Laboratorio de Redes Biológicas, Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile.
CGNA (Agriaquaculture Nutritional Genomic Center), Temuco, Chile.
PeerJ. 2023 Jul 7;11:e15235. doi: 10.7717/peerj.15235. eCollection 2023.
The Andean condor () is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome.
This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways.
Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with , a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for and , respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.
安第斯神鹫（Andean condor）是南美洲最大的食腐动物。这种掠食性鸟类通过清除腐肉在其生态位中发挥着至关重要的作用。我们报告了安第斯神鹫肠道微生物组的首次宏基因组分析。
这项工作分析了来自 15 只智利圈养安第斯神鹫混合物的鸟枪法宏基因组数据。为了过滤真核生物的污染，我们使用了 BWA-MEM v0.7。使用 Kraken2 和 MetaPhlAn v2.0 进行分类群分配，所有过滤后的reads 都使用 IDBA-UD v1.1.3 进行组装。使用 MetaCompass 对两种最丰富的物种进行基因组参考指导组装。最后，我们使用 Prodigal 进行基因预测，每个预测的基因都进行了功能注释。InterproScan v5.31-70.0 还用于基于蛋白质结构域检测同源性，KEGG mapper 软件用于重建代谢途径。
我们的结果与其他新世界秃鹫的肠道微生物组数据一致。在安第斯神鹫中，厚壁菌门是最丰富的门，而 ，一种对其他动物具有潜在致病性的细菌，是肠道微生物组中的主要物种。我们组装了对应于在神鹫肠道微生物组中发现的前两种物种的所有reads，发现 和 的完整性分别达到 94%到 98%。我们的工作强调了安第斯神鹫作为环境储库和潜在传播媒介的能力，这些媒介可能携带关键优先病原体，其中包含相关的遗传元件。在这些遗传元件中，我们发现了 71 个抗生素耐药基因和 1786 个毒力因子，我们将这些基因与几种适应过程联系起来。
