Description of Microbacterium dauci sp. nov., a plant growth hormone indoleacetic acid-producing and nitrogen-fixing bacterium isolated from carrot rhizosphere soil.

A plant growth hormone indoleacetic acid-producing strain LX3-4T was isolated from a carrot rhizosphere soil sample collected in Shandong Province, China. It is Gram-stain-positive, non-motile, and has irregular short rod-shaped cells. LX3-4T shared high 16S rRNA gene sequence identity with Microbacterium oleivorans DSM 16091T (99.4%), M. testaceum NBRC 12675T (98.6%), M. marinum DSM 24947T (98.5%), M. resistens NBRC 103078T (98.4%), and M. paraoxydans NBRC 103076T (98.3%). Phylogenetic analysis based on the concatenated gene sequences of 16S rRNA gene, housekeeping genes gryB and rpoB also showed the distinction between strain LX3-4T and other Microbacterium species. Furthermore, analysis of the average nucleotide identities (ANI), the average amino acid identity (AAI), and the digital DNA-DNA hybridization (dDDH) values between strain LX3-4T and its relatives revealed that strain LX3-4T represents a distinct species. The genomic DNA G + C content of the strain is 69.5%. It can grow at 25-37 °C (optimum 37 °C), pH 5.0-10.0 (optimum pH 6.0-8.0), and the range of NaCl concentration is 0-7% (w/v) (optimum 1-5%). The colonies on agar plates are smooth, translucent, and pale yellow. The main cellular fatty acids of strain LX3-4T are anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The predominant respiratory quinones are MK-12 and MK-11. Diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, and an unidentified phosphoglycolipid are major polar lipids. The cell-wall sugar of strain LX3-4T is glucose. The cell-wall peptidoglycan contains glycine, alanine, lysine, and glutamic acid. In addition, this strain carries nitrogen fixation genes and can grow in nitrogen-free medium. Based on the polyphasic data, strain LX3-4T represents a novel species of the genus Microbacterium, for which the name Microbacterium dauci sp. nov. is proposed with strain LX3-4T (= CCTCC AB 2023103T = LMG 33159T) designated as the type strain.

Faecalibacterium hominis Liu et al. 2023 is a later heterotypic synonym of Faecalibacterium duncaniae Sakamoto et al. 2022.

A strain of the recently validated species Faecalibacterium hominis shares 99.0 % 16S rRNA gene sequence similarity with the type strain of Faecalibacterium duncaniae. The aim of this study was to evaluate the taxonomic relationship between F. hominis and F. duncaniae. F. duncaniae JCM 31915T showed 73.0 % digital DNA-DNA hybridization (dDDH) value with F. hominis JCM 39347T. The average nucleotide identity (ANI) value between these two strains was 96.7 %. These results indicate that F. duncaniae JCM 31915T and F. hominis JCM 39347T represent members of the same species. Based on these data, we propose Faecalibacterium hominis as a later heterotypic synonym of Faecalibacterium duncaniae. An emended description is provided.

Isolation and genomics of ten novel Shewanella species from mangrove wetland.

Mangrove bacteria largely compose the microbial community of the coastal ecosystem and are directly associated with nutrient cycling. In the present study, 12 Gram-negative and motile strains were isolated from a mangrove wetland in Zhangzhou, China. Pairwise comparisons (based on 16S rRNA gene sequences) and phylogenetic analysis indicated that these 12 strains belong to the genus Shewanella. The 16S rRNA gene sequence similarities among the 12 Shewanella strains and their related type strains ranged from 98.8 to 99.8 %, but they still could not be considered as known species. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between the 12 strains and their related type strains were below the cut-off values (ANI 95-96% and dDDH 70 %) for prokaryotic species delineation. The DNA G+C contents of the present study strains ranged from 44.4 to 53.8 %. The predominant menaquinone present in all strains was MK-7. The present study strains (except FJAT-53532T) also contained ubiquinones (Q-8 and Q-7). The polar lipid phosphatidylglycerol and fatty acid iso-C15 : 0 was noticed in all strains. Based on phenotypic, chemotaxonomic, phylogenetic and genomic comparisons, we propose that these 12 strains represent 10 novel species within the genus Shewanella, with the names Shewanella psychrotolerans sp. nov. (FJAT-53749T=GDMCC 1.2398T=KCTC 82649T), Shewanella zhangzhouensis sp. nov. (FJAT-52072T=MCCC 1K05363T=KCTC 82447T), Shewanella rhizosphaerae sp. nov. (FJAT-53764T=GDMCC 1.2349T=KCTC 82648T), Shewanella mesophila sp. nov. (FJAT-53870T=GDMCC 1.2346T= KCTC 82640T), Shewanella halotolerans sp. nov. (FJAT-53555T=GDMCC 1.2344T=KCTC 82645T), Shewanella aegiceratis sp. nov. (FJAT-53532T=GDMCC 1.2343T=KCTC 82644T), Shewanella alkalitolerans sp. nov. (FJAT-54031T=GDMCC 1.2347T=KCTC 82642T), Shewanella spartinae sp. nov. (FJAT-53681T=GDMCC 1.2345T=KCTC 82641T), Shewanella acanthi sp. nov. (FJAT-51860T=GDMCC 1.2342T=KCTC 82650T) and Shewanella mangrovisoli sp. nov. (FJAT-51754T=GDMCC 1.2341T= KCTC 82647T).

Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species.

Enterococcus species have been described as core members of the microbial community of Spodoptera frugiperda (Lepidoptera: Noctuidae) and have been previously reported as insecticide degrading agents. This study aimed to investigate the molecular composition of these microbial symbionts of S. frugiperda to better understand their association with the host and their potential for insecticide metabolization. Through phenotypic assays and comparative genomic analyses of several pesticide-degrading Enterococcus isolated from the gut of S. frugiperda larvae, we identified two new species: Enterococcus entomosocium n. sp. and Enterococcus spodopteracolus n. sp. Their identities as new species were confirmed by whole genome alignment, utilizing cut-offs of 95-96% for the average nucleotide identity (ANI) and 70% for the digital DNA: DNA hybridization (dDDH) values. The systematic positioning of these new species within the genus Enterococcus was resolved using genome-based analysis, revealing Enterococcus casseliflavus as a sister group of E. entomosocium n. sp., and Enterococcus mundtii as a sister group of E. spodopteracolus n. sp. Comparative genomic analyses of several isolates of E. entomosocium n. sp. and E. spodopteracolus n. sp. provided a better assessment of the interactions established in the symbiotic association with S. frugiperda and led to the discovery of misidentified new species of Enterococcus associated with insects. Our analyses indicated that the potential of E. entomosocium n. sp. and E. spodopteracolus n. sp. to metabolize different pesticides arises from molecular mechanisms that result in rapid evolution of new phenotypes in response to environmental stressors, in this case, the pesticides their host insect is exposed to.

Genome-based, phenotypic and chemotaxonomic classification of Faecalibacterium strains: proposal of three novel species Faecalibacterium duncaniae sp. nov., Faecalibacterium hattorii sp. nov. and Faecalibacterium gallinarum sp. nov.

Faecalibacterium prausnitzii is one of the most important butyrate-producing bacteria in the human gut. Previous studies have suggested the presence of several phylogenetic groups, with differences at the species level, in the species, and a taxonomic re-evaluation is thus essential for further understanding of ecology of the important human symbiont. Here we examine the phenotypic, physiological, chemotaxonomic and phylogenomic characteristics of six F. prausnitzii strains (BCRC 81047T=ATCC 27768T, A2-165T=JCM 31915T, APC918/95b=JCM 39207, APC942/30-2=JCM 39208, APC924/119=JCM 39209 and APC922/41-1T=JCM 39210T) deposited in public culture collections with two reference strains of Faecalibacterium butyricigenerans JCM 39212T and Faecalibacterium longum JCM 39211T. Faecalibacterium sp. JCM 17207T isolated from caecum of broiler chicken was also included. Three strains of F. prausnitzii (BCRC 81047T, JCM 39207 and JCM 39209) shared more than 96.6 % average nucleotide identity (ANI) and 69.6 % digital DNA-DNA hybridization (dDDH) values, indicating that the three strains are members of the same species. On the other hand, the remaining three strains of F. prausnitzii (JCM 31915T, JCM 39208 and JCM 39210T) were clearly separated from the above three strains based on the ANI and dDDH values. Rather, JCM 39208 showed ANI and dDDH values over the cut-off values of species discrimination (>70 % dDDH and >95-96 % ANI) with F. longum JCM 39211T, whereas JCM 31915T, JCM 39210T and JCM 17207T did not share dDDH and ANI values over the currently accepted cut-off values with any of the tested strains, including among them. Furthermore, the cellular fatty acid patterns of these strains were slightly different from other F. prausnitzii strains. Based on the collected data, F. prausnitzii JCM 31915T, F. prausnitzii JCM 39210T and Faecalibacterium sp. JCM 17207T represent three novel species of the genus Faecalibacterium, for which the names Faecalibacterium duncaniae sp. nov. (type strain JCM 31915T=DSM 17677T=A2-165T), Faecalibacterium hattorii sp. nov. (type strain JCM 39210T=DSM 107841T=APC922/41-1T) and Faecalibacterium gallinarum sp. nov. (type strain JCM 17207T=DSM 23680T=ic1379T) are proposed.

The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis.

The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Candidatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in implementation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and databases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thousands of newly discovered but uncultured species.

Taxonomic reassessment of the genus Pseudocitrobacter using whole genome sequencing: Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis and description of Pseudocitrobacter vendiensis sp. nov.

The taxonomic status of all Pseudocitrobacter species was re-evaluated by comparative genomics based on whole genome sequencing. As a result, it is obvious that Pseudocitrobacter anthropi is a later heterotypic synonym of Pseudocitrobacter faecalis. In addition, genome-based analysis of strain CPO20170097T, isolated from a patient in northern Denmark was allocated to the genus Pseudocitrobacter. This strain showed significant genotypic and phenotypic differences from P. faecalis and it is proposed that this strain represents a novel species of the genus, for which the name Pseudocitrobacter vendiensis sp. nov. is proposed with the type strain CPO20170097T (=CCUG 73096T=LMG 31042T).

Reclassification of Sphingomonas aeria as a later heterotypic synonym of Sphingomonas carotinifaciens based on whole-genome sequence analysis.

The 16S rRNA gene sequences of Sphingomonas carotinifaciens L9-754T and Sphingomonas aeria B093034T possess 99.71 % sequence similarity. Further studies were undertaken to clarify the taxonomic assignments of these species. Whole-genome comparisons showed that S. aeria B093034Tand S. carotinifaciens L9-754T shared 96.9 % average nucleotide identity, 98.4 % average amino acid identity and 76.1 % digital DNA-DNA hybridization values. These values exceeded or approached the recommended species delineation threshold values. Furthermore, a phylogenetic tree based on 41 of the most conserved genes provided additional evidence that S. aeria B093034T and S. carotinifaciens L9-754T are very closely related. Based on this evidence we propose the reclassification of S. aeria Xue et al. 2018 as a later heterotypic synonym of S. carotinifaciens Madhaiyan et al. 2017.

Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae.

Phylogenetic analyses based on 16S rRNA gene sequences of members of the family Staphylococcaceae showed the presence of para- and polyphyletic genera. This finding prompted a thorough investigation into the taxonomy of the Staphylococcaceae family by analysing their core genome phylogeny complemented with genome-based indices such as digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity. The resulting data suggested the following proposals: Auricoccus indicus was reduced in taxonomic rank as a later heterotypic synonym of Abyssicoccus albus; Staphylococcus petrasii subsp. jettensis as a later heterotypic synonym of Staphylococcus petrasii subsp. petrasii; the unification of Staphylococcus aureus subsp. anaerobius and Staphylococcus aureus subsp. aureus as Staphylococcus aureus; the unification of Staphylococcus carnosus subsp. utilis and Staphylococcus carnosus subsp. carnosus as Staphylococcus carnosus; the unification of Staphylococcus saprophyticus subsp. bovis and Staphylococcus saprophyticus subsp. saprophyticus as Staphylococcus saprophyticus; Staphylococcus succinis subsp. casei as the novel species Staphylococcus casei; Staphylococcus schleiferi subsp. coagulans as the novel species Staphylococcus coagulans; Staphylococcus petrasii subsp. croceilyticus as the novel species Staphylococcus croceilyticus; Staphylococcus petrasii subsp. pragensis as the novel species Staphylococcus pragensis; Staphylococcus cohnii subsp. urealyticus as the novel species Staphylococcus urealyticus; the reassignment of Staphylococcus sciuri, Staphylococcus fleurettii, Staphylococcus lentus, Staphylococcus stepanovicii and Staphylococcus vitulinus to the novel genus Mammaliicoccus with Mammaliicoccus sciuri as the type species; and the formal assignment of Nosocomiicoccus as a member of the family Staphylococcaceae.

Genome sequence-based criteria for demarcation and definition of species in the genus Rickettsia.

Over recent years, genomic information has increasingly been used for prokaryotic species definition and classification. Genome sequence-based alternatives to the gold standard DNA-DNA hybridization (DDH) relatedness have been developed, notably average nucleotide identity (ANI), which is one of the most useful measurements for species delineation in the genomic era. However, the strictly intracellar lifestyle, the few measurable phenotypic properties and the low level of genetic heterogeneity made the current standard genomic criteria for bacterial species definition inapplicable to Rickettsia species. We evaluated a range of whole genome sequence (WGS)-based taxonomic parameters to develop guidelines for the classification of Rickettsia isolates at genus and species levels. By comparing the degree of similarity of 74 WGSs from 31 Rickettsia species and 61 WGSs from members of three closely related genera also belonging to the order Rickettsiales (Orientia, 11 genomes; Ehrlichia, 22 genomes; and Anaplasma, 28 genomes) using digital DDH (dDDh) and ANI by orthology (OrthoANI) parameters, we demonstrated that WGS-based taxonomic information, which is easy to obtain and use, can serve for reliable classification of isolates within the Rickettsia genus and species. To be classified as a member of the genus Rickettsia, a bacterial isolate should exhibit OrthoANI values with any Rickettsia species with a validly published name of ≥83.63 %. To be classified as a new Rickettsia species, an isolate should not exhibit more than any of the following degrees of genomic relatedness levels with the most closely related species: >92.30 and >99.19 % for the dDDH and OrthoANI values, respectively. When applied to four rickettsial isolates of uncertain status, the above-described thresholds enabled their classification as new species in one case. Thus, we propose WGS-based guidelines to efficiently delineate Rickettsia species, with OrthoANI and dDDH being the most accurate for classification at the genus and species levels, respectively.

Reclassification of Ochrobactrum lupini as a later heterotypic synonym of Ochrobactrum anthropi based on whole-genome sequence analysis.

The genus Ochrobactrum belongs to the family Brucellaceae and its members are known to be adapted to a wide range of ecological niches. Ochrobactrum anthropi ATCC 49188T and Ochrobactrum lupini LUP21T are strains isolated from human clinical and plant root nodule samples, respectively, which share high similarity for phylogenetic markers (i.e 100 % for 16S rRNA, 99.9 % for dnaK and 99.35 % for rpoB). In this work, multiple genome average nucleotide identity (ANI) approaches, digital DNA-DNA hybridization (dDDH) and phylogenetic analysis were performed in order to investigate the taxonomic relationship between O. anthropi ATCC 49188T, O. lupini LUP21T, and other five type strains from the genus Ochrobactrum. Whole-genome comparisons demonstrated that O. lupini LUP21T and the Ochrobactrum genus type species, O. anthropi ATCC 49188T, share 97.55 % of ANIb, 98.25 % of ANIm, 97.99 % of gANI, 97.94 % of OrthoANI and 83.9 % of dDDH, which exceed the species delineation thresholds. These strains are also closely related in phylogenies reconstructed from a concatenation of 1193 sequences from single-copy ortholog genes. A review of their profiles revealed that O. anthropi ATCC 49188T and O. lupini LUP21T do not present pronounced differences at phenotypic and chemotaxonomic levels. Considering phylogenetic, genomic, phenotypic and chemotaxonomic data, O. lupini should be considered a later heterotypic synonym of O. anthropi.

Minimal standards for the description of new genera and species of rhizobia and agrobacteria.

Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.

Characterization and comprehensive genome analysis of novel bacteriophage, vB_Kpn_ZCKp20p, with lytic and anti-biofilm potential against clinical multidrug-resistant Klebsiella pneumoniae.

Introduction: The rise of infections by antibiotic-resistant bacterial pathogens is alarming. Among these, Klebsiella pneumoniae is a leading cause of death by hospital-acquired infections, and its multidrug-resistant strains are flagged as a global threat to human health, which necessitates finding novel antibiotics or alternative therapies. One promising therapeutic alternative is the use of virulent bacteriophages, which specifically target bacteria and coevolve with them to overcome potential resistance. Here, we aimed to discover specific bacteriophages with therapeutic potential against multiresistant K. pneumoniae clinical isolates. Methods and Results: Out of six bacteriophages that we isolated from urban and medical sewage, phage vB_Kpn_ZCKp20p had the broadest host range and was thus characterized in detail. Transmission electron microscopy suggests vB_Kpn_ZCKp20p to be a tailed phage of the siphoviral morphotype. In vitro evaluation indicated a high lytic efficiency (30 min latent period and burst size of ∼100 PFU/cell), and extended stability at temperatures up to 70°C and a wide range of (2-12) pH. Additionally, phage vB_Kpn_ZCKp20p possesses antibiofilm activity that was evaluated by the crystal violet assay and was not cytotoxic to human skin fibroblasts. The whole genome was sequenced and annotated, uncovering one tRNA gene and 33 genes encoding proteins with assigned functions out of 85 predicted genes. Furthermore, comparative genomics and phylogenetic analysis suggest that vB_Kpn_ZCKp20p most likely represents a new species, but belongs to the same genus as Klebsiella phages ZCKP8 and 6691. Comprehensive genomic and bioinformatics analyses substantiate the safety of the phage and its strictly lytic lifestyle. Conclusion: Phage vB_Kpn_ZCKp20p is a novel phage with potential to be used against biofilm-forming K. pneumoniae and could be a promising source for antibacterial and antibiofilm products, which will be individually studied experimentally in future studies.

Identification of Peptoniphilus vaginalis-Like Bacteria, Peptoniphilus septimus sp. nov., From Blood Cultures in a Cervical Cancer Patient Receiving Chemotherapy: Case and Implications.

A 39-year-old woman with a 3-year human papillomavirus (HPV) 18 infection history was admitted to the hospital for a 16-day history of vaginal bleeding after sex. She was diagnosed with cervical cancer based on the results of the electronic colposcopy, cervical cytology, microscopy, and magnetic resonance imaging (MRI). Then, she received chemotherapy, with paclitaxel 200 mg (day 1), cisplatin 75 mg (day 2), and bevacizumab 700 mg (day 3) twice with an interval of 27 days. During the examination for the diagnosis and treatment, many invasive operations, including removal of intrauterine device, colposcopy, and ureteral dilatation, were done. After that, the patient was discharged and entered the emergency department about 2.5 months later with a loss of consciousness probably caused by septic shock. The patient finally died of multiple organ failure and bacterial infection, although she has received antimicrobial therapy. The blood cultures showed a monobacterial infection with an anaerobic Gram-positive bacterial strain, designated as SAHP1. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) indicated that the patient was infected with Peptoniphilus asaccharolyticus, while molecular analysis and genome-based taxonomy confirmed the infection with a novel Peptoniphilus species that has a close genetic relationship with Peptoniphilus vaginalis and proposed provisionally as Peptoniphilus septimus sp. nov., which may also act as a commensal of the human vagina. Genomic features of SAHP1 have been fully described, and comparative genomic analysis reveals the known prokaryote relative of Peptoniphilus septimus sp. nov. in the genus Peptoniphilus. The invasive operations on the genital tract during the diagnosis and treatment of the patient and the tumor tissue damage and bleeding may have a certain role in the bloodstream infection. This study casts a new light on the Peptoniphilus bacteria and prompts clinicians to include anaerobic blood cultures as part of their blood culture procedures, especially on patients with genital tract tumors. Furthermore, due to the incomplete database and unsatisfying resolution of the MALDI-TOF MS for Peptoniphilus species identification, molecular identification, especially whole-genome sequencing, is required for those initially identified as bacteria belonging to Peptoniphilus in the clinical laboratory.

The Next Million Names for Archaea and Bacteria.

Latin binomials, popularised in the 18th century by the Swedish naturalist Linnaeus, have stood the test of time in providing a stable, clear, and memorable system of nomenclature across biology. However, relentless and ever-deeper exploration and analysis of the microbial world has created an urgent need for huge numbers of new names for Archaea and Bacteria. Manual creation of such names remains difficult and slow and typically relies on expert-driven nomenclatural quality control. Keen to ensure that the legacy of Linnaeus lives on in the age of microbial genomics and metagenomics, we propose an automated approach, employing combinatorial concatenation of roots from Latin and Greek to create linguistically correct names for genera and species that can be used off the shelf as needed. As proof of principle, we document over a million new names for Bacteria and Archaea. We are confident that our approach provides a road map for how to create new names for decades to come.

Genome-Based Taxonomy of Brevundimonas with Reporting Brevundimonas huaxiensis sp. nov.

Brevundimonas is a genus of Gram-negative bacteria widely distributed in nature and is also an opportunistic pathogen causing health care-associated infections. Brevundimonas strain 090558T was recovered from a blood culture of a cancer patient and was subjected to genome sequencing and analysis. The average nucleotide identity and in silico DNA-DNA hybridization values between 090558T and type strains of Brevundimonas species were 78.76% to 93.94% and 19.8% to 53.9%, respectively, below the cutoff to define bacterial species. Detailed phenotypic tests were performed, suggesting that 090558T can be differentiated from other Brevundimonas species by its ability to assimilate sodium acetate but not to utilize glucose, trypsin, or ß-glucosidase. Strain 090558T (GDMCC 1.1871T or KCTC 82165T) therefore represents a novel Brevundimonas species, for which the name Brevundimonas huaxiensis sp. nov. is proposed. All Brevundimonas genomes available in GenBank (accessed on 25 January 2021) were retrieved, discarding those labeled "excluded from RefSeq" by GenBank, and included 82 genomes for precise species curation. In addition to the 21 Brevundimonas species with genomes of type strains available, we identified 29 Brevundimonas taxa that either belong to the 12 Brevundimonas species without available genomes of type strains or represent novel species. We found that more than half (57.3%) of the 82 Brevundimonas genomes need to be corrected for species assignation, including species mislabeling of a type strain. Our analysis highlights the complexity of Brevundimonas taxonomy. We also found that only some Brevundimonas species are associated with human infections, and more studies are warranted to understand their pathogenicity and epidemiology. IMPORTANCEBrevundimonas is a genus of the family Caulobacteraceae and comprises 33 species. Brevundimonas can cause various infections but remains poorly studied. In this study, we reported a novel Brevundimonas species, Brevundimonas huaxiensis, based on genome and phenotype studies of strain 090558T recovered from human blood. We then examined the species assignations of all Brevundimonas genomes (n = 82) in GenBank and found that in addition to the known Brevundimonas species with genome sequences of type strains available, there are 29 Brevundimonas taxa based on genome analysis, which need to be further studied using phenotype-based methods to establish their species status. Our study significantly updates the taxonomy of Brevundimonas and enhances our understanding of this genus of clinical relevance. The findings also encourage future studies on the characterization of novel Brevundimonas species.

LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes.

BACKGROUND: Computing genomic similarity between strains is a prerequisite for genome-based prokaryotic classification and identification. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments. Since this is computationally expensive, faster and computationally cheaper alignment-free methods have been developed to estimate ANI. However, these methods do not reach the level of accuracy of alignment-based methods. METHODS: Here we introduce LINflow, a computational pipeline that infers pairwise genomic similarity in a set of genomes. LINflow takes advantage of the speed of the alignment-free sourmash tool to identify the genome in a dataset that is most similar to a query genome and the precision of the alignment-based pyani software to precisely compute ANI between the query genome and the most similar genome identified by sourmash. This is repeated for each new genome that is added to a dataset. The sequentially computed ANI values are stored as Life Identification Numbers (LINs), which are then used to infer all other pairwise ANI values in the set. We tested LINflow on four sets, 484 genomes in total, and compared the needed time and the generated similarity matrices with other tools. RESULTS: LINflow is up to 150 times faster than pyani and pairwise ANI values generated by LINflow are highly correlated with those computed by pyani. However, because LINflow infers most pairwise ANI values instead of computing them directly, ANI values occasionally depart from the ANI values computed by pyani. In conclusion, LINflow is a fast and memory-efficient pipeline to infer similarity among a large set of prokaryotic genomes. Its ability to quickly add new genome sequences to an already computed similarity matrix makes LINflow particularly useful for projects when new genome sequences need to be regularly added to an existing dataset.

Genome-based Taxonomy for Bacteria: A Recent Advance.

Prokaryotic taxonomic assignments are shifting to genome-based algorithms. A recent study (Parks et al., 2020) has advanced genome-based taxonomy by constructing reference databases, computing average nucleotide identity and assigning tentative placeholder species names. However, prokaryotic taxonomy should be carefully curated and updated in a timely fashion; this requires coordinated efforts of prokaryotic taxonomists, genomicists, and database curators.

Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris.

Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA. The bean rhizobia were found in 16 defined species and nine putative novel species; in addition, 35 strains previously described as Rhizobium etli, Rhizobium phaseoli, Rhizobium vallis, Rhizobium gallicum, Rhizobium leguminosarum and Rhizobium spp. should be renamed. The phylogenetic patterns of symbiotic genes nodC and nifH were highly host-specific and inconsistent with the genomic phylogeny. Multiple symbiovars (sv.) within the Rhizobium species were found as a common feature: sv. phaseoli, sv. trifolii and sv. viciae in Rhizobium anhuiense; sv. phaseoli and sv. mimosae in Rhizobium sophoriradicis/R. etli/Rhizobium sp. III; sv. phaseoli and sv. trifolii in Rhizobium hidalgonense/Rhizobium acidisoli; sv. phaseoli and sv. viciae in R. leguminosarum/Rhizobium sp. IX; sv. trifolii and sv. viciae in Rhizobium laguerreae. Thus, genomic comparison revealed great species diversity in bean rhizobia, corrected the species definition of some previously misnamed strains, and demonstrated the MLSA a valuable and simple method for defining Rhizobium species.