A comprehensive analysis of antibiotic resistance genes in the giant panda gut

Deng, Feilong; Han, Yanhua; Huang, Yushan; Li, Desheng; Chai, Jianmin; Deng, Linhua; Wei, Ming; Wu, Kai; Zhao, HuaBin; Yang, Guan; Zhao, Jiangchao; Li, Ying; Wang, Chengdong

doi:10.1002/imt2.171

Cited by 9 publications

(1 citation statement)

References 19 publications

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“…Contigs from each sample were binned using the MetaBAT2 v2.12.1 [32]. A total of 2758 MAGs were obtained, which were then assessed for completeness and contamination using the CheckM v1.2.2 [33]; MAGs with completeness greater than 50% and contamination less than 10% were retained [34,35], resulting in 1302 MAGs. Finally, the MAGs were deduplicated using dRep v3.4.5 [36] with the following parameters: -comp 50 -con 10 -sa 0.99 -p 30.…”

Section: Bioinformaticsmentioning

confidence: 99%

Exploring the Intestinal Microbial Community of Lantang Pigs through Metagenome-Assembled Genomes and Carbohydrate Degradation Genes

Yang,

Fan,

Jin

et al. 2024

Fermentation

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High-fiber, low-cost agricultural byproducts offer a sustainable alternative for mitigating the competition for crops between humans and livestock. Pigs predominantly utilize dietary fibers through the process of microbial fermentation within the gut. This study explored the gut microbiota and the capacity for carbohydrate degradation in 30 individual Lantang pigs, a breed indigenous to China. Through metagenomic analysis, a total of 671 metagenome-assembled genomes (MAGs) were assembled and assigned into 14 bacterial and 1 archaeal phylum, including 97 species from uncultured microbes. The phylum with the highest abundance were identified as Bacillota_A, Bacteroidota, and Bacillota. Remarkably, the investigation revealed nearly 10,000 genes implicated in the degradation of carbohydrates, with a pronounced prevalence within five principal bacterial genera: Prevotella, Cryptobacteroides, Gemmiger, Vescimonas, and Faecousia. Additionally, 87 distinct types of carbohydrate-degrading enzymes were exclusively identified within the gut microbiota of the Lantang pig. These insights not only enhance our understanding of the microbial diversity specific to native Chinese pig breeds but also augment the body of research regarding porcine fiber degradation capabilities. The implications of this study are twofold: it provides strategic directions for optimizing feed efficiency and reducing breeding costs, and it furnishes an expanded gene pool for the microbial synthesis of industrial enzymes in the future.

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Section: Bioinformaticsmentioning

confidence: 99%

Exploring the Intestinal Microbial Community of Lantang Pigs through Metagenome-Assembled Genomes and Carbohydrate Degradation Genes

Yang,

Fan,

Jin

et al. 2024

Fermentation

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iMetaOmics: Advancing human and environmental health through integrated meta‐omics

Shi,

Chen,

Lan

et al. 2024

iMetaOmics

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Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition

Ma,

Lyu,

Zeng

et al. 2024

iMeta

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The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome‐assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region‐specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic‐resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.

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A comprehensive analysis of antibiotic resistance genes in the giant panda gut

Cited by 9 publications

References 19 publications

Exploring the Intestinal Microbial Community of Lantang Pigs through Metagenome-Assembled Genomes and Carbohydrate Degradation Genes

Exploring the Intestinal Microbial Community of Lantang Pigs through Metagenome-Assembled Genomes and Carbohydrate Degradation Genes

iMetaOmics: Advancing human and environmental health through integrated meta‐omics

Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition

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