Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

Abstract

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species ( Chryseobacterium arachidiradicis , Chryseobacterium bovis , Chryseobacterium caeni , Chryseobacterium hispanicum , Chryseobacterium hominis , Chryseobacterium hungaricum , Chryseobacterium molle , Chryseobacterium pallidum and Chryseobacterium zeae ) to the genus Epilithonimonas and eleven ( Chryseobacterium anthropi , Chryseobacterium antarcticum , Chryseobacterium carnis , Chryseobacterium chaponense , Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum , Chryseobacterium palustre , Chryseobacterium solincola , Chryseobacterium treverense and Chryseobacterium yonginense ) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.

Kangsaoukella pontilimi gen. nov., sp. nov., a new member of the family Rhodobacteraceae isolated from a tidal mudflat

“…The calculated AAI, ANI and dDDH values between the genome sequences of strain GH1-50 T and all the type strains compared in were <70.0, <84.1 and <20.5 %, respectively. Although there is no generalized boundary in prokaryotic genus delineation, a threshold (76 %) for the AAI value was suggested for delineation of bacteria genera [27, 28]. The indices for overall genomic similarity calculated in this study indicated that strain GH1-50 T could be a member of a new genus in the family Rhodobacteraceae .…”

Pareuzebyella sediminis gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae, isolated from a tidal flat sediment

“…These values were below the threshold values of recommended species delineation of ANI at 95–96% [19] and AAI at 95 % [20], indicating that strain S2-4-21 T and MT2-5-19 could be considered to be a novel species. AAI values were also below the cutoff (74–76%) for a novel genus delineation, which were recommended in analysis of Chryseobacterium and its close relatives within the family Weeksellaceae [21]. The genomic relatedness of strains S2-4-21 T and MT2-5-19 in comparison with close relatives together with phylogenetic reconstruction supported that they were distinctly separated from Euzebyella and Pseudozobellia , indicating that strain S2-4-21 T could be considered as a novel species of a novel genus ().…”

Antrihabitans stalactiti gen. nov., sp. nov., a new member of the family Nocardiaceae isolated from a cave

“…On the other hand, the ANI and dDDH values between strain YC2-7 T and members of the family Nocardiaceae were <73.2 and <19.2 %, respectively. These values obtained for the overall genome similarities revealed that the isolates could be assigned to a member of a new genus in the family Nocardiaceae [28, 29].…”