Fems Microbiology Letters最新文献

Formaldehyde is a highly reactive and cytotoxic compound, and its efficient detoxification is essential for cellular survival. This requirement is particularly critical in methylotrophic microorganisms, where formaldehyde serves as a central intermediate in methanol assimilation. Despite the toxicity of this compound, methylotrophic and methanotrophic bacteria have evolved mechanisms that allow limited tolerance, yet the isolation of highly resistant variants remains extremely challenging due to the intrinsic difficulties of cultivating and purifying these organisms. Here, we report the isolation and complete genome sequence of a Methylomicrobium alcaliphilum 20Z derivative capable of sustained growth at 30 mM formaldehyde-representing a six-fold increase over the parental strain and positioning it among the most formaldehyde-tolerant methanotrophs described to date. The strain was obtained after prolonged adaptation and successful purification of a single resistant colony, a technically demanding process in this species. In parallel, we re-sequenced and re-annotated the wild-type genome, generating an improved genetic reference for M. alcaliphilum 20Z. Comparative genome analysis revealed 168 mutations affecting 31 open reading frames in the adapted strain. These mutations span genes involved in stress response, membrane remodeling, macromolecular repair, and regulatory functions, suggesting multifactorial adaptive strategies beyond canonical formaldehyde detoxification pathways. The genomic data provided here constitute a valuable foundation for future mechanistic studies and offer a resource for researchers aiming to understand or engineer aldehyde tolerance in methylotrophic bacteria.

Plasmids of the incompatibility group H (IncH) are large mobile elements that confer multidrug resistance and are prevalent in Enterobacterales from clinical and environmental sources. We analyzed 1308 globally distributed IncH plasmid sequences to assess their genomic features and functional potential. IncH plasmids were classified into IncHI1 and IncHI2, with IncHI1 subdivided into IncHI1B and IncHI1AB based on co-occurring replication proteins. These subtypes exhibited distinct host preferences and genomic patterns. IncH plasmids carried antimicrobial resistance genes and other adaptive determinants at comparable frequencies across environments. They encoded multiple replication and relaxase proteins, supporting broad host range and plasmid exclusion. Core genes included the Hha regulator, involved in virulence and conjugation; a DNA (cytosine-5)-methyltransferase contributing to AT-rich content; Cobamide synthase, potentially linked to metal tolerance; and the ter operon, associated with tellurium resistance and stress adaptation. Integron-associated genes such as qacEΔ1, sul1, and blaIMP promoted resistance to quaternary ammonium compounds, sulfonamides, and carbapenems. Notably, ~60% of nonredundant IncH plasmids encoded sulfonamide, quaternary ammonium compound, and β-lactam resistance, while over 70% harbored aminoglycoside resistance genes. These findings highlight IncH plasmids as reservoirs of clinically relevant genes and stress-response functions, reinforcing their importance for monitoring antibiotic resistance dissemination and environmental adaptability within Enterobacterales.

Recent studies utilizing 16S rRNA amplicon sequencing have challenged the notion of urine sterility, yet urine is a low-biomass specimen in which apparent community profiles can be strongly influenced by background signal from reagents and processing. To address this interpretability gap, we integrate culture-independent absolute 16S rRNA gene quantification with urinary 16S amplicon sequencing in a negative-control-anchored workflow. Bacterial load provides a biomass-aware quality control gate that defines interpretable low-biomass thresholds and objective exclusion criteria. As a pilot application, we compared midstream urine collected prior to instrumentation from healthy volunteers and newly diagnosed bladder cancer (BC) patients, quality filtering retained 29 controls and 5 BC cases. Samples > 106 copies/ml typically produced > 10 000 reads; near 105 copies/ml read counts dropped sharply yet remained distinguishable from background. Thirteen negative controls (V3-V4 PCR and stabilization buffer; median 90, mean 124 reads) supported excluding samples with < 1000 reads. Median bacterial load was lower in BC than in controls (7.0  × 103 vs 1.07 × 106 copies/ml), although not significant in this underpowered cohort (P = 0.07). This cohort-size-independent framework enables load-based triage for sequencing, reduces background-driven over-interpretation in low-biomass urine datasets, and supports modeling bacterial load as a covariate or stratifier in future studies of the bladder cancer microbiome.

Honeybees (Apis mellifera) are essential pollinators that sustain biodiversity and global food security but are increasingly threatened by bacterial infections and antimicrobial resistance (AMR). This study investigated the bacterial composition and resistance profiles of beehives from three floral micro-regions of Misurata city, Libya: Spring Flower, Thyme, and Sidr. A total of 120 isolates (40 per area) were identified using biochemical assays and tested for susceptibility to tetracycline, erythromycin, ampicillin, and chloramphenicol. Bacillus species predominated (56.7%), followed by Staphylococcus (28.3%), with minor occurrences of Pseudomonas, Enterococcus, Klebsiella, and Acinetobacter. Marked interspecific differences were detected for tetracycline, erythromycin, and ampicillin, while no chloramphenicol resistance occurred (0/120; 0%, 95% CI upper bound ≈ 3.1%). Staphylococcus aureus and Enterococcus spp. exhibited the highest resistance, contrasting with the largely susceptible Bacillus isolates, except for ampicillin resistance in B. cereus (34/40; 85.0%) and B. subtilis (6/28; 21.4%). Less frequent species tended to display stronger resistance, whereas no significant differences were observed among the three sampling areas. These findings establish the first baseline of bacterial diversity and AMR in Libyan beehives, emphasizing the need for responsible antibiotic use and continuous monitoring within apicultural ecosystems.

This study optimizes sustainable ectoine production in reduced salinity and minimal media to meet demands in pharmaceuticals, food, and cosmetics, isolating a halophilic bacterium 99.1% similarity to Halomonas smyrnensis from Sambhar Salt Lake. Optimization of ectoine production was performed using the one-variable-at-a-time method and response surface methodology, assessing variables such as carbon and nitrogen sources, incubation time, pH, temperature, inoculum density, agitation rate, and salinity. High-performance liquid chromatography confirmed total ectoine production, which increased from 0.54 to 6.5 g/l, a 12.03-fold enhancement compared to initial unoptimized conditions. The optimal ectoine yield by H. smyrnensis IIIM VA-6 was achieved after 72 h under conditions of 5% (w/v) salinity, 2.5 % monosodium glutamate, pH 5.0, 10.0 g/l lactose, and 250 rpm agitation, and characterized by Fourier transform infrared spectroscopy, nuclear magnetic resonance, and liquid chromatography mass spectrometry. This study represents a significant improvement in sustainable production of ectoine under reduced salinity conditions using a halophilic strain.

Barley (Hordeum vulgare) is susceptible to Puccinia hordei (leaf rust), a biotrophic foliar pathogen contributing to global yield losses. With rising food demand and increasing disease pressure, sustainable crop protection strategies are urgently needed to support UN Sustainable Development Goal 2: Zero Hunger. Arbuscular mycorrhizal (AM) fungi, including Rhizophagus irregularis, form symbioses with barley roots and can modulate host immunity through mycorrhiza-induced resistance (MIR). Here, we tested whether R. irregularis colonization alters barley growth and defence responses during P. hordei infection. AM fungal colonization did not significantly reduce disease severity or mitigate pathogen-associated biomass loss at a single post-infection time point. However, co-infected plants showed enhanced expression of defence genes (PR1, PR2, PR3, and WRKY28), which remained low in plants colonized by AM fungi alone, consistent with immune priming. RNA sequencing revealed AM fungal-associated reprogramming of the leaf transcriptome, including enrichment of defence, metabolism and ubiquitination-related processes. These results indicate that R. irregularis reshapes barley immune regulatory networks at transcriptional and post-translational levels. Although these molecular changes did not translate into measurable phenotypic protection within the short experimental timeframe, they highlight the complexity and context dependence of MIR in cereal-rust interactions.

Periodontal disease is a chronic inflammatory condition primarily caused by Porphyromonas gingivalis (P. gingivalis), which plays a pivotal role in disease progression and biofilm formation. Conventional oral hygiene products often contain strong disinfectants, which can be unsuitable for children and older adults. Thus, identifying natural, low-irritant antibacterial agents is essential for safe and effective prevention. This study investigated fig (Ficus carica) leaves, an underutilized food biomass, as a source of antibacterial compounds. Ethanol extracts were fractionated using five solvents, and the ethyl acetate fraction showed the most potent growth inhibition against P. gingivalis, but not against Aggregatibacter actinomycetemcomitans. TLC and HPLC analyses revealed the presence of psoralen, bergapten, and several unidentified compounds. The ethyl acetate fraction was rich in polyphenols. Although individual HPLC-separated fractions showed limited activity, mixtures retained antibacterial effects, suggesting synergistic or additive interactions. The fraction also inhibited hyper-virulent P. gingivalis W83, Prevotella intermedia, and Staphylococcus epidermidis, but not Escherichia coli, indicating selective antibacterial activity. Known fig leaf compounds were not the main contributors to the observed effects. These findings suggest that fig leaf ethyl acetate extract may be a promising natural antibacterial agent for oral hygiene products, particularly targeting P. gingivalis, and may help prevent periodontal and related systemic diseases.

The study of archaeal viruses is important for understanding microbial life in extreme environments. However, this study is difficult mainly because they predominantly exhibit a chronic lifestyle, where viral particles are released without causing host cell death. Therefore, conventional plaque assays, which are well-suited for studying lytic viruses, usually fail to detect chronically infecting viruses due to their nonlytic nature. To address this limitation, we developed an optimized plaque assay protocol for detecting chronically infecting viruses of haloarchaea, focusing on species within the Haloferax genus. By enhancing viral diffusibility and infectivity through adjustments in agar concentration and incubation temperature, this modified protocol improved plaque formation, enabling the detection of viruses that cause mild growth delays. We successfully demonstrate plaque formation for two chronically infecting viruses, Haloferax volcanii pleomorphic virus 1 (HFPV-1) and lemon-shaped virus of Haloferax strain Atlit 48 N (LSV-48 N), on representative Haloferax strains. This assay is an effective method for the detection and quantification of chronically infecting archaeal viruses, providing a new tool for discovering new viral families in extreme environments. Here, we present a high-sensitivity plaque assay protocol tailored specifically to detect archaeal viruses that produce chronic productive infections, which traditional methods have failed to identify. Our findings offer a novel tool that can be adapted for studying virus-host interactions within extreme environments, potentially expanding our understanding of the ecological roles and diversity of archaeal viruses. This protocol also represents a valuable advancement for microbiologists seeking to discover new archaeal viral viruses.

Whole-genome sequencing has transformed microbial genomics since the first bacterial genome was published in 1995. Advances in sequencing technology, together with decreasing costs, now enable high-resolution investigation of bacterial pathogens for epidemiological surveillance, and infection control. A major breakthrough has been the advent of third-generation long-read sequencing (LRS) platforms, such as Pacific Biosciences and Oxford Nanopore Technologies, which overcome the limitations of short-read sequencing by producing long continuous reads. LRS facilitates accurate de novo genome assembly, resolution of repetitive and structurally complex regions, and precise characterization of plasmids and other mobile genetic elements that frequently harbor antimicrobial resistance genes (ARGs). A particular strength of LRS lies in its ability to reveal the complete genomic architecture of ARGs, including their localization, copy number, and surrounding genetic environment. Such contextual information is essential, since e.g. the interpretation of antimicrobial resistance (AMR) depends not only on the presence of specific genes but also on their structural organization, mobility potential, and genomic integration. By contrast, LRS provides a reliable foundation for understanding AMR evolution and dissemination through both clonal expansion and horizontal gene transfer. Recent developments in bioinformatics, including dedicated tools for plasmid reconstruction, typing, and annotation, further enhance the analytical value of LRS and hybrid approaches. Beyond isolate-level analyses, LRS enables plasmid surveillance and the tracing of ARG transmission across strains, hosts, and healthcare settings. This review sets out to give readers a brief overview of LRS technology and its capabilities and outlines current approaches and tools to analyze bacterial plasmids.

We developed a STEAM (science, technology, engineering, arts, and mathematics) outreach program that integrates tardigrade biology with smartphone microscopy and 3D printing in a public science program hosted by the Kanagawa Institute of Industrial Science and Technology (KISTEC), Japan. Building on prior educational activities that introduced tardigrades mainly through conventional light microscopy, our approach links smartphone-based observation to the creation of 3D-printed models in a single, low-cost workflow. Between 2023 and 2025, five workshops were conducted with 249 students in grades 3-6. Participants collected local moss, recovered and enriched tardigrades from the samples, and observed their revival from anhydrobiosis using a smartphone microscope, followed by the creation of 3D-printed tardigrade models. Pre-activity questionnaires showed that although 92% of students had at least heard of tardigrades, fewer than 10% had ever used a smartphone microscope or a 3D printer, and about 90% reported high interest in these topics. Post-activity surveys indicated that interest remained high and increased modestly: 93%-95% of students reported 'very high' or 'somewhat high' interest in tardigrades, smartphone microscopes, and 3-D printers, and 95% rated the workshop as 'interesting' or 'very interesting'. In total, 74% (182/245) successfully located tardigrades in their own samples. Grade-level comparisons showed older students achieved higher understanding and fluency. This demonstrates that tardigrade biology, smartphone microscopy, and 3D printing provide an effective, low-cost microbiology outreach model for elementary education.