Assembly of hundreds of novel bacterial genomes from the chicken caecum

Abstract

9Chickens are a highly important source of protein for a large proportion of the human population. The 10 caecal microbiota plays a crucial role in chicken nutrition through the production of short chain fatty acids, 11 nitrogen recycling and amino acid production. In this study we sequenced DNA from caecal contents 12 samples taken from 24 chickens belonging to either a fast or slower growing breed consuming either a 13 vegetable-only diet or a diet containing fish meal. We utilised 1.6T of Illumina data to construct 469 draft 14 metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species and 42 novel 15 genera. We compared our genomes to data from eight EU countries and show that these genomes are 16 abundant within European chicken flocks. We also compared the abundance of our genomes, and the 17 carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are 18 both breed-and diet-specific microbiomes, as well as an overlapping core microbiome. This data will form 19 the basis for future studies examining the composition and function of the chicken caecal microbiota. 20 21 Background: 22 157 Data availability 158 Paired-read fastq files have been submitted to the European Nucleotide Archive under project PRJEB33338. 159 MAG fasta files have been submitted to Edinburgh DataShare (https://doi.org/10.7488/ds/2584). 160

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

“…While there is high variability present between the microbiota of chickens in different trials [21] it does seem as though there are taxonomies which are consistently present in the chicken gut [1]. Identifying these shared taxa and elucidating their function within birds could lead to a greater understanding of the microbial ecology of the chicken gut and the development of technologies which could be widely applied to improve chicken health or productivity.…”

“…Improvements in sequencing technologies have led to a better understanding of the microbiota of many livestock species [1][2][3][4], leading some to suggest that we could optimise the composition of microbiota in these economically important animals to improve production and sustainability [5]. However, to do so would require a good understanding of the types of microbes which naturally occur in these animals and the role they play in nutrition and health.…”

A Genomic Blueprint of the Chicken Gut Microbiome

“…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].…”

“…Two strategies have proven productive for exploring taxonomic and functional diversity in complex microbial communities [12,13]. Culture-independent approaches rely on shotgun metagenomic sequencing of DNA extracted from relevant samples, followed by bioinformatics-based community pro ling and analysis [12,14,15]. Culture-dependent approaches (often termed "culturomics") combine large-scale isolation of microorganisms in pure culture with whole-genome sequencing and…”

Development of the duodenal, ileal, jejunal and caecal microbiota in chickens

“…While there is high variability present between the microbiota of chickens in different trials [21] it 251 does seem as though there are taxonomies which are consistently present in the chicken gut [1]. 252 Sequences were removed if they were >275 bp in length, contained ambiguous bases, had 299 homopolymers of >9bp in length, did not align to the V4 region of the 16S rRNA gene or they did not 300 originate from bacteria.…”