Seasonal dynamics in sheep fecal microbiome and soil bacterial communities under grazing management
Data files
Jun 01, 2026 version files 97.94 MB
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asvTable_raw.txt
97.93 MB
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metadati.csv
7 KB
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README.md
3.78 KB
Abstract
The gut microbiome plays a key role in animal health, productivity, and environmental sustainability. As it represents a valuable proxy for animal welfare, its investigation has become increasingly important in livestock studies. With the growing focus on promoting sustainable livestock, supporting rural areas at risk of abandonment is receiving particular attention. Indeed, sheep grazing offers a promising strategy in improving sustainability, biodiversity, and land management. This study focuses on the interconnected dynamics between the sheep gut and soil microbiomes, assessing how seasonal changes and grazing activity shape microbial diversity and community structure across the animal–soil interface. Fecal and soil samples were collected throughout 2024 in a commercial farm in Tuscany, Italy: 215 fecal and 46 soil samples (23 pasture and 23 meadow – i.e., not grazed) were stored. Alpha and Beta diversity were assessed using the Kruskal-Wallis test and PERMANOVA, respectively, and the Differential abundance analysis was carried out. The relative abundance analysis at the family and genus level revealed an increase in the number of taxa from winter to autumn in both fecal and soil samples. When the Chao1 index was considered, alpha diversity was higher in fecal samples, followed by soils. Principal Coordinate Analysis revealed distinct clustering between animal and soil microbiota, with slightly reduced differentiation in Summer. In fecal samples, the five most abundant bacterial families were Ruminococcaceae, Spirochaetaceae, Porphyromonadaceae, Lachnospiraceae, and Rikenellaceae, whose abundance varied seasonally. Ruminococcaceae, Lachnospiraceae, and Rikenellaceae decreased in Summer, while Spirochaetaceae and Porphyromonadaceae increased. These families that increased in abundance during Summer may reflect heat stress in animals. Differential abundance analysis also suggested potential microbial transfer from animals to soil: Peptostreptococcaceae and Erysipelotrichaceae were enriched in grazed soils across multiple seasons. Cross-sectional studies like this are essential for understanding microbiome dynamics and animal–soil interactions in grazing systems.
Dataset DOI: 10.5061/dryad.hdr7sqvzh
Description of the data and file structure
This dataset contains raw amplicon sequence variant (ASV) counts and associated metadata from a study investigating seasonal dynamics of sheep fecal microbiota and soil bacterial communities under different grazing management conditions during 2024.
Samples were collected once per season (Winter, Spring, Summer, and Autumn) from:
- sheep fecal microbiome samples obtained using rectal FLOQSwabs® (Copan, Italy);
- soil bacterial communities collected from grazed and non-grazed pasture areas.
All samples were transported on dry ice immediately after collection and stored at −80°C until DNA extraction and sequencing.
Sampling design
Sheep fecal samples
A total of 215 lactating sheep were sampled during milking procedures to minimize animal stress.
Seasonal distribution of fecal samples:
| Season | Number of samples |
|---|---|
| Winter | 50 |
| Spring | 54 |
| Summer | 70 |
| Autumn | 41 |
Soil samples
A total of 46 soil samples were collected randomly from grazed (GRAZED) and non-grazed (NGRAZED) pasture perimeters in equal proportions within each season.
Seasonal distribution of soil samples:
| Season | Number of samples |
|---|---|
| Winter | 6 |
| Spring | 12 |
| Summer | 12 |
| Autumn | 16 |
File descriptions
File: asvTable_raw.txt
Raw ASV abundance table generated from 16S rRNA gene amplicon sequencing data.
Structure
- Rows represent ASVs (Amplicon Sequence Variants).
- Columns represent samples and taxonomic assignments.
Columns
| Column | Description |
|---|---|
ASV_seq |
Nucleotide sequence of the ASV |
ASV |
Unique ASV identifier |
| Sample columns | Raw read counts for each sample |
Kingdom |
Taxonomic assignment at kingdom level |
Phylum |
Taxonomic assignment at phylum level |
Class |
Taxonomic assignment at class level |
Order |
Taxonomic assignment at order level |
Family |
Taxonomic assignment at family level |
Genus |
Taxonomic assignment at genus level |
Species |
Taxonomic assignment at species level |
Notes
- Sample identifiers in this table correspond to the
Samplecolumn inmetadati.csv. - Read counts are unnormalized raw abundances.
File: metadati.csv
Metadata associated with all biological samples included in the ASV table.
Columns
| Column | Description |
|---|---|
Sample |
Unique sample identifier |
GROUP |
Sample category |
Sampling |
Season |
GROUP categories
| Category | Description |
|---|---|
GRAZED |
Soil samples collected from grazed pasture |
NGRAZED |
Soil samples collected from non-grazed pasture |
ANIMAL |
Sheep fecal microbiome samples |
Notes
- Metadata rows correspond to sample columns in
asvTable_raw.txt. - The value
Nin theSamplingcolumn indicates valid samples included in downstream analyses.
Bioinformatics processing
Raw sequencing reads were processed in R using the DADA2 pipeline for quality filtering, denoising, chimera removal, and ASV inference.
