Pedobacter schmidteae sp. nov., a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea

Luis Johnson Kangale (1) , Didier Raoult (2, 1) , Eric Ghigo (1) , Pierre-Edouard Fournier (3, 1)

1 IHU Marseille - Institut Hospitalier Universitaire Méditerranée Infection
2 MEPHI - Microbes évolution phylogénie et infections
3 VITROME - Vecteurs - Infections tropicales et méditerranéennes

Pedobacter schmidteae sp. nov. strain EGT (Collection de Souches de l’Unité des Rickettsie CSUR P6417 = Colección Española de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp–long with a G + C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter schmidteae sp. nov.

Mots clés: Bacteria; Bacterial genomics; Microbiology

Domaines: Bactériologie; Cardiologie et système cardiovasculaire; Maladies émergentes; Maladies infectieuses; Parasitologie; Virologie

Luis Johnson Kangale, Didier Raoult, Eric Ghigo, Pierre-Edouard Fournier. Pedobacter schmidteae sp. nov., a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea. Scientific Reports, 2020, 10 (1), ⟨10.1038/s41598-020-62985-x⟩. ⟨hal-02543781⟩