Metagenomic reconstructions of gut microbial metabolism in weanling pigs

Wang, Weilan; Hu, Huifeng; Zijlstra, R. T.; Zheng, Jinshui; Gänzle, Michael G.

doi:10.1186/s40168-019-0662-1

Cited by 95 publications

(93 citation statements)

References 84 publications

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“…Due to improvements in computational power and sequencing technologies, and the development of new computational approaches [22,23], it is now possible to accurately bin short-read metagenomic data into highquality genomes. Using this technique, thousands of MAGs have been generated from various environments, including humans [24,25], chickens [26], the rumen [27,28], pig faeces [29], marine surface waters [30,31], an underground aquifer system [32], and other public datasets [33].…”

Section: Introductionmentioning

confidence: 99%

Assembly of hundreds of novel bacterial genomes from the chicken caecum

et al. 2020

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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.

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Section: Introductionmentioning

confidence: 99%

Assembly of hundreds of novel bacterial genomes from the chicken caecum

et al. 2020

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“…Due to improvements in computational power and sequencing technologies, and the development of new computational approaches (21, 22), it is now possible to accurately bin short-read metagenomic data into high-quality genomes. Using this technique thousands of MAGs have been generated from various environments, including humans (23, 24), chickens (25) the rumen (26, 27), pig faeces (28), marine surface waters (29, 30), an underground aquifer system (31) and other public datasets (32).…”

Section: Introductionmentioning

confidence: 99%

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Glendinning

Stewart

Pallen

et al. 2019

Preprint

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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

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“…Recent studies have proposed metagenomic binning as a culture-independent method to extract genomes from samples (Albertsen, et al 2013: 533, Pasolli, et al 2019: 649-62.e20, Tully, et al 2018: 170203, Wang, et al 2019: 48). However, one of the main pitfalls of metagenomic binning is that metagenomic assemblers struggle to assemble contigs of closely related taxa, especially if the organisms are found in low abundance (Ayling, et al 2019).…”

Section: Discussionmentioning

confidence: 99%

The Gut Microbiota composition of Feral and Tamworth Pigs determined using High-Throughput Culturomics and Metagenomics Reveals Compositional Variations When Compared to the Commercial Breeds

Fenske

Ghimire

Antony

et al. 2019

Preprint

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Bacterial communities in the hindguts of pigs have a profound impact on health and disease. Yet very limited studies have been performed outside intensive swine farms to determine pig gut microbiome composition in natural populations. Feral pigs represent a unique situation where the microbiome structure can be observed outside the realm of modern agriculture. Additionally, Tamworth pigs that freely forage were included to characterize the microbiome structure of this rare breed. In this study, gut microbiome of feral and Tamworth pigs were determined using metagenomics and culturomics. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. In total, 46 distinct species were successfully isolated from 1000 colonies selected. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. Furthermore, the naturally raised Tamworth pig microbiome contained more number of antibiotic resistance genes when compared to feral pig microbiome. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function by assembling simple to complex microbiota communities in bioreactors or germfree animal models.

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Metagenomic reconstructions of gut microbial metabolism in weanling pigs

Cited by 95 publications

References 84 publications

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Assembly of hundreds of novel bacterial genomes from the chicken caecum

The Gut Microbiota composition of Feral and Tamworth Pigs determined using High-Throughput Culturomics and Metagenomics Reveals Compositional Variations When Compared to the Commercial Breeds

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