DNA analysis reveals diversity of chicken gut microbiome

A collaboration between researchers in the UK and Scotland to characterize new microbes using DNA analysis has more than doubled the number of known species residing in the chicken gut.

Monika Wisniewska | Dreamstime.com
Monika Wisniewska | Dreamstime.com

A collaboration between researchers in the UK and Scotland to characterize new microbes using DNA analysis has more than doubled the number of known species residing in the chicken gut.

“We have barely begun to understand what a healthy gut microbiome looks like in chickens, despite the clear importance of this bird. I would even go as far as to say that until this study, we knew more about the far side of the moon than what lives inside chickens,” said Mark Pallen, study author and Research Leader of Bacterial Genomics and Metagenomics at the Quadram Institute.

The study, published in the open access journal PeerJ, could serve as an important resource for future research on the chicken microbiome.

“Only by gaining a complete view of microbial diversity, can we begin to work out how microbes are interacting and what they are doing in this important habitat. This will underpin efforts to devise new feed additives, new probiotics and other approaches to manipulation of the microbiome. Working out which components are common to most birds will help us select interventions that are broadly applicable,” he added.

The power of DNA analysis

The researchers used two cutting edge DNA analysis approaches to identify and classify microorganisms that were obtained from over 500 chicken fecal samples collected across 12 countries.

“We used two approaches. We cultured isolates from chicken samples and then sequenced their genomes to work out which represented new species. In parallel, we analyzed DNA that had been extracted from samples without prior culture — an approach called ‘metagenomics.’ Sophisticated computer-based analyses allowed us to identify and characterize novel bacterial genomes and species from the chicken gut,” Pallen explained.

More than 20 million microbial genes and over 5,000 microbial genomes were characterized. The researchers identified over 800 bacterial species, only 158 of which were previously known. 

The research team worked with Israeli nomenclature expert Aharon Oren to give each of the newly discovered bacterial species a Latin name, resulting in the largest number of microbial taxonomic names created within a single study.

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