README.md

Manuscript title: Kiwi development through a microbial lens: How time, local environment, and disease history influence the Brown Kiwi (Apteryx mantelli) gut microbiome

Submitted to Microbiome

Repository name: kiwi_2020

What: Repository for Kiwi gut microbiome project
When: February 2020 longitudinal sampling
Where: National Kiwi Hatchery, Rotorua, Aotearoa, New Zealand

Authors: 
- Priscilla A. San Juan
- Emma Bean
- Helen McCormick
- Arapata Reuben
- Manpreet K. Dhami

Processed data and script used for microbiome analysis available in this repository.

Data (bacteria):
- sample metadata sheet (filename: sample_datasheet_kiwi_2020.csv)
- Operational taxonomic unit (OTU) table (filename: bac_otu.csv)
- Taxonomic assignment table (filename: bac_tax.csv)

Data (fungi):
- sample metadata sheet (filename: sample_datasheet_kiwi_2020.csv)
- Operational taxonomic unit (OTU) table (filename: fun_otu.csv)
- Taxonomic assignment table (filename: fun_tax.csv)

Script:
- R_kiwi_mic_2020_analysis_code_submit.R

Raw data available in NeSI directory 
Location of raw data (not available until published):
/nesi/project/landcare02543/data/priscilla/kiwi2020