Comeault Aaron A, Orta Alberto H, Fidler David B, Nunn Tobias, Ellison Amy R, Anspach Tayte A, Matute Daniel R
School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Prifysgol Bangor University, Bangor, United Kingdom.
Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA.
mSystems. 2025 Jul 2:e0002725. doi: 10.1128/msystems.00027-25.
Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from communities associated with six species of drosophilid flies collected from "anthropogenic" environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera , , , , and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions, including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera , , , and others on the performance of their insect hosts across diverse environments.IMPORTANCEWhile much attention has been given to catalogue the taxonomic diversity intrinsic to host-associated microbiomes, much less is known about the functional consequences of this variation, especially in wild, non-model host species. In this study, we use long-read sequencing to generate and analyze 103 high-quality metagenome-assembled genomes from host-associated bacterial communities from six species of wild fruit fly (). We find that the genomes of drosophilid-associated bacteria possess diverse metabolic pathways and biosynthetic gene clusters that are predicted to generate metabolites involved in nutrition and disease resistance, among other functions. Using functional gene predictions, we show that different bacterial lineages that comprise the insect microbiome differ in predicted functional capacities. Our findings highlight the functional variation intrinsic to microbial communities of wild insects and provide a step towards disentangling the ecological and evolutionary processes driving host-microbe symbioses.
与宿主相关的微生物群落可以介导宿主与生物和非生物环境之间的相互作用。虽然已经开展了大量工作来记录微生物群如何因物种和环境而异，但对于这种变异的功能后果却知之甚少。在这里，我们通过进行牛津纳米孔长读长测序，并从北美、欧洲和非洲“人为”环境中采集的六种果蝇相关群落中生成宏基因组组装基因组（MAG），来测试果蝇相关细菌之间的功能变异。通过系统发育分析，我们发现果蝇拥有多样化的微生物群，其中包括与 属、 属、 属、 属及其他属密切相关的核心成员。与公开可用的细菌基因组进行比较表明，这些属中的许多与系统发育上不同的昆虫肠道微生物群有关。使用功能注释和预测的次生代谢物生物合成基因簇，我们表明属于不同细菌目和属的MAG在基因含量和预测功能上存在差异，包括代谢能力以及它们对环境应激源的反应方式。我们的结果提供了证据，表明野生果蝇拥有系统发育和功能多样的微生物群落。这些发现凸显了需要量化来自 属、 属、 属及其他属的昆虫相关细菌的丰度和功能对其昆虫宿主在不同环境中的表现的影响。
重要性
虽然人们已经非常关注编目宿主相关微生物群固有的分类多样性，但对于这种变异的功能后果却知之甚少，尤其是在野生的、非模式宿主物种中。在本研究中，我们使用长读长测序从六种野生果蝇（ ）的宿主相关细菌群落中生成并分析了103个高质量的宏基因组组装基因组。我们发现，果蝇相关细菌的基因组拥有多样的代谢途径和生物合成基因簇，预计这些基因簇会产生参与营养和抗病等功能的代谢物。通过功能基因预测，我们表明构成昆虫微生物群的不同细菌谱系在预测的功能能力上存在差异。我们的发现凸显了野生昆虫微生物群落固有的功能变异，并朝着解开驱动宿主 - 微生物共生的生态和进化过程迈出了一步。
