Metagenomics comparison identifies shared pathogenic microbiome in humans, pigs and chickens

Area of Science:

• Microbiome research
• Infectious disease epidemiology
• One Health

Background:

• Emerging infectious diseases often originate from zoonotic sources, with 60-75% estimated globally.
• Integrating human, animal, and environmental health is critical for disease control.

Purpose of the Study:

• To estimate microbial sharing at the species-level genome bins (SGBs) resolution across humans, pigs, and chickens.
• To understand the influence of host species and geography on gut microbial community structure.

Main Methods:

• Analysis of 1274 shotgun metagenomic faecal samples from humans, pigs, and chickens across multiple countries.
• Alpha and beta diversity analyses to assess community structure.
• LEfSe analysis to identify distinctive microbial signatures.

Main Results:

• Host species significantly structures gut microbial communities, outweighing geographical influence.
• Substantial cross-host sharing of SGBs was observed, including known pathogens like Escherichia coli and Clostridium perfringens.
• Core microbial taxa were predominantly host-specific, while non-core taxa were more frequently shared.

Conclusions:

• Geographically distant humans and livestock can harbor similar microbial populations with pathogenic potential.
• Findings support the need for integrated One Health surveillance to prevent zoonotic and reverse zoonotic transmission.
• Understanding microbial sharing is key to managing infectious disease risks in interconnected systems.