Comparative genomic analysis ofFlavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis
Comparative genomic analysis ofFlavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis
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DOI：
10.1186/s12864-020-06971-7
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发表时间：
2020-08-20
期刊：
影响因子：
4.4
通讯作者：
Sipkema, Detmer
中科院分区：
文献类型：
--
作者：
Gavriilidou, Asimenia;Gutleben, Johanna;Sipkema, Detmer
背景黄杆菌科（Flavobacteriaceae）是一个广泛分布于海洋环境中的细菌家族，常与藻类、鱼类、碎屑或海洋无脊椎动物共生。然而，人们对它们在不同生态位中无处不在的特征知之甚少。在这里，我们提供了一个概述的功能性状共同的家庭flavobacteriaceae从不同的环境来源的分类学上不同的成员，重点是海洋分支。我们包括七个新测序的海洋海绵衍生菌株，也进行了滑行运动和抗菌活性的测试。结果比较基因组学显示，基因组相似性与16S rRNA基因和基因组遗传相关，而差异主要与营养物质的获取有关，如碳水化合物代谢和滑行运动。高分子降解酶基因的高频率和多样性，往往安排在多糖利用位点（普尔斯），支持海洋黄杆菌利用不同碳源的能力。滑动蛋白的同源物广泛存在于所有研究的Flavobacteriaceae中，与其他门的成员形成对比，突出了拟杆菌中这种特征的特殊存在。值得注意的是，并非所有预测滑动的细菌都形成了扩散菌落。基因组挖掘揭示了一个多样化的次生代谢物生物合成库的黄杆菌科与高流行率的基因簇编码途径的生产抗菌剂，抗氧化剂和细胞毒性化合物。然而，抗微生物活性测试表明，表型与七种测试菌株的基因组预测不同。结论我们的研究阐明了海洋黄杆菌科的功能库，并强调需要联合收割机基因组和实验数据，同时使用适当的刺激，以解锁其未知的代谢潜力。
Background Members of the bacterial familyFlavobacteriaceaeare widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the familyFlavobacteriaceaefrom different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. Results Comparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marineFlavobacteriaceaeto utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studiedFlavobacteriaceaein contrast to members of other phyla, highlighting the particular presence of this feature within theBacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal ofFlavobacteriaceaewith high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains. Conclusions Our study elucidates the functional repertoire of marineFlavobacteriaceaeand highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.