Search Results (840)

Ammonia-oxidizing bacteria (AOB) are the rate-limiting microbial group in biological nitrogen removal. However, difficulties in isolation and cultivation, along with unclear metabolic regulation mechanisms, have long constrained their engineering applications. Existing research has mostly focused on the responses of model strains to environmental factors, while studies on the growth regulation mechanisms driven by key medium components remain scarce. Moreover, there is a lack of efficient strains suitable for complex wastewater with high ammonia and high salinity. To isolate an efficient strain and optimize its culture conditions for high-ammonia wastewater treatment, we collected water samples from a polluted river in Zhongshan City. After enrichment, a strain was isolated via gradient dilution and silica gel plating, identified by scanning electron microscopy and 16S rDNA sequencing as Nitrosomonas europaea W4 (99.93% similarity to the type strain). Single-factor medium optimization examined CaCO₃ and Fe²⁺/Fe³⁺, while temperature and initial ammonia nitrogen effects were tested, and landfill leachate was used for verification. CaCO₃ shortened the lag phase without affecting maximum specific growth rate; replacing Fe³⁺ with Fe²⁺ further reduced lag and enhanced the ammonia oxidation rate. Optimal growth occurred at 25–30 °C and an initial ammonia nitrogen concentration of ~2000 mg/L. In landfill leachate, the strain increased the ammonia degradation rate 6.3-fold, from 4.64 ± 0.11 mg L⁻¹ d⁻¹ in the uninoculated control group to 29.32 ± 0.07 mg L⁻¹ d⁻¹, and importantly, nitrite can be rapidly degraded by indigenous denitrifiers, posing no secondary pollution risk. Overall, N. europaea W4 exhibits high ammonia oxidation efficiency, and the optimized medium and conditions improve its proliferation and metabolic stability, providing a basis for cultivation and application in treating high-strength ammonia nitrogen wastewater. Full article

Background/Objectives: Schisandrin B (Sch B), a bioactive lignan of Schisandra chinensis has been commonly investigated for its antitumor activities, yet its radiosensitizing effect and mechanism remain unclear. This study was conducted to investigate the radiosensitizing effects of Sch B in breast cancer (BC) and elucidate its molecular mechanisms, with a specific focus on the gut microbiota–immune axis. Methods: In vitro, CCK-8, colony formation, and 3D spheroid assays were used to evaluate the effects of Sch B on proliferation inhibition and radiosensitization, flow cytometry and immunofluorescence were used to elucidate the mechanisms involved. In vivo, 4T1 tumor-bearing mice were treated with Sch B, and 16S rDNA sequencing and LC-MS/MS were used to analyze the gut microbiota and short-chain fatty acid (SCFA) metabolism. IHC and qPCR detected antitumor immune responses. Results: Sch B inhibited the proliferation of BC cells in a time- and dose-dependent manner with negligible toxicity to the mammary epithelial cell line MCF-10A. Furthermore, Sch B enhanced the radiosensitivity (sensitization enhancement ratio: 1.20~1.77) of BC by inducing G1 phase cell cycle arrest and delaying radiation-induced DNA double-strand break repair. In vivo, Sch B suppressed BC growth in BALB/c mice without causing obvious systemic toxicity. Sch B reversed tumor-induced gut microbiota dysbiosis (restoring species abundance and the Firmicutes/Bacteroidetes ratio, enriching beneficial genera such as Lactobacillus and Butyrobacter) and normalized SCFA profiles (correlative evidence). Furthermore, Sch B modulated systemic immune responses by increasing the expression of Ifng, Cxcl10, Ddx58 and promoting CD3⁺ and CD8⁺ T-cell infiltration in tumors. Conclusions: Sch B exerts BC radiosensitization through dual mechanisms, direct regulation of the cell cycle and DNA repair, and indirect modulation of the gut microbiota-immune axis (correlative evidence), highlighting it as a safe and effective candidate for improving the efficacy of BC radiotherapy. Full article

Inadequate surface sanitization represents a significant risk to sterility assurance and regulatory compliance. Therefore, an effective cleaning and disinfection program is a critical component of contamination control strategies in pharmaceutical facilities manufacturing sterile medicinal products. This study aimed to standardize a carrier-based methodology for evaluating the efficacy of disinfectants against in-house environmental isolates recovered from a pharmaceutical industry facility. Nine representative strains were selected from five different groups—Gram-positive non-spore-forming bacteria (Micrococcus luteus and Kocuria spp.), Gram-positive spore-forming bacteria (two Bacillus spp. strains), Gram-negative bacteria (Pseudomonas aeruginosa and Acinetobacter haemolyticus), yeasts (Candida parapsilosis and Rhodotorula mucilaginosa), and filamentous fungus (Penicillium spp.)—based on historical environmental monitoring data (2012–2022), and were characterized using matrix-assisted laser desorption/ionization-time-of-flight/mass spectrometry (MALDI-TOF MS) and molecular sequencing (16S rRNA or D2 LSU rDNA). Disinfectant efficacy was assessed on stainless-steel and low-density polyethylene surfaces using NF T 72-281:2014 with adaptations, testing alcohol 70%, sodium hypochlorite 0.5%, quaternary ammonium 0.05%, peracetic acid 0.5%, and accelerated hydrogen peroxide wipes. All agents demonstrated ≥5 log₁₀ reductions against vegetative bacteria and fungi on both surfaces. However, variable sporicidal performance was observed, particularly for one Bacillus cereus group strain (B1342/15), which showed limited viability reduction on stainless steel. These findings highlight inter-strain variability and the greater tolerance of surface-associated spores. The study reinforces the importance of carrier-based testing using in-house isolates to ensure realistic validation of disinfectants and to strengthen microbiological risk management within pharmaceutical contamination control strategies. Full article

Objectives: Allergic asthma (AA) is an increasing public health concern. The aim of this study was to investigate the potential effects of immune responses against AA in rats following intervention with Lacticaseibacillus paracasei DMLA16017 and vitamin D (VD). Methods: L. paracasei DMLA16017 was identified using 16S rDNA sequencing, while a rat model of AA was established via ovalbumin (OVA) induction. Subsequently, samples were collected for biomarker analysis in peripheral blood and lung tissue (including serum OVA-immunoglobulin E (IgE) and cytokines) using enzyme-linked immunosorbent assays and assessment of the composition of the intestinal microbiota and species diversity using 16S rRNA sequencing. Results: In the rat model, OVA-induced sensitization induced significant physiological alterations, including pulmonary tissue damage, elevated white cell counts, increased serum levels of OVA-IgE and cytokines interleukin (IL)-4 and IL-17, and reduced levels of IFN-γ and TGF-β. These changes were accompanied by dysbiosis of the gut microbiota and decreased species diversity. Co-administration of VD and DMLA16017 effectively ameliorated the physiological disturbances and histopathological abnormalities in rats with AA, restored the balance between cellular and immune responses, and improved the composition of the gut microbiota and species diversity. Conclusions: Combined intervention with VD and DMLA16017 can be used to treat AA disorders, with potential long-term modulation of the immune system. Full article

Macrococcus is a genus of Gram-positive cocci in the Staphylococcaceae family and a close phylogenetic relative of Staphylococcus. It is not a significant human pathogen but is known to widely colonize different environments, including animal skin and food products. Phylogenetically, Macrococcus is distinct from yet closely related to Staphylococcus, particularly the sciuri group. The species is effectively identified through such molecular markers as hsp60 and 16S rDNA. A key biochemical feature is an identified FAD-dependent oleate hydratase in Macrococcus equipercicus (M. equipercicus). Critically, Macrococcus carries various mobile antibiotic-resistance genes, especially against β-lactams (e.g., mecB, mecD) and macrolides (e.g., mef(F), msr(G)); these genes are located on plasmids, SCCmec-like elements, or resistance islands (e.g., McRI_mecD), which facilitates their horizontal transfer. Surveillance confirms the widespread presence of methicillin-resistant Macrococcus, often with a multidrug-resistant phenotype, in food animals and their products. Although its own pathogenicity is low, Macrococcus acts as a reservoir and transmission platform for resistance genes: through horizontal gene transfer, it can potentially confer resistance to pathogenic Staphylococcus, thereby posing a threat to animal and public health. This review summarizes the basic biological characteristics and drug resistance-related research progress of the genus Macrococcus; it aims to provide a reference for subsequent studies as well as to establish technical support and a theoretical basis for the epidemiological investigation, drug-resistant strain identification, and clinical drug-resistance risk prevention and control of Macrococcus. Full article

Background: We aimed to evaluate the prognostic significance of bone pain at presentation in metastatic castration-sensitive prostate cancer (mCSPC) and its association with radiographic progression-free survival (rPFS), independent of established prognostic factors. Methods: We retrospectively analyzed 205 patients with mCSPC treated at our center. Data were obtained from patient files and hospital records. rPFS was estimated using the Kaplan–Meier method and compared using the log-rank test. Baseline characteristics according to bone pain status were compared using the χ² test for categorical variables and the Wilcoxon test for continuous variables. Results: Median rPFS for the entire cohort was 23.8 months (95% CI: 18.6–29.0). In univariate analysis, median rPFS was significantly shorter in patients with bone pain compared to those without (16.9 vs. 29.5 months, p < 0.001). Other factors associated with worse rPFS included ECOG PS ≥ 1, DNA repair mutations, high disease volume, liver metastasis, hemoglobin < 12 g/dL, and albumin < 3.5 g/dL. In multivariate analysis, bone pain (HR = 2.37, 95% CI: 1.29–4.34; p = 0.005), albumin < 3.5 g/dL (HR = 1.99; p = 0.034), hemoglobin < 12 g/dL (HR = 2.00; p = 0.005), and liver metastasis (HR = 3.07; p = 0.024) remained independent predictors of shorter rPFS. Conclusions: Bone pain at presentation is an independent prognostic factor for shorter rPFS and may help guide risk stratification and treatment decisions in mCSPC. Full article

Gram-stain-positive, endospore-producing, mesophilic and rod-shaped strain O16^T was isolated from a copper mine’s soil and characterized using a polyphasic taxonomic approach. The 16S rRNA gene-sequence analysis revealed that strain O16^T belongs to the genus Saccharibacillus. It exhibited the highest sequence similarity to Saccharibacillus endophyticus JM-1350^T (97.2%), followed by ‘Saccharibacillus alkalitolerans’ VR-M41^T (97.1%), Saccharibacillus sacchari GR21^T (96.8%), Saccharibacillus kuerlensis HR1^T (96.6%), and Saccharibacillus deserti WLJ055^T (95.7%). Genome-based comparisons revealed that the digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain O16^T and its closest relatives, S. endophyticus JM-1350^T and ‘S. alkalitolerans’ VR-M41^T, were 21.3% and 22.3%, and 76.6% and 77.6%, respectively, which are well below the recommended thresholds for species delineation. The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. Phosphatidylglycerol and diphosphatidylglycerol were the major polar lipids in strain O16^T. The predominant menaquinone was MK-7. The DNA G+C content was 53.4%. The major cellular fatty acids present were anteiso-C_15:0 (60.8%), iso-C_16:0 (9.5%) and C_16:1 ω11c (7.4%). On the basis of phenotypic, chemotaxonomic, and genotypic evidence, strain O16^T is considered to represent a novel species within the genus Saccharibacillus. This data strongly supports the classification of the strain O16^T as a novel species in the genus Saccharibacillus, for which we propose the name Saccharibacillus soli sp. nov. strain O16^T (=CCM 8781^T = KCTC 33898^T). Full article

Oocyte maturation is a pivotal event in teleost reproduction that directly determines egg quality, fertilization success, and the developmental competence of early embryos. However, the transcriptional and post-transcriptional regulatory mechanisms operating within oocytes during maturation in marine teleosts remain poorly understood. In the present study, the orange-spotted grouper (Epinephelus coioides), an economically important marine aquaculture species, was used as a model. Oocytes at four distinct maturation stages were obtained by microscopically removing the surrounding follicular layers, followed by integrated mRNA-seq and miRNA-seq analyses to characterize the molecular regulatory landscape underlying oocyte maturation and hydration. The results showed that, as maturation progressed, oocyte diameter and wet weight increased significantly, accompanied by a marked decrease in Na⁺ content, a significant increase in K⁺ content, and the continuous accumulation of most free amino acids, indicating the gradual establishment of an osmotic basis favorable for oocyte hydration. Transcriptomic analysis further revealed extensive transcriptional remodeling during both the early and late phases of maturation. Differentially expressed genes were significantly enriched in pathways related to oocyte meiosis, cytokine signaling, lipid metabolism, DNA replication, cell cycle regulation, ribosome biogenesis, spliceosome function, oxidative phosphorylation, and mitochondrial activity, suggesting that oocyte maturation is a dynamic process characterized by a shift from basal growth maintenance to metabolic reprogramming, maternal transcript remodeling, and terminal maturation responses. miRNA profiling identified a large number of stage-specific differentially expressed miRNAs, including let-7d-5p, miR-22a-3p, and novel-miR-20/27/118, whose predicted target genes were mainly enriched in ribosome-related pathways, oxidative phosphorylation, DNA replication, transcriptional regulation, and signal transduction. Moreover, the miRNA–TF–mRNA regulatory network demonstrated that miRNAs may not only directly repress target genes, but also mediate hierarchical regulatory cascades through transcription factors, thereby coordinately participating in cell cycle progression, cytoskeletal remodeling, vesicular transport, and immune- and cell communication-related responses. Collectively, this study provides the first systematic temporal atlas of mRNA and miRNA regulation during oocyte maturation and hydration at the oocyte level in a marine teleost, thereby deepening our understanding of the molecular basis of meiotic resumption and egg quality formation, and offering valuable theoretical support for the optimization of artificial breeding and the identification of key molecular targets in grouper reproduction. Full article

Background/Objectives: Bisulfite-based cell-free DNA (cfDNA) methylation assays enable the detection of clinically valuable epigenetic biomarkers but often cause DNA degradation and inconsistent conversion efficiency, limiting performance in low-input liquid biopsy samples. We aimed to develop and evaluate a fully enzymatic cfDNA methylation workflow that preserves DNA integrity and supports quantitative clinical detection. Methods: The assay integrates TET2-mediated oxidation and APOBEC3A deamination with RNase H2-guided primer design, uracil-DNA glycosylase error suppression, and dual-probe detection compatible with quantitative PCR (qPCR) and digital PCR (dPCR). Performance was assessed using serial dilutions of methylated HT29 DNA, unmethylated controls, and plasma cfDNA from colorectal cancer (CRC) patients and healthy donors. Analytical sensitivity, linearity, and concordance between platforms were evaluated. Results: The 40-marker panel demonstrated higher cumulative methylation scores and more frequent methylation-positive signals in CRC cfDNA compared to controls. dPCR confirmed single-molecule resolution and clear discrimination between methylated and unmethylated templates, with occasional double-positive partitions consistent with mixed allelic methylation. Signal intensity across the dilution series followed a four-parameter logistic model, achieving detection sensitivity below 0.2% methylated DNA. qPCR and dPCR results showed strong correlation across the HT29 dilution series (R² = 0.80) and high concordance in classifying CRC and healthy samples. Conclusions: This TET2–APOBEC-based enzymatic cfDNA assay enables sensitive, quantitative, sequencing-free methylation detection under gentle conditions, supporting its application in early colorectal cancer screening and routine clinical liquid biopsy workflows. Full article

The global incidence of nonalcoholic fatty liver disease (NAFLD) is rising, with no approved pharmacotherapy available. Medicinal plants offer a potential preventive strategy. Anacyclus pyrethrum root exhibits anti-inflammatory and glucose-regulating properties, but its role in NAFLD prevention is unclear. This study aims to investigate the preventive effect of Anacyclus pyrethrum root ethanol extract (APE) against NAFLD and its underlying mechanisms. The chemical composition of APE was analyzed by UHPLC-HRMS. Network pharmacology predicted the potential signaling pathways underlying its protective effects against NAFLD. In a 12-week high-fat diet mice model, APE treatment led to measurements of blood glucose, lipid profiles, liver function parameters, histopathological changes in liver and colon, and gut microbiota alterations via 16S rDNA sequencing. In animal experiments, APE lowered fasting and random blood glucose, total cholesterol, triglycerides, LDL-C, AST, ALT, and serum lipopolysaccharide while increasing HDL-C, and alleviated hepatic steatosis. Network pharmacology suggested APE acts via TLR, NF-κB, and TNF pathways. In vivo, APE suppressed hepatic TLR4, MyD88, p-NF-κB p65, the p-NF-κB p65/NF-κB p65 ratio, and TNF-α/IL-6 levels. Gut microbiota analysis showed increased Akkermansiaceae and decreased Desulfovibrionaceae. APE also upregulated intestinal Occludin and ZO-1, and downregulated intestinal TNF-α and IL-6. APE prevents NAFLD progression, potentially by regulating gut microbiota, protecting the intestinal mucosal barrier, and inhibiting the LPS/TLR4/MyD88/NF-κB pathway. Full article

Monacha cartusiana (O. F. Müller, 1774), native to the Mediterranean region and Europe, is a terrestrial gastropod recognized as a highly destructive agricultural pest that causes significant damage to crop plants, fruit trees, vegetables, ornamentals, and natural ecosystems. Despite its broad geographic distribution, the evolutionary history and phylogeographic relationships of M. cartusiana populations remain globally unexplored. This study reports the first molecularly confirmed record of M. cartusiana in Pakistan and investigates its genetic diversity and phylogeographic structure within a global context using mitochondrial markers. After morphological identification, genomic DNA was extracted from collected specimens using the CTAB method, followed by amplification and sequencing of the mitochondrial COI and 16S rRNA genes. The resulting sequences were subsequently analyzed using DnaSP and PopART software to estimate genetic diversity, perform neutrality tests, and construct haplotype networks. Published sequences of M. cartusiana retrieved from GenBank were incorporated to provide a global comparative framework. The COI dataset (555 bp) revealed 52 haplotypes, whereas the 16S rRNA dataset (269 bp) identified 14 haplotypes across global populations. High haplotype diversity (Hd = 0.946 for COI; Hd = 0.831 for 16S rRNA) and moderate nucleotide diversity (π = 0.010 for COI; π = 0.01253 for 16S rRNA) indicated substantial genetic variability within the species. Neutrality tests produced negative and insignificant values for Tajima’s D for COI and significant values for 16S rRNA (−1.428 for COI; −0.20586 for 16S rRNA) and Fu’s Fs (−29.776 for COI; −1.263 for 16S rRNA), suggesting historical population expansion. Phylogenetic reconstruction and haplotype network analyses identified two major clades (Clade A and Clade B), reflecting genetic relationships among populations from different geographic regions. AMOVA based on COI and 16S rRNA sequences revealed significant population structuring, with 29.98–51.30% of the total genetic variation occurring among populations and high fixation indices (FST = 0.299–0.51398, p = 0.001), indicating pronounced genetic differentiation and restricted gene flow. Pairwise FST analyses indicated that the Pakistani population is most closely related to populations from Italy and Central Europe, suggesting a closer genetic affinity with Southern or Central European populations. However, FST alone does not allow definitive inference of introduction directionality, and additional analyses would be required to robustly identify the source population. Overall, this study provides the first comprehensive molecular and phylogeographic assessment of the M. cartusiana species from Pakistan within a global context. These findings contribute important baseline data for understanding the evolutionary dynamics, dispersal history, and population connectivity of this economically important pest species. The pronounced genetic differentiation among populations and the suggested genetic affinity of the Pakistani population with European lineages have direct implications for biosecurity monitoring, invasion pathway tracing, and targeted pest management strategies. Future research integrating nuclear markers with the mitochondrial data presented here will be essential for a more complete understanding of gene flow and local adaptation in this species. Full article

Spi-1 Proto-Oncogene (SPI1) encodes Purine-rich box 1 Transcription Factor (PU.1), a transcription factor of the ETS family that regulates hematopoietic lineage commitment and immune cell differentiation. Alteration of PU.1 dose or ETS domain integrity may interfere with transcriptional programs, which adds to hematopoietic dysregulation and leukemogenesis. Even though changes in SPI1 expression have been associated with acute myeloid leukemia (AML), the structural and regulatory effects of missense mutations at the PU.1 ETS domain have not been entirely studied, and targeting the PU.1 ETS domain by ligands is an area of computational analysis that should be further pursued. To computationally describe deleterious missense variants of SPI1 in terms of structural stability, evolutionary conservation, post-translational modification (PTM) context and interaction networks, and to measure ADMET-mediated molecular docking of cinnamic acid with the PU.1 ETS domain (8EQG) as a potential modulator. Missense nsSNPs were obtained through Ensembl and narrowed down by consensus prediction of pathogenicity (PredictSNP, combining SIFT, PolyPhen, SNAP and PhD-SNP and other tools). InterPro/UniProt was used for domain mapping. SWISS-MODEL was used to produce wild-type and mutant PU.1 versions, which were analyzed on the structural alignment and Cα–Cα displacement parameters in UCSF Chimera (v1.19). The estimation of stability change was carried out with I-Mutant and MUpro. Prediction of PTM sites was done using MusiteDeep and exploration of functional partners was done using STRING. Human, mouse and zebrafish orthologue conservation was measured by means of MAFFT alignment. GEPIA2 was used to compare the expression of SPI1 in AML (TCGA-LAML) and normal tissues (GTEx). AutoDock Vina (grid center 6, −2, −9 A; 20 × 20 × 20 A; 16 exhaustiveness) was used to prepare cinnamic acid and dock it into the PU.1 ETS domain (8EQG), with SwissDock being used for consistency checks. SwissADME and ADMETlab 2.0 were used to predict drug-likeness, pharmacokinetics, and toxicity. Nine missense mutations were routinely considered as deleterious with the majority of them being located in or near the ETS DNA-binding domain. Structural comparisons showed local perturbations of the structure and I189F and H211P yielded the greatest conformational changes between prioritized variants whereas other forms had minimal movements. A predominantly destabilizing trend was supported by stability prediction whereby V241G had the strongest destabilization signal with further destabilizations being predicted in I189F and R259C. PTM mapping revealed several potential regulatory residues (phosphorylation, acetylation, ubiquitination, and methylation), which indicated that there could be crosstalk between the sequence variation and the transcriptional regulation. The SPI1 was placed in a central hematopoietic transcriptional module (containing RUNX1, CEBP members, GATA1 and IRF factors) by the STRING network. The cross-species alignment showed that there was high conservation of a number of the mutation sites, which would support functional constraint at the ETS region. The expression analysis revealed that the level of SPI1 mRNA in AML was significantly elevated compared to normal tissues. Docking also indicated a slight and reproducible interaction of cinnamic acid with the ETS domain (top affinity −4.27 kcal/mol), with a solitary leading polar anchor and supportive hydrophobic interactions, which is akin to interaction between fragments. The ADMET profiling revealed the likelihood of success in the oral drug-likeness and low CYP inhibition liability, as well as signifying the presence of a possible hepatotoxicity signal that needs further confirmation through experiments. Comprehensive computational studies suggest that certain pathogenic variants of SPI1 missense defects, especially in the ETS domain, can result in loss of PU.1 structural stability and regulatory environment, which are in line with the disturbed hematopoietic regulation and AML-related dysregulation. Cinnamic acid demonstrates moderate yet reproducible binding to the PU.1 ETS domain and has an overall favorable developability profile, which indicates that it is better considered as a starting scaffold, as opposed to an active inhibitor. The results give a logical basis of focused biochemical validation and structure-directed optimization of ETS domain modulators in hematologic disease settings. Full article

A microbial community study using a culture-dependent method was conducted on dehydrated sludge collected from a steel factory’s wastewater treatment plant. One isolate, designated QWL-01^T, was a strictly anaerobic, Gram-stain-negative, non-motile, non-spore-forming bacterium with coccoid cells measuring 0.6–0.9 μm in diameter. The growth of strain QWL-01^T was observed at 4–40 °C (optimum at 28–35 °C), pH 5.5–8.0 (optimum at pH 7.1), and a range of 0–3% NaCl (optimum at 0.5%). An analysis of the Biolog AN plate revealed positive carbon source utilization only for palatinose, α-ketovaleric acid, and pyruvic acid. The predominant fatty acids were iso-C_13:0 (17.0%), C_16:0 dimethyl acetal (12.0%), and anteiso-C_13:0 (9.2%). A 16S rRNA gene sequence analysis through BLASTN demonstrated that the nearest phylogenetic neighbors of the novel strain were Youngiibacter multivorans DSM 6139^T (93.82%) and Proteiniclasticum ruminis JCM 14817^T (93.75%). The genome size of strain QWL-01^T was 3.69 Mbp, with a G+C content of 50.8 mol%. Comparing strain QWL-01^T with closely related species of genera Proteiniclasticum and Youngiibacter, the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) values ranged from 26.60% to 36.80%, 65.89% to 68.30%, and 49.27% to 51.58%, respectively. Based on phenotypic, physiological, phylogenetic, and genomic relatedness evidence, strain QWL-01^T represents a novel genus in the family Clostridiaceae, for which the name Anaerococcoides asporogena gen. nov. sp. nov. is proposed. Strain QWL-01^T (=BCRC 81396^T = CICC 25258^T = NBRC 117088^T) is the type strain of the proposed novel species. Full article

A newly discovered facultative anaerobic strain, designated as LXY-3^T, was obtained from a soil sample collected at an industrial site in Guangxi, China, known for heavy metal processing. An investigation including phenotypic, chemotaxonomic, and genomic traits was conducted. Phylogenetic analysis based on 16S rRNA showed that LXY-3^T belonged to the genus Paenibacillus. The closest phylogenetic relative of this strain was Paenibacillus anaericanus MH21^T with the similarity of 97.03%. Iso-C_15:0, antéiso-C_15:0, and C_16:1 ω7c alcohol were the major cellular fatty acids. The predominant polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), unidentified phospholipids (PL1-PL8), unidentified resistant material (RM1–RM4), and lipids (L1–L3). For genome sequencing, the genomic DNA G+C content of the strain is 51.2 mol%. Comparative genomic analysis revealed that the average nucleotide identity (ANI) values between strain LXY-3^T and its closest phylogenetic relatives within the genus Paenibacillus (represented by type strains) were consistently below the 95% species demarcation threshold. Nitrogen fixation gene cluster (nifB, nifE, nifK, nifN, nifV, nifX, nifD, and nifH) was conserved in the strain. Correspondingly, digital DNA–DNA hybridization (dDDH) values remained below the 70% cutoff for species delineation. These genomic metrics provide compelling evidence that strain LXY-3^T represents a novel species within the genus Paenibacillus. The type strain LXY-3^T (=CGMCC 1.64949^T = JCM 37600^T) is proposed. Full article

Endophytic bacteria from plants adapted to arid and semi-arid environments represent an underexplored reservoir of microbial diversity with potential agricultural applications. Here, we report a polyphasic taxonomic and genome-based characterization of Achromobacter sp. isolates recovered from root and foliar tissues of Citrullus colocynthis and Peganum harmala, two medicinal plants thriving under harsh environmental conditions. Whole-genome sequencing, phylogenomic analyses, average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), multilocus sequence typing, and detailed phenotypic profiling revealed three previously undescribed species, for which we propose the names Achromobacter colocynthi sp. nov., Achromobacter maghribensis sp. nov., and Achromobacter semiaridum sp. nov. Genome assemblies were highly complete (98.7–99.2%) with minimal contamination (<1%), supporting robust taxonomic inference. All three species displayed ANI and dDDH values below accepted thresholds relative to their closest phylogenetic neighbors, despite partial inconsistencies in 16S rRNA similarity for one isolate, highlighting the value of genome-wide metrics for species delineation. Phylogenomic analyses placed the novel taxa within Achromobacter sp. as distinct evolutionary lineages. Phenotypic characterization indicated broad metabolic versatility, including utilization of carbohydrates, organic acids, and amino acids, tolerance to moderate salinity and acidic pH, and resistance to multiple antimicrobial compounds, traits likely linked to adaptation to endophytic lifestyles under semi-arid conditions. Beyond their taxonomic novelty, the isolates exhibited in vitro traits associated with plant adaptation and stress tolerance, including IAA production, ACC deaminase activity, and tolerance to Zn, Cu, and Cd. Genomic analyses further indicated functions related to phosphate acquisition and stress response. These findings expand the taxonomic framework of Achromobacter sp., establish C. colocynthis and P. harmala as reservoirs of novel endophytic bacteria, and highlight their potential relevance for agricultural biotechnology in stress-prone environments. Full article