Data from: Social organization and habitat use shape the gut microbiome of a marine fish
Data files
Jun 15, 2026 version files 6.74 MB
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DATASET_A_def.xlsx
2.07 MB
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DATASET_B_def.xlsx
230.53 KB
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README.md
9.90 KB
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Table_A1.csv
41.85 KB
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Table_A2.csv
5.06 KB
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Table_A3.csv
5.25 KB
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Table_A4.csv
5.68 KB
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Table_A5.csv
8.39 KB
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Table_A6.csv
4.17 MB
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Table_B1.csv
193.01 KB
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Table_B2.csv
6.07 KB
Abstract
The gut microbiome hosts diverse bacterial communities that can influence individual behaviour, social interactions, and ecological processes in animal populations. This dataset was generated to investigate the links between gut microbiome composition, social organization, and spatial ecology in a wild marine fish population. Using a high-resolution acoustic telemetry system, we quantified individual movement patterns, habitat use, and social interactions of 232 pearly razorfish (Xyrichtys novacula) (153 females and 79 males) inhabiting coastal waters of Mallorca, western Mediterranean Sea. A subset of tracked individuals was subsequently recaptured for gut microbiome characterization using 16S rRNA gene amplicon sequencing (Illumina platform). The dataset integrates biometric information, movement and habitat-use metrics, social association networks, and gut microbial community composition, including both core and non-core operational phylogenetic units (OPUs). These data provide a unique resource for studying the relationships among microbiome diversity, social behaviour, and space use in natural populations, and for advancing research at the interface of microbial ecology, behavioural ecology, and movement ecology.
Dataset DOI: 10.5061/dryad.vdncjsz9x
Description of the data and file structure
This DATASET contains the data of the manuscript: Social organization and habitat use shape the gut microbiome of a marine fish. Publication in Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.70286
- File “DATASET_A_def.xlsx” contains biological and movement data (acoustic tracking) in the pearly razorfish:
- Table_A1.csv: Biometric data of all individuals.
- Table_A2.csv: Associations found between individuals at a distance of 5 m.
- Table_A3.csv: Associations found between individuals at a distance of 10 m.
- Table_A4.csv: Associations found between individuals at a distance of 20 m.
- Table_A5.csv: Social network measures of all individuals at 5-minute intervals at a minimum distance of 5 meters.
- Table_A6.csv: All measures required for the calculation of space and habitat use characterization: activity, home range, and distance to P. oceanica.
- File “DATASET_B_def.xlsx” contains data of the composition (r16) of the gut microbiota:
- Table_B1.csv: Relative abundances of all OPUs in the gut microbiome of the pearly razorfish, followed by the OPU number, the genus of the species, and the species number of the genus. The table also presents the occurrence and the average abundance of each OPU in every individual. The OPUs were identified from the original dataset in Viver et al. 2023, following the same nomenclature.
- Table_B2.csv: Relative abundances of the core members in the gut microbiome of the pearly razorfish.
Files and variables
File: DATASET_B_def.xlsx
Description: Table A1: Biometric data of all individuals.
- Table A2: Associations found between individuals at a distance of 5 m.
- Table A3: Associations found between individuals at a distance of 10 m.
- Table A4: Associations found between individuals at a distance of 20 m.
- Table A5: Social network measures of all individuals at 5-minute intervals at a minimum distance of 5 meters.
- Table A6: All measures required for the calculation of space and habitat use characterization: activity, home range, and distance to P. oceanica.
Variables
- Movement metric
Variable Dictionary
- Table A1. Biometric data of all individuals
- Variable | Description | Units / Levels
- date | Date of tagging and release | YYYY-MM-DD
- id | Unique individual identifier | Character
- tag.id.hex | Acoustic transmitter identifier (hexadecimal format) | Character
- tag.id.dec | Acoustic transmitter identifier (decimal format) | Integer
- type | Tag type/model | Character
- battery.life | Expected transmitter battery life | days
- species | Scientific species name | Character
- common.name | Common species name | Character
- sex | Sex of the individual | M = male, F = female
- total.length | Total body length | cm
- weight | Body mass | cm
- hour.release | Release time | HH:MM
- aquarium.no | Aquarium holding tank number before release | Integer
- recapture.date | Date of recapture | YYYY-MM-DD
- hook | Hook type or identifier used during recapture | Type
- n.detect | Total number of acoustic detections | Count
- n.detect.days | Number of days with detections | Days
- last.detection | Date/time of last acoustic detection | Date-time
- n.pos.total | Total number of estimated positions | Count
- n.pos.filtered | Number of filtered positions retained for analyses | Count
- n.pos.days | Number of days with positioning data | Days
- last.position | Date/time of last estimated position | Date-time
- Table A2. Social associations at 5 m
- Variable | Description | Units / Levels
- from | Focal individual identifier | Character
- to | Associated individual identifier | Character
- association_index | Strength of association between the pair of individuals | index
- Table A3. Social associations at 10 m
- Variables identical to Table A2. Associations were calculated using a 10 m distance threshold.
- Table A4. Social associations at 20 m
- Variables identical to Table A2. Associations were calculated using a 20 m distance threshold.
- Table A5. Social network metrics
- Variable | Description | Units / Levels
- id | Individual identifier | Character
- degree | Number of social connections | Count
- strength | Weighted sum of social associations | Unitless
- betweenness_centrality | Betweenness centrality metric | Unitless
- eigen_centrality | Eigenvector centrality metric | Unitless
- Table A6. Space use and habitat use metrics
- Variable | Description | Units / Levels
- id.xn | Individual identifier | Character
- id.hex | Acoustic transmitter identifier (hexadecimal format) | Character
- date | Observation date | YYYY-MM-DD
- n.pos.crawl | Number of positions used for movement analyses | Count
- center.x | X coordinate of activity centre | UTM
- center.y | Y coordinate of activity centre | UTM
- area.ud.50 | Core home range area (50% utilization distribution) | M2
- area.ud.95 | Home range area (95% utilization distribution) | [m2
- dist.cent.mean | Mean distance from activity centre | m
- dist.cent.sd | Standard deviation of distance from activity centre | m
- dist.cent.max | Maximum distance from activity centre | m
- dist.border.mean | Mean distance to home-range border | m
- dist.border.sd | Standard deviation of distance to home-range border | m
- dist.border.max | Maximum distance to home-range border | m
- total.dist | Total distance travelled | m
- effective.dist | Net displacement distance | m
- max.extent | Maximum spatial extent | m
- total.time | Total tracking duration | m
- speed.mean | Mean movement speed | m
- speed.sd | Standard deviation of movement speed | m
- speed.max | Maximum movement speed | m
- angle.mean | Mean turning angle | Radians or degrees
- angle.kappa | Concentration parameter of turning angles | Unitless
- dist_posi | Distance to Posidonia oceanica habitat | m
File: DATASET_A_def.xlsx
Description: Table B1: Relative abundances of all OPUs in the gut microbiome of the pearly razorfish, followed by the OPU number, the genus of the species, and the species number of the genus. The table also presents the occurrence and the average abundance of each OPU in every individual. The OPUs were identified from the original dataset in Viver et al. 2023, following the same nomenclature.
Table B2: Relative abundances of the core members in the gut microbiome of the pearly razorfish.
Variables
- OPUs
Variable Dictionary
- Table B1. Relative abundances of all OPUs in the gut microbiome
- This table contains the relative abundance (%) of all Operational Phylogenetic Units (OPUs) detected in the gut microbiome of individual Xyrichtys novacula. Each row corresponds to one OPU and each individual fish is represented by a separate column.
- Variable | Description | Units / Levels
- 1211, 9281, 8DC8, 751C, ... | Unique fish identifiers (acoustic tag IDs) corresponding to individual fish microbiome samples | Character
- OPU | Operational Phylogenetic Unit identifier following Viver et al. (2023) nomenclature | Character
- Genus | Taxonomic genus assigned to the OPU | Character
- Species nr. | Species designation within genus used in the OPU classification scheme | Character
- Occurrence | Number of individuals in which the OPU was detected | Count
- Average abundance | Mean relative abundance of the OPU across all individuals | Percentage (%)
- Values in individual fish columns: Relative abundance of each OPU within the gut microbiome of a given individual fish, expressed as a percentage of total sequence reads.
- Table B2. Relative abundances of core gut microbiome members
- This table contains the subset of OPUs classified as members of the core microbiome.
- Variable | Description | Units / Levels
- 1211, 9281, 8DC8, 751C, ... | Unique fish identifiers (acoustic tag IDs) corresponding to individual fish microbiome samples | Character
- OPU | Operational Phylogenetic Unit identifier following Viver et al. (2023) nomenclature | Character
- Genus | Taxonomic genus assigned to the OPU | Character
- Species nr. | Species designation within genus used in the OPU classification scheme | Character
- Occurrence | Number of individuals in which the OPU was detected | Count
- Phylum | Taxonomic phylum assigned to the OPU | Character
- Average abundance | Mean relative abundance of the OPU across all individuals | Percentage (%)
- Values in individual fish columns: Relative abundance of each core OPU within the gut microbiome of a given individual fish, expressed as a percentage of total sequence reads.
- Taxonomic abbreviations
- Term | Description
- OPU | Operational Phylogenetic Unit
- Sp. | Species designation within a genus when a formal species name was not assigned
- Data units
- Relative abundance values are expressed as percentages of total reads per individual sample.
- Occurrence represents the number of individuals in which a given OPU was detected.
- Average abundance is calculated across all analysed individuals.
Missing Values
Some cells in the dataset contain the value "NA". These indicate missing information that was not available for a given individual or sample at the time of data collection or processing. Missing values arise for several reasons, including:
- The individual was not recaptured and therefore no microbiome sample was available.
- A metric could not be calculated because the required observations were insufficient.
- The variable was not applicable to a particular sample or analysis.
No values were imputed or estimated. Users should interpret "NA" as a missing value and handle these records according to the requirements of their analyses.