DOI: 10.5061/dryad.ghx3ffbzd
title: The global network of domestic mammal hosts and zoonotic bacteria: Implications for disease transmission and detection

description: Zoonotic diseases, defined as those transmitted from animals to humans,
 represent over 75% of emerging infectious diseases and pose ongoing
 challenges to public health. Understanding the structure of host–pathogen
 interactions is critical for anticipating and mitigating such threats. In
 this study, we analysed the global bipartite network formed by zoonotic
 bacteria and their domestic mammal hosts. A bipartite network links two
 distinct sets of nodes—in this case, bacteria and hosts—through documented
 interactions. We aimed to (1) describe the structure of this host–bacteria
 (H–B) network using ecological network metrics, and (2) assess whether
 host traits, namely time since domestication and phylogenetic proximity to
 humans, predict the number of associated zoonotic bacteria per host
 species. The network, built from literature-based associations involving
 24 domestic mammals and 51 zoonotic bacteria, exhibited high nestedness (a
 pattern where specialist bacteria infect subsets of hosts used by
 generalist bacteria) and low modularity (indicating weak
 compartmentalisation into distinct host–pathogen clusters) compared with
 null models. This suggests a non-random, core–periphery structure. Hosts
 with longer domestication histories hosted significantly more bacterial
 species, whereas phylogenetic distance from humans had no significant
 effect. These findings suggest that early-domesticated hosts may act as
 key nodes for pathogen accumulation and redistribution. The nested
 architecture also revealed likely “missing links” (unreported but
 plausible host–pathogen interactions), offering a practical basis for
 targeted surveillance. While network analysis is already established in
 zoonotic research, our global-scale findings highlight its continued
 potential to uncover structure and dynamics in increasingly complex
 host–pathogen systems.
description: # The global network of domestic mammal hosts and zoonotic bacteria:
 Implications for disease transmission and detection **María del Rosario
 Belén Pacheco & Mariano Devoto** Dataset DOI:
 [10.5061/dryad.ghx3ffbzd](https://doi.org/10.5061/dryad.ghx3ffbzd) ##
 Description of the data and file structure This dataset was assembled to
 analyse the global bipartite network formed by zoonotic bacteria and their
 domestic mammal hosts. It compiles documented interactions between 24
 domestic mammal species and 51 zoonotic bacterial species, drawn from
 published reviews and literature spanning 2002–2022, as well as classic
 compendia. The aim was to describe the structure of the host–bacteria
 network (nestedness, modularity, connectance) and to test whether
 domestication history and phylogenetic proximity to humans predict
 bacterial richness per host. ## Files and variables The dataset includes
 four files: ### 1. `zoo_bac_dom2.csv` Contains the host–bacteria
 interaction data in **long (edge-list) format**. Each row corresponds to a
 recorded interaction between one domestic mammal species and one zoonotic
 bacterial species. Columns are: * **bacterium_name**: Scientific name of
 the zoonotic bacterium (character string; e.g., *Brucella abortus*). *
 **host_name**: Scientific name of the domestic mammal species (character
 string; matches the names in `domestic_year.csv`; e.g., *Bos taurus*). *
 **bacterium_num**: Numeric identifier assigned to each bacterial species
 (integer index). * **host_num**: Numeric identifier assigned to each
 mammal species (integer index). Presence of a row indicates a documented
 host–bacterium association (equivalent to a “1” in a binary matrix).
 Absence of a pair indicates no reported interaction (equivalent to “0”).
 ### 2. `domestic_year.csv` Provides metadata on each domestic mammal
 species included in the network. Columns are: * **Order**: Taxonomic order
 of the mammal species (categorical). * **host_name**: Scientific name of
 the domestic mammal species (character string; matches the rows in
 `zoo_bac_dom2.csv`). * **DOMYear**: Estimated year of first domestication,
 expressed as years **before present (BP)** (integer; e.g., `4514` =
 domesticated ~4514 years ago). Missing values are indicated by `NA`. *
 **domestic_category**: Broad functional category of domestication
 (categorical; e.g., “Livestock”, "Small Livestock", “Utility”,
 “Pet”). * **publ_number**: Number of publications that reported bacterial
 associations for this species (integer count; unit = publications). *
 **global_livestock**: Estimated global population size for the species
 (numeric; unit = number of individuals). Missing values are indicated by
 `NA`. ### 3. `cytb_supertree.tree` A phylogenetic tree in Newick format,
 representing relationships among the 24 domestic mammal species plus
 humans. The topology is derived from mitochondrial cytochrome b data. No
 tabular variables apply beyond the tree structure itself. ### 4.
 `OIK11077_R2.R` An R script containing the full analysis workflow. It
 reads the three data files, builds and analyses the host–bacteria
 bipartite network, calculates network- and node-level metrics, conducts
 null model comparisons, computes phylogenetic distances and Mantel tests,
 fits phylogenetic GLMMs, and generates figures. ## Code/software All
 analyses were performed in R (version 4.0 or later). Required open-source
 packages include **igraph**, **bipartite**, **ape**, **vegan**, and
 **phyr**. The workflow is entirely contained in `OIK11077_R2.R`, which
 imports the data files and runs the analyses sequentially. Users can
 reproduce the figures and statistical models by running this script with
 the datasets in the same working directory.