Puribacter membranae gen. nov., sp. nov., isolated from a biofilm of a membrane bioreactor (MBR) treating sewage

A Gram-stain-negative, non-motile, aerobic, yellow, convex, rod-shaped mesophilic bacterial strain, designated strain D33T, was isolated from rhizosphere soil of ancient mulberry in Dezhou city, Shandong province, PR China. The strain grew at 8-37 °C (optimum, 30 °C), pH 4-9 (optimum, pH 7) and growth occurred at 0.5-5.5 % (w/v) NaCl (optimally at 1 %). The results of the phylogenetic analyses of 16S rRNA gene and whole genome sequences indicated that D33T was closely related to members of the genus Flavobacterium and had the highest 16S rRNA gene sequence similarity with 'Flavobacterium agri' KACC 19300 (95.4 %), Flavobacterium ichthyis NST-5T (94.6 %), Flavobacterium ahnfeltiae KCTC 32467T (93.6 %) and Flavobacterium longum JCM 19141T (93.6 %). The genome size of D33T was 3.8 Mb and the DNA G+C content was 48.0 mol%. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and average amino acid identity (AAI) values among D33T and reference strains were lower than the threshold values for species delineation. The only respiratory quinone of D33T was menaquinone 6 (MK-6). The predominant fatty acids (>5 %) were C15:0, C16 : 0, C18 : 0, iso-C15:0, iso-C17 : 0 3-OH, anteiso-C15 : 0 and summed feature 9 . The polar lipid profile contained phosphatidylethanolamine, two unidentified aminophospholipids, three unidentified aminolipids and two unidentified lipids. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that D33T is a representative of a novel species of the genus Flavobacterium, for which the name Flavobacterium selenitireducens sp. nov. is proposed. The type strain is D33T (=GDMCC 1.1946T=KACC 22131T).

Microbial taxonomy and nomenclature have been challenged by methodological advances in high-throughput sequencing and high-performance computing. While taxonomy appears to adapt rapidly and has benefited enormously from the availability of whole-genome sequences, nomenclature still struggles to embrace these changes. Here, we present two independent initiatives that have resulted from the transitions of taxonomic practices in microbiology from a phenotypic and single gene-driven framework to a genome-based driven framework. The first initiative, the Genome Taxonomy Database (GTDB), was developed to address the needs of microbial taxonomists to classify rapidly accumulating genome sequences from both cultured and uncultured microorganisms. Availability of growing numbers of metagenome-assembled genomes (MAGs) and single amplified genomes (SAGs), combined with the genomes from cultured species, created a perfect opportunity for building a consensus classification based on an evolutionary framework. This has been realised in the GTDB, a knowledgebase that provides phylogenetically consistent and rank-normalised taxonomies for bacterial and archaeal genomes. A distinctive feature of GTDB is a complete classification of genomes from species to domain using an automated approach combining average nucleotide identity (ANI) and relative evolutionary divergence (RED), followed by manual curation. GTDB has become an essential taxonomic resource for microbiologists worldwide, attracting ~3,500 users per month. GTDB mainly relies on two public databases, the National Center for Biotechnology Information (NCBI) Assembly database to which GTDB releases are indexed and the List of Prokaryotic names with Standing in Nomenclature (LPSN), as the primary nomenclatural reference. The database operates according to the FAIR (Findable, Accessible, Interoperable, Reusable) data principles and incorporates its own internal (e.g., standards for delineating taxa) as well as external standards. The latter are often directly adopted from the NCBI since it is used as a primary source of genomes as well as metadata. Examples of such standards include Darwin Core data standards from Biodiversity Information Standards (TDWG), Minimum Information (MI) about any (x) Sequence (MIxS) and MISAG and MIMAG standards (Bowers et al. 2017) from the Genomic Standards Consortium. GTDB is used by many third-party resources and provides direct links to external public resources used for curation and validation of taxonomies. Importantly, GTDB contributes to the further generation of knowledge by enabling users to classify their own genomes within the GTDB taxonomic framework using our open-source GTDB-Tk tool. To our knowledge, GTDB is the only database that provides a comprehensive systematic de novo taxonomy for prokaryotes, which serves a multitude of purposes to its global users. The second initiative, the Code of Nomenclature of Prokaryotes Described from Sequence Data or SeqCode, was developed in response to the need for formal naming of uncultured microbial diversity. This need has become even more evident with the establishment of the GTDB taxonomy, which highlighted many issues with nomenclature of uncultured taxa at scale. These include the absence of nomenclatural types, proposed higher taxon names without named children, and the lack of priority for Candidatus names (a prefix indicating a provisional status for the names of organisms falling outside the existing Prokaryotic Code). All these issues arise from one core issue: the absence of regulations for naming uncultured taxa because the International Code of Nomenclature of Prokaryotes (ICNP; Oren et al. 2023) only applies to microorganisms able to be obtained in pure culture. To solve this problem and ultimately to be able to express taxonomic affiliations of uncultured taxa in a regulated manner, genome sequences are proposed to serve as nomenclatural types under the SeqCode. This new code has many common aspects with the ICNP and recognises names that are validly published under the ICNP. It operates via an online Registry that allows registration and validation of names following one of two paths: new names are registered and reviewed prior to publication and validated upon the notification about effective publication, or existing names such as names of Candidatus taxa are registered and reviewed with a validation certificate granted upon the satisfaction of all checks. new names are registered and reviewed prior to publication and validated upon the notification about effective publication, or existing names such as names of Candidatus taxa are registered and reviewed with a validation certificate granted upon the satisfaction of all checks. To avoid naming ambiguity and ensure accurate species descriptions, SeqCode requires that genome sequences designated as types satisfy recommendations on minimal standards for DNA sequences, which are largely adopted from the MISAG and MIMAG standards. The SeqCode Registry also embraces FAIR principles, and was developed with interoperable data structures to facilitate the sharing of its names across global biodiversity resources including GTDB. Recently, we illustrated how SeqCode can be applied, along with the ICNP, by proposing new names for GTDB-defined higher taxonomic names under the two codes (Chuvochina et al. 2023). While it is not ideal to operate under two Prokaryotic codes, we believe that this development is a necessary step towards a unified nomenclatural system.

A novel endophytic actinomycete with antagonistic activity against Fusarium moniliforme, designated strain NEAU-BLH26T, was isolated from the root of Adonis amurensis Regel collected at the horticultural experiment station of Northeast Agricultural University, Heilongjiang Province, northeast China. Strain NEAU-BLH26T exhibited morphological and chemotaxonomic features of the genus Streptomyces. The diamino acid present in its cell wall was identified as LL-diaminopimelic acid, while galactose detected in whole-cell hydrolysates. The menaquinones were identified as MK-9(H6), MK-9(H8), and MK-9(H4). The phospholipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified phospholipids and two unidentified aminolipids. The major fatty acids were determined to be iso-C16:0 and C16:0. The DNA G + C content, based on the genome sequence, was 70.5mol%. Phylogenetic analyses of 16S rRNA gene and whole genome sequences analyses indicated that strain NEAU-BLH26T was most closely related to Streptomyces geranii A301T, with a 16S rRNA gene sequence similarity of 98.69%. However, the average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values confirmed that strain NEAU-BLH26T represents a distinct species. This conclusion was further supported by phenotypic and chemotaxonomic differences between strain NEAU-BLH26T and its closest relative. Additionally, the secondary metabolite biosynthetic gene clusters in strain NEAU-BLH26T were predicted and analyzed. Based on phenotypic, chemotaxonomic and genotypic evidence, strain NEAU-BLH26T is proposed as a novel species of the genus Streptomyces, for which the name Streptomyces adonidis sp. nov. is suggested. The type strain is NEAU-BLH26T (= JCM 36414T = MCCC 1K08678T).

Currently, Lactococcus garvieae contains two subspecies: L. garvieae subsp. bovis and L. garvieae subsp. garvieae. In a study by Varsha and Nampoothiri, high pheS (99.7 %) and rpoA (99.6 %) sequence similarities indicated that L. garvieae subsp. bovis and Lactococcus formosensis probably have a close taxonomic relationship; low pheS (92.2 %) and rpoA (97.8 %) sequence similarities and relatively low DNA-DNA hybridization value (75.8 %) indicated that L. garvieae subsp. bovis and L. garvieae subsp. garvieae probably represent two different species. In the present study, the taxonomic relationships between L. garvieae subsp. bovis, L. garvieae subsp. garvieae and L. formosensis were re-examined based on sequence analyses of 16S rRNA, pheS, recA, rpoA and rpoB genes, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) values, average amino acid identity (AAI), fatty acid methyl ester analysis and phenotypic characterization. L. garvieae subsp. bovis LMG 30663T exhibited 97.3 % ANI, 78.3 % dDDH and 96.4 % AAI values to L. formosensis NBRC 109475T, higher than the threshold for species demarcation (95-96, 70 and 95-96 %, respectively), indicating that L. garvieae subsp. bovis LMG 30663T and L. formosensis NBRC 109475T belong to the same species. L. garvieae subsp. bovis LMG 30663T had 91.2 % ANI, 43.3 % dDDH and 92.9-93.0% AAI values with the type strain of L. garvieae subsp. garvieae, indicating that they represent two different species. Because L. formosensis has been proposed and validated before L. garvieae subsp. bovis, L. garvieae subsp. bovis is transferred to L. formosensis as L. formosensis subsp. bovis comb. nov. The type strain of L. formosensis subsp. bovis is BSN307T (=DSM 100577T=MCC 2824T=KCTC 21083T=LMG 30663T). The type strain of L. formosensis subsp. formosensis is 516T (=NBRC 109475T=BCRC 80576T).

In this study, we report the draft genome sequence of strain A2. The genome size was 3.8 Mbp, the GC content was 67.4%, and it was predicted to contain 3520 protein-coding genes, 62 tRNA genes, 8 rRNA genes, and 4 snRNA genes. Phylogenetic analysis of the 16S rRNA gene in different databases suggests that strain A2 belongs to Halomonas salifodinae. Also, Multilocus Sequence Typing analysis confirms that A2 is closely related to H. salifodinae. Phylogenomic of the core genes and comparative genomic analysis using the Average Nucleotide Identity, digital DNA-DNA Hybridization, Average Amino acid Identity, the Percentage of Conserved Proteins values indicators, and the Genome Taxonomy Database indicates that strain A2 is identified as H. salifodinae and suggest that this species has a closer phylogenetic relationship with the genus Bisbaumannia than with Halomonas. The pangenomic analysis of A2 against 100 reference genomes of described Halomonas and another related genus shows 136,122 genes that comprise the pangenome with 317 core genes, 3457 shell genes, 132,332 accessory genome genes, and 691 unique genes. A2 has 261 signature genes that it shares only with Bisbaumannia and Halomonas salifodinae. For strain A2 we found 29 genes for secretion systems, 23 genes for Na+ and K+ ion transport, 6 Biosynthetic Gene Clusters groups, a total of 12 genomic islands, an 8.2 kb gene prophage region, 15 regions associated with CRISPR and one CAS-TypeIF cas gene cluster region, 12 genes of biotechnological importance, 38 unique genes essential for adaptability and biotechnological relevance, as well as, 35 genes for the synthesis of compatible solutes. Comparative genomics analysis shows that strain A2 has multiple unique genetic features that could be useful for biotechnological applications. The result of this study places the species Halomonas salifodinae in a very close relationship with the genus Bisbaumannia than with Halomonas, so its reclassification to the genus Bisbaumannia is proposed for future validation.

Three Gram-stain-negative, aerobic, non-motile and coccobacilli-shaped bacterial strains, designated as NPKOSM-4T, NPKOSM-8 and MO-31T, were isolated from rice paddy soil. They had 96.5-100 % 16S rRNA gene sequence similarity to each other, and strains NPKOSM-4T and NPKOSM-8 showed 100 % 16S rRNA gene sequence similarity, confirming that they were the same species. Comparative analysis of 16S rRNA genes with closely related type strains showed that three isolates were most closely related to Falsiroseomonas terricola EM0302T (96.1-97.8 %), Falsiroseomonas wooponensis WW53T (95.51-96.3 %) and Falsiroseomonas bella CQN31T (96.0-96.5 %), respectively. The genomes of strains NPKOSM-4T and MO-31T consisted of 4 632 875 and 6 455 771 bps, respectively, with 72.0 and 72.1 mol% G+C content. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strains NPKOSM-4T and MO-31T and type strains of Falsiroseomonas species were lower than the cut-offs (≥95 % for ANI, ≥95-96 % for AAI and ≥ 70 % for dDDH) required to define a bacterial species. The major fatty acids of strains NPKOSM-4T, NPKOSM-8 and MO-31T were C18 : 1 ω7c and C18 : 1 2-OH (<10 %) and the predominant quinone was Q-10. The polar lipids of strain NPKOSM-4T were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and three unidentified aminolipids. The polar lipid profiles of strain MO-31T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminolipid and three unidentified lipids. Based on their distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, strains NPKOSM-4T, NPKOSM-8 and MO-31T are considered to represent two novel species of the genus Falsiroseomonas, for which the names Falsiroseomonas oryziterrae sp. nov. [to accommodate strains NPKOSM-4T (= KACC 22135T=JCM 34745T), NPKOSM-8 (=KACC 22134=JCM 34746)] and Falsiroseomonas oryzae sp. nov. [to accommodate strain MO-31T (= KACC 22465T=JCM 35532T)] are proposed.

Motilibacter deserti sp. nov. and Motilibacter aurantiacus sp. nov., two novel actinobacteria isolated from soil of Cholistan Desert and emended description of the genus Motilibacter

A novel bacterial strain, designated as PHS-Z3T, was isolated from a marine sponge belonging to the genus Theonella on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3T were Gram-stain-positive, motile, oxidase- and catalase-positive, white-pigmented, spore-forming, short rods that could grow at 10-40 °C (optimum, 20 °C), pH 6.0-9.5 (optimum, pH 7.5) and with 2-16 % (w/v) NaCl (optimum, 7 %). The 16S rRNA gene sequence of PHS-Z3T showed 97.9 %, 96.7 %, and 96.2 % identities to Paenibacillus mendelii C/2T, Paenibacillus oenotherae DT7-4T and Paenibacillus aurantiacus RC11T, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PHS-Z3T formed an independent cluster with Paenibacillus mendelii C/2T. The total genome of PHS-Z3T was approximately 7 613 364 bp in size with a DNA G+C content of 51.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between PHS-Z3T and other type strains of species of the genus Paenibacillus were 68.0-81.4 % [ANI by blast (ANIb)], 83.0-88.0 % [ANI by MUMmer (ANIm)] and 12.7-32.1 % (dDDH). The dDDH and ANI values were below the standard cut-off criteria for delineation of bacterial species. The percentage of conserved proteins (POCP) values between the genome of PHS-Z3T and those of members of the genus Paenibacillus were 39.7-75.7 %, while the average amino acid identity (AAI) values were 55.9-83.7 %. The sole respiratory quinone in the strain was MK-7, and the predominant fatty acids were anteiso-C15 : 0 and C16 : 0. The major polar lipids of PHS-Z3T consisted of diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The characteristic amino acid in the cell wall of PHS-Z3T was diamino heptanoic acid (meso-DAP). On the basis of the molecular, physiological, biochemical and chemotaxonomic features, strain PHS-Z3T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus spongiae sp. nov. is proposed, with the type strain PHS-Z3T (=MCCC 1K07848T=KCTC 43443T).

Three bacterial strains, C9, H5 and TLL-A3, were isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of 16S rRNA genes indicated that the strains belonged to the Muribaculaceae, and shared 91.6-99.9 % sequence identity with the recently described Duncaniella muris DSM 103720T. Genome-sequencing of the isolates was performed to compare average nucleotide identities (ANI) between strains. The ANI analysis revealed that all isolates shared highest ANI with D. muris DSM 103720T, with strain C9 being most similar (ANI: 98.0 %) followed by strains H5 (ANI: 76.4 %) and TLL-A3 (ANI: 74.4 %). Likewise, digital DNA-DNA hybridization (dDDH) indicated high similarity of strain C9 (dDDH: 86.6 %) to D. muris DSM 103720T, but strains H5 and TLL-A3 showed lower similarity (dDDH <35 %) to either of the three type species of the Muribaculaceae (Muribaculum intestinale DSM 28989T , Paramuribaculum intestinale DSM 100749T, D. muris DSM 103720T). MK-10 and MK-11 were abundant in all three isolates, but concentrations varied between species. Based on genotypic, phylogenetic and phenotypic differences, the strains TLL-A3 and H5 are considered to represent novel species of the genus Duncaniella, for which the names Duncaniella freteri sp. nov., and Duncaniella dubosii sp. nov., are proposed. The respective type strains are TLL-A3T (=DSM 108168T=KCTC 15769T), and H5T (=DSM 107170T=KCTC 15734T). Strain C9 reveals limited sequence dissimilarity and minor differences in morphological properties with Duncaniella muris DSM 103720T and is therefore proposed to belong to the same species. The respective strain is C9 (=DSM 107165=KCTC 15733).

A Gram-stain-negative, strictly aerobic and filamentous bacterial strain, designated as DQS-5T, was isolated from the activated sludge of a municipal sewage treatment plant in Shenzhen, PR China. Optimal growth was observed at 28 °C and pH 7.5. Catalase and oxidase activities were detected. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DQS-5T was most closely related to the genera Chitinimonas and Chitinivorax (91.0-93.4 % and 92.5 % 16S rRNA gene sequence similarity, respectively) and was close to the member of the family Burkholderiaceae. The complete genome sequence of strain DQS-5T contains 5 653 844 bp and 57.3 mol% G+C. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between the genome of strain DQS-5T and those of its close relatives were 75.9-77.2, 19.0-20.3 and 57.2-61.8 %, respectively. Chemotaxonomic analysis of strain DQS-5T indicated that the sole respiratory quinone was ubiquinone-8, the predominant cellular fatty acids were C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and aminolipid. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrate that strain DQS-5T represents a novel species in a novel genus within the family Burkholderiaceae, for which the name Parachitinimonas caeni gen. nov., sp. nov., is proposed. Strain DQS-5T (=KCTC 92788T=CCTCC AB 2022320T) is the type and only strain of P. caeni.

A novel bacterial strain, designated as WHS-Z9T, was isolated from marine sponge Hymeniacidon sp. collected from Weihai (37° 25' N, 121° 58' E), Shandong Province, PR China. Cells of strain WHS-Z9T were Gram-stain-positive, non-spore-forming, non-motile, short-rod-shaped and light yellow-pigmented. The strain could grow at 10-40 °C (optimum, 20 °C), pH 4.5-9.5 (optimum, pH 8.5) and 2-14 % (w/v) NaCl (optimum, 4 %). The 16S rRNA gene sequence of strain WHS-Z9T showed 98.7 % similarity to that of Brevibacterium epidermidis NBRC 14811T, 98.5 % to Brevibacterium sediminis FXJ8.269T and 98.4 % to Brevibacterium oceani BBH7T. The phylogenetic tree based on 16S rRNA gene sequences revealed that strain WHS-Z9T was clustered with Brevibacterium limosum o2T. The whole genome of WHS-Z9T was approximately 4 217 721 bp in size with a G+C content of 65.2 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among WHS-Z9T and other Brevibacterium type strains were 83.3-85.5 % (ANI based on blast), 86.4-87.9 % (ANI based on MUMmer) and 41.9-57.5 % (dDDH). Percentage of conserved protein values between the genomes of strain WHS-Z9T and members of genera Brevibacterium were 76.8-82.9 %, while the average amino acid identity (AAI) values were 83.7-87.0 %. The dDDH, ANI, AAI and POCP values were below the standard cut-off criteria for the delineation of bacterial species. The sole respiratory quinone in strain WHS-Z9T was MK-8(H2), and the predominant fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipids of WHS-Z9T consisted of diphosphatidylglycerol and glycolipid. The diagnostic cell-wall diamino acid of strain WHS-Z9T was meso-diaminopimelic acid. Based on the data obtained in this study, strain WHS-Z9T (=MCCC 1K07845T=KCTC 49848T) should be classified as the type strain of a novel species of the genus Brevibacterium, for which the name Brevibacterium spongiae sp. nov. is proposed.

Coral reefs are declining due to the rising seawater temperature. Bacteria within and surrounding corals play key roles in maintaining the homeostasis of the coral holobiont. Research on coral-related bacteria could provide benefits for coral reef restoration. During the isolation of coral-associated bacteria, a Gram-stain-negative, motile bacterium (D5M38T) was isolated from seawater surrounding corals in Daya Bay, Shenzhen, PR China. Phylogenetic analysis revealed that strain D5M38T represents a novel species in the genus Cognatishimia. The temperature range for strain D5M38T growth was 10-40 °C, and the optimum temperature was 37 °C. The salinity range for the growth of this isolate was from 0 to 4.0 %, with an optimal salinity level of 0.5 %. The pH range necessary for strain D5M38T growth was between pH 5.0 and 9.0, with an optimal pH being 7.5. The predominant fatty acid was summed feature 8 (65.0 %). The major respiratory quinone was Q-10. The DNA G+C content was 56.8 %. The genome size was 3.88 Mb. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain D5M38T and its two closest neighbours, Cognatishimia activa LMG 29900T and Cognatishimia maritima KCTC 23347T, were 73.2/73.6%, 73.2/73.6% and 19.7/19.5%, respectively. Strain D5M38T was clearly distinct from its closest neighbours C. activa LMG 29900T and C. maritima KCTC 23347T, with 16S rRNA gene sequence similarity values of 97.5 and 97.3 %, respectively. The phylogenetic analysis, along with the ANI, AAI, and dDDH values, demonstrated that strain D5M38T is a member of the genus Cognatishimia, and is distinct from the other two recognized species within this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain D5M38T. Thus, strain D5M38T is considered to be classified as representing a novel species in the genus Cognatishimia, for which the name Cognatishimia coralii sp. nov. is proposed. The type strain is D5M38T (=MCCC 1K08692T=KCTC 8160T).

Polyphasic characterization of a novel species in the Lactobacillus casei group from cow manure of Taiwan: Description of L. chiayiensis sp. nov.

Strain Mg02T was isolated from roots of Eucommia ulmoides Oliv. collected from Changde City, Hunan Province, China. Strain Mg02T, which exhibited distinct chemotaxonomic characteristics of the genus Nocardiopsis: cell-wall chemotype III/C, i.e., meso-diaminopimelic acid as diagnostic amino acid in whole-cell hydrolysates and menaquinone MK-10 with variable degrees of saturation in the side chain as the predominant isoprenoid quinone, was investigated by a polyphasic approach to determine their taxonomic position. Sequence analysis of the 16S rRNA gene indicated that strain Mg02T is affiliated to the genus Nocardiopsis, having highest sequence similarity to Nocardiopsis flavescens CGMCC 4.5723T (99.1%) and <98.7% to other species of the genus Nocardiopsis with validly published names. Phylogenetic analysis of 16S rRNA gene indicated strain Mg02T formed a separate evolutionary clade, suggesting that it could be a novel Nocardiopsis species. Phylogenomic analysis showed that strain Mg02T was closely related to N. flavescens CGMCC 4.5723T and distinct from the latter according to the clustering patterns. The Average Nucleotide Identity and digital DNA-DNA hybridization values between strain Mg02T and N. flavescens CGMCC 4.5723T were far below the species-level thresholds. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, we think that strain Mg02T should represent a novel Nocardiopsis species, for which the name Nocardiopsis changdeensis sp. nov. is proposed. The type strain is Mg02T (=MCCC 1K06174T = JCM 34709T).

Recently, the Bork group published a tool called GUNC (the Genome UNClutter) that detects chimerism and contamination in prokaryotic genomes. Disturbingly, they estimated that 3.2% (1009) of all species in release 95 of the Genome Taxonomy Database (GTDB) consist entirely of contaminated genomes, which could inflate estimates of phylogenetic diversity and taxonomic novelty. We applied GUNC to the latest release of GTDB and found the situation is even worse, with 6.0% (3,958) of all species in release 207 estimated to be comprised entirely of contaminated genomes.To address the question of whether this contamination compromises the GTDB taxonomy by inflating phylogenetic diversity, we split putative chimeric genomes into halves according to their GUNC contamination scores. We then inferred phylogenetic trees from the genome halves as per the standard GTDB workflow, i.e. based on a concatenated alignment of up to 120 single copy marker genes, to determine any changes in genus to phylum classifications between pairs of genome halves. We also subjected the genome halves to average nucleotide identity (ANI)-based analysis, which is how species are assigned in GTDB. These analyses allowed us to quantify taxonomic inflation caused by genomic contamination, and the extent to which the GTDB taxonomy has been compromised. Tune in to find out the results!