Shiella aurantiaca gen. nov., sp. nov., a novel bacterium isolated from activated sludge, and proposal of Shiellaceae fam. nov

A novel Gram-stain-negative, long rod-shaped, aerobic, non-motile, non-spore-forming and orange-pigmented bacterium, designated LB-30T, was isolated from activated sludge. Growth was observed at 15-40 °C (optimum 30 °C), pH 6.0-9.0 (optimum 7.0) and salinities of 0-3.0 % (w/v; optimum 2.0 %). LB-30T showed less than 89.9 % sequence similarities to the recognized taxa of the order Cytophagales. The results of phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic tree indicated that LB-30T formed a distinct lineage within the order Cytophagales. The average amino acid identity (AAI) values between LB-30T and members of the related families Cyclobacteriaceae, Fulvivirgaceae, Roseivirgaceae, Reichenbachiellaceae, Cesiribacteraceae, Cytophagaceae and Hymenobacteraceae in the order Cytophagales were 50.5-54.6 %. The sole respiratory quinone of LB-31T was menaquinone 7 (MK-7). The major polar lipids were phosphatidylethanolamine, aminolipid and four unidentified lipids. The major fatty acids were iso-C15 : 0, iso-C15 : 1G and iso-C17 : 0 3-OH. The DNA G+C content was 43.8 mol%, calculated from the genome sequence. On the basis of differences in the phenotypic, physiological and biochemical characteristics, and distinct phylogenetic relationships, strain LB-30T is proposed to represent a novel species in a novel genus for which the name Shiella aurantiaca gen. nov., sp. nov is proposed, within a novel family Shiellaceae fam. nov. of the order Cytophagales. The type strain is LB-30T (=GDMCC 1.3629T= KCTC 92689T).

Proposal to reclassify Aquiflexum aquatile into a novel genus as Cognataquiflexum aquatile gen. nov., comb. nov., and description of Cognataquiflexum nitidum sp. nov. and Cognataquiflexum rubidum sp. nov., isolated from freshwater lakes on the Tibetan Plateau

Thousands of lakes harbouring different characteristics (pH, salinity, temperature) are located on the Tibetan Plateau, and the mining of microbial resources inhabited in these lakes has great value. Two Gram-stain-negative, aerobic, rod-shaped, non-motile strains (LQ15W^T and AIY15W^T) were isolated from freshwater lakes on the Tibetan Plateau. Comparisons based on the 16S rRNA gene sequences showed that both strains LQ15W^T and AIY15W^T share 16S rRNA gene sequence similarities 98.4 % with Aquiflexum aquatile Z0201^T, but only about 95.0 % with Aquiflexum balticum DSM 16537^T. The 16S rRNA gene sequence similarity between strains LQ15W^T and AIY15W^T was 98.9 %. The phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains LQ15W^T and AIY15W^T take A. aquatile Z0201^T as their closest neighbour and these three strains form a tight cluster. In the phylogenomic tree, the genus Aquiflexum was splited into two clusters by Mariniradius saccharolyticus. Strains LQ15W^T, AIY15W^T and A. aquatile Z0201^T still formed a close cluster, and A. balticum DSM 16537^T and Aquiflexum lacus CUG 91378^T formed another cluster. The calculated OrthoANIu, average amino acid identity and digital DNA-DNA hybridization values among strains LQ15W^T, AIY15W^T, A. aquatile Z0201^T, A. balticum DSM 16537^T and A. lacus CUG 91378^T were less than 91.0, 92.9 and 42.1 %, respectively. The major respiratory quinones of both strains LQ15W^T and AIY15W^T were MK-7 (32 %) and MK-8 (68 %), and their major fatty acids were iso-C_15 : 0, C_18 : 1  ω9c, summed feature 3 and summed feature 9. The predominant polar lipids of both strains were phosphatidylethanolamine, unidentified aminophospholipids, unidentified phospholipids and lipids. Strain AIY15W^T also contained phosphatidylglycerol and unidentified glycolipid. Considering the distinct phylogenetic relationships and chemotaxonomic characteristics between strains A. aquatile Z0201^T and A. balticum DSM 16537^T, it is proposed to reclassify A. aquatile into a novel genus Cognataquiflexum gen. nov. as Cognataquiflexum aquatile comb. nov., and strains LQ15W^T and AIY15W^T should represent two independent novel species of the genus Cognataquiflexum, for which the names Cognataquiflexum nitidum sp. nov. (type strain: LQ15W^T=CICC 24711^T=JCM 34222^T) and Cognataquiflexum rubidum sp. nov. (type strain: AIY15W^T=CICC 24708^T=JCM 34612^T) are proposed.

Penaeicolahalotolerans gen. nov., sp. nov., a novel bacterium of the family Cyclobacteriaceae isolated from a shrimp pond

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium (designated as LMIT005^T) was isolated from shrimp ponds in Shantou, China. The new isolate was characterized taxonomically using a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain LMIT005^T was found to be affiliated with the family Cyclobacteriaceae of the order Cytophagales while appearing as a distinct lineage. The 16S rRNA gene sequence similarity between strain LMIT005^T and Algoriphagus yeomjeoni KCTC 12309^T, the closest type strain in the family, was 91.3 %. Strain LMIT005^T grew optimally at 25 °C, pH 7 and in the presence of 2.0 % (w/v) NaCl. The DNA G+C content (data from genome sequence) was 40.5 mol%. Compared with reference strain A. yeomjeoni KCTC 12309^T, the average nucleotide identity (ANI) of LMIT005^T was 70 %. The sole respiratory quinone of LMIT005^T was menaquinone (MK-7), and the major fatty acids were summed feature 3 (C_16 : 1 ω6c / C_16 : 1 ω7c). The polar lipids of strain LMIT005^T were mainly composed of phosphatidylethanolamine, phosphatidylcholine, two unidentified amino lipids, two unidentified lipids, one unidentified glycolipid and one unidentified phospholipid. The draft genome of strain LMIT005^T comprised 3 089 781 bp (3.09 Mb) nucleotides and 2773 genes. Antimicrobial resistant-related genes (blal, mexA, and mexb) were annotated in the genome of strain LMIT005^T, which indicated that it might be able to resist β-lactam antibiotics. This was further verified by antimicrobial resistant test. Given its distinct genomic, morphological, and physiological differences from previously described type strains, strain LMIT005^T is proposed as a representative of a novel genus of the family Cyclobacteriaceae, with the name Penaeicola halotolerans gen. nov., sp. nov. The type strain is LMIT005^T (=KCTC 82616^T=CICC 25047^T).

Pararhodonellum marinum gen. nov., sp. nov., isolated from deep-sea sediment

A Gram-stain-negative, non-motile bacterial strain, designated SW124^T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. SW124^T was aerobic and catalase-positive. The strain grew at 4-40 °C (optimum, 30 °C), at pH 5.0-8.6 (optimum, pH 7.0) and in the presence of 0.5-9.5 % (w/v) NaCl (optimum, 3.0%). The results of comparative analyses of the 16S rRNA gene sequence indicated that SW124^T was grouped in the vicinity of the genus Rhodonellum in the family Cyclobacteriaceae. The quinone system contained menaquinone MK-7. The predominant cellular fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c). SW124^T contained phosphatidylethanolamine (PE) as the major polar lipid. The genomic DNA G+C content of SW124^T was 41.7 mol%. On the basis of its phenotypic characteristics and phylogenetic data, we propose that strain SW124^T (=CGMCC 1.16171^T=KCTC 82235^T) represents a novel species of a novel genus, with the name Pararhodonellum marinum gen. nov., sp. nov.

Arthrospiribacter ruber gen. nov., sp. nov., a novel bacterium isolated from Arthrospira cultures

Polyphasic analysis of ten isolates of the red-pigmented bacteria isolated from ten Arthrospira cultures originating from different parts of the world is described. The 16S rRNA analysis showed <95 % identity with the known bacteria on public databases, therefore, additional analyses of fatty acids profiles, MALDI-TOF/MS, genome sequencing of the chosen isolate and following phylogenomic analyses were performed. Gram-stain-negative, strictly aerobic rods were positive for catalase, negative for oxidase, proteolytic and urease activity. Major fatty acids were 15 : 0 iso, 17:0 iso 3 OH and 17:1 iso w9c/16:0 10-methyl. The whole phylogenomic analyses revealed that the genomic sequence of newly isolated strain DPMB0001 was most closely related to members of Cyclobacteriaceae family and clearly indicated distinctiveness of newly isolated bacteria. The average nucleotide identity and in silico DNA-DNA hybridisation values were calculated between representative of the novel strains DPMB0001 and its phylogenetically closest species, Indibacter alkaliphilus CCUG57479 (LW1)^T (ANI 69.2 % is DDH 17.2 %) and Mariniradius saccharolyticus AK6^T (ANI 80.02 % isDDH 26.1 %), and were significantly below the established cut-off <94 % (ANI) and <70 % (isDDH) for species and genus delineation. The obtained results showed that the analysed isolates represent novel genus and species, for which names Arthrospiribacter gen nov. and Arthrospiribacter ruber sp. nov. (type strain DPMB0001=LMG 31078=PCM 3008) is proposed.

Pleomorphovibrio marinus gen. nov., sp. nov., isolated from deep-sea sediment

A Gram-stain-negative, non-motile bacterial strain, designated SW125^T, was isolated from a deep-sea vsediment sample collected from the Indian Ocean. Cells were aerobic, catalase-positive and oxidase-positive. The strain grew at 4-42 °C (optimum, 30 °C), at pH 5.0-10.0 (optimum, pH 7.0-7.6) and in the presence of 0.5-9.0 % (w/v) NaCl (optimum, 2.0-3.0 %). Comparative analyses of the 16S rRNA gene sequence showed that strain SW125^T was grouped in the vicinity of the genus Negadavirga with the highest sequence similarity of 91.6 % to the type strain of Negadavirga shengliensis. The quinone system contained menaquinone MK-7 as the predominant component. The predominant cellular fatty acids of strain SW125^T were iso-C_15 : 0, iso-C_17 : 0 3-OH and summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c). Strain SW125^T contained phosphatidylethanolamine as the major polar lipid. The genomic DNA G+C content of strain SW125^T was 43.2 mol%. On the basis of its phenotypic characteristics and phylogenetic data, strain SW125^T represents a novel species of a new genus, for which the name Pleomorphovibrio marinus gen. nov., sp. nov. is proposed. The type strain is SW125^T (=CGMCC 1.16172^T=DSM 107180^T=KCTC 62653^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.