global abundance filter (0.005%)
• Read count after individual abundance filter (0.1%)
• Read counts after rarefaction to 5000 reads

Delimiter: ;

File: Suppl._table_2-_Microsatellite_primers_sequences_W1_W2.xlsx

Description: Microsatellite loci used in the study, including locus name, motif, number of repeats, amplicon size, primer sequences, sequencing coverage, and genotyping metrics.

Column description

• Multiplex — multiplex panel used for amplification (e.g., W1, W2).
• Locus name — unique identifier of the microsatellite locus.
• ReadID+ — reference sequence ID used for locus mapping.
• Microsatellite motif — repeated motif (e.g., ATAG).
• Number of repeats — number of motif repetitions.
• Amplicon size — expected PCR product length (bp).
• Forward primer sequence* — forward primer (5’→3’).
• Reverse primer sequence — reverse primer (5’→3’).
• Mean coverage/loci/sample — average sequencing depth per locus per sample.
• SD coverage/loci/sample — standard deviation of sequencing depth.
• Analysis strategy — genotyping strategy (e.g., FullLength).
• Parameter set* — parameter set used for genotyping.
• NallelesSequence — number of alleles detected by sequence.
• NalleleSize — number of alleles detected by size.
• Raw missing genotype $ — proportion of missing genotypes.
• Allelic error — allelic error rate.