Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria
Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria
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DOI：
10.1128/msphere.00475-23
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发表时间：
2024-02
期刊：
影响因子：
4.8
通讯作者：
Lluvia Vargas-Gastélum;Alexander S. Romer;M. Ghotbi;J. Dallas;N. Alexander;Kylie C. Moe;Kerry L. McPhail;George F Neuhaus;Leila Shadmani;J. Spatafora;J. Stajich;Javier F. Tabima;Donald M Walker
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作者：
Lluvia Vargas-Gastélum;Alexander S. Romer;M. Ghotbi;J. Dallas;N. Alexander;Kylie C. Moe;Kerry L. McPhail;George F Neuhaus;Leila Shadmani;J. Spatafora;J. Stajich;Javier F. Tabima;Donald M Walker
摘要 爬行动物和两栖动物（爬行动物）是地球上最濒危和受威胁的物种之一，为了确保物种恢复，正在实施许多保护策略。然而，人们对野生爬行动物的肠道微生物组及其与这些种群健康的关系知之甚少。在这里，我们报告了对爬行动物进行广泛调查的肠道微生物组特征的结果，以及真菌 Basidiobolus 和细菌群落之间的相关性，这些结果得到了更深入、更密集的 Plethodon gluinosus（称为粘滑蝾螈）采样的支持。我们证明，从青蛙、蜥蜴和蝾螈中取样的细菌群落是由宿主分类法构建的，并且担子菌是这些野生肠道微生物组的常见且天然的组成部分。对田纳西州生态区多个寄主的密集采样表明，地理和寄主与地理之间的相互作用是特定寄主内存在的不同担子菌操作分类单元的有力预测因素。 Basidiobolus 和细菌群落多样性的共现分析支持 Basidiobolus 和细菌之间的相关性和相互作用，表明 Basidiobolus 可能在构建细菌群落中发挥作用。我们进一步假设，这种相互作用是通过源自细菌水平基因转移到 Basidiobolus 的独特的专门代谢来促进的，并证明 Basidiobolus 能够产生多种专门代谢物，包括小环肽。重要性这项工作显着增进了我们对爬行动物微生物组中生物多样性和微生物相互作用、真菌作为爬行动物肠道微生物组结构和功能成员的作用以及构建微生物组表型的化学功能的理解。我们还提供了一个重要的观察系统，了解肠道微生物组如何代表一个独特的环境，通过真菌和细菌之间的水平基因转移选择新的代谢功能。需要进行此类研究，以更好地了解自然界肠道微生物组的复杂性，并为受威胁的爬行动物物种的保护策略提供信息。这项工作极大地增进了我们对爬行动物微生物组中生物多样性和微生物相互作用、真菌作为爬行动物肠道微生物组结构和功能成员的作用以及构建微生物组表型的化学功能的理解。我们还提供了一个重要的观察系统，了解肠道微生物组如何代表一个独特的环境，通过真菌和细菌之间的水平基因转移选择新的代谢功能。需要进行此类研究，以更好地了解自然界肠道微生物组的复杂性，并为受威胁的爬行动物物种的保护策略提供信息。
ABSTRACT Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides. IMPORTANCE This work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna. This work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.