RESEARCHERS say that they have more than doubled the number of microbial species known to live in chicken guts.

The new study used DNA analysis to uncover and characterise microbes taken from samples of chicken guts.

See also: UK Trials begin of new poultry gut health bacteria

A healthy gut microbiome underpins the health of birds and productivity of poultry farming.

Despite this, there is not a complete picture of what lives in the guts of healthy chickens.

Researchers from the Quadram Institute and Earlham Institute on the Norwich Research Park collaborated with partners at the University of Surrey to carry out the largest ever study of microbial diversity within the chicken gut.

The study was funded by the Biotechnology and Biological Sciences Research Council, part of UKRI.

‘Complex community’

The University of Surrey’s Roberto La Ragione said: “Understanding the complex microbial communities that live in the chicken gut is fundamental to improving poultry health and welfare.

“Moreover, in-depth exploration of this community has the potential to improve food security and contribute to the development of interventions to reduce the carriage of foodborne pathogens such as Campylobacter and Salmonella.”

The team of investigators took two approaches.


The first, called metagenomics, relied on extracting and sequencing DNA from faecal or gut samples and then analysing DNA sequences to reconstruct the associated microbes’ genetic blueprints (genomes).  

The second approach involves high-throughput recovery and DNA sequencing of cultured isolates.

Both approaches facilitate discovering new microorganisms while also allowing them to be classified and assigned an accurate position with the family tree of life.

The investigation started with just fifty faecal samples from two breeds of chicken reared in the UK.


However, it was soon expanded to include computer-based analysis of over five hundred DNA datasets from similar samples collected across twelve countries.

The investigators compiled a set of 20 million microbial genes from the chicken gut and reconstructed over 5000 microbial genomes.

These fell into over 800 bacterial species, only 158 of which possessed validly published names, while the majority ranked as previously unknown.

The team also isolated over 280 bacterial cultures, which allowed them to describe thirty newly cultured bacteria species.

‘Remarkable biodiversity’

The Quadram Institute’s Mark Pallen said: “We were surprised to find such remarkable biodiversity within this commonplace livestock ecosystem – diversity that rivals that associated with the human gut.

“Our work has more than doubled the number of bacterial species known to reside in the chicken gut and has resulted in the creation of an unprecedented number of new species names.

“The availability of so many novel genes, genome and species represents a substantial step forward in understanding this system and lays the groundwork for future comparative and intervention studies.”

Gilroy et al. (2021) Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture, has been published in PeerJ