Assembly of hundreds of novel bacterial genomes from the chicken caecum

Abstract

Background: Chickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short-chain fatty acids, nitrogen recycling, and amino acid production. In this study, we sequence DNA from caecal content samples taken from 24 chickens belonging to either a fast or a slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. Results: We utilise 1.6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species, and 42 novel genera. We compare our genomes to data from 9 European Union countries and show that these genomes are abundant within European chicken flocks. We also compare the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed-and diet-specific microbiomes, as well as an overlapping core microbiome. Conclusions: This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

A Genomic Census of the Chicken Gut Microbiome using Metagenomics and Culture

“…Only two species appeared to be restricted (at ≥1x coverage) to just a single sample: Aliarcobacter thereius and Candidatus Avibacteroides faecavium. Correlation clustering con rmed structure in the data linked to BioProject ( Figure S2b) -for example, the BioProject from the study by Glendenning et al [15] clearly shows enhancement of clostridial species compared to other BioProjects, re ected samples sourced from chicks with no post-hatching contact with an adult bird.…”

“…We performed a search of PubMed with the species name and "chicken", leaving aside the 33 species named by Glendenning et al [15]. This suggested that our study provides the rst-evidence-in-chickens for the majority (81/125) of these species (Table S14).…”

“…Pan-genome analysis was conducted using Roary v3.11.2 and visualised using the roary2svg.pl script [54]. Comparison of our derived metagenomes with those of Glendinning et al [15] was performed at 95% ANI using dRep and visualised using web-tool BioVenn [55] [49].…”

“…Of the 853 de-replicated bacterial metagenomic species, 321 represented previously delineated species catalogued in publicly available databases (Table S13). Following direct comparison, a further 165 metagenomic species had been previously identi ed by Glendenning et al [15], with these sequences not currently available in public archives. However, only 158 of our metagenomic species possess validly published names based on Latin binomials.…”

Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

“…Metagenomics is a powerful tool which allows us to examine the entire genetic repertoire of the rumen microbiota without the need for culturing. Our group has previously published thousands of metagenome assembled genomes from cattle rumen samples (19, 20) and hundreds of genomes from chicken caecal samples (21), many of which were identified as novel species.…”