# Airborne Microbiome of Tropical Ostrich Farms: Diversity, Antibiotic Resistance, and Biogeochemical Cycling Potential

## TL;DR

This study explores the airborne microbes and antibiotic resistance in tropical ostrich farms, showing they can spread antibiotic resistance genes and impact biogeochemical cycles.

## Contribution

The study reveals the airborne microbiome and antibiotic resistance gene diversity in tropical ostrich farms, linking them to ecological and health risks.

## Key findings

- Airborne bacteria in ostrich farms include Staphylococcus, Bacillus, and Acinetobacter, shaped by seasons and particle size.
- Over 638 antibiotic resistance genes were detected, including clinically relevant ones like mcr-1 and blaTEM.
- Airborne microbes show potential for carbon and nitrogen cycling, with high CAZyme activity and nitrogen assimilation pathways.

## Abstract

Ostrich farming is rapidly developing in tropical regions, but little attention has been given to the microorganisms and antibiotic resistance carried in farm air. In this study, we collected airborne bioaerosols from different seasons, functional areas, and particle size fractions of an ostrich farm in Hainan, China, and analyzed them using 16S rRNA sequencing and metagenomics. The airborne bacterial community was mainly composed of Bacillota, Proteobacteria, and Actinobacteriota, with genera such as Staphylococcus, Bacillus, and Acinetobacter being dominant. Seasonal changes, farming activities, and particle size characteristics jointly shaped the structure of the airborne microbiome. We detected a wide range of ARGs, including β-lactam resistance genes dominated by OXA-type determinants and fluoroquinolone resistance genes such as gyrA, gyrB, and parC. Functional genes indicated that airborne microorganisms may participate in carbon and nitrogen cycling, suggesting potential ecological importance. These findings show that bioaerosols in ostrich farms may act as a reservoir of antibiotic resistance and functionally active microbes, highlighting the need for enhanced environmental monitoring and One Health-based risk management.

The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1–3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65–1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and blaTEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies.