Elmassry Moamen M, Farag Mohamed A, Preissner Robert, Gohlke Björn-Oliver, Piechulla Birgit, Lemfack Marie C
Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States.
Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Giza, Egypt.
Front Microbiol. 2020 Sep 30;11:557253. doi: 10.3389/fmicb.2020.557253. eCollection 2020.
Microorganisms are diverse in their genome sequences and subsequently in their encoded metabolic pathways, which enabled them to adapt to numerous environmental conditions. They produce thousands of small molecules, many of which are volatiles in nature and play important roles in signaling in intra- and inter-species to kingdom and domain interactions, survival, or virulence. Many of these compounds have been studied, characterized, and organized in the mVOC 2.0 database. However, such dataset has not been investigated comprehensively in terms of its phylogeny to determine key volatile markers for certain taxa. It was hypothesized that some of the volatiles described in the mVOC 2.0 database could function as a phylogenetic signal since their production is conserved among certain taxa within the microbial evolutionary tree. Our meta-analysis revealed that some volatiles were produced by a large number of bacteria but not in fungal genera such as dimethyl disulfide, acetic acid, 2-nonanone, dimethyl trisulfide, 2-undecanone, isovaleric acid, 2-tridecanone, propanoic acid, and indole (common bacterial compounds). In contrast, 1-octen-3-ol, 3-octanone, and 2-pentylfuran (common fungal compounds) were produced primarily by fungal genera. Such chemical information was further confirmed by investigating genomic data of publicly available databases revealing that bacteria or fungi harbor gene families involved in these volatiles' biosynthesis. Our phylogenetic signal testing identified 61 volatiles with a significant phylogenetic signal as demonstrated by phylogenetic statistic -value < 0.05. Thirty-three volatiles were phylogenetically conserved in the bacterial domain (e.g., cyclocitral) compared to 17 volatiles phylogenetically conserved in the fungal kingdom (e.g., aristolochene), whereas 11 volatiles were phylogenetically conserved in genera from both bacteria and fungi (e.g., geosmin). These volatiles belong to different chemical classes such as heterocyclic compounds, long-chain fatty acids, sesquiterpenoids, and aromatics. The performed approaches serve as a starting point to investigate less explored volatiles with potential roles in signaling, antimicrobial therapy, or diagnostics.
微生物的基因组序列多种多样，其编码的代谢途径也各不相同，这使它们能够适应多种环境条件。它们产生数千种小分子，其中许多在本质上是挥发性的，在种内和种间信号传递、界与域间相互作用、生存或毒力方面发挥着重要作用。许多此类化合物已在mVOC 2.0数据库中得到研究、表征和整理。然而，就其系统发育而言，尚未对该数据集进行全面研究以确定某些分类群的关键挥发性标记物。据推测，mVOC 2.0数据库中描述的一些挥发性物质可能作为系统发育信号发挥作用，因为它们在微生物进化树中的某些分类群中产量是保守的。我们的荟萃分析表明，一些挥发性物质由大量细菌产生，但在真菌属中不产生，如二甲基二硫醚、乙酸、2-壬酮、二甲基三硫醚、2-十一烷酮、异戊酸、2-十三烷酮、丙酸和吲哚（常见细菌化合物）。相比之下，1-辛烯-3-醇、3-辛烷酮和2-戊基呋喃（常见真菌化合物）主要由真菌属产生。通过研究公开可用数据库的基因组数据进一步证实了此类化学信息，表明细菌或真菌含有参与这些挥发性物质生物合成的基因家族。我们的系统发育信号测试确定了61种具有显著系统发育信号的挥发性物质，系统发育统计值<0.05证明了这一点。与真菌界中17种系统发育保守的挥发性物质（如马兜铃烯）相比，有33种挥发性物质在细菌域中系统发育保守（如环柠檬醛），而有11种挥发性物质在细菌和真菌的属中系统发育保守（如土臭素）。这些挥发性物质属于不同的化学类别，如杂环化合物、长链脂肪酸、倍半萜类化合物和芳香族化合物。所采用的方法作为一个起点，用于研究在信号传递、抗菌治疗或诊断中具有潜在作用但较少被探索的挥发性物质。
