Dynamics of archaeal diversity and functionality in the piglet gut microbiome under common antimicrobial treatments

Engineering notes

Key topics: autonomous driving. See the paper for implementation details and experimental results.

Chinese explanation / 中文解读

中文解读待补充：本站会优先为端到端自动驾驶、BEV感知、3D目标检测、轨迹预测、路径规划、LiDAR感知等高价值论文补充中文说明。

Original abstract

Introduction The gut microbiota comprises a diverse and dynamic community of microorganisms that collectively enhance host metabolism, physiology, and overall functionality. In this context, the swine archaeome remains largely underexplored despite growing evidence that archaea may greatly influence host health. Advances in high-throughput approaches provide new opportunities to reveal the dynamics and composition of archaea. Herein, we uncover the taxonomic and functional landscape of the piglet archaeome during the weaning transition under multiple experimental conditions, integrating shotgun metagenomic and metatranscriptomic analyses to elucidate its contribution to gut microbial ecology. Methods The seven experimental conditions included four antibiotic treatments for post-weaning diarrhoea (trimethoprim/sulfamethoxazole, colistin, gentamicin, amoxicillin), an oral vaccine, acidifiers in drinking water, and a no-intervention group. A total of 280 faecal samples were collected longitudinally one day before weaning (ST1), three days (ST2), two weeks (ST3), and four weeks (ST4) after the start of the treatment. Treatment was initiated eleven days after arrival at the experimental farm following the onset of clinical signs. Shotgun metagenomics was used to assess archaeal taxonomic diversity and recover archaeal metagenome-assembled genomes (aMAGs), while metatranscriptomics was integrated to assess differentially expressed genes at ST1, ST2, and ST4. Results The results revealed archaea as the second most abundant microorganism, exhibiting a longitudinal increase in diversity over the experimental time. The most predominant genus was Methanobrevibacter , including Methanobrevibacter smithii . Eleven high-quality aMAGs were recovered, belonging to the Methanobacteriota and Thermoplasmatota phyla. Genome-inferred functional analyses revealed that the predominant metabolic processes included the biosynthesis of nucleic acids, amino acids, organic anions, and vitamins. Additional functional traits suggested potential roles in the degradation of sugars, amino acids, and antibiotics were also observed. Moreover, significant differences were detected on the archaeal metatranscriptome between the experimental groups treated with antibiotics and the rest of the groups, underscoring their response to changes in microbial interactions, substrate availability and, in some cases, direct effect of the antimicrobials on metabolic pathways. Discussion Altogether, this study highlights the biological significance of archaeal dynamics during initial life stages and demonstrates how combining metagenomics and metatranscriptomics uncovers their functional potential and the pathways actively expressed in the piglets’ gut.

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