International Journal of Systematic and Evolutionary Microbiology

A novel endophytic actinobacterium, designated strain EGI 650086T, was isolated from the roots of Anabasis elatior (C.A.Mey.) Schischk. collected in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic taxonomic approach. Growth occurred at 15–40 °C, pH 6.0–8.0 and in the presence of 0–6 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence and concatenation of 22 protein marker genes revealed that strain EGI 650086T formed a monophyletic clade within the genus Amycolatopsis and shared the highest sequence similarities with Amycolatopsis nigrescens JCM 14717T (97.1 %) and Amycolatopsis sacchari DSM 44468T (97.0 %). Sequence similarities with type strains of other species of the genus Amycolatopsis were less than 97.0 %. The average nucleotide identity and DNA–DNA hybridization values between strain EGI 650086T and the reference strains were 78.1–79.8 % and 22.1–23.0 %, respectively. The genome of strain EGI 650086T was 10.9 Mb, with a DNA G+C content of 70.1 mol%. The diagnostic diamino acid in the peptidoglycan was meso-diaminopimelic acid. The major whole-cell sugars contained arabinose, galactose, glucose and ribose. The predominant menaquinones were MK-9 (H4) and MK-9 (H2). Major fatty acids were iso-C16 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The polar lipid profile of strain EGI 650086T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids, an unknown glycolipid and an unknown lipid. Polyphasic taxonomic characteristics indicated that strain EGI 650086T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis anabasis sp. nov. is proposed. The type strain is EGI 650086T (=KCTC 49044T=CGMCC 4.7188T).

A novel obligately anaerobic, thermophilic and formate-utilizing bacterium K32T was isolated from Shengli oilfield of China. Cells were straight rods (0.4–0.8 µm × 2.5–8.0 µm), Gram-stain-positive, non-spore-forming and slightly motile. Optimum growth occurred with pH of 7 and 0.5 g l–1 NaCl under temperature of 55–60 °C. Nitrate could be reduced into nitrite, syntrophic formate oxidation to methane and carbon dioxide occurred when co-culturing strain K32T and Methanothermobacter thermautotrophicus ΔH. The main cellular fatty acids were iso-C15 : 0 (24.0 %), anteiso-C15 : 0 (21.7 %), C16 : 0 (12.7 %) and C14 : 0 (10.8 %), and the main polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 46.3 mol%. The 16S rRNA gene sequence of K32T shared ≤90.4 % of sequence similarity to closest type strains of Desulfitibacter alkalitolerans , Calderihabitans maritimus and members of the genus Moorella . Based on the phenotypic, biochemical and genotypic characterization, Zhaonella formicivorans gen. nov., sp. nov. is proposed with K32T (=CCAM 584T =DSM 107278T=CGMCC1.5297T) as the type strain, which is the first representative of Zhaonellaceae fam. nov. In addition, the order Thermoanaerobacterales and family Peptococcaceae were reclassified, and three novel families in the novel order of Moorellales ord. nov. were also proposed.

In prokaryotic taxonomy, a set of criteria is commonly used to delineate species. These criteria are generally based on cohesion at the phylogenetic, phenotypic and genomic levels. One such criterion shown to have promise in the genomic era is average nucleotide identity (ANI), which provides an average measure of similarity across homologous regions shared by a pair of genomes. However, despite the popularity and relative ease of using this metric, ANI has undergone numerous refinements, with variations in genome fragmentation, homologue detection parameters and search algorithms. To test the robustness of a 95–96 % species cut-off range across all the commonly used ANI approaches, seven different methods were used to calculate ANI values for intra- and interspecies datasets representing three classes in the Proteobacteria . As a reference point, these methods were all compared to the widely used blast-based ANI (i.e. ANIb as implemented in JSpecies), and regression analyses were performed to investigate the correlation of these methods to ANIb with more than 130000 individual data points. From these analyses, it was clear that ANI methods did not provide consistent results regarding the conspecificity of isolates. Most of the methods investigated did not correlate perfectly with ANIb, particularly between 90 and 100% identity, which includes the proposed species boundary. There was also a difference in the correlation of methods for the different taxon sets. Our study thus suggests that the specific approach employed needs to be considered when ANI is used to delineate prokaryotic species. We furthermore suggest that one would first need to determine an appropriate cut-off value for a specific taxon set, based on the intraspecific diversity of that group, before conclusions on conspecificity of isolates can be made, and that the resulting species hypotheses be confirmed with analyses based on evolutionary history as part of the polyphasic approach to taxonomy.

A novel actinobacterial strain, designated K81G1T, was isolated from a soil sample collected in Kantulee peat swamp forest, Surat Thani Province, Thailand, and its taxonomic position was determined using a polyphasic approach. Optimal growth of strain K81G1T occurred at 28–30 °C, at pH 5.0–6.0 and without NaCl. Strain K81G1T had cell-wall chemotype IV (meso-diaminopimelic acid as the diagnostic diamino acid, and arabinose and galactose as diagnostic sugars) and phospholipid pattern type II, characteristic of the genus Amycolatopsis . It contained MK-9(H4) as the predominant menaquinone, iso-C16 : 0, C17 : 0 cyclo and C16 : 0 as the major cellular fatty acids, and phospholipids consisting of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids. Based on 16S rRNA gene sequence similarity and phylogenetic analyses, strain K81G1T was most closely related to Amycolatopsis rhizosphaerae TBRC 6029T (97.8 % similarity), Amycolatopsis acidiphila JCM 30562T (97.8 %) and Amycolatopsis bartoniae DSM 45807T (97.6 %). Strain K81G1T exhibited low average nucleotide identity and digital DNA–DNA hybridization values with A. rhizosphaerae TBRC 6029T (76.4 %, 23.0 %), A. acidiphila JCM 30562T (77.9 %, 24.6 %) and A. bartoniae DSM 45807T (77.8 %, 24.3 %). The DNA G+C content of strain K81G1T was 69.7 mol%. Based on data from this polyphasic study, strain K81G1T represents a novel species of the genus Amycolatopsis , for which the name Amycolatopsis acidicola sp. nov. is proposed. The type strain is K81G1T (=TBRC 10047T=NBRC 113896T).

Genome analysis is one of the main criteria for description of new taxa. Availability of genome sequences for all the actinobacteria with a valid nomenclature will, however, require another decade’s works of sequencing. This paper describes the rearrangement of the higher taxonomic ranks of the members of the phylum ‘ Actinobacteria ’, using the phylogeny of 16S rRNA gene sequences and supported by the phylogeny of the available genome sequences. Based on the refined phylogeny of the 16S rRNA gene sequences, we could arrange all the members of the 425 genera of the phylum ‘ Actinobacteria ’ with validly published names currently in use into six classes, 46 orders and 79 families, including 16 new orders and 10 new families. The order Micrococcales Prévot 1940 (Approved Lists 1980) emend. Nouioui et al. 2018 is now split into 11 monophyletic orders: the emended order Micrococcales and ten proposed new orders Aquipuribacterales , Beutenbergiales , Bogoriellales , Brevibacteriales , Cellulomonadales , Demequinales , Dermabacterales , Dermatophilales , Microbacteriales and Ruaniales . Further, the class ‘ Actinobacteria ’ Stackebrandt et al. 1997 emend. Nouioui et al. 2018 was described without any nomenclature type, and therefore the name ‘ Actinobacteria ’ is deemed illegitimate. In accordance to Rule 8 of the International Code of Nomenclature of Prokaryotes, Parker et al. 2019, we proposed the name Actinomycetia which is formed by using the stem of the name Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009, to replace the name ‘ Actinobacteria ’. The nomenclature type of the proposed new class Actinomycetia is the order Actinomycetales Buchanan 1917 (Approved Lists 1980) emend. Zhi et al. 2009.

An obligately anaerobic, Gram-stain-positive and coccus-shaped bacterium, designated strain YH-panp20T, was isolated from pig faeces. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belongs to the family Erysipelotrichaceae , and is most closely related to Catenisphaera adipataccumulans KCTC 15517T (93.5 % sequence similarity), followed by Faecalitalea cylindroides KCTC 5815T (92.2 %), Faecalicoccus acidiformans KCTC 15521T (90.2 %) and Holdemanella biformis KCTC 5969T (89.6 %). Average nucleotide identity values between YH-panp20T and its closest relatives were lower than 71 %. The G+C content of the isolate was 38.4 mol%, and its cell-wall peptidoglycan was found to be of A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C18 : 1 cis 9, C18 : 0 DMA and C16 : 0. The major end-products of glucose fermentation were lactate, acetate and formate. Therefore, based on the phenotypic, phylogenetic and chemotaxonomic properties, a novel genus and species, Absicoccus porci gen. nov., sp. nov., is proposed for isolate YH-panp20T (=KCTC 15747T=JCM 32769T).

A novel Gram-stain-positive, rod shaped and anaerobic bacterium, designated as W6T, was isolated from Shengli oilfield in China. Strain W6T was observed to grow from 20 to 45 °C with pH 6.5–9.0 (optimally at 40 °C and pH of 7.5) and without addition of NaCl. The major cellular fatty acids were iso-C15 : 0 (29.1%), C14 : 0 (27.0%) and C16 : 0 (12.2%), and the main polar lipids were lipids (L) and aminolipids (AL). The DNA G+C content is 42.9 mol%. Based on 16S rRNA gene sequence analysis, strain W6T showed highest similarities to Tissierella creatinini DSM 9508T (94.9%) and Soehngenia saccharolytica DSM 12858T (94.1%). The morphological, physiological, biochemical, phylogenetic and phylogenomic analyses demonstrated strain W6T (CCAM 534T=DSM 28124T=CGMCC 1.5291T) represents a novel species in a new genus, for which the name Gudongella oleilytica gen. nov. sp. nov. is proposed. The family Tissierellaceae is proposed as a new family containing the genera Anaerosalibacter , Gudongella, Keratinibaculum , Soehngenia , Sporanaerobacter , Tepidimicrobium , Tissierella , Urmitella and species Clostridium ultunense based on the phylogenetic and phylogenomic analyses.