Porter Hailee I, Alas Imraan, Krull Nyssa K, Braun Doug R, Rajski Scott R, Murphy Brian T, Bugni Tim S
School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA.
Microorganisms. 2025 Jul 4;13(7):1576. doi: 10.3390/microorganisms13071576.
The purpose of this study was to investigate the taxonomic and phylogenomic placement of the proposed genus '' within the context of other marine genera using a dual-omics approach. Initially, we isolated bacteria from marine tunicates, squirts, and sponges, which were morphologically similar to an emerging genus (identified as '_E' by the GTDB-tk2 database using whole genome sequence data) by colony shape, size, and clustering pattern, but only found five strains in our dataset belonging to this distinction. Due to the minimally explored nature of this genus, we sought to identify more bacterial strains with similar morphology to '_E' by whole genome sequencing (WGS). Within our collection, we noted 35 strains that met this criterion and extracted genomic information to perform WGS on these strains. With this information, we studied taxonomic and phylogenomic relationships among these organisms. Using the data gathered from WGS, we were able to identify an additional five strains labeled by the GTDB-tk2 database as '_E', as well as construct phylogenomic trees to examine the evolutionary relationships between these strains. ANI values were calculated between strains from our dataset and type strains of and as well as against an outgroup strain. No type strains are available for ''. Using MALDI-TOF MS, we positively identified '', which was supported by the phylogenomic tree showing '_E' ('') in a distinct clade from and . Additionally, we discovered gene cluster families (GCFs) in alignment with genera, as well as a large representation of biosynthetic gene clusters (BGCs) coming from the '' strains. These findings suggest significant potential to discover novel chemistry from '', adding to the importance of investigating this new genus of bacteria.
本研究的目的是使用双组学方法，在其他海洋属的背景下研究拟议的属“”的分类学和系统基因组学定位。最初，我们从海洋被囊动物、海鞘和海绵中分离细菌，这些细菌通过菌落形状、大小和聚类模式在形态上与一个新兴属（使用全基因组序列数据，GTDB-tk2数据库将其鉴定为“E”）相似，但在我们的数据集中仅发现五株属于该分类的菌株。由于该属的研究程度极低，我们试图通过全基因组测序（WGS）来鉴定更多形态与“E”相似的细菌菌株。在我们的样本中，我们注意到35株符合该标准的菌株，并提取了基因组信息以对这些菌株进行WGS。利用这些信息，我们研究了这些生物体之间的分类学和系统基因组学关系。使用从WGS收集的数据，我们能够鉴定出另外五株被GTDB-tk2数据库标记为“E”的菌株，并构建系统基因组树以检查这些菌株之间的进化关系。计算了我们数据集中的菌株与_和_的模式菌株以及一个外群菌株之间的ANI值。“”没有模式菌株。使用基质辅助激光解吸电离飞行时间质谱（MALDI-TOF MS），我们明确鉴定出了“”，系统基因组树支持这一结果，该树显示“E”（“”）在一个与_和_不同的分支中。此外，我们发现了与各属一致的基因簇家族（GCF），以及来自“”菌株的大量生物合成基因簇（BGC）。这些发现表明从“”中发现新化学物质具有巨大潜力，这增加了研究这一新细菌属的重要性。
