Pets Pooled Analysis

Introduction

This repository contains the code and supplementary material for the companion animal pooled analysis study presented in the following manuscript:

"A comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods"

Tobyn Branck^1,2,3, Zhiji Hu^1,2, William A. Nickols^1,2,4, Aaron M. Walsh^1,2,4, Amrisha Bhosle^1,2,4, Meghan I. Short^1,2,4, Jacob T. Nearing^1,2,4, Francesco Asnicar⁵, Lauren J. McIver^1,2, Sagun Maharjan^1,2,4, Ali Rahnavard⁶, Artemis Louyakis³, Dayakar V. Badri³, Christoph Brockel³, Kelsey N. Thompson^1,2,4, Curtis Huttenhower^1,2,4,7

¹Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA, ²Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA, ³Science and Technology Center, Hill’s Pet Nutrition, Inc., Topeka, KS, USA, ⁴Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA, ⁵CIBIO Department, University of Trento, Trento, Italy, ⁶Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA, ⁷Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA

Contents

Custom scripts:

• See "scripts" directory for the code used to generate all main and supplemental figures in the manuscript. A detailed README.txt is provided which contains the input files and output files/figures generated by each script.

Supplemental Tables

Includes tables describing individual study characteristics and sample information.

• Supplemental Table 1: Public and private data sources of cat, dog, and human gut metagenomic samples.
• Supplemental Table 2: By-sample taxonomic profiles generated by MetaPhlAn 4 for all companion animal gut metagenomes
• Supplemental Table 3: By-sample taxonomic profiles generated by MetaPhlAn 4 for HMP1-II baseline (time 0 samples) gut metagenomic samples
• Supplemental Table 4: By-sample taxonomic profiles generated by MetaPhlAn 4 for Madagascar cohort gut metagenomes
• Supplemental Table 5: SGB prevalence by host
• Supplemental Table 6: Helicobacteraceae spp. distribution across hosts.
• Supplemental Table 7: Campylobacter spp. distributed across hosts.
• Supplemental Table 8: Feature-wise testing (multivariate linear model) for differences in dog gut microbiome, at the SGB-level, based on housing (facility vs. household).
• Supplemental Table 9: Feature-wise testing (multivariate linear model) for differences in gut microbiome, at the SGB-level, across host species (cats, dogs, and humans).
• Supplemental Table 10: Feature-wise testing for differences in ARGs across host species (cats, dogs, and humans). Multivariate linear models ran with MaAsLin 2 for all samples.
• Supplemental Table 11: Feature-wise testing for differences in ARGs (organized into antibiotic superclasses) across host species (cats, dogs, and humans). Multivariate linear models ran with MaAsLin 2.
• Supplemental Table 12: Oct22 to Jun23 database taxonomy mapping for SGBs
• Supplemental Table 13: ARG abundance table
• Supplemental Table 14: Abundance table for ARGs grouped into ABX targets (ABX superclasses)
• Supplemental Table 15: Sample-specific metadata