Search Results (581)

Perfluorobutane sulfonamide (FBSA), an emerging short-chain perfluorooctanesulfonate (PFOS) alternative used in semiconductor manufacturing and fire suppression, has been detected in environmental matrices and poses environmental risks via industrial emissions and product leaching. However, the microbial degradation characteristics of FBSA are still unclear. In this study, two FBSA-transforming bacterial strains (designated LH-1 and BO-1) were isolated from the contaminated sediments of the Liaohe Estuary and the Bohai Sea, northeastern China. Based on 16S rDNA gene sequence analysis, strain LH-1 showed 99.66% sequence similarity with Neobacillus cucumis C7-N-8-8, while strain BO-1 showed 100% similarity with Glutamicibacter nicotianae OTC-16. Genomic analysis identified key degradation-related genes, including oxidoreductases, hydrolases, and genes involved in chloroalkane (LH-1) or fluorobenzoate (BO-1) degradation pathways, providing genetic evidence that supported their FBSA biotransformation potential. After 5 days of incubation with 133.8 nmol/mL FBSA, LH-1 and BO-1 removed 8.78% and 11.37% of FBSA, respectively. Perfluorobutanesulfonic acid (PFBS), perfluorobutanoic acid (PFBA), and perfluoropropionic acid (PFPrA) were detected as biodegradation products, with PFBS and PFPrA as the main products in strains LH-1 and BO-1, respectively. Genome annotation revealed candidate genes associated with deamination, oxidation, desulfonation, decarboxylation, and defluorination, as well as strain-specific enrichment of chloroalkane degradation genes in LH-1 and fluorobenzoate degradation genes in BO-1. Neither strain showed detectable degradation of perfluorooctanoic acid (PFOA) or PFOS, suggesting an apparent preference for the sulfonamide precursor FBSA over terminal perfluoroalkyl acids (PFAAs). This study provides the first genomic and metabolic insights into FBSA biotransformation by coastal sediment bacteria and improves our understanding of the environmental fate of sulfonamide-based PFAS precursors. Full article

Background/Objectives: The aim of this study was to investigate primary colonizers adhering to the oral biofilm on five adhesive restorative materials. Methods: For each material (Admira Fusion, Clearfil AP-X, Durafill VS, Filtek Supreme XTE, and Venus Diamond), sixteen test specimens were prepared according to a standardized protocol. For pellicle formation, the specimens were incubated for two hours at 37 °C with sterile-filtered inactivated human saliva. The bacteria (Streptococcus oralis (S. oralis), Streptococcus gordonii (S. gordonii), Streptococcus sanguinis (S. sanguinis), Streptococcus mitis (S. mitis), and Actinomyces naeslundii (A. naeslundii)) were cultivated and suspended. A bacteria mix was prepared from the suspensions. The specimens with pellicles were wetted with the bacterial mix and incubated at 37 °C for 8 h. The total genomic DNA of the adhered bacteria was isolated and subsequently quantified using SYBR Green qPCR. Results: For S. gordonii, S. oralis, and A. spp., no significant differences in the amount of adhered bacterial DNA were found between the different materials. S. mitis DNA concentration was significantly higher on Filtek Supreme XTE compared to the other materials. Significantly higher DNA concentrations of S. sanguinis could also be detected on Filtek Supreme XTE compared to Clearfil AP-AX and Durafill VS. Conclusions: The investigated restorative materials showed species-specific differences in bacterial adhesion, with Filtek Supreme XTE exhibiting higher adhesion of S. mitis and S. sanguinis, whereas no differences were observed for the other tested species. Full article

This study characterizes AP-20-A, a lytic podovirus infecting Sinorhizobium meliloti, isolated from agricultural chernozem. Its 49.4 kbp genome shows negligible intergenomic similarity with known rhizobiophages (<2%). Core structural proteins—the major capsid protein (MCP) and terminase large subunit (TerL)—show closest homology to podoviruses infecting Paenibacillus, rather than to alphaproteobacterial viruses, suggesting cross-phylum horizontal gene transfer. This exchange is ecologically plausible, as Paenibacillus and Sinorhizobium co-exist in the rhizosphere. Over 63% of predicted proteins are functionally uncharacterized, with structural homologs detected in bacteria, archaea, and eukaryotes. We report the first identification in a rhizobiophage of a Tad2-like domain, predicted to block the bacterial Thoeris type II anti-phage defense. AP-20-A infected 56% of native S. meliloti strains; agrocenose isolates showed higher resistance than phytocenose isolates, evidence of local co-evolution. Among susceptible strains, 60% entered putative pseudolysogeny (with one strain exhibiting growth stimulation), whereas a symbiotically elite inoculant strain was completely lysed within hours. Some host strains carry additional AbiE systems; whether these independent defense–counterdefense layers interact during infection remains unknown. We conclude that resident phages represent a selective force that can disrupt inoculant establishment, underscoring the need to integrate soil virome assessment into agricultural microbiome management. Full article

Several strategies can be employed for the identification of novel microbial lipases. Despite the increasing importance of metagenomics in bioprospecting, significant limitations in the expression of recombinant proteins, and lipases in particular, remain. Culture-based bioprospecting approaches are, therefore, still valuable. In this work, a collection of bacterial isolates, mainly of marine origin, was screened for lipase activity through a culture-based approach. Screening for lipolytic bacteria was performed in solid media containing olive oil emulsions and rhodamine B. Positive isolates were subsequently grown in liquid media, to confirm lipase production. Significant hydrolytic activity towards the triglyceride substrates tributyrin and triolein could be observed with the biomass produced, although no lipase activity could be detected in the culture supernatants. Six isolates presenting high activity were characterized as whole-cell biocatalysts, and all were found to be active at temperatures ranging between 25 and 65 °C, and at pH values between 6 and 10.5. Genomic analyses of two of these Gram-negative lipase-producing isolates revealed the presence of several hypothetical genes encoding for lipolytic enzymes, including outer cell-bound enzymes, predicted through the application of machine-learning tools. These natural isolates, containing cell-associated lipases, may therefore be of special interest for application as whole-cell biocatalysts. Full article

Background/Objectives: The global spread of carbapenemase-producing Gram-negative bacteria (CP-GNB) represents a major clinical challenge, causing severe hospital-acquired infections with limited treatment options. Accurate and rapid detection is essential for guiding antimicrobial therapy and implementing infection control measures. Lateral flow immunoassays (LFIAs) targeting the five main carbapenemase families are increasingly used in routine diagnostics, and many new commercial assays have recently become available, often without thorough assessment. The continuous evolution of these enzymes under antibiotic pressure requires regular reassessment of assay performance. Methods: In this study, we evaluated the Beright Carba-5 assay (Alltest Biotech, Hangzhou, China) targeting the five main carbapenemases (KPC, NDM, OXA-48-like, IMP, and VIM), on a panel of 77 whole-genome sequenced Gram-negative bacterial (GNB) isolates exhibiting reduced susceptibility to carbapenems. Seventy-three were carbapenemase-producing (CP) GNBs, including six VIM-, 18 OXA-48-, 14 KPC-, 9 NDM-, 8 IMP-, 10 multiple carbapenemase-, and eight non-targeted carbapenemase-producers. Results: The assay was rapid and easy to use, showing 100% (CI: 73.54% to 100%) specificity, with no false positive results. However, overall sensitivity of CP-GNB detection was lower than expected at 63.08% (CI: 50.20% to 74.72%), with numerous false negatives, particularly among IMP and NDM producers, and to a lesser extent, KPC producers. Detection was more reliable for VIM and OXA-48-like variants. Practical limitations, including insufficient buffer supply, reduced the number of tested isolates from the planned 100 to 77. Conclusions: Overall, the Beright assay demonstrated insufficient sensitivity for routine diagnostic use. Full article

Background/Objectives: Antimicrobial resistance (AMR), driven by high-risk bacterial pathogens, is a major healthcare threat. This scoping review mapped artificial intelligence/machine learning (AI/ML) and computational approaches integrated with whole-genome sequencing (WGS), genomic surveillance, rapid typing, epidemiological data, or clinical metadata for early warning of AMR outbreak clones. Methods: Following PRISMA-ScR guidance and the Population–Concept–Context (PCC) framework, PubMed/MEDLINE, Scopus, and Web of Science were searched for English-language studies published between 2010 and 2026. Eligible studies addressed AI/ML or computational approaches for AMR outbreak detection, clone surveillance, transmission analysis, or infection prevention and control (IPC). Results: Thirty-eight studies were grouped into five domains: genomic surveillance; rapid typing; resistance, risk-factor, and lineage prediction; transmission reconstruction; and IPC-oriented genomic epidemiology. AI/ML supported automation, isolate prioritization, typing triage, prediction, transmission modelling, and electronic health record (EHR)-linked route identification. Conclusions: AI/ML may enhance WGS-based AMR surveillance, but validation, dataset dependence, heterogeneity, and limited IPC outcome reporting remain key gaps. Full article

Background and Aims: Helicobacter pylori is a major cause of chronic gastritis and peptic ulcer disease. The increasing global spread of antibiotic-resistant strains, particularly against amoxicillin and clarithromycin, poses a significant challenge to eradication therapies. Moreover, treatment-related adverse effects, often linked to antibiotic-induced intestinal dysbiosis, frequently lead to a poor patient compliance; this, in turn, promotes the persistence of resistant bacterial populations. Probiotics may mitigate these effects and improve treatment adherence. This study aimed to assess the genomic safety of new probiotics intended for adjuvant use in H. pylori eradication regimens. Methods: Whole-genome sequencing was performed on three probiotic strains: one of Lactobacillus acidophilus, and two of Bifidobacterium animalis subsp. lactis. Genomes were compared with corresponding wild-type reference strains to identify genetic variations and detect mobile genetic elements. Results: Comparative genomic analysis revealed differences between selected and wild-type strains. Importantly, no plasmids or transposons were identified, suggesting a reduced theoretical risk of horizontal transfer of antimicrobial resistance determinants. Genomic findings were consistent with in vitro phenotypic observations. Conclusions: Whole-genome sequencing provided a robust assessment of the safety profile of these strains. The absence of transferable resistance elements supports their potential use as probiotic candidates to improve tolerability and adherence to H. pylori eradication therapies, contributing to more effective treatment outcomes. Full article

Lactobacilli species have emerged as a focal point in food microbiology due to their core probiotic properties, including the regulation of intestinal homeostasis and the enhancement of immunity. This study focuses on Lacticaseibacillus rhamnosus MG0718 (hereinafter referred to as MG0718), employing a combined approach of phenotypic evaluation and whole-genome sequencing to assess its probiotic potential and analyze the correlation between its phenotype and genotype. In vitro experiments demonstrated that MG0718 possesses broad-spectrum antibacterial activity against pathogenic bacteria. In vitro experiments showed that MG0718 had broad-spectrum antibacterial activity against pathogenic bacteria such as Escherichia coli (E. coli), with an inhibition zone diameter of up to 13.67 ± 1.56 mm. It survived pH 2.5 for 6 h with only a 1.72 log10 reduction, and showed 0.78 and 1.11 log10 CFU/mL reductions in artificial gastric and intestinal fluids after 2 h. DPPH scavenging was 56.7% and total reducing power was 91.1%. In vivo, 7-day preventive administration maintained 100% survival against S. Typhimurium infection and alleviated weight loss. Bacterial loads in spleen, liver, and cecum dropped from 4.5, 4.5, and 4.2 to 3.6, 1.8, and 2.5 lg CFU/g, respectively. Whole-genome sequencing analysis indicated that the complete genome of MG0718 is 2,574,565 bp in length, containing 2813 CDS. Among these genomic components, 203 stress-related protein genes elucidate its superior environmental tolerance; one bacteriocin gene cluster, one EPS gene cluster and two secondary metabolite gene clusters provide the genetic basis for its antibacterial activity. Notably, no virulence factors were detected, ensuring the safety of the strain for application. In summary, the functional phenotypes of MG0718 are highly consistent with its genetic characteristics, identifying it as a probiotic candidate of significant developmental value. Future research should focus on clinical trials to further verify its practical benefits for human intestinal health and immunomodulation, thereby providing a robust scientific basis for its application in functional foods. Full article

Infectious diseases remain a major global health concern, with a growing burden of antimicrobial resistance and consequent higher mortality in the human population. Accurate bacterial identification is fundamental across clinical, veterinary, agricultural, and research settings, supporting effective diagnosis, antimicrobial stewardship, infection control, food safety, and environmental monitoring; however, conventional approaches are limited by time constraints, reduced sensitivity, and challenges in detecting fastidious or uncultivable organisms. This review provides a comprehensive overview of classical and advanced methods, including microscopy, culture, biochemical testing, immunological and serological assays, proteomic and spectroscopy-based techniques, and molecular approaches, such as polymerase chain reaction (PCR), digital PCR, DNA hybridization, 16S rRNA gene sequencing, whole-genome sequencing, and metagenomics. The integration of artificial intelligence has further enhanced analytical performance. Nevertheless, harmonization of bioinformatics frameworks remains essential, as variability in algorithm-defined cut-off values limits standardized implementation of whole-genome sequencing in routine laboratories. Emerging technologies, including CRISPR-based diagnostics and phage- and nanomaterial-based detection systems, offer promising alternatives. Overall, the integration of these approaches is expected to improve the accuracy, speed, and applicability of bacterial identification across diverse settings; however, these advances should be implemented cautiously, with standardization remaining a key priority alongside technological modernization. Full article

Camel milk is widely consumed in the world’s arid and semi-arid regions because of its favorable nutritional profile and associated human health benefits. The indigenous microbiota of raw camel milk is diverse and composed of different bacterial and fungal groups. This community drives spontaneous milk fermentation, resulting in a variety of traditional products, including Gariss, Shubat, Chal, Dhanaan, Lfrik, and Suusac (or Suusa), depending on geographic region and cultural practice. This fermented milk has improved sensory, nutritional, and health profiles, as well as an extended shelf life, compared to raw milk. Fermentation alters the microbial community structure, with lactic acid bacteria (LAB) consistently becoming dominant, while yeasts and molds are also detected in some products. These patterns have been identified using both culture-dependent and culture-independent approaches, including 16S rRNA gene sequencing and whole-genome shotgun metagenomics. However, the milk’s microbial composition is highly variable and is influenced by the original composition, geographical location, fermentation and hygiene practices. The detection of opportunistic pathogens such as E. coli, Salmonella and Listeria in some traditional products raises important food safety concerns. This review presents current knowledge on fermented camel milk microbiology using a cross-regional approach, identifying key gaps in microbial safety and process standardization to support wider acceptance and potential commercialization. Full article

Potato (Solanum tuberosum L.) is an important staple and food security crop to many communities in the world. However, potato production and quality is greatly constrained by bacterial wilt, a disease caused by a soil-borne pathogen, Ralstonia solanacearum. Ralstonia solanacearum can be managed through clean seed systems and therefore laboratory testing is a pre-requisite for seed certification to confirm the absence of the pathogen in potato seeds before planting. Molecular diagnostics is the gold standard for detection of R. solanacearum in potato seeds. However, the extraction of genomic DNA from R. solanacearum for molecular diagnostics is complex, tedious, lengthy and/or costly procedure. A simple, rapid and reliable DNA extraction protocol is required for use in routine molecular diagnosis of R. solanacearum, a high-risk quarantine pathogen. In this study, we developed a simple and rapid protocol for extracting genomic DNA from symptomatic and asymptomatic potato tubers infected with R. solanacearum and verified its efficiency for the detection and molecular characterization of the pathogen. The protocol was developed from the evaluation of distilled water, Tris-EDTA (TE) and Tris buffer as a base solution for tissue maceration. The DNA quantity and integrity was determined using the NanoDrop 2000C spectrophotometer and agarose gel electrophoresis, respectively. Both hot and cold solutions produced intact high molecular weight genomic DNA of sufficient yield and purity for molecular-based applications. The detection and determination of phylotypes of R. solanacearum, based on conventional and multiplex polymerase chain reaction (PCR), amplified the expected 280 and 372 bp amplicons, respectively, confirming that the quantity and quality of the extracted pathogen genomic DNA was sufficient for molecular diagnostic applications. The sequencing of the amplified products of the endoglucanase gene produced good quality sequences, which confirmed the R. solanacearum isolates to be members of phylotype II sequevar 1. This protocol is a simple, fast and reliable tool for the extraction of sufficient genomic DNA with high quality, directly from R. solancearum-infected potato tubers for PCR and sequencing applications. Its simplicity and throughput make it valuable for use in routine diagnostics and can be adopted by certification programs to ensure distribution of clean potato seeds to farmers. Full article

Background/Objectives: Probiotic feed additives are increasingly used in livestock production as antimicrobial-sparing tools, yet viable microbial products should not introduce clinically relevant antimicrobial resistance genes (ARGs) into the intestinal resistome. This study evaluated farm-animal probiotic products using an integrated phenotypic, metagenomic and mobilome-aware safety framework. Methods: Seven commercially available products intended for poultry, pigs, cattle or horses were assessed using product metadata, culture-based recovery, broth microdilution minimum inhibitory concentration (MIC) profiling and Illumina short-read sequencing as a screening-level resistome approach. Reads were quality controlled, assembled, screened using the Comprehensive Antibiotic Research Database (CARD)/Resistance Gene Identifier (RGI) workflow and interrogated for plasmid-, phage- and insertion sequence/mobile genetic element-associated genomic context. Results: MIC profiles were generated for viable bacterial isolates representing Enterococcus faecium, Pediococcus acidilactici, Pediococcus pentosaceus and Bacillus subtilis. One labelled Lactobacillus plantarum component was not recovered as viable culture, and one labelled P. acidilactici component was recorded as P. pentosaceus. Sequencing-based resistome screening identified 30 antimicrobial resistance (AMR)-associated CARD antibiotic-resistant organism (ARO) hits belonging to 13 determinants across six ARG-positive coded products, while one coded product had no retained CARD/RGI hit. Profiles were dominated by recurrent Enterococcus-associated background determinants, including aac(6′)-Ii, msrC and eatAv. Plasmid prediction was positive for five hits, whereas no iMGE- or phage-associated ARG context was detected. No vanA/vanB, mcr, optrA, poxtA, cfr, extended-spectrum β-lactamase (ESBL) or carbapenemase gene was detected. Conclusions: The investigated products did not show evidence of high-priority mobile ARG carriage. Nevertheless, AMR-associated determinants and occasional predicted mobile contexts support routine integrated MIC-sequencing-based resistome–mobilome assessment of veterinary probiotic products. Because short-read assemblies do not fully resolve plasmid architecture or transferability, mobile-context predictions should be considered screening-level indicators requiring confirmatory long-read or functional testing for higher-priority findings. Full article

Live virus inoculation (LVI) is widely used for porcine reproductive and respiratory syndrome virus (PRRSV) stabilization, yet preparation practices and pathogen composition remain poorly characterized. This study aimed to evaluate variability in LVI preparation, quantify PRRSV genomic load, and detect additional swine pathogens. A survey was conducted to document LVI preparation methods, and samples were analyzed using reverse-transcription quantitative PCR (RT-qPCR) for PRRSV quantification and next-generation sequencing for PRRSV and the metagenomic characterization of additional pathogens. Among 61 LVI samples, substantial variability was observed in preparation practices and viral composition, with 31 distinct PRRSV variants identified and seven samples containing multiple strains. PRRSV RNA concentrations ranged from 10^1.69 to 2.52 × 10⁸ copies/mL. Metagenomic analysis detected a complete or near-complete genome for PRRSV, porcine parvovirus, and porcine circovirus type 2. Genome fragments of porcine sapovirus, porcine rotavirus, porcine astrovirus, and bacterial genetic material from Salmonella spp., Pseudomonas spp., Streptococcus spp., and Escherichia coli were also detected. These findings highlight substantial heterogeneity in LVI materials and encourage the use of next-generation sequencing to verify LVI PRRSV composition and screen for co-existing pathogens, reinforcing the need for standardized preparation protocols and further investigation into optimal viral dosing for effective immunization. Full article

The double-crested cormorant (Nannopterum auritum), a piscivorous bird endemic to North America, frequently forages in aquaculture ponds during migration and wintering, contributing to economic losses in catfish-producing regions of the southern United States. While interactions between cormorants and aquaculture systems are well documented, their associated microbial communities and genetic elements remain less characterized. In this exploratory study, Hi-C-enabled metagenomics was applied to fecal samples from two cormorants to generate a genome-resolved, descriptive analysis of gut microbial composition and to associate bacterial genomes with mobile genetic elements (MGEs), antimicrobial resistance genes (ARGs), and putative virulence-associated genes. Metagenome-assembled genomes (MAGs) included taxa reported in aquatic or animal-associated environments, including Edwardsiella tarda, Plesiomonas shigelloides, Clostridium perfringens, and Campylobacter volucris. ARGs were detected across multiple MAGs, with E. tarda harboring the greatest diversity. Hi-C-enabled linkage of plasmids and phages to putative hosts, providing structural insight into microbial organization. Analyses are descriptive (n = 2) and do not include statistical comparisons or diversity metrics. These findings demonstrate the utility of Hi-C for resolving gene–host associations and provide a framework for future studies of microbial connectivity in One Health contexts. Full article

The two-spotted spider mite, Tetranychus urticae, poses significant agricultural challenges due to its rapid population growth and high capacity for developing chemical resistance. This study evaluated the acaricidal activity of bacterial strain TAM1, isolated from naturally deceased mites in Taiwan. In bioassays, TAM1 caused over 90% adult mite mortality within 48 h. Infected mites showed symptoms of body darkening and deformation of the ventral abdominal crest lines. Enzymatic analysis confirmed significant chitinase and gelatinase activities. Whole genome sequence of TAM1 was acquired with a 5,066,903 bp circular chromosome (CP120954) and a 164,574 bp circular plasmid (CP120955). Refined functional profiling identified a sophisticated enzymatic arsenal including core chitin-active families (GH18, GH20, AA10) and 157 proteases, with a high prevalence of metallopeptidases that correlate with the detected gelatinase activities. Secretome analysis predicted 42 extracytoplasmic proteases primarily utilizing the Sec-dependent pathway, while the presence of multiple CBM50 modules suggests a potential for targeted substrate anchoring. These genomic insights provide a plausible molecular basis for the observed enzymatic potential and the localized ultrastructural disruption of the T. urticae cuticle. The alignment between phenotypic observations, microscopic evidence, enzymatic activities, and genomic data suggests that TAM1 utilizes synergistic, multi-target mechanisms to exert its acaricidal effects. Based on analyses of whole-genome sequence and 16S rRNA gene sequence, TAM1 was tentatively designated as a strain of Kosakonia sacchari. The bacterial strain reported here represents a promising microbial agent for integrated pest management (IPM) programs. Full article