DOI: 10.5281/zenodo.10987293
title: Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population

description: Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population

 

These files contain data on bacteria present in the guts of wild great tit (Parus major)  obtained from faecal samples and sequenced using Illumina MiSeq. These data resulted from an experiment which provided supplementary mealworms at the nest during the breeding season at number of woodland sites in Cork, Ireland. Approximately half of these nests were given mealworms covered in a freeze dried bacterial powder containing the bacteria Lactobacillus kimchicus, which had been isolated from great tit faeces from the previous season. This treatment aimed to disrupt the gut microbiota of the treatment birds in order to provide evidence for the gut microbiotas role in birds health and fitness. Included here are the 3 elements necessary to create a 'phyloseq object' containing the sample metadata, ASV (Amplicon Sequence Variant) count table and a taxonomy table. The metadata file includes the alpha diversity scores for each individual. The data include all negative control samples taken during sample collection and library preparation, which were removed before the main analyses. All analyses, except for the beta-diversity analyses, were conducted in R. All R code is available on GitHub (https://github.com/shan-e-s\). Raw Sequence data are available in the European Nucleotide Archive under access number PRJEB74941, and ERS18960426-ERS18960697.

 

## Description of the data and file structure 

Taxonomy, ASV and metadata files required to create a phyloseq object in R. metadata.csv file contains data on individual birds (i.e. individual samples). The metadata includes descriptions of the bird itself and it's environment, namely:



Rownames: unique sample ID for each sample, corresponds with asvTable.csv. 

Nest: unique identifier for the nest box associated with the bird being sampled. 

Sample.ID: unique identifier for the faecal sample or control sample.

Bird.ID: Identity of the bird the sample came from, note some individuals sampled twice so some bird.ID's may reoccur in metadata with different Sample.ID.

Date: Date the sample was taken dd/mm/yyyy.

Day: Date the sample was taken, in days since 1st March.

Ring.Mark: British Trust for Ornithology (BTO) metal ring ID where applicable. Birds only ringed at D15 so some young birds do not have IDRings.

Site: ID of woodland site  that bird was sampled at.

Chick.LetterID: ID letter differentiates between different birds from the same nest. Either 'A'-'F' for nestlings, 'Fe' for females or 'M' for males.

Age.code: BTO age code.

Age.category: Age category that bird is in. D8 = 8 days post hatching, D15 = 15 days post hatching, adult = 1+ years post hatching.

Sex: Bird's sex, only determined for adult birds. Fe = Female, M = Male.

Wing_mm: Wing length in mm.

Tarsus_mm: minimum tarsus length of bird in mm.

Weight_g: bird's weight in grams.

Faecal.Sample: bird's age at sampling.

newRing: whether bird was fitted with a new BTO ring. Only relevant to adults.

Treatment: the experimental treatment group that the bird was in. Either 'Treatment' when nest given L. kimchicus treated mealworms or 'Control' when nest given plain mealworms.

Notes: field notes.

Main.sample: indicates whether this sample was the main sample to be used for analysis, an alternative sample taken as a backup.

Plate: the ID of the PCR plate which the sample was amplified on.

Azenta_noPeriod: sample ID given to sequencing facility without special characters. Corresponds to fastq files and ASV table counts.

Qubit_prePool: samples qubit score before pooling.

Date_extracted: date the sample was extracted on dd/mm/yyyy.

SampleType: whehther the sample was a 'main' sample intended for downstream analysis, a 'control' sample for detecting contamination during library preparation, a 'duplicate' for detecting PCR issues, a 'label_error' where sample was suspected of being mislabelled at some point, a 'repeat' sample intended to detect errors or issues, a 'contam' sample which was suspected of being contaminated,  a 'common' sample used across different PCR plates to detect issues. Extraction_notes: notes regarding the DNA extraction of the sample.  

LibPrep_notes: notes regarding the library preparation of the sample.

Ring.Mark.lab: the ring or sample ID written on the sample tube, recorded to help detect mislabelling.

Post_lab_notes: notes regarding issues found post sequencing.

NumberOfReads: number of sequence reads associated with the sample.   

DistanceToEdge: distance between nest and woodland edge in metres.   

BroodSize.D8: number of nestlings in the nest at day-8 post hatching.   

BroodSize.D15: number of nestlings in the nest at day-15 post hatching.

firstEggLayDate: Date the first egg in the clutch was laid, in days since 1st March.

lastEggLayDate: Date the last egg in the clutch was laid, in days since 1st March.

Observed: number of unique ASV's (or taxa) detected in the sample.

Chao1: Chao1 diversity of the sample.

Shannon: Shannon diversity of the sample.


The file 'taxonomy.csv' contains the taxonomic breakdown of each bacterial Amplicon Sequence Variant (ASV) found in the dataset from Phylum to Species. Obtained by using the Naive Bayes Classifier against the Silva (v138) taxonomic database.

The file 'asvTable.csv' contains counts of each amplicon sequence variant's occurrence for each individual sample. Samples are rows and taxa are columns.

 

Sharing/Access information 

All R code is available on GitHub (https://github.com/shan-e-s\).  Raw Sequence data are available in the European Nucleotide Archive under access number PRJEB74941, and ERS18960426-ERS18960697.