Laboratoire de Valorisation et Conservation des Ecosystèmes Arides (LVCEA), Faculté des Sciences de la Nature et de la Vie et Sciences de la Terre, Université de Ghardaia, Ghardaïa, Algeria.
Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure de Kouba, Algiers, Algeria.
PLoS One. 2024 Aug 22;19(8):e0307299. doi: 10.1371/journal.pone.0307299. eCollection 2024.
The classification of Microbispora, a bacterial genus of significant ecological, agricultural, biotechnological, and clinical importance, has traditionally been carried out based on 16S rRNA gene sequences or phenotypic characteristics, which may lead to equivocal conclusions and it is not in line with the current standards. Moreover, some of the recent species descriptions have not been made using whole genome sequences (WGS), or when used, not all the species were included in the analyses. Consequently, some of the taxonomic conclusions drawn are equivocal, and therefore some currently accepted species should be synonymized. In this study, we revised the taxonomy of the genus Microbispora using digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values, and by reconstructing phylogenetic relationships using whole genome sequences. Based on the clear phylogenomic separations and on the sequence divergence values, we propose to elevate Microbispora rosea subsp. rosea and Microbispora rosea subsp. aerata to the species level, and therefore to create Microbispora aerata sp. nov. with JCM 3076T (= DSM 43176T = ATCC 15448T = IFO 14624T = NBRC 14624T = VKM Ac-1507T) as the type strain. Hence, with this proposition, the correct name for Microbispora rosea subsp. rosea is M. rosea. Furthermore, we propose to reclassify M. camponoti as a subspecies within M. bryophytorum. Consequently, we propose the creation of the following two subspecies: Microbispora bryophytorum subsp. bryophytorum subsp. nov. with DSM 46710T (= CGMCC 4.7138T = NEAU TX2-2T) as the type strain, and Microbispora bryophytorum subsp. camponoti subsp. nov., comb. nov. with DSM 2C-HV3T (= DSM 100527T = CGMCC 4.7281T) as the type strain. In addition, we propose to reinstate M. amethystogenes as an independent species and not as a M. rosea synonym, and reclassify "M. cellulosiformans" as a subspecies within M. amethystogenes. Hence, we propose the creation of the following two subspecies: Microbispora amethystogenes subsp. amethystogenes subsp. nov. with NBRC 101907T (= DSM 43164T = JCM 3021T = NRRL B-2637T) as the type strain, and Microbispora amethystogenes subsp. cellulosiformans subsp. nov., comb. nov. with Gxj-6T (= DSM 109712T = CGMCC 4.7605T) as the type strain. Lastly, we propose M. fusca NEAU-HEGS1-5T and "M. tritici" MT50T as later homotypic synonyms of M. triticiradicis NEAU-HRDPA2-9T.
微杆菌属（Microbispora）是一个具有重要生态、农业、生物技术和临床意义的细菌属，其分类传统上基于 16S rRNA 基因序列或表型特征进行，但这可能导致模棱两可的结论，不符合当前的标准。此外，最近的一些物种描述并未使用全基因组序列（WGS）进行，或者在使用时，并非所有物种都包含在分析中。因此，得出的一些分类结论存在模棱两可的情况，因此一些当前被接受的物种应该被同义化。在本研究中，我们使用数字 DNA-DNA 杂交（dDDH）和平均核苷酸同一性（ANI）值，以及通过使用全基因组序列重建系统发育关系，对微杆菌属的分类进行了修订。基于明显的系统发育分离和序列分歧值，我们建议将玫瑰色微杆菌亚种玫瑰色亚种和玫瑰色微杆菌亚种 aerata 提升为种水平，并因此创建微杆菌 aerata sp. nov.，以 JCM 3076T（=DSM 43176T=ATCC 15448T=IFO 14624T=NBRC 14624T=VKM Ac-1507T）为模式菌株。因此，根据这一提议，玫瑰色微杆菌亚种玫瑰色的正确名称为 M. rosea。此外，我们建议将 M. camponoti 重新分类为 M. bryophytorum 的一个亚种。因此，我们提出创建以下两个亚种：微杆菌 bryophytorum 亚种 bryophytorum 亚种 nov.，以 DSM 46710T（=CGMCC 4.7138T=NEAU TX2-2T）为模式菌株，和微杆菌 bryophytorum 亚种 camponoti 亚种 nov.，组合新种，以 DSM 2C-HV3T（=DSM 100527T=CGMCC 4.7281T）为模式菌株。此外，我们建议恢复 M. amethystogenes 为独立物种，而不是 M. rosea 的同义词，并将“M. cellulosiformans”重新分类为 M. amethystogenes 的一个亚种。因此，我们提出创建以下两个亚种：微杆菌 amethystogenes 亚种 amethystogenes 亚种 nov.，以 NBRC 101907T（=DSM 43164T=JCM 3021T=NRRL B-2637T）为模式菌株，和微杆菌 amethystogenes 亚种 cellulosiformans 亚种 nov.，组合新种，以 Gxj-6T（=DSM 109712T=CGMCC 4.7605T）为模式菌株。最后，我们提议将 M. fusca NEAU-HEGS1-5T 和“M. tritici”MT50T 作为 M. triticiradicis NEAU-HRDPA2-9T 的后同型同义词。
