Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
Instituto de Ciencias Agropecuarias y Rurales, Universidad Autónoma del Estado de México, Toluca, Mexico.
Microb Genom. 2024 Jan;10(1). doi: 10.1099/mgen.0.001181.
Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of skin microbiome differed between . infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.
两栖动物的皮肤微生物组可以通过保护宿主免受病原体侵害，在宿主对抗新兴疾病方面发挥关键作用。虽然有大量生物和非生物因素被证明会影响两栖动物皮肤微生物组的分类多样性，但功能基因组多样性是否会因时间和环境因素而变化仍不清楚。在这里，我们采用宏基因组学方法来评估季节性、不同海拔的不同生境和病原体的存在是否会影响皮肤微生物组的功能基因组多样性。我们获得了 92107 个非冗余注释基因的基因目录和 50 个独特的宏基因组组装基因组 (MAG)。我们的分析表明，与一般和潜在抗真菌特性相关的基因在不同季节和不同海拔的采样地点存在显著差异。此外，我们发现，只有在冬季，受感染和未受感染的蝾螈的皮肤微生物组的功能基因组多样性存在差异，这表明季节性和病原体感染之间存在相互作用。此外，我们还发现了与潜在抗真菌功能相关的基因和生物合成基因簇 (BGC) 的存在，如生物膜形成、群体感应、分泌系统、次生代谢物生物合成和几丁质降解。有趣的是，与这些潜在抗真菌特性相关的基因主要在伯克霍尔德氏菌目和噬几丁质菌目 MAG 中被鉴定出来。总的来说，无论功能多样性在季节、海拔/生境和病原体存在方面存在差异，我们的研究结果都确定了与皮肤微生物组中潜在抗真菌功能相关的功能特征。我们的研究结果表明，在伯克霍尔德氏菌目和噬几丁质菌目分类群中发现的潜在抗真菌特性可能与蝾螈在 Bd 存在下生存的能力有关，尽管需要进一步的实验分析来验证这一假设。
