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PubMed2026

AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.

MOTIVATION: Satellite DNA has long posed challenges for genome assembly and analysis due to its low sequence complexity and poor mappability. These large heterochromatic arrays of tandem repeats are ubiquitous across eukaryotic genomes, yet remain understudied. Current methods for annotating satellite regions, and other classes of tandem repeat arrays, are limited in their ability to annotate divergent or novel sequences. RESULTS: In this work, we introduce AniAnn's, an algorithm for annotating large blocks of tandemly repeating DNAs. AniAnn's exploits the high Average Nucleotide Identity (ANI) shared between repeat units of the same array to quickly and accurately infer the boundaries of such arrays. We show that AniAnn's improves the annotation of satellites and other tandem repeats within a variety of plant and animal genomes, while requiring only a fraction of the runtime compared to previous approaches. We conclude by exploring several use cases of AniAnn's as a lightweight method for masking repeats prior to whole-genome alignment as well as the de novo annotation and classification of satellite repeats. AVAILABILITY: AniAnn's is open source software and available at github.com/marbl/anianns.

Algorithms↗

PubMed2026

Halosimplex yunnanense sp. nov., a novel haloarchaeon from an underground salt mine.

Strain J119T, a halophilic archaeon, was isolated from a salt mine sample collected in Yunnan Province, China. Cells are spherical (diameter 0.5-0.7 µm) or short‑rod‑shaped (0.4-0.5 × 0.7-0.8 µm), non‑motile, Gram‑stain‑negative, and can grow at 20-55°C (optimum 42°C), with NaCl tolerance ranging from 15% to 30% (w/v) (optimum 20%) and a pH growth range of 5.5-9.0 (optimum pH 7.0). Strain J119T's nearly complete 16S rRNA gene sequence (1,452 bp; accession MW736888.1) shows the highest sequence similarity (97.32%) to Halosimplex salinum YPL4T; this value is lower than the species boundary threshold of 98.65%. Its rpoB' gene (1,830 bp; NZ_JBTJEL000000000.1) shares the highest similarity (95.52%) with Halosimplex aquaticum XZYJT29T. Genomic analyses revealed that the average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values between strain J119T and strains YPL4T and XZYJT29T were 78.58%, 82.59%, 25.50% and 82.61%, 85.70%, 29.20%, respectively. The genomic DNA G + C content of strain J119T is 66.5%. Phenotypic, phylogenetic, and genome-based analyses suggest that strain J119T (= KCTC 4326T = MCCC 4K00178T) represents a novel species of the genus Halosimplex, for which the name Halosimplex yunnanense sp. nov. is proposed.

RNA, Ribosomal, 16S↗

PubMed2026

Description of Dorea chungnamensis sp. nov., an Aerotolerant Anaerobe Isolated from Pig Feces.

A Gram-stain-positive, rod-shaped aerotolerant anaerobe was isolated from pig feces and designated as strain YH-dor228T. Phylogenetic analysis using 16 S rRNA gene sequence revealed that the strain was most closely related to Dorea hominis NSJ-36T, with 96.6% similarity. The phylogenomic tree revealed that the strain formed a distinct cluster within the genus Dorea. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between the strain and the most closely related strains within genus Dorea ranged from 73.4 to 74.9, 66.4-70.5, and 20.0-22.2%, respectively. The major fatty acids were C14:0, C16:0, and C16:1 ω9c DMA. The cell wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G + C content of the strain was 40.7%. The chemotaxonomic, phenotypic, and phylogenetic properties of YH-dor228T (= KCTC 25915T=NBRC 117235T) suggested that it represented a novel species of the genus Dorea, for which the name Dorea chungnamensis sp. nov. is proposed.

Animals↗

PubMed2026

Proposal of three novel species of the family Xanthobacteraceae: Xanthobacter pollutisoli sp. nov., Xanthobacter luteus sp. nov. and Aquabacter albus sp. nov., isolated from oil-contaminated soils.

Three Gram-stain-negative bacterial strains, KR7-65T, KR7-225T and CN5-332T isolated from oil-contaminated soil in Korea and China were identified. Phylogenetic analysis based on 16S rRNA gene sequences placed the strains within the family Xanthobacteraceae, with KR7-65T and KR7-225T affiliated with the genus Xanthobacter and CN5-332T with the genus Aquabacter. Sequence similarities to type strains of validly published species were below 98.5%. Core genome phylogeny showed that the four strains formed distinct clusters occupying different positions in the phylogenetic tree and exhibited different closest relatives. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization (dDDH) values between KR7-65T and KR7-225T and members of Xanthobacter were 78.7-87.0%, 74.8-87.8% and 22.7-32.3%, respectively, whereas those between CN5-332T and members of Aquabacter were 80.2-80.7%, 79.6-80.5% and 23.4-23.9%, supporting their assignment as novel species. The DNA G+C contents were 68.0, 69.9 and 66.5 mol% for KR7-65T, KR7-225T and CN5-332T, respectively. Strains KR7-65T and KR7-225T contained phosphatidylcholine, phosphatidylglycerol, phosphatidyl monomethyl ethanolamine, diphosphatidylglycerol (DPG) and an unidentified glycolipid as major polar lipids, whereas DPG was absent in strain CN5-332T. The primary fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), cyclo C19 : 0ω8c and C16 : 0. On the basis of phylogenetic, genomic and phenotypic evidence, strains KR7-65T and KR7-225T represent two novel species of the genus Xanthobacter, for which the names Xanthobacter pollutisoli sp. nov. (type strain KR7-65T=KACC 23453T=NBRC 116939T) and Xanthobacter luteus sp. nov. (type strain KR7-225T=KACC 23282T=NBRC 116940T) are proposed. Strain CN5-332T represents a novel species of the genus Aquabacter, for which the name Aquabacter albus sp. nov. (type strain CN5-332T=KACC 23276T=CCTCC AB 2024343T) is proposed.

Phylogeny↗

PubMed2026

Routine methods misidentify Serratia spp.: Limitations of MALDI-TOF MS revealed by whole-genome sequencing.

Accurate species-level identification within the genus Serratia remains challenging due to extensive phenotypic overlap and high genomic relatedness among closely related and recently described taxa. This study presents an evaluation of routine and genome-based identification approaches applied to clinical Serratia isolates, integrating phenotypic assays, MALDI-TOF MS (Bruker Daltonics), 16S rRNA gene sequencing, and Whole-Genome Sequencing (WGS). A total of 103 isolates collected from a teaching hospital were analyzed. WGS was performed on a subset of isolates. Conventional biochemical methods classified all isolates as Serratia marcescens, whereas MALDI-TOF MS identified 60.1% as S. marcescens, 11.6% as S. ureilytica, and 28.1% just at the genus level. Peak analysis from MALDI-TOF MS revealed specific peaks associated with S. marcescens and S. ureilytica, but limited discriminatory power. WGS of six isolates initially identified as S. ureilytica by MALDI-TOF MS revealed reclassification as Serratia sarumanii (n = 5) and Serratia montpellierensis (n = 1), supported by Average Nucleotide Identity (ANI), Average Amino Acid Identity (AAI), and Digital DNA-DNA Hybridization (dDDH) thresholds. In contrast, 16S rRNA analysis showed limited species-level resolution. Phylogenomic and SNP-based analyses confirmed these classifications with strong support. Overall, this study underscores the critical role of high-resolution genomic approaches for precise species identification and highlights the need for continuous expansion and curation of MALDI-TOF MS reference databases to support reliable clinical diagnostics and epidemiological surveillance of emerging Serratia species.

Spectrometry, Mass, Matrix-Assisted Laser Desorpti↗

PubMed2026

Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir.

Comprehensive phylogenomic and comparative genomic analyses were conducted to clarify the taxonomic boundaries of the genus Metabacillus. Phylogenetic trees reconstructed from a set of single-copy orthologous proteins (SCOPs) revealed that the genus, as currently defined, is polyphyletic. The type species of the genus Metabacillus and its closest relatives formed a consistent clade, herein designated as Metabacillus sensu stricto. The remaining species were grouped into three well-supported clades: Kandeliae, Indicus, and Mangrovi, and two single-taxon lineages: M. arenae and M. lacus. The phylogenomic delineation found in these divergent taxa was corroborated by either inconsistent distribution patterns or the absence of previously defined conserved signature indels (CSIs) specific to Metabacillus. Genomic metrics, including Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), and digital DNA-DNA hybridization (dDDH) further supported the taxonomic delineation proposed here. The observed genomic divergence was mirrored by phenotypic differences, including variations in GC content ranges. Based on this polyphasic evidence, we propose the reclassification of the genus Metabacillus taxa into five novel genera: Chryseobacillus gen. nov. (encompassing the Kandeliae clade), Cohnibacillus gen. nov. (M. lacus), Salimetabacillus gen. nov. (M. arenae), Pantoeobacillus gen. nov. (Indicus clade), and Lutimetabacillus gen. nov. (Mangrovi clade). The core lineage is retained as Metabacillus sensu stricto, for which an emended description of the genus Metabacillus is also provided. A novel bacterial strain, designated as MAU-250T, was isolated from a soil sample collected on the shore of an artificial reservoir in the Andean foothills of the Maule Region in central Chile. Public metagenome screening supported a low-abundance taxon with broad ecological adaptability, preferentially associated with soil habitats. A polyphasic analysis based on phenotypic traits and genomic distances (78.0% ANIb and 19.8% dDDH against its closest relative) also supported its designation as a novel species, for which the name Chryseobacillus diguaensis sp. nov. is proposed. The type strain is MAU-250T (=RGM 3146T = IMI 507634T).

Phylogeny↗

PubMed2026

Halolitoreus marinus gen. nov., sp. nov. and Halolitoreus rarus sp. nov., halophilic archaea isolated from diverse coastal tidal flats, and proposal of the novel family Halolitoreaceae fam. nov. in the order Halobacteriales within the class Halobacteria.

Coastal tidal flats represent dynamic saline environments that harbor largely unexplored haloarchaeal communities. In this study, amplicon sequencing, metagenomic analyses, and cultivation-based approaches revealed substantial haloarchaeal diversity in tidal flats from four provinces of eastern China despite their relatively low salinity. Five haloarchaeal strains, designated YSMS36T, DYSN1, QDMS2, CMSO5T, and ZSTT2, were isolated from diverse tidal flats. Theses strains shared 16S rRNA gene sequence similarities of 92.1-92.2% with their closest validly named relative, Salinilacihabitans rarus AD-4T. Phylogenetic analyses based on 16S rRNA and rpoB' gene sequences showed that the five strains formed a distinct and well-supported monophyletic lineage, separated from currently recognized members of the class Halobacteria. Average amino acid identity (AAI), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) values between these five strains and the related Halobacteria representatives were 49.3-62.7%, 66.9-74.9%, and 16.2-29.5%, respectively, and well below the accepted thresholds for species and genus delineation. Phylogenomic analyses further supported their placement within a novel family of the order Halobacteriales. Based on phylogenetic, genomic, chemotaxonomic, and phenotypic analyses, these five strains represent two novel species of a novel genus within a novel family. The names, Halolitoreaceae fam. nov., Halolitoreus marinus gen. nov., sp. nov., and Halolitoreus rarus sp. nov. are herein proposed.

Coastal tidal flat↗

PubMed2026

Albidovulum molybdatiresistens sp. nov., a molybdate-resistant bacterium isolated from river water.

A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, white rod-shaped strain, RF13T, was isolated from water samples of the Qingliang River in Fucheng County, Hebei Province, China, and was grown at 15-42 °C (optimum 35 °C), pH 6.0-8.0 (optimum pH 7), and 0-0.5% (w/v) NaCl (optimum concentration 0%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RF13T belonged to the genus Albidovulum, with closest sequence similarity to Albidovulum salinarum MCCC 1K0602T (97.2%), Frigidibacter oleivorans CGMCC 1.3778T (97.2%), Allgaiera indica MCCC 1A01802T (96.8%), and Pseudothioclava arenosa KCTC 52190T (96.4%). The genome size of strain RF13T was 3.7 Mb, and the DNA G+C content was 64.6%. The DNA-DNA hybridisation value (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) between strain RF13T and the reference strain were less than 20.0%, 78.8%, and 72.8%, respectively. Chemotaxonomic analysis revealed Summed feature 8 (48.4%) (C18:1 ω6c and/or C18:1 ω7c), C18:1 ω7c 11-methyl (22.1%), C18:0 3OH (7.9%), and C10:0 3OH (5.0%) as predominant fatty acids. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminolipids, two unidentified phospholipids, and three unidentified lipids. The predominant isoprenoid quinone was ubiquinone-10 (Q-10), and a small amount of Q-9 was also detected. In addition, strain RF13T exhibited a minimum inhibitory concentration (MIC) of 20 mM for molybdate in R2A broth medium and was capable of reducing molybdate to molybdenum blue. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with 16S rRNA gene sequence analyses and draft genome sequence comparisons, strain RF13T was considered to represent a novel species of the genus Albidovulum, and was therefore named Albidovulum molybdatiresistens sp. nov. The type strain was RF13T (= GDMCC 1.3414T= JCM 35643T).

Phylogeny↗

PubMed2025

KpSC-ID: a multiplex real-time PCR assay for the simultaneous detection of the Klebsiella pneumoniae species complex and specific identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae and Klebsiella variicola.

The Klebsiella pneumoniae species complex (KpSC) comprises five closely related bacterial species, namely Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola, Klebsiella quasivariicola and Klebsiella africana. The KpSC is ubiquitous in the environment and is also an important human pathogen, particularly associated with healthcare-associated infections. The accurate detection and differentiation of the KpSC is challenging owing to the close phenotypic and genotypic identity (93-95% average nucleotide identity) shared between these members. Current diagnostic assays either fail to detect and identify all KpSC members or misidentify some KpSC members as K. pneumoniae sensu stricto. It is currently estimated that ~20% of human infections are caused by members of the KpSC other than K. pneumoniae. This leads to underreporting of some KpSC members in both clinical and environmental settings, which impacts our understanding of the importance of each species. Furthermore, it limits our understanding of the global and local epidemiological impact of some members of the KpSC. In this study, a rapid multiplex real-time PCR assay (KpSC-ID) was designed and developed to detect all KpSC members while simultaneously identifying the predominant human pathogens K. pneumoniae, K. quasipneumoniae and K. variicola. Assay performance was verified in silico using a panel of over 1,000 publicly available genome sequences and experimentally validated using a panel of genomic DNA extracted from 54 Enterobacteriaceae. The assay displayed excellent specificity against over 1,000 genome sequences tested in silico. During in vitro validation, the pan-KpSC assay detected each (29/29) KpSC species and strains tested. For the species-specific assays, 100% specificity was demonstrated in the K. pneumoniae, K. quasipneumoniae and K. variicola assays, respectively. Sensitivity of 10 genomic equivalents was demonstrated for each assay. Ultimately, the diagnostic assay developed in this study can improve our understanding of the significance of KpSC members, which is important when investigating their routes of transmission and epidemiology.

Klebsiella↗

PubMed2026

Description and genomic characterization of Aquipuribacter aurantiacus sp. nov., isolated from saline lake sediment.

Strains MA13-6T and MA13-13, two Gram-stain-positive, aerobic, short rod-shaped actinobacteria, were isolated from a saline lake in Ngari Prefecture, Xizang Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these two strains belonged to the genus Aquipuribacter, with the closest relationship to Aquipuribacter hungaricus IV-75T (98.47% sequence similarity) and Aquipuribacter nitratireducens AMV4T (97.36% sequence similarity). Phylogenetic analysis based on genomes further confirmed their classification as a distinct cluster within the genus Aquipuribacter. The average nucleotide identity and digtal DNA-DNA hybridization values between these two strains and their closest relative Aquipuribacter hungaricus IV-75T, were 82.44-82.49% and 23.00%, respectively, clearly indicating that strains MA13-6T and MA13-13 represent a novel species. The 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA-DNA hybridization values between these two strains were 99.79%, 99.97% and 99.40%, respectively, unequivocally confirming their classification within the same species. However, DNA fingerprinting analysis distinguished them as non-clonal variants. The polar lipids comprised phosphatidylglycerol, two unidentified phospholipids, two unidentified glycolipids, and two unidentified lipids. The predominant respiratory quinone was MK-10 (H4). The major fatty acids were anteiso-C15:0, C18:1ω9c, isoC16:0 and anteiso-C17:0. The cell wall diagnostic diamino acid was meso-diaminopimelic acid. Based on phylogenetic analyses combined with phenotypic and chemotaxonomic characterization, strains MA13-6T and MA13-13 represent a novel species of the genus Aquipuribacter, for which the name Aquipuribacter aurantiacus sp. nov. is proposed. The type strain is MA13-6T (=MCCC 1K10045T = KCTC 59572T).

Phylogeny↗

PubMed2026

Salinimicrobium molybdatiresistens sp. nov., a novel molybdate-resistant and selenite-reducing bacterium isolated from river silt.

Strain TH3T was isolated from the river bottom silt collected in Hengshui, Hebei Province, China. The bacterium is a yellow-pigmented, rod-shaped, Gram-staining negative and aerobic organism. It was able to grow between 10 and 37 °C (optimum 30 °C), at pH values from 5.0 to 9.0 (optimum pH 7.0), and tolerated NaCl concentrations ranging from 0 to 13% (w/v, optimum 2%). The 16 S rRNA gene sequence of strain TH3T was found to be most closely related to Salinimicrobium sediminilitoris ASW11-47T (99.7%). Nevertheless, genome comparison revealed the relatedness indices below species delineation thresholds: digital DNA-DNA hybridization was 49.7%, and average nucleotide identity was 93.2%, and average amino acid identity was 94.2% compared to Salinimicrobium sediminilitoris ASW11-47T. Strain TH3T had a genome size of 3.7 Mb and a DNA G + C content of 41.0%. The major fatty acids observed for strain TH3T (≥ 5%) were iso-C14:0, iso-C15:0, anteiso-C15:0, iso-C16:0, iso-C16:0 3-OH, iso-C17:0 3-OH, and summed feature 3. The polar lipid composition included phosphatidylethanolamine, one unidentified phospholipid, two aminolipids, along with five unknown lipids. The sole respiratory quinone in strain TH3T was menaquinone-6. In addition, strain TH3T was highly resistant to molybdate (500 mM) and selenite (20 mM), and could completely reduce 1 mM selenite to red elemental SeNPs within 3 d. Strain TH3T contains several putative selenite-reducing genes, including sodA, serA, serC, cysH, deoC, tktA, and pdhC. Based on polyphasic characterization, strain TH3T was found to be a novel species in the genus Salinimicrobium, and the proposed name is Salinimicrobium molybdatiresistens sp. nov. The type strain is TH3T (= GDMCC 1.3399T = JCM 35713T).

Rivers↗

PubMed2026

Comparative genomics reveals population structure and functional differentiation in Limosilactobacillus fermentum.

Limosilactobacillus fermentum is a widely distributed lactic acid bacterium frequently detected in fermented foods and host-associated microbiota, yet its global genomic diversity and functional variability remain insufficiently characterized. Here, we performed a large-scale comparative genomic analysis of 336 high-quality L. fermentum genomes curated from public databases. Species identity was validated using average nucleotide identity (ANI), and population structure was examined using pairwise ANI comparisons together with Mash-based phylogenetic reconstruction. Clustering at ≥ 99% ANI resolved the dataset into 15 genomic clusters, with four dominant lineages comprising the majority of genomes. Pangenome reconstruction identified 5,853 gene clusters, including 1,325 core genes (22.6%) and a large accessory component dominated by low-frequency genes. Heap's law modeling (λ = 0.19) indicated a weakly open pangenome, suggesting ongoing gene acquisition as additional genomes are sampled. Functional annotation revealed that core genes were primarily associated with essential cellular processes, whereas accessory genes were enriched in carbohydrate metabolism, membrane-associated functions, and defense-related systems. Variation in carbohydrate-active enzymes (CAZymes), transport systems, and stress-response genes was observed across lineages, indicating strain-level functional diversity. Although genomes from human and food sources were broadly distributed across phylogenetic lineages, multivariate analysis showed that gene-content variation was more strongly associated with genomic lineage than with isolation source. These results provide a population genomic framework for understanding genomic diversity and functional potential in L. fermentum.

Phylogeny↗

PubMed2026

Pseudaquabacterium prasiolae sp. nov., Isolated from the Freshwater Green Alga Prasiola japonica, and Rubrivivax soli sp. nov., Isolated from Soil, with Reclassification of Aquabacterium humicola as Pseudaquabacterium humicola comb. nov.

Two Gram-stain-negative, catalase- and oxidase-positive, strictly aerobic, non-flagellated rod-shaped bacteria, designated OR-4T and RP6-9T, were isolated from the freshwater green alga Prasiola japonica and soil in Republic of Korea, respectively. Strain OR-4T exhibited gliding motility, whereas strain RP6-9T lacked gliding motility. Strain OR-4T grew at 10-30 °C, pH 6.0-9.0, and 0-1.5% (w/v) NaCl, while strain RP6-9T grew at 20-35 °C, pH 6.0-9.0, and 0-1.0% (w/v) NaCl. Both strains contained ubiquinone-8 as the sole respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; strain OR-4T additionally possessed an unidentified phospholipid and an unidentified polar lipid. The predominant fatty acids of OR-4T were C12:0, C16:0, summed feature 3 (C16:1ω6c and/or C16:1ω7c), and summed feature 8 (C18:1ω7c and/or C18:1ω6c), whereas RP6-9T contained C12:0, C16:0, and summed feature 3 as major components. The genomic DNA G + C content of both strains was 71.0 mol%. Whole-genome-based phylogenomic analyses placed OR-4T and RP6-9T within the genera Pseudaquabacterium and Rubrivivax, respectively, forming distinct lineages. Comparative analyses of average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity further supported their assignment to these genera while confirming their separation from previously described species. Based on combined phenotypic, chemotaxonomic, and genomic evidence, strains OR-4T and RP6-9T represent novel species, for which the names Pseudaquabacterium prasiolae sp. nov. (type strain OR-4T =KACC 22752T =NBRC 116024T) and Rubrivivax soli sp. nov. (type strain RP6-9T =KACC 24055T =DSM 119932T) are proposed. Phylogenomic analyses also support the reclassification of Aquabacterium humicola as Pseudaquabacterium humicola comb. nov. (type strain RJY3T =KCTC 92105T =NBRC 115831T).

Phylogeny↗

PubMed2026

Burkholderia arboris bacteremia initially identified as Burkholderia cepacia complex: a genome-based case report.

We report a bloodstream Burkholderia arboris isolate from a 75-year-old man without cystic fibrosis. The organism was recovered from both aerobic bottles of two separately collected blood-culture sets and was initially assigned to the Burkholderia cepacia complex (Bcc) by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Whole-genome sequencing yielded three circular chromosomes and one circular plasmid. DFAST_QC identified B. arboris as the only type-strain match above the species threshold, with an average nucleotide identity of 99.48%; the next-highest match was B. seminalis at 93.33%. Multilocus sequence typing identified ST-2575, and ResFinder detected no acquired antimicrobial resistance genes. The patient improved after 14 days of meropenem therapy without recurrent B. arboris bacteremia. This report adds a clinically supported bloodstream infection, a complete genome resource, and detailed susceptibility data, while illustrating the importance of up-to-date reference genomes for species-level interpretation of unusual Bcc isolates.

Humans↗

PubMed2025

Rapid Radiations Outweigh Reticulations During the Evolution of a 750-Million-Year-Old Lineage of Cyanobacteria.

Species are a fundamental unit of biodiversity. Yet, the existence of clear species boundaries among bacteria has long been a subject of debate. Here, we studied species boundaries in the context of the phylogenetic history of Nostoc, a widespread genus of photoautotrophic and nitrogen-fixing cyanobacteria that includes many lineages that form symbiotic associations with plants (e.g. cycads and bryophytes) and fungi (e.g. cyanolichens). We found that the evolution of Nostoc was characterized by eight rapid radiations, many of which were associated with major events in the evolution of plants. In addition, incomplete lineage sorting associated with these rapid radiations outweighed reticulations during Nostoc evolution. We then show that the pattern of diversification of Nostoc shapes the distribution of average nucleotide identities (ANIs) into a complex mosaic, wherein some closely related clades are clearly isolated from each other by gaps in genomic similarity, while others form a continuum where genomic species boundaries are expected. Nevertheless, recently diverged Nostoc lineages often form cohesive clades that are maintained by within-clade gene flow. Boundaries to homologous recombination between these cohesive clades persist even when the potential for gene flow is high, i.e. when closely related clades of Nostoc co-occur or are locally found in symbiotic associations with the same lichen-forming fungal species. Our results demonstrate that rapid radiations are major contributors to the complex speciation history of Nostoc. This underscores the need to consider evolutionary information beyond thresholds of genomic similarity to delimit biologically meaningful units of biodiversity for bacteria.

Phylogeny↗

PubMed2026

Halorubrum marinum sp. nov., Halorubrum rarum sp. nov., Halorubrum wangae sp. nov., Halorubrum shenae sp. nov., and Halorubrum zhoui sp. nov., halophilic archaea from coastal tidal flats, a saline lake, and a marine solar saltern.

Five novel halophilic archaeal strains, designated DTA46T, DTA98T, HHNYT27T, N11T, and SY-15T, were isolated from diverse saline environments across various regions of China. Amplicon and metagenome analyses revealed that three amplicon reads were affiliated with strains DTA46T, HHNYT27T, and N11T while two MAGs related to strains N11T and SY-15T. The sequence similarities among these five strains and current species of the genus Halorubrum were 93.1%-99.1% and 86.0%-95.9% judged by 16S rRNA and rpoB' genes, respectively. Phylogenomic and comparative genomic analyses revealed their close affiliation with Halorubrum. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between these strains and existing Halorubrum species ranged from 74.9%-93.6%, 22.3%-58.3%, and 68.3%-93.7%, respectively. All are below the recommended thresholds for species delineation, which supports their classification as novel taxa. The growth characteristics of strains DTA46T, DTA98T, HHNYT27T, N11T, and SY-15T were determined as follows: temperature range 20-60 °C (optima: 35, 37-42, 37, 35, and 42 °C), NaCl concentration 1.4-5.5 M (optima: 2.6, 3.1, 3.1, 3.1, and 5.1 M), and pH range 5.5-9.5 (optima: 8.0, 8.0, 7.0, 7.5, and 7.0). Based on the polyphasic characterization integrating phenotypic, chemotaxonomic, phylogenetic, and phylogenomic evidence, strains DTA46T, DTA98T, HHNYT27T, N11T, and SY-15T are proposed to represent five novel species of the genus Halorubrum, for which the names Halorubrum marinum sp. nov., Halorubrum rarum sp. nov., Halorubrum wangae sp. nov., Halorubrum shenae sp. nov., and Halorubrum zhoui sp. nov. are designated, respectively.

Phylogeny↗

PubMed2026

Rhizobium zaerense sp. nov., a novel member of the Rhizobium leguminosarum species complex with a broad geographic distribution and multiple legume hosts.

A novel nitrogen-fixing rhizobial strain, designated Z1P35ᵀ, was isolated from root nodules of Pisum sativum grown in the Zaër region of Morocco. Phylogenetic analysis of the 16S rRNA gene placed strain Z1P35ᵀ within the genus Rhizobium, showing 100% sequence identity with several undescribed genospecies of the Rhizobium leguminosarum species complex (Rlc). Strain Z1P35ᵀ exhibited low average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with all described Rhizobium species, but high ANI and dDDH values (97.62 and 78.8%, respectively) with Rhizobium sp. SRDI565, representing genospecies M (GsM) of the Rlc, suggesting that Z1P35ᵀ represents a novel species corresponding to GsM within this complex. FastANI screening against all Rhizobium genomes available in GenBank revealed that Z1P35ᵀ shares ANI values above the bacterial species delimitation threshold with 17 unclassified strains, which, together with Z1P35ᵀ and Rhizobium sp. SRDI565 (GsM), form a distinct lineage within the Rlc. These 17 strains originate from root nodules of diverse legume hosts and are distributed across the Mediterranean region and Australia, including representatives of the symbiovars viciae and trifolii. Phylogenomic analysis further confirms the clustering of Z1P35ᵀ with Rhizobium sp. SRDI565 (GsM) and several undescribed Rhizobium strains, forming a unique taxonomic unit clearly distinct from other members of the Rlc. Strain Z1P35ᵀ has a genome of 7.6 Mb with a G+C content of 61 mol% and carries numerous genes associated with chemotaxis, nodulation, nitrogen fixation, phosphate solubilization, iron acquisition and abiotic stress tolerance. Differentiation of Z1P35ᵀ from described Rhizobium species was further supported by phenotypic and chemotaxonomic analyses. Based on these results, we conclude that Z1P35T belongs to a novel species, corresponding to genospecies M within the Rlc, for which we propose the name Rhizobium zaerense sp. nov. The type strain is Z1P35ᵀ (DSM 120601ᵀ=CCMM B1365ᵀ).

Phylogeny↗

PubMed2024

Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.

UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566T, delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566T. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HST (DSM 115941T = NRRL B-65665T). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology. IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.

Phylogeny↗