Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions |
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| Affiliation: | 1. School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, People’s Republic of China;2. School of Agricultural Engineering, Jiangsu University, Zhenjiang 212013, People’s Republic of China;1. Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia;2. Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia;1. LSTM, Univ Montpellier, CIRAD, INRAE, IRD, Institut Agro Montpellier, Montpellier, France;2. Laboratory of Microbiology, Dept. Biochemistry and Microbiology, Ghent University, Ghent, Belgium;3. Montpellier GenomiX, Montpellier, 141 rue de la Cardonille, 34 094 Montpellier Cedex, France;4. Faculty of Agronomy II, Damascus University, and Faculty of Medicine, Syrian Private University, Damascus, Syria;1. Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain;2. Grup Microbiologia del Medi Ambient, Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain;1. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal;2. CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal;3. Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg;4. The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Luxemburg;5. Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal |
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| Abstract: | Many genera closest to the family Comamonadaceae have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-Comamonadaceae (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S rRNA gene and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family Comamonadaceae, thereby proposing the CTC group as a novel family, Sphaerotilaceae fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed Sphaerotilaceae-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family Sphaerotilaceae and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors. |
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| Keywords: | Taxonomic classification Phylogenomic analysis Genus-defined threshold Taxonomic revision |
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