Burkholderia sensu lato is a collection of closely related genera within the family Burkholderiaceae that includes species of environmental, industrial, biotechnological, and clinical importance. Multiple species within the complex are the source of diverse specialized metabolites, many of which have been identified through genome mining of their biosynthetic gene clusters (BGCs). However, the full, true genomic diversity of these species and genera, and their biosynthetic capacity have not been investigated. This study sought to cluster and classify over 4000 Burkholderia sensu lato genome assemblies into distinct genomic taxa representing named and uncharacterized species. We delineated 235 species groups by average nucleotide identity analyses that formed seven distinct phylogenomic clades, representing the genera of Burkholderia sensu lato: Burkholderia, Paraburkholderia, Trinickia, Caballeronia, Mycetohabitans, Robbsia, and Pararobbisa. A total of 137 genomic taxa aligned with named species possessing a sequenced type strain, while 93 uncharacterized species groups were demarcated. The 95% ANI threshold proved capable of delineating most genomic species and was only increased to resolve several closely related species. These analyses enabled the assessment of species classifications of over 4000 genomes, and the correction of over 400 genome taxonomic assignments in public databases into existing and uncharacterized genomic species groups. These species groups were genome mined for BGCs, their specialized metabolite capacity calculated per species and genus, and the number of distinct BGCs per species estimated through kmer-based de-replication. Mycetohabitans species dedicated a larger proportion of their relatively small genomes to specialized metabolite biosynthesis, while Burkholderia species harbored more BGCs on average per genome and possessed the most distinct BGCs per species compared to the remaining genera. Exploring the hidden genomic diversity of this important multi-genus complex contributes to our understanding of their taxonomy and evolutionary relationships, and supports future efforts toward natural product discovery.

伯克霍尔德菌sensu lato 是伯克霍尔德氏菌科中密切相关属的集合，包括具有环境、工业、生物技术和临床重要性的物种。该复合体中的多个物种是多种特殊代谢物的来源，其中许多已通过对其生物合成基因簇 (BGC) 的基因组挖掘进行鉴定。然而，尚未研究这些物种和属的完整、真实的基因组多样性及其生物合成能力。本研究试图对 4000 多个伯克霍尔德菌sensu lato 基因组组装成不同的基因组分类群，代表命名和未表征的物种。我们通过平均核苷酸同一性分析划定了 235 个物种组，这些分析形成了七个不同的系统发育进化枝，代表了伯克霍尔德菌 感觉： 伯克霍尔德菌, 帕拉伯克霍尔德菌, 特里尼基亚, 卡巴莱罗尼亚, 栖菌者, 罗布夏， 和 帕罗比萨。共有 137 个基因组分类群与具有已测序类型菌株的命名物种对齐，同时划定了 93 个未表征的物种组。95% 的 ANI 阈值证明能够描绘大多数基因组物种，并且仅用于分辨几个密切相关的物种。这些分析能够评估 4000 多个基因组的物种分类，并将公共数据库中的 400 多个基因组分类分配更正为现有和未表征的基因组物种组。这些物种组是为 BGC 挖掘的基因组，按物种和属计算它们的专门代谢物容量，以及通过基于 kmer 的去复制估计每个物种的不同 BGC 的数量。栖菌者 物种将较大比例的相对较小的基因组用于专门的代谢物生物合成，而 伯克霍尔德菌与其余属相比，物种平均每个基因组具有更多的 BGC，并且每个物种拥有最独特的 BGC。探索这个重要的多属复合体隐藏的基因组多样性有助于我们了解它们的分类和进化关系，并支持未来对天然产物发现的努力。