Pelagihabitans pacificus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a deep-sea seamount

The Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, strictly aerobic, rod-shaped bacterial strain, designated TP-CH-4^T, was isolated from a seamount near the Yap Trench in the tropical western Pacific. The optimal growth conditions were determined to be at pH 7-8, 25-30 °C and in the presence of 2 % (w/v) NaCl. The major respiratory quinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and three unidentified polar lipids. The predominant cellular fatty acids were iso-C_15 : 0 and summed feature 1 (composed of C_13 : 03-OH and/or iso-C_15 : 1H). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain TP-CH-4^T was a member of the family Flavobacteriaceae and formed a distinct lineage. Strain TP-CH-4^T displayed highest sequence similarities to Pseudozobellia thermophila KMM 3531^T (95.1 %) and Flagellimonas flava A11^T (93.9 %). Genome sequencing revealed the strain TP-CH-4^T has a genome size of 4.5 Mbp and a G+C content of 44.5 mol%. Collectively, based on phenotypic, chemotaxonomic, phylogenetic and genomic evidence, strain TP-CH-4^T represents a novel species of a novel genus of the family Flavobacteriaceae, for which the name Pelagihabitans pacificus gen. nov., sp. nov. is proposed. The type strain of Pelagihabitans pacificus is TP-CH-4^T (=CGMCC 1.17120^T=KCTC 72434^T).

Wocania indica gen. nov., sp. nov., isolated from deep sea hydrothermal sulfide in the northwest Indian Ocean, and proposal to reclassify Flaviramulus ichthyoenteri as Wocania ichthyoenteri comb. nov

A novel Gram-stain-negative, non-motile, strictly aerobic, rod-shaped bacterium was isolated from deep-sea hydrothermal sulfide in the northwest Indian Ocean Ridge and designated as strain IOP_32^T. Strain IOP_32^T could grow at 4-40 °C (optimum, 37 °C), pH 5-9 (optimum, pH 7-8) and salinity of 0-12 % NaCl (w/v; optimum, 2-3 %). The 16S rRNA gene sequence of strain IOP_32^T is most similar to Bizionia fulviae EM7^T, Bizionia berychis RA3-3-1^T, Bizionia paragorgiae KMM 6029^T and Oceanihabitans sediminis S9_10^T with 95.5-95.3 % similarity. The phylogenomic analysis indicated that strain IOP_32^T forms a distinct lineage with Flaviramulus ichthyoenteri Th78^T within the family Flavobacteriaceae. The average nucleotide identity, average amino acid identity and percentage of conserved protein values between strain IOP_32^T and the type strains of close genera were 72.3-78.5 %, 67.4-76.9 % and 56.3-61.6 %, respectively. The major cellular fatty acid was anteiso-C_15 : 0. The respiratory quinone was MK-6. The polar lipids were mainly composed of phosphatidylethanolamine, an unidentified aminophospholipid and five unidentified polar lipids. Strain IOP_32^T is significantly different from related genera, which is reflected by the wide adaptability to temperature and salinity levels, the composition of phospholipids and fatty acids, and the results of phylogenetic analyses. The phenotypic properties and phylogenetic data suggest that the lineage represents a novel genus and species within the family Flavobacteriaceae, for which the name Wocania indica gen. sp. nov. is proposed, with the type strain IOP_32^T (=MCCC 1A14017 ^T=KCTC 62660 ^T). We also propose the reclassification of Flaviramulus ichthyoenteri as Wocania ichthyoenteri comb. nov. (Th78^T=DSM 26285^T=JCM 18634^T=KCTC 32142^T).

Pontimicrobium aquaticum gen. nov., sp. nov., a bacterium in the family Flavobacteriaceae isolated from seawater

A Gram-stain-negative, yellow-pigmented, non-spore-forming, non-motile, rod-shaped, catalase-positive, strictly aerobic bacterial strain, designated CAU 1491^T, was isolated from seawater and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1491^T grew optimally at 30 °C, pH 7.5 and in 2.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1491^T showed that it formed a distinct lineage within the family Flavobacteriaceae as a separate deep branch, with 97.0 % or lower sequence similarity to representatives of the genera Lacinutrix, Gaetbulibacter and Aquibacter. The major cellular fatty acids of strain CAU 1491^T were iso-C_15 : 0, iso-C_15 : 1 G, iso-C_17 : 0 3-OH and summed feature 3. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylserine, phosphatidylethanolamine and an unidentified phospholipid. The strain contained MK-6 as the sole respiratory quinone. Genome sequencing revealed that strain CAU 1491^T has a genome size of 3.13 Mbp and a G+C content of 32.4 mol%. On the basis of the phenotypic, chemotaxonomic and genomic data, strain CAU 1491^T represents a new genus and species in the family Flavobacteriaceae for which the name Pontimicrobium aquaticum gen. nov., sp. nov. is proposed. The type strain of Pontimicrobium aquaticum is CAU 1491^T (=KCTC 72003^T=NBRC 113695^T).

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.