摘要
      肠道微生物组是鸟类健康的重要组成部分，影响营养吸收和免疫功能。虽然对农业上重要鸟类的肠道微生物组进行了研究，但野生鸟类的微生物组仍有待探索。填补这一知识空白可能会对圈养鸟类的微生物重新繁殖和抗生素耐药性细菌（ARB）的鸟类宿主管理产生影响。使用基因组解析的宏基因组学，我们从野生和圈养的西方卡氏锥虫（Tetrao urogallus）的粪便中回收了112个宏基因组组装基因组（MAG）（n=8）。对野生和圈养刺五加细菌多样性的比较表明，圈养个体的多样性降低可能是由于饮食差异。通过对517657个直向同源群（COG）的分析进一步证实了这一点，这表明与氨基酸和碳水化合物代谢相关的基因功能在野生山柑中更丰富。对耐药组的宏基因组学挖掘鉴定了751个抗生素耐药基因（ARG），其中40.7%是野生山柑属特有的，这表明山柑属可能是宿主ARG相关细菌的潜在宿主。此外，野生和圈养卡氏菌之间共享的核心耐药性表明，鸟类可以从环境中自然获得这些ARG相关细菌（占ARG的43.1%）。26个MAG与120个ARG和378个病毒操作分类单元（vOTU）的关联也表明这些元素之间可能存在相互作用，其中假定的噬菌体可能在调节鸟类宿主的肠道微生物群中发挥作用。这些发现可能对保护和人类健康具有重要意义，例如鸟类肠道微生物群的重建，识别噬菌体与微生物相互作用带来的新威胁或机会，以及监测野生鸟类种群中ARG相关细菌的潜在传播。
Abstract
The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.

https://www.sciencedirect.com/science/article/pii/S0944501323000745