Paramixta manurensis gen. nov., sp. nov., a novel member of the family Erwiniaceae producing indole-3-acetic acid isolated from mushroom compost

There are numerous species in the Erwiniaceae family that are important for agricultural and clinical purposes. Here we described the Erwiniaceae bacterium PD-1 isolated from mushroom (Pleurotus eryngii) compost. Comparative genomic and phylogenetic analyses showed that the strain PD-1 was assigned to a new genus and species, Paramixta manurensis gen. nov., sp. nov. in the family Erwiniaceae. From the average amino acid index, we identified the five AroBEKAC proteins in the shikimate pathway as a minimal set of molecular markers to reconstruct the phylogenetic tree of the Erwiniaceae species. The strain PD-1 containing annotated genes for ubiquinone and menaquinone produced a higher level of ubiquinone (Q8) than demethylmenaquinone (DMK8) and menaquinone (MK8) in anaerobic condition compared to aerobic condition, as similarly did the reference strains from the genera Mixta and Erwinia. Results from fatty acid methyl ester and numerical analyses of strain PD-1 showed a similarity to species of the genera Mixta and Winslowiella. This study revealed that the strain's ability to utilize polyols, such as glycerol, erythritol, and D-arabitol, distinguished the strain PD-1 from the nearest relative and other type strains. The analyzed genetic markers and biochemical properties of the strain PD-1 suggest its potential role in the process of mushroom compost through the degradation of carbohydrates and polysaccharides derived from fungi and plants. Additionally, it can produce a high concentration of indole-3-acetic acid as a plant growth-promoting agent.

Genomic delineation and description of species and within-species lineages in the genus Pantoea

As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.

Diverse Virulence Attributes of Pantoea alfalfae sp. nov. CQ10 Responsible for Bacterial Leaf Blight in Alfalfa Revealed by Genomic Analysis

Alfalfa is widely grown worldwide for its excellent nutritional value. Pantoea species living in alfalfa seeds can easily spread over great distances with frequent trade. However, the pathogenic properties of this dangerous hitchhiker on alfalfa have not been evaluated. Here, we identified the taxonomic status of Pantoea strain CQ10 isolated from the interior of alfalfa seeds based on the whole genome sequence. The diverse virulence attributes of strain CQ10 during host infection were characterized through pathogenicity assays and functional and genomic analyses. We report that strain CQ10 belongs to a novel species in the genus Pantoea, which was phylogenetically close to Pantoea vagans and Pantoea agglomerans. Strain CQ10 caused bacterial leaf blight of alfalfa after inoculation from the roots. We found that strain CQ10 possesses a large number of pathogenic genes involved in shaping the virulence properties during bacteria-host interactions, including motility, biofilm, type VI secretion system, and nutrient acquisition. Compared with P. vagans and P. agglomerans, the unique virulence factors of strain CQ10 were mainly involved in motility and biofilm, which were confirmed by in vitro experiments. Taken together, our results suggest that strain CQ10 is the first Pantoea species to infect alfalfa, and it possesses diverse virulence attributes among which motility and biofilm may be the best weapons.

Increased Leaf Bacterial Network Complexity along the Native Plant Diversity Gradient Facilitates Plant Invasion?

Understanding the mechanisms of biological invasion is critical to biodiversity protection. Previous studies have produced inconsistent relationships between native species richness and invasibility, referred to as the invasion paradox. Although facilitative interactions among species have been proposed to explain the non-negative diversity-invasibility relationship, little is known about the facilitation of plant-associated microbes in invasions. We established a two-year field biodiversity experiment with a native plant species richness gradient (1, 2, 4, or 8 species) and analyzed the effects of community structure and network complexity of leaf bacteria on invasion success. Our results indicated a positive relationship between invasibility and network complexity of leaf bacteria of the invader. Consistent with previous studies, we also found that native plant species richness increased the leaf bacterial diversity and network complexity. Moreover, the results of the leaf bacteria community assembly of the invader suggested that the complex bacteria community resulted from higher native diversity rather than higher invader biomass. We concluded that increased leaf bacterial network complexity along the native plant diversity gradient likely facilitated plant invasion. Our findings provided evidence of a potential mechanism by which microbes may affect the plant community invasibility, hopefully helping to explain the non-negative relationship between native diversity and invasibility.

First case of bloodstream infection caused by Mixta hanseatica sp. nov., a novel species within the Mixta genus of the Erwiniaceae family

Members of the Erwiniaceae family very rarely cause infections in humans. Here we describe the first case of a bloodstream infection due to Mixta hanseatica sp. nov., a novel member of the Erwiniaceae family.

Transfer of Erwinia toletana and Erwinia iniecta to a novel genus Winslowiella gen. nov. as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov. and description of Winslowiella arboricola sp. nov., isolated from bleeding cankers on broadleaf hosts

Following a screening campaign of bleeding cankers of broadleaf hosts in Great Britain, numerous bacterial strains were isolated, identified by 16S rRNA and protein-coding gene sequencing and ultimately classified. During the course of the study, several Gram-negative, facultatively anaerobic strains were isolated from bleeding Platanus x acerifolia (London plane) and Tilia x europaea (common lime) cankers that could not be assigned to an existing species. Partial 16S rRNA gene sequencing placed these strains in the genus Erwinia, as a close phylogenetic relative of Erwinia toletana. In an effort to determine the taxonomic position of the strains, a polyphasic approach was followed including genotypic, genomic, phenotypic, and chemotaxonomic assays. Multilocus sequence analysis based on four protein-coding genes (gyrB, rpoB, infB, and atpD) confirmed the phylogenetic position of the strains as a novel taxon of subgroup 3 of the genus Erwinia, along with E. toletana and E. iniecta, and furthermore, provided support for their reclassification in a novel genus. Whole genome comparisons allowed the delimitation of the novel species and also supported the proposed transfer of subgroup 3 species to a novel genus in the Erwiniaeae. Phenotypically the novel species could be differentiated from E. toletana and E. iniecta, and the novel genus could be differentiated from the closely related genera Erwinia and Mixta. Therefore, we propose (1) the reclassification of E. toletana and E. iniecta in a novel genus, Winslowiella gen. nov., as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov., with W. toletana comb. nov. as the type species (type strain A37T = CFBP 6631T = ATCC 700880T = CECT 5263T), and (2) classification of the novel strains as Winslowiella arboricola sp. nov. (type strain BAC 15a-03bT = LMG 32576T = NCPPB 4696T).

First Report of Bacterial Wilt Caused by Enterobacter mori of Strawberry in Beijing, China

Strawberry (Fragaria × ananassa) is an economically important crop in China, and a crucial part of urban agriculture in Beijing. In November 2020, wilt symptoms were observed in strawberry seedlings in several greenhouses in the Pinggu District of Beijing city (40.14° N; 117.12° E). The average disease incidence was 20%. Water-soaked lesions appeared along the veins of diseased strawberry leaves and bacterial ooze was also present on severely affected leaves. Bisected crowns had a reddish-brown discoloration in the xylem which later turned black. Three diseased strawberry seedlings were collected for pathogen identification. Isolations were conducted from stem, crown, leaf, and roots of diseased strawberry plants. Samples were surface sterilized by immersion in 70% ethanol for 30 s and rinsed three times with sterile distilled water, before being placed on potato dextrose agar (PDA) medium and incubated at 28℃. Several bacterial colonies grew on the medium after 24 h. Colonies were then purified on Lysogeny broth (LB) agar plates using the streak plate method. Twenty-nine isolates were obtained from 36 diseased tissue samples, which were from stem(10), crown(12), leaf(2) and roots(5) separately. All isolates appeared white, round, opaque and smooth on LB plates. To identify the isolates, genomic DNA was extracted from nine purified bacterial colonies (CM1 to CM9). The fragments of atpD, gyrB, infB and rpoB gene were amplified and sequenced with primers atpD 01-F/ atpD 02-R, gyrB 01-F/ gyrB 02-R, and infB 01-F/ infB 02-R (Brady et al. 2008) and RpoB-F/ RpoB-R (Mollet et al. 1997), respectively. All atpD, gyrB, infB and rpoB sequences belonging to the isolates were identical. The sequences of atpD, gyrB, infB and rpoB gene of isolates CM1 and CM3 were deposited in GenBank under accession numbers ON055247, ON055248, ON055249, ON055250, ON055251, ON055252, OL771192 and OL771193. BLAST searches were conducted with the sequences of atpD, gyrB, infB and rpoB. The atpD, gyrB, infB and rpoB sequences of the obtained isolate showed 99.53%, 99.06%, 99.19% and 99.80% identity with the corresponding sequences of Enterobacter mori strains, respectively. Phylogenetic analysis was performed using the maximum likelihood (ML) method with the CIPRES Science Gateway platform (http://www.phylo.org/) based on the combined atpD, gyrB, infB and rpoB sequences (Brady et al. 2013; Palmer et al. 2018). In the phylogenetic tree, the isolates were clustered together with E. mori strain LMG 25706. To confirm the pathogenicity, 200 μL of bacterial suspensions (108 CFU/mL) of the two isolates were injected into the crown of six healthy Fragaria × ananassa cv. Bennihope strawberry seedlings respectively with 1 mL sterilized syringe, and the control seedlings were injected with sterile water. The seedlings were kept in a moist chamber (28°C, 16-h light and 8-h dark period) for 2 days. Then all the seedlings were transferred to the greenhouse with conditions similar to those where the diseased plants were collected. Forty days after inoculation, old leaves started to wilt and leaf midvein necrosis, along with xylem discoloration, was observed in inoculated plants. No symptoms were observed in the control group. Pathogenicity tests were conducted three times with similar results. The bacteria were re-isolated from the symptomatic diseased strawberry plants and confirmed as E. mori by morphological and sequence analyses as above, fulfilling Koch's postulates. To the best of our knowledge, this is the first report of strawberry bacterial wilt caused by E. mori. Due to the significant crop loss from this disease, more research is needed in epidemiology and disease management.

Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type

Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.

Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov

To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.

Genomics-Informed Multiplex PCR Scheme for Rapid Identification of Rice-Associated Bacteria of the Genus Pantoea

The genus Pantoea forms a complex of more than 25 species, among which several cause diseases of various crop plants, including rice. Notably, strains of Pantoea ananatis and P. stewartii have been repeatedly reported to cause bacterial leaf blight of rice, whereas other authors have observed that P. agglomerans can also cause bacterial leaf blight of rice. The contribution of these and perhaps other species of Pantoea to plant diseases and yield losses of crop plants is currently not well documented, partly due to the lack of efficient diagnostic tools. Using 32 whole-genome sequences of the three major plant-pathogenic Pantoea spp., a set of PCR primers that detect each of the three species P. agglomerans, P. ananatis, and P. stewartii was designed. A multiplex PCR scheme which can distinguish these three species and also detects members of other Pantoea spp. was further developed. Upon validation on a set of reference strains, 607 suspected Pantoea strains that were isolated from rice leaves or seed originating from 11 African countries were screened. In total, 41 P. agglomerans strains from 8 countries, 79 P. ananatis strains from 9 countries, 269 P. stewartii strains from 9 countries, and 218 unresolved Pantoea strains from 10 countries were identified. The PCR protocol allowed detection of Pantoea bacteria grown in vitro, in planta, and in rice seed. The detection threshold was estimated as total genomic DNA at 0.5 ng/µl and heated cells at 1 × 10⁴ CFU/ml. This new molecular diagnostic tool will help to accurately diagnose major plant-pathogenic species of Pantoea. Due to its robustness, specificity, sensitivity, and cost efficiency, it will be very useful for plant protection services and for the epidemiological surveillance of these important crop-threatening bacteria.

Antibiotic susceptibility of human gut-derived facultative anaerobic bacteria is different under aerobic versus anaerobic test conditions

Facultative anaerobes are the most common cause of infections in anoxic parts of the human body, including deep wound, vagina, periodontal pockets, gastrointestinal tract, genitourinary tract and lungs. Generally, antibiotic susceptibility tests (AST) for facultative anaerobes are performed under aerobic conditions due to ease of handling and rapid growth. However, variation in susceptibility of facultative anaerobes to antibiotics under aerobic and anaerobic conditions can lead to failure of antibiotic treatment. Our study evaluated the susceptibility of facultative anaerobic microorganisms to antibiotics during growth under anaerobic or aerobic conditions. We compared the resistance patterns of representatives from 15 bacterial genera isolated from the human-gastrointestinal tract against 22 different antibiotics from six classes under aerobic and anaerobic conditions. Preliminary results obtained by a disc diffusion method were verified using minimum inhibitory concentration (MIC) testing. The results demonstrated that 7-strains had a similar pattern of drug resistance under both conditions, while the remaining ten strains had significant differences in resistance patterns between aerobic and anaerobic conditions for at least one antibiotic. We conclude that successful antibiotic therapy for host-associated pathogens requires proper assessment of the oxygen condition of the growth environment and MIC testing of each pathogen under anaerobic and aerobic conditions.

The Complete Genome Sequence of Xanthomonas theicola, the Causal Agent of Canker on Tea Plants, Reveals Novel Secretion Systems in Clade-1 Xanthomonads

Xanthomonas theicola is the causal agent of bacterial canker on tea plants. There is no complete genome sequence available for X. theicola, a close relative of the species X. translucens and X. hyacinthi, thus limiting basic research for this group of pathogens. Here, we release a high-quality complete genome sequence for the X. theicola type strain, CFBP 4691^T. Single-molecule real-time sequencing with a mean coverage of 264× revealed two contigs of 4,744,641 bp (chromosome) and 40,955 bp (plasmid) in size. Genome mining revealed the presence of nonribosomal peptide synthases, two CRISPR systems, the Xps type 2 secretion system, and the Hrp type 3 secretion system. Surprisingly, this strain encodes an additional type 2 secretion system and a novel type 3 secretion system with enigmatic function, hitherto undescribed for xanthomonads. Four type 3 effector genes were found on complete or partial transposons, suggesting a role of transposons in effector gene evolution and spread. This genome sequence fills an important gap to better understand the biology and evolution of the early-branching xanthomonads, also known as clade-1 xanthomonads.

Draft genome and description of Mixta mediterraneensis strain Marseille-Q2057T sp.nov., a new bacterium isolated from human healthy skin

In 2019, by culturing a skin swab from the hand of a 30-year-old healthy woman using the culturomic method, we isolated the new bacterial strain Marseille-Q2057^T (= CSUR-Q2057). Matrix-assisted desorption–ionization time-of-flight mass spectrometry (MALDI-TOF MS) failed to identify this isolate. Analysis of the 16S rRNA gene and Genome-to-Genome comparison suggested that this taxon belongs to a novel bacterial species within the family Erwiniaceae, phylum Proteobacteria. We describe here its main phenotypic characteristics, genome sequence and annotation of Mixta mediterraneensis strain Marseille-Q2057^T, a new member of the Mixta genus, that we propose as type strain.

Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov

The genera Proteus and Cosenzaea are closely related members of the family Morganellaceae. The genus Cosenzaea consists of the species Cosenzaea myxofaciens originally separated from the genus Proteus by rpoB gene analysis. Due to the high similarity of the 16S rRNA genes between species of both genera, the taxonomic status is here re-evaluated by a genome-based approach. Based on a core genome phylogeny and genome relatedness indices, it is shown that the taxonomy and nomenclature given for the basonym Proteus myxofaciens is more appropriate. Therefore, we propose to use this name in preference. Furthermore, the species status of Proteus terrae and Proteus cibarius was reassessed. Both species are related at subspecies level by digital DNA-DNA hybridization (dDDH) analysis. Additionally, average amino acid identity (AAI) and average nucleotide identity (ANI) do not support a separate species status, and therefore it is proposed to classify P. cibarius as a subspecies of P. terrae. Consequently, both species are being renamed Proteus terrae subsp. cibarius subsp. nov. and Proteus terrae subsp. terrae subsp. nov., respectively. The genome relatedness indices revealed a close relationship of the Proteus genomospecies 5 with P. terrae subsp. terrae. Thus, it has been assigned to the same subspecies.

Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019

Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.

Neonatal Thoracic Infection with Mixta

The Erwiniaceae are a family of gram-negative, aerobic coliforms which are pathogenic to a number of plants. Recently described within this family are the Pantoea, strains of which have been associated with infection in immunocompromised children and post-surgical meningitis but also colonisation of a healthy human subject's gastrointestinal tract, as well as a variety of agricultural diseases. In 2015, a further clade of this family was established as the genus Mixta.

In this case report, we describe infection of the pleural space and lung parenchyma with members of Mixta in a term neonate following an anastomic leak post-primary repair of congenital trache-oesophageal fistula, causing a respiratory and cardiovascular deterioration. Mixta were identified by MALDI-TOF. The child made a full recovery with use of intravenous piperacillin-tazobactam.

The Mixta genus must be added to a list of opportunistic pathogens responsible for infection following perforation of the gastrointestinal tract.

First Report of Pathogenic Bacterium Kalamiella piersonii Isolated from Urine of a Kidney Stone Patient: Draft Genome and Evidence for Role in Struvite Crystallization

Uropathogenic bacteria are widely distributed in the environment and urinary tract infection is implicated in kidney stone disease. Here, we report on a urease negative bacterium Kalamiella piersonii (strain YU22) isolated from the urine of a struvite stone (MgNH₄PO₄·6H₂O) patient. The closest species, K. piersonii IIIF1SW-P2^T was reported from International Space Station samples. However, there are no earlier reports on its human association. Using whole genome and experimental analysis, its involvement in urinary tract colonization and struvite crystallization was explored. The strain YU22 showed many virulence factors that are needed for host cell invasion and colonization including cell adhesion factors, swimming and swarming motilities, biofilm and siderophore among others. In vitro infection studies in HEK-293T cells demonstrated the host cell attachment and killing. It was able to utilize amino acids as sole carbon source and showed growth in synthetic and healthy urine establishing metabolic adaptation to urinary tract. Increased pH and availability of ammonium ions from amino acid breakdown promoted struvite crystallization. The results from this study support the involvement of urease negative uropathogen in the struvite lithogenesis. Further studies on other isolates of K. peirsonii are warranted to assess its health risks.

Complete Genome Sequence of Pantoea ananatis Strain NN08200, an Endophytic Bacterium Isolated from Sugarcane

Stain NN08200 was isolated from the surface-sterilized stem of sugarcane grown in Guangxi province of China. The stain was Gram-negative, facultative anaerobic, non-spore-forming bacteria. The complete genome SNP-based phylogenetic analysis indicate that NN08200 is a member of the genus Pantoea ananatis. Here, we summarize the features of strain NN08200 and describe its complete genome. The genome contains a chromosome and two plasmids, in total 5,176,640 nucleotides with 54.76% GC content. The chromosome genome contains 4598 protein-coding genes, and 135 ncRNA genes, including 22 rRNA genes, 78 tRNA genes and 35 sRNA genes, the plasmid 1 contains 149 protein-coding genes and the plasmid 2 contains 308 protein-coding genes. We identified 130 tandem repeats, 101 transposon genes, and 16 predicted genomic islands on the chromosome. We found an indole pyruvate decarboxylase encoding gene which involved in the biosynthesis of the plant hormone indole-3-acetic acid, it may explain the reason why NN08200 stain have growth-promoting effects on sugarcane. Considering the pathogenic potential and its versatility of the species of the genus Pantoea, the genome information of the strain NN08200 give us a chance to determine the genetic background of interactions between endophytic enterobacteria and plants.

Reclassification of genus Izhakiella into the family Erwiniaceae based on phylogenetic and genomic analyses

The genus Izhakiella was established and designated as a member of the family Enterobacteriaceae in 2016. Although the taxonomical classification of most members in this family has been relatively resolved after two reclassifications in 2016 and 2017, the classification of the genus Izhakiella remains ambiguous. In this study, a polyphasic approach was used to provide evidence supporting the fact that the genus Izhakiella should no longer be considered a member of Enterobacteriaceae and proposes its reclassification into the family Erwiniaceae. The phylogenetic tree of type species in the families Enterobacteriaceae and Erwiniaceae based on the sequences of the 16S rRNA gene, rpoB housekeeping gene, and the whole-genome comprising the 92 core genes revealed that the genus Izhakiella forms a phylogenetic lineage within the family Erwiniaceae. The average nucleotide identity (ANI) value of the type species with genus Izhakiella was found to be higher for the family Erwiniaceae than that for the family Enterobacteriaceae. Notably, 12 conserved signature indels (CSIs) that are exclusively shared among the Erwiniaceae clade members were found in the type strains of the genus Izhakiella. Based on these analyses, this study suggests the reclassification of I. capsodis and I. australiensis into the family Erwiniaceae.

Proposed nomenclature or classification changes for bacteria of medical importance: taxonomic update 5

A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy continues to change at a very rapid rate in the era of molecular diagnostics including whole genome sequencing. This update focuses on taxonomic changes and proposals that may be of medical importance from 2018 to 2020.

Mixta tenebrionis sp. nov., isolated from the gut of the plastic-eating mealworm Tenebrio molitor L

A bacterial strain, BIT-26^T, was isolated from the gut of plastic-eating mealworm Tenebrio molitor L. The taxonomic position of this new isolate was investigated by using a polyphasic approach. Cells of the strain were Gram-stain-negative, facultatively anaerobic, motile rods with peritrichous flagella. The 16S rRNA gene sequence (1412 bp) of strain BIT-26^T showed the highest similarity (97.4 %) to Erwinia piriflorinigrans CFBP 5888^T, followed by Citrobacter sedlakii NBRC 105722^T (97.3 %), Mixta calida LMG 25383^T (97.3 %), Cronobacter muytjensii ATCC 51329^T (97.2 %) and Mixta theicola QC88-366 ^T (97.2 %). The results of phylogenetic analyses, based on the 16S rRNA gene and concatenated sequences of four housekeeping genes (atpD, gyrB, infB and rpoB), placed strain BIT-26^T within the genus Mixta of the family Erwiniaceae. This affiliation was also supported by the chemotaxonomic data. Strain BIT-26^T had similar predominant fatty acids, including C_12 : 0, C_14 : 0, C_16 : 0, C_17 : 0 cyclo and C_19 : 0 cyclo ω8c, to species of the genus Mixta. In silico DNA-DNA hybridization and average nucleotide identity calculations plus physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain BIT-26^T from other species of the genus Mixta with validly published names. Therefore, strain BIT-26^T is considered to represent a novel species, for which the name Mixta tenebrionis sp. nov is proposed. The type strain is BIT-26^T (=CGMCC 1.17041^T=KCTC 72449^T).

Molecular validation of clinical Pantoea isolates identified by MALDI-TOF

The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.

Taxogenomics and Systematics of the Genus Pantoea

Members of the genus Pantoea are Gram-negative bacteria isolated from various environments. Taxonomic affiliation based on multilocus sequence analysis (MLSA) is used routinely for inferring accurate phylogeny and identification of bacterial species and genera. Partial sequences of five housekeeping genes (fusA, gyrB, leuS, rpoB, and pyrG) were extracted from 206 draft or complete genomes of Pantoea strains publicly available in databases and analyzed together with the representative sequences of the 25 validly published Pantoea type strains to verify and assess their phylogenetic assignations. Of a total of 159 strains assigned to species level, 11.3% of the non-type strains were incorrectly assigned within suitable Pantoea species. The highest proportion of misidentified strains was recorded in Pantoea vagans, 8 out of 15 (53.3%) inaccurate assignations at the species level. One probable reason for this incorrect classification could be the method previously used for strain identification. Forty-seven (22.8%) genome sequences were from strains identified at the genus level only (Pantoea sp.). A combination of MLSA, average nucleotide identities [ANI and MuMmer-based ANI (ANIm)], tetranucleotide usage pattern (TETRA), and genome-based DNA-DNA hybridization (gDDH) data was used to accurately assign 25 of the 47 strains to validly published Pantoea species, while 17 strains could be assigned as putative novel species within the genus Pantoea. Four genomes designed as Pantoea sp. were identified as Mixta calida. Positive and significant correlation coefficients were computed between MLSA and all the indices derived from whole-genome sequences being proposed for species delimitation. gDDH exhibited the best correlation with MLSA while TETRA was the worst. Accurate species-level identification is key to a better understanding of bacterial diversity and evolution. The MLSA scheme used here could be instrumental to determine the correct taxonomic status of new whole-genome sequenced Pantoea strains, especially non-type strains, before depositing into public databases.

Pantoea endophytica sp. nov., novel endophytic bacteria isolated from maize planting in different geographic regions of northern China

Four endophytic bacterial strains were isolated from root, stem and leaf of maize planted in different regions of northern China. The four strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. Furthermore, the average nucleotide identity (ANI) values among them were higher than 95%, suggesting they all belong to one species. Based on 16S rRNA gene phylogeny, the four strains were clustered together with Pantoea rodasii LMG 26273^T and Pantoea rwandensis LMG 26275^T, but on a separate branch. Multilocus sequence analysis (MLSA) indicated that the four strains form a novel Pantoea species. Authenticity of the novel species was confirmed by ANI comparisons between strain 596^T and its closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. The genome size of 596^T was 5.1Mbp, comprising 4896 predicted genes with DNA G+C content of 57.8mol%. The respiratory quinone was ubiquinone-8 (Q-8) and the polar lipid profile consisted of phosphatidylethanolamin, diphosphatidylglycerol, phosphatidylglycerol, unidentified aminophospholipid and unidentified phospholipid. The major fatty acids of strain 596^T were C_16:0, summed feature 2 (C_12:0 aldehyde), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, the four isolates are considered to represent a novel species of the genus Pantoea, for which the name Pantoea endophytica sp. nov., is proposed, with 596^T (=DSM 100,785^T=CGMCC 1.15280^T) as type strain.

Metagenome to phenome approach enables isolation and genomics characterization of Kalamiella piersonii gen. nov., sp. nov. from the International Space Station

Several evolutionarily distinct, near full-length draft metagenome-resolved genomes (MRG), were assembled from sequences recovered from the International Space Station (ISS) environments. The retrieval of MRGs facilitated the exploration of a large collection of archived strains (~ 500 isolates) and assisted in isolating seven related strains. The whole genome sequences (WGS) of seven ISS strains exhibited 100% identity to the 4.85 × 10⁶ bp of four MRGs. The "metagenome to phenome" approach led to the description of a novel bacterial genus from the ISS samples. The phylogenomics and traditional taxonomic approaches suggested that these seven ISS strains and four MRGs were not phylogenetically affiliated to any validly described genera of the family Erwiniaceae, but belong to a novel genus with the proposed name Kalamiella. Comparative genomic analyses of Kalamiella piersonii strains and MRGs showed genes associated with carbohydrate (348 genes), amino acid (384), RNA (59), and protein (214) metabolisms; membrane transport systems (108), pathways for biosynthesis of cofactors, vitamins, prosthetic groups, and pigments (179); as well as mechanisms for virulence, disease, and defense (50). Even though Kalamiella genome annotation and disc diffusion tests revealed multidrug resistance, the PathogenFinder algorithm predicted that K. piersonii strains are not human pathogens. This approach to isolating microbes allows for the characterization of functional pathways and their potential virulence properties that can directly affect human health. The isolation of novel strains from the ISS has broad applications in microbiology, not only because of concern for astronaut health but it might have a great potential for biotechnological relevance. The metagenome to phenome approach will help to improve our understanding of complex metabolic networks that control fundamental life processes under microgravity and in deep space.