G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi 0160, Georgia.
Richard Lugar Center for Public Health Research, National Center for Disease Control and Public Health, Tbilisi 0198, Georgia.
Mar Drugs. 2020 Nov 14;18(11):558. doi: 10.3390/md18110558.
Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage-host interactions; however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecosystems in this regard. This study was aimed at to fill this gap by analyzing microbial diversity and bacteriophage-host interactions in the waters of Eastern Black Sea using a metagenomic approach. To this end, prokaryotic and viral metagenomic DNA from two sampling sites, Poti and Gonio, were sequenced on the Illumina Miseq platform and taxonomic and functional profiles of the metagenomes were obtained using various bioinformatics tools. Our metagenomics analyses allowed us to identify the microbial communities, with , , , and found to be the most dominant bacterial phyla and and phages found to be the most dominant viral groups in the Black Sea. As minor groups, putative phages specific to human pathogens were identified in the metagenomes. We also characterized interactions between the phages and prokaryotic communities by determining clustered regularly interspaced short palindromic repeats (CRISPR), prophage-like sequences, and integrase/excisionase sequences in the metagenomes, along with identification of putative horizontally transferred genes in the viral contigs. In addition, in the viral contig sequences related to peptidoglycan lytic activity were identified as well. This is the first study on phage and prokaryote diversity and their interactions in the Eastern coastal area of the Black Sea using a metagenomic approach.
病毒在海洋生态系统中拥有最丰富的数量和最高的遗传多样性。病毒与其宿主之间的相互作用是海洋生态学的热点之一。除了在各种生态系统中具有重要作用外，病毒（尤其是噬菌体及其基因库）对于开发具有高创新价值的新型基因产物也具有巨大的兴趣。在不同的生态系统中进行了各种研究，以了解微生物多样性和噬菌体-宿主相互作用；然而，黑海，特别是其东部沿海地区，在这方面仍然是研究最少的生态系统之一。本研究旨在通过使用宏基因组学方法分析黑海东部水域的微生物多样性和噬菌体-宿主相互作用来填补这一空白。为此，在 Illumina Miseq 平台上对来自波季和格尼奥两个采样点的原核生物和病毒宏基因组 DNA 进行了测序，并使用各种生物信息学工具获得了宏基因组的分类和功能图谱。我们的宏基因组学分析使我们能够识别微生物群落，其中、、、和被发现是黑海最占优势的细菌门，而和噬菌体被发现是最占优势的病毒组。作为次要群体，在宏基因组中鉴定出了针对人类病原体的假定噬菌体。我们还通过确定宏基因组中的聚类规则间隔短回文重复序列 (CRISPR)、类噬菌体序列和整合酶/切除酶序列，以及鉴定病毒基因座中的假定水平转移基因，来表征噬菌体与原核生物群落之间的相互作用。此外，还在与肽聚糖裂解活性相关的病毒基因座序列中鉴定出了。这是首次使用宏基因组学方法对黑海东部沿海地区的噬菌体和原核生物多样性及其相互作用进行的研究。
