International Journal of Systematic and Evolutionary Microbiology

Four rhizobial strains isolated from root nodules of tropical leguminous plants in Costa Rica were characterized. Strain LEGMi-135b was isolated from Lonchocarpus felipei root nodules, LEGMi-12c from Cojoba arborea, LEGMi-198b from Calliandra haematocephala and Rhizobium altiplani LEGMi-166a from Mimosa pigra. Phylogenetic analyses based on the 16S rRNA gene and four concatenated housekeeping genes (recA, atpD, GATase and gyrB) placed these strains within the genera Martinezella (LEGMi-12c, LEGMi-135b, and LEGMi-198b) and Rhizobium (LEGMi-166a). Genome-based analyses showed that strain LEGMi-135b exhibited an average nucleotide identity (ANI) value of 94% and a digital DNA-DNA hybridization (dDDH) value of 53.2% compared with its closest related species, Martinezella hainanensis CCBAU 57015T, supporting its classification as a distinct species. LEGMI-12c exhibited ANI and dDDH values of 98% and 87%, respectively, compared with Martinezella hainanensis CCBAU 57015T. LEGMi-198b showed the highest similarity to Rhizobium cerradonense CNPSo 3464, with ANI and dDDH values of 98% and 81.4%, respectively; however, this taxon has not been validly published. LEGMi-166a exhibited ANI and dDDH values of 100% and 99.3%, respectively, compared with Rhizobium altiplani BR 10423, confirming its assignment to this species. Additionally, differentiation of strains LEGMi-135b and LEGMi-198b from their closest phylogenetic relatives was supported by phenotypic, physiological, and biochemical analyses. Based on the combined genomic, phenotypic, and biochemical evidence, we propose the establishment of the novel rhizobial species Martinezella legmii sp. nov., with strain LEGMi-135b designated as the type strain (LEGMi-135b), and Martinezella ivanii sp. nov., with strain LEGMi-198b designated as the type strain (LEGMi-198b). This study expands our understanding of rhizobial diversity associated with nitrogen-fixing symbioses, particularly among tropical leguminous plants from Costa Rica

A Gram-stain-negative, aerobic, moderately halophilic, non-motile, rod-shaped bacterium, designated MC10-B4T, was isolated from the coral Oulastrea crispata collected from Hong Kong waters. The strain showed the ability to persist in a coral holobiont during an eight-month monitoring period in a field trial, indicating a long-term association with the coral host. Growth occurred at 10-37 {degrees}C (optimum, 28-30 {degrees}C), at NaCl concentrations up to 4.0% (w/v; optimum, 0.5-2.0%), and at pH 7.0-10.0 (optimum, pH 7.0-8.0) under standard laboratory conditions. Colonies on Marine Agar 2216 were round, smooth, convex, white, opaque, and had entire margins. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MC10-B4T belongs to the genus Ruegeria and shares the highest sequence similarity with Ruegeria conchae TW15T (99.64%), followed by Ruegeria profundi ZGT108T (98.92%), Ruegeria lacuscaerulensis ITI-1157T (98.46%), Ruegeria denitrificans CECT 5091T (98.31%), Ruegeria arenilitoris G-M8T (97.69%), Ruegeria atlantica NBRC 15792T (97.55%), Ruegeria halocynthiae MA1-6 (97.11%), Ruegeria atlantica IAM 14463T (96.98%), Ruegeria meonggei MA-E2-3 (96.83%), and Ruegeria pomeroyi DSS-3T (96.65%). Genome sequencing revealed a genome size of 4.55 Mbp and a DNA G+C content of 57.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain MC10-B4T and Ruegeria conchae TW15T were 77.6% and 18.2-22.8%, respectively. These values are below the recommended thresholds for species delineation (95% and 70%). Strain MC10-B4T shares the same predominant fatty acid, summed feature 8 (consisting of C18:1 {omega}7c and/or C18:1 {omega}6c), with other Ruegeria strains; however, it also contains C19:0 cyclo {omega}8c, which was not detected in Ruegeria conchae TW15T and Ruegeria pomeroyi DSS-3T. The type strain is MC10-B4T (= GDMCC 1.6889T = KCTC 18785T).

Pectobacterium comprises Gram-negative, pectinolytic plant pathogens that cause soft rot and blackleg diseases on numerous economically important crops. During sampling in 2018 in taro (Colocasia esculenta) fields in Hawaii, two bacterial strains PL152T and PL155 were isolated from taro. Peliminary molecular characterization placed both strains in the genus Pectobacterium. However, their taxanomic postions could not be resoved at the species level. A polyphasic taxonomic approach incorporating phenotypic characterization, 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), whole genome based phylogeny, average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) was therefore employed to determine their taxonomic status. Phylogenetic and phylogenomic analyses consistently placed PL152 and PL155 together in a distinct and well supported lineage within the genus Pectobacterium, separate from currently recognized species. The two strains exhibited high genomic relatedness to each other, whereas the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, were lower than the accepted species delineation thresholds of 95% and 70%, respectively, supported the delineation of a novel bacterial species. The genomic characteristic of PL152 included a genome size of 5.02 Mb and a DNA G+C content of 52%. Collectively, based on a polyphasic approach including phylogenetic, phlyogenomic, biochemical, and phenotypic evidences supports the classification of strains PL152 and PL155 as representatives of a novel species within the genus Pectobacterium, for which the name Pectobacterium pacificum sp. nov. is proposed. Strain PL152 (ICMP 2436274, LMG 32536) is designated as the type strain.

A strictly anaerobic bacterial strain, F2T, was isolated from an anaerobic bioreactor fermenting source-separated organic waste. Cells of strain F2T are non-spore-forming, rod-shaped (1.5-2.5 x 0.27-0.33 m), and Gram-negative, although they possess a monoderm cell wall architecture. The strain grew at 37 degrees C within a pH range of 5 to 8 and produced short-, branched-, and medium-chain carboxylates as well as ammonium, H2 and CO2, with acetate and propanoate produced or consumed depending on fermentation conditions. The genome consists of a single 2.4 Mbp chromosome with a G+C content of 50.2% and 2,131 predicted genes. Phylogenetic analysis of the 16S rRNA gene against other isolates revealed that strain F2T is most similar to Eubacterium pyruvativorans I-6T (92.06% 16S rRNA identity). Based on further phenotypic, genomic, and phylogenetic analysis, strain F2T represents a novel genus and species within the family Anaerovoracaceae with the proposed name Peptonella octanoica gen. nov. sp. nov. The type strain is F2T (strain accession pending). As a member of this same genus-level clade, we propose reclassifying Eubacterium pyruvativorans as Peptonella pyruvativorans comb. nov. These findings disambiguate Peptonella spp. from the phylogenetically distant and phenotypically distinct Eubacterium limosum ATCC 8486T.

Two thermophilic bacterial strains, designated OKO1 and KUI1, were isolated from hot springs within the Taup[o] Volcanic Zone of New Zealand. Analysis of the 16S rRNA gene identified both as members of the genus Venenivibrio, sharing 99.13% and 98.82% sequence similarity with Venenivibrio stagnispumantis CP.B2T, respectively. The novel isolates were characterised using a polyphasic taxonomic approach alongside V. stagnispumantis. Despite their close phylogenetic relationship, the strains differed markedly in cell morphology, physiology and genomic content. Both isolates exhibited broad tolerance to temperature and pH, while re-examination V. stagnispumantis CP.B2T revealed substantially wider physiological capabilities than previously reported, bringing its phenotype into closer agreement with the new isolates. Comparative genomic analyses identified key differences in genes encoding cytochromes, hydrogenases, and nitrogen metabolism, suggesting distinct metabolic potential among the strains. Although the genomes shared average nucleotide identity (ANI) values of 95-96%, placing them near the accepted species boundary, the combined phenotypic and genomic evidence support recognition of OKO1T and KUI1T as two species within the genus. We therefore propose Venenivibrio orakeikorakoensis sp. nov. (type strain OKO1T, ACCESSION) and Venenivibrio aotearoaensis sp. nov. (type strain KUI1T, ACCESSION) as new members within the genus, and emend the descriptions of Venenivibrio stagnispumantis and the genus Venenivibrio to incorporate the expanded phenotypic and genomic diversity revealed in this study.

The genus Xanthomonas comprises a phylogenetically and ecologically diverse group of bacteria, historically characterized by economically important plant-pathogenic members affecting a wide range of agricultural crops. However, an increasing number of non-pathogenic and endophytic lineages have been recognized within the genus, expanding understanding of its taxonomic and ecological breadth. While it has been known for the last 30 years that non-pathogenic Xanthomonas (NPX) are present in diverse plants, studies from our lab over the last decade on the rice microbiome have revealed the presence of multiple, diverse NPX species as a community associated with a particular plant host. In this study, we identify two novel citrus plant-associated NPX species and provide evidence for the existence of an NPX community composed of multiple, diverse species, as in rice. Biochemical analysis, along with phylogenomic and genome-based taxonomic investigations, revealed that these strains represent two novel species within the genus Xanthomonas, providing evidence for a citrus-associated NPX community composed of multiple, diverse species, analogous to that described in rice. The lack of a canonical type III secretion system, along with multiple antimicrobial biosynthetic loci, as in the rice NPX community, points to their importance in plant microbiomes. Hence, such systematic studies of the NPX community need to be extended to all other plants. Accordingly, we propose that strain LMG 8992 (DSM =122509T) be classified as a novel species, Xanthomonas pateli sp. nov., and strain LMG 8993 (DSM = 122444T) be classified as a novel species, Xanthomonas hingoranii sp. nov.

Henriciella is the only genus with reported non-prosthecate members in the family Hyphomonadaceae, a large group of dimorphic prosthecate bacteria. Using type strains, we reinvestigated growth in media shown to support prosthecate morphotypes in marine caulobacters. We report that Marine Broth (MB) and Peptone Yeast Extract (PYE)-derived media supported prosthecate populations for all Henriciella species. Surprisingly, we observed that H. aquimarina, H. mobilis, and H. pelagia reproduce by tip budding whereas H. marina and H. liltoralis reproduce by asymmetric binary fission. These two observed reproductive strategies resemble those characterized for the model prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. Phylogenomic analysis indicates that H. marina, H. litoralis, H. algicola, and H. barbarensis form a monophyletic subgenus that reproduces by asymmetric binary fission. We propose genus and species emendations that correct the record on this fascinating genus.

Abstract The Bacillus cereus group is a complex of closely related species, which vary in terms of their geographic spread, industrial utility, and pathogenic potential. In addition to encompassing well-known species represented by thousands of genomes (e.g., bioterrorism agent B. anthracis, foodborne pathogen B. cereus, biopesticide B. thuringiensis), the B. cereus group houses "rare" species discovered/first sequenced over a decade ago. Until recently, four rare species (B. manliponensis, B. bingmayongensis, B. gaemokensis, "B. clarus") were each represented by a single unique genome; as such, virtually nothing is known about these species beyond their type strains. We hypothesized that additional representatives of rare B. cereus group species may already be present in public databases as yet-unassembled metagenomes. To this end, we used species-specific markers to identify 7 metagenomic samples in NCBI's Sequence Read Archive, which harbored B. manliponensis, B. bingmayongensis, or B. gaemokensis. Metagenomic assembly and binning yielded an isolate-quality B. manliponensis metagenome-assembled genome (MAG) from avocado orchard soil in Israel, plus a partial B. bingmayongensis MAG from commercial spinach spiked with Shiga toxin-producing Escherichia coli. For rare species represented by >1 unique genome, we compared our novel MAGs to all available genomes and identified strain- and lineage-specific genomic elements (e.g., sphingomyelinase C and hemolysin BL homologs, variably present in B. manliponensis and B. bingmayongensis, respectively). Altogether, our study indicates that some rare B. cereus group species may be more common and geographically widespread than previously thought, and highlights the utility of culture-independent methods for recovering rare/under-isolated taxa. Impact Statement Individual B. cereus group strains vary in terms of their pathogenic potential and industrial utility. While some strains cause illness in humans and/or animals (e.g., anthrax, emetic intoxication, diarrheal toxicoinfection, non-gastrointestinal illnesses), other strains have important biotechnological applications (e.g., biocontrol, plant growth promotion, production of antimicrobials and other natural products). Because many virulence- and biotechnological-related phenotypes are strain-dependent (rather than species-dependent), phenotypes associated with an individual strain (e.g., a species type strain) cannot be extrapolated to an entire B. cereus group species. Within this context, rare B. cereus group species represent a major gap in our understanding of B. cereus group evolution, ecology, and pathogenicity, as until 2021, each rare species was represented solely by its type strain genome. Here, we aggregate all publicly available genomes/MAGs of rare B. cereus group species and supplement them with their first novel representatives since 2024. Our efforts bring the total number of unique B. manliponensis and B. bingmayongensis genomes/MAGs to >2, allowing us to conduct the first-ever phylogeographic survey and strain-level assessment of functional potential for each species. Overall, our study represents a critical first step toward understanding rare B. cereus group species beyond their type strains.

The genus Erwinia comprises a diverse group of bacteria associated with plants, insects, and the environment, including several economically important phytopathogens. The genus has been revised taxonomically many times, yet a thorough and genome-wide assessment of its evolutionary relationships and genomic diversity has been lacking. In this research, we carried out an extensive phylogenomic and comparative genomic analyses of the genus Erwinia using 104 genomes including historically important strains. Genome-wide analyses integrating average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), core-genome phylogenomics, pan-genome analysis, and comparative genomics resolved evolutionary relationships across the genus and identified multiple taxonomic inconsistencies. The pan-genome analysis revealed a relatively small core genome alongside an extensive accessory genome, underscoring the substantial genomic plasticity and ongoing diversification within the genus. The comparative analyses further showed pronounced lineage-specific variation in secretion systems, exopolysaccharide biosynthetic loci, flagellar gene clusters, genomic islands, prophages, and iron acquisition systems, suggesting that virulence-associated determinants have evolved through differential gene gain, loss, and conservation across distinct lineages, thereby facilitating host and ecological niche adaptation. This lineage-specific variation indicates that pathogenicity in the genus is not driven by a single conserved set of virulence determinants but instead reflects distinct combinations of virulence-associated genes. These findings refine the genomic framework of the genus Erwinia, provide evidence for taxonomic revision of several lineages, and improve our understanding of the evolutionary relationships, genomic diversification, and lineage-specific adaptations associated with host interactions and ecological specialization. Impact StatementThis study provides the first comprehensive genome-wide phylogenomic framework for the genus Erwinia, integrating taxonomy, pan-genome diversity, virulence-associated determinants, and mobile genetic elements across all 18 currently recognized species. Analyses resolve evolutionary relationships, uncover multiple taxonomic inconsistencies, identify previously unrecognized species-level lineages, including a putative novel Erwinia species PL328 isolated from Cornus florida (dogwood), and reveal lineage-specific genomic features. These findings establish a valuable genomic foundation for future studies of Erwinia evolution, taxonomy, and plant-microbe interactions. Data SummaryGenomes sequenced in this study were submitted to the NCBI database under the accession numbers: JCBCPT000000000

Currently, the fungal class Paraglomeromycetes (phylum Glomeromycota) consists of one order, Paraglomerales, with two families: Paraglomeraceae, comprising the genera Paraglomus with ten species and Innospora with one species, and the monogeneric and monospecific Pervetustaceae represented by Pervetustus with Pe. simplex. However, our morphological analyses of these species and an undescribed specimen morphologically resembling other Paraglomeromycetes species, as well as analyses of sequences of these fungi and environmental sequences, indicated that the current taxonomic composition of this class should be updated. We did so here by creating in Paraglomeromycetes Pervetustales ord. nov. with Pervetustus and Opikia catenata gen. nov. and sp. nov., as well as transferring Innospora with In. majewskii to Innosporaceae fam. nov. These novelties were introduced primarily based on strong genetic divergences of the analyzed taxa, as many morphological and histochemical features of their spores and mycorrhizal structures overlap. Only Op. catenata possesses the unique trait of occasionally producing spores in chains. This mode of sporulation has also not been recognized in any other Glomeromycota species. Unlike species of Pervetustales and Innosporaceae, which produce single-walled spores, the subcellular spore structure of Paraglomus species contains one or two walls.

The obscure life histories of many kickxellalean genera remain a bottleneck for comprehensive taxon sampling and phylogenetic reconstruction of the order. While Kickxellales has long been regarded as saprobes inhabiting soil or dung, the discovery of "amphibious fungi" such as Unguispora, which exhibits dimorphic growth between the animal gut and feces, suggests a cryptic gut-dwelling stage within these genera. Given its phylogenetic proximity to Unguispora, ecophysiological traits of Linderina were investigated to evaluate its potential association with the animal gut. Two isolates of L. macrospora were obtained from Japanese soil, representing the first record of this species in Japan. Physiological assays revealed that the optimal temperature for both vegetative growth and sporulation was 25-30 {degrees}C. Furthermore, comparative growth assays on different media demonstrated that sporocladium abundance per sporangiophore is sensitive to nutrient availability, and nutrient-poor media were determined to be the most suitable for evaluating morphological characterization. Under anaerobic, nutrient-rich conditions which are known to induce yeast-like growth in Unguispora, sporangiospores of L. macrospora produce arthrospores. Although marked morphological plasticity was observed during the arthrospore formation, the occurrence of yeast-like unicellular proliferation suggests a potential relationship with the animal gut. Additionally, vegetative growth and sporulation were markedly inhibited by white light exposure; notably, a lethal effect on growth was observed during incubation at 20 {degrees}C, indicating that the natural niche of the species is restricted to light-shielded environments. Our findings will help to elucidate the cryptic life cycles and evolutionary trajectories within Kickxellales.

Microsporidia are a group of parasites that exhibit vast morphological, ecological, and genetic diversity. To catalog this diversity, we previously generated a database of attributes for microsporidia species. Here we expand this database to include species described since 2021, previously missed descriptions, and provisional species defined by clustering GenBank 18S rRNA sequences, resulting in 1,795 species. Using these data, we describe when and where microsporidia have been reported, their hosts and host habitats, the tissues they infect, and their spore morphology. A phylogeny of 18S sequence clusters shows that closely related microsporidia tend to infect closely related hosts, such that sequence identity is predictive of host taxonomy. Clustering also reveals previously unappreciated genetic diversity within some named species, in particular the human pathogen Vittaforma corneae, suggesting that these may comprise multiple species. We have also generated a web portal through which new species information can be submitted, which will facilitate regular updates. This database provides a resource for systematic analysis of microsporidia properties and a reference for taxonomic descriptions.

The bile acid-converting Peptacetobacter hiranonis is a Gram-positive, anaerobic, potentially spore-forming bacterium. It was first isolated from human feces and was subsequently shown to convert bile acids (BA) in both in vitro and in vivo experiments. The conversion of BA relies on the presence of the 7alpha-dehydroxylation multi-step pathway, encoded by the BA-inducible (bai) operon, harbored by P. hiranonis. In companion animals, P. hiranonis has been characterized as a biomarker for intestinal health, with its loss associated with dysbiosis. However, characterization of P. hiranonis cultured from companion animals is limited. An in-depth characterization of P. hiranonis was published by Chen et al. recently, including the proposal of a new species, Peptacetobacter hominis. We have sequenced the whole genome of both canine- and feline-derived strains of P. hiranonis, characterized these strains biochemically, and assessed their in vitro BA-converting ability as well as their antimicrobial resistance profiles. The strains described here can convert primary into secondary BAs and are whole-genome inhibited by low concentrations of amoxicillin-clavulanate, cefepime, ceftriaxone, chloramphenicol, ciprofloxacin, clindamycin, and metronidazole. Based on whole genome analysis, we propose dividing P. hiranonis into two host-adapted subspecies: P. hiranonis subsp. deconjugans and P. hiranonis subsp. nondeconjugans, based on their genomic differences and divergent ability to deconjugate BAs; a function that appears widely distributed among P. hiranonis strains cultured from dogs, but absent from those cultured from cats. Taken together, our results confirmed the BA conversion ability of P. hiranonis cultured from dogs and cats and reveal host-associated genomic and functional differences within the species.

Prevotella melaninogenica is a Gram-negative bacterium that has been implicated in numerous disorders such as chronic obstructive pulmonary disease (COPD) and cystic fibrosis, and despite its abundance in the human microbiome, there is still limited knowledge on the fundamental physiology describing Prevotella melaninogenica. To properly advance Prevotella biology, it is critical to report and document such characterizations of Prevotella; therefore, the purpose of this study is to examine and define the phenotypic and growth characteristics of P. melaninogenica ATCC 25845. In this study, we found that Prevotella melaninogenica ATCC 25845 is a Gram-negative bacterium that is predominantly short and medium rod-shaped, with occasional filamentous rods. SEM imaging revealed that this filamentation may serve as division centers, points from which multiple daughter cells form. We also describe the antibiotic profile, which showed susceptibility to four classes and resistance to six classes of antibiotics. Carbon source growth kinetic characterization revealed a preference for carbohydrate sources.

Knowledge of the family Lactobacillaceae rests largely on isolates from foods and a few repeatedly sampled hosts. Reference databases give an unrecognised sequence the name of its nearest relative, so a lineage with no entry of its own is renamed rather than flagged. Here we classify the family across the public plant and invertebrate amplicon record to locate the hosts carrying undescribed lineages. Across 3,344 independent 16S rRNA gene amplicon studies, every sequence cluster was tested against a type-strain reference and placed at the deepest rank it supports. Of 204,813 classified clusters, 20,516 were named to species and 127,906 to genus, while 4,741 matched no described species. Six published datasets whose authors could name their Lactobacillaceae only as "Lactobacillus", or not at all, are reclassified here. Genera described from one habitat occur far beyond it, three bee-associated genera occurring on Rosaceae and Brassicaceae at several times their rate on wind-pollinated grasses, and we found no published Bombilactobacillus record from a plant. Undescribed lineages concentrate in the least-cultured hosts, reaching 86.1% and 77.4% of studies in the stingless bees Melipona and Tetragonula, and are most divergent in the turtle ant Cephalotes and, among plants, in tea, Camellia. An independent genome-resolved survey of pot honey converges on the same two genera. The primary descriptions of forty-eight species from these hosts specify a supplemented medium, so the hosts carrying undescribed lineages also indicate how to culture them.

Flavobacterium psychrophilum is a devastating pathogen of fish reared in freshwater worldwide. Serotyping is a relevant method for epidemiological surveillance and outbreak detection, as well as for a better understanding of host-pathogen interactions. Serological diversity may also have important consequences for the selection of appropriate strains for vaccine development and for selective breeding for increased disease resistance. F. psychrophilum serotyping relies on structural variations in the O-polysaccharide (O-PS) moiety of the cell surface lipopolysaccharide (LPS). However, conventional serotyping is costly, labor-intensive and requires significant technical expertise. Moreover, divergent scheme proposals highlighted the absence of harmonization among laboratories. In this context, the development of an mPCR-based serotyping scheme targeting wzy genes greatly improved the reliability and standardization of serotyping. Nevertheless, the proposed mPCR scheme did not capture the entire diversity of genomic variability. The aim of this study was to establish a robust and publicly available tool for F. psychrophilum genome-based serotyping. Extensive genome analysis of the O-antigen biosynthesis locus allowed the identification of biomarkers enabling the development of FlavoTyper, an in-silico-based serotyping tool. The FlavoTyper tool was evaluated on all F. psychrophilum genome assemblies publicly available, providing sound and sensitive predictions and easily interpretable results. When applied to a curated collection of publicly available genomes, the in-silico O-types assigned by the tool were statistically significantly associated with host fish species, confirming previous studies (coho salmon with O:0, rainbow trout with O:1 and O:2, and ayu with O:3) and their distribution across MLST clonal complexes revealed that the O-antigen locus is frequently rearranged independently of the core-genome lineage, consistent with the extensive recombination that shapes the evolution and genomic diversity of this species.

Plant growth-promoting bacterial endophytes represent a sustainable strategy for enhancing agricultural productivity while reducing reliance on synthetic fertilizers and pesticides. This study focused on the genomic and functional characterization of two endophytic bacterial strains, R11F and R19M, isolated from bean and maize roots, respectively. Comparative analyses based on 16S rRNA gene sequences, average nucleotide identity (ANI), and genome-to-genome distance calculations (GGDC) classified both isolates as Pseudomonas palleroniana. Comparative genomic analyses revealed highly conserved genomes containing genes associated with plant colonization, phosphate solubilization, stress adaptation, heavy metal resistance, and hydrocarbon degradation. Genome mining further identified 17 and 18 biosynthetic gene clusters (BGCs) in R11F and R19M, respectively, including non-ribosomal peptide synthetases (NRPS), pyoverdine, NRP-metallophores, RiPP-like compounds, arylpolyenes, {beta}-lactones, terpenes, NAGGN, and hydrogen cyanide. Strain-specific BGCs associated with syringomycin and viscosin biosynthesis were identified in R11F, whereas R19M harbored clusters related to asplenin and kolossin biosynthesis. In vitro assays confirmed indole production, phosphate solubilization, and siderophore production, as well as the ability of both strains to grow in nitrogen-free medium. Both strains significantly inhibited the growth of Fusarium oxysporum, Phytophthora cinnamomi, and Colletotrichum gloeosporioides. Furthermore, plant inoculation assays demonstrated host-dependent growth promotion, with R11F showing the most consistent improvements in plant growth parameters in tomato, wheat, and lentil. Overall, the integration of comparative genomics and experimental validation demonstrates that P. palleroniana R11F and R19M possess complementary traits associated with plant growth promotion, pathogen suppression, saline stress adaptation, and bioremediation.

Bartonella henselae is a zoonotic pathogen associated with cat-scratch disease. Although multilocus sequence typing (MLST) has been used for strain classification, its resolution for distinguishing between B. henselae isolates remains limited. We herein developed a B. henselae-specific core genome MLST (cgMLST) scheme based on whole-genome sequencing data and examined the genetic and phenotypic diversities of 80 strains derived from cats, humans, mongooses, and masked palm civets. Using the conventional MLST scheme, the 80 strains were classified into nine sequence types (STs), while cgMLST subdivided them into 72 cgSTs, demonstrating a marked improvement in discriminatory power. The cgMLST scheme comprised 1,183 core genes and showed high applicability across the 80 strains. A phylogenetic analysis revealed that ST1, which has been associated with cat-scratch disease, was further subdivided into three major clusters and two singletons, indicating high genetic heterogeneity within this ST. We also found that the bafA subtypes clustered in a manner that was largely consistent with the cgMLST-based phylogenetic structure, suggesting a close relationship between bafA variations and the genomic background of B. henselae strains. In a human umbilical vein endothelial cell proliferation assay, strains belonging to distinct cgSTs exhibited strain-dependent differences in proliferative capacity, which were associated with the bafA subtype classification. Some strains induced focal cell fragmentation and a reduced cell density at a high multiplicity of infection, indicating strain-dependent differences in endothelial cell injury. Collectively, the present results establish a high-resolution cgMLST framework for B. henselae and demonstrate that genetically distinct strains have diverse endothelial cell phenotypes.

Scrub typhus, caused by Orientia tsutsugamushi, is an obligate intracellular gram-negative pathogen that remains a cause of acute febrile illness in India. Culture isolation of Orientia tsutsugamushi clinical isolates is infrequent because it is technically more challenging than PCR-based molecular identification. In this report, we describe the culture isolation of Orientia from the whole blood of a 64-year-old farmer with acute febrile illness. Whole blood was inoculated onto an 80% confluent L929 cell line. Real-time PCR targeting the 47-kDa and 56-kDa genes, combined with Sanger sequencing, confirmed the isolate. Transmission electron microscopy of infected L929 cells revealed multiple oval-shaped bacteria within the host cytoplasm. Confocal microscopy demonstrated progressive accumulation of CFSE-labelled bacteria within infected cells over time. These findings support the successful isolation and visualization of a blood-derived O. tsutsugamushi isolate and provide a platform for downstream assays of host-pathogen interactions, antimicrobial susceptibility testing, and vaccine development.

Chinese bahaba (Bahaba taipingensis) is a fish species endemic to China and listed as a Class I nationally protected wild animal. Although significant breakthroughs have been achieved in its artificial breeding, high mortality rates persist during cultivation. Beginning in August 2024, sustained mass mortalities occurred in artificially farmed Chinese bahaba at a farm in Guangdong Province. Diseased fish exhibited pronounced skin ulcers, ascites, gastroenteritis, and splenomegaly. Histopathological examination revealed severe necrotizing gastroenteritis, gill necrosis and edema, muscle congestion with inflammatory cell infiltration, hepatic congestion with marked vasculitis, renal interstitial necrosis with tubular atrophy, and abundant melanomacrophage centers in the spleen. Based on biochemical characterization and whole-genome phylogenomic analysis, the isolated strain HCY1 was identified as Vibrio harveyi. Artificial infection experiments with this strain resulted in 100% mortality and reproduced clinical signs similar to those in naturally infected fish. Antimicrobial susceptibility testing showed that HCY1 remained susceptible to florfenicol and trimethoprim-sulfamethoxazole, but was resistant to multiple antibiotics, including {beta}-lactams and tetracyclines. Comparative genomic analysis revealed that HCY1 carries various antimicrobial resistance genes primarily conferring resistance to {beta}-lactam and tetracycline antibiotics, consistent with the phenotypic resistance profile. The strain also harbored numerous virulence genes, including complete type III and type VI secretion systems (T3SS and T6SS), tlh, hap/vvp, and rtxB. Its plasmids encoded multiple virulence-enhancing genes, such as mcpA, pal, and esiB. To our knowledge, this is the first systematic investigation of a disease outbreak in cultured Chinese bahaba, and provides valuable insights for disease control and population conservation of this endangered species.