Fems Microbiology Letters最新文献

Sheep and sheep products play a notable role in Albanian culture and economy, particularly in rural regions. This sector is defined by small-scale activities and often faces challenges linked to safety and productivity. These issues necessitate the development of reforms to protect public health, boost productivity, and comply with regulatory requirements. Escherichia coli is a frequent ovine commensal, with an association with pathotypes like Shiga Toxin-encoding E. coli. The relationship between ovine bacteria and antibiotic resistance further remains poorly characterized. In this study, E. coli isolates from sheep across Albania were sequenced using Oxford Nanopore Technologies™ and characterized in silico for serotype, virulence, resistance genes, and phylogenetic relationships as isolates were compared to a global collection of animal and environmentally associated genomes. Isolates exhibited diverse serotypes and a conserved resistome comprising four genes, including EC-type β-lactamases. Four isolates were Shiga toxin-positive (stx1c predominant). Phylogenetic analyses revealed high similarity with European ovine E. coli, indicating regional relatedness and potential for resistance gene dissemination. This work provides the first genomic insight into ovine E. coli in Albania and highlights their potential role in antimicrobial resistance dynamics within livestock systems. These findings are crucial to understand for the development of Albanian agricultural practices.

Bradyrhizobium, the largest rhizobial genus, is characterized by a variety of exopolysaccharide (EPS) components, such as penta- and tetrasaccharides, depending on the species. However, several genes involved in EPS synthesis remain unknown. In this study, we investigated whether 186 Bradyrhizobium strains possess homologous genes in the EPS cluster I, which is responsible for the synthesis of a pentasaccharide EPS by B. diazoefficiens USDA110. The absence of homologous genes in the B. elkanii and Photosynthetic Bradyrhizobium supergroups, in contrast to the B. japonicum supergroup, suggests that these lineages may utilize distinct and uncharacterized genes involved in tetrasaccharide EPS biosynthesis.

Methanogens rely on compatible solutes to withstand osmotic stress, yet their responses to high ammonium concentrations, common in biogas digesters, remain poorly understood. In this study, intracellular osmolyte accumulation was examined in four Methanoculleus bourgensis strains (MAB1, MAB2, MAB3, and BA1), isolated from high-ammonia biogas digesters, under progressive increase in concentrations of ammonium and sodium chloride. Their responses were compared with those of the type strain Methanoculleus bourgensis MS2T and the halophilic Methanoculleus submarinus Nankai-1T. All investigated strain grew to 12 g l-1 NH4+-N (0.3 mg l-1 NH3), and gradual adaptation increased ammonium/ammonia tolerance in some strains to 25 g l-1 NH4+-N. Whereas the reference strains accumulated glycine betaine under both ammonium and sodium chloride stress, the M. bourgensis strains from high ammonia biogas systems uniquely accumulated Nε-acetyl-β-lysine during increasing levels of ammonium chloride. This β-amino acid derivative is known as a NaCl-induced osmoprotectant in methanogens, but it´s association with high ammonium/ammonia levels in pure cultures has not previously been demonstrated. Our findings identify Nε-acetyl-β-lysine biosynthesis as a potential mechanism underpinning the exceptional ammonium/ammonia tolerance of M. bourgensis, a taxon frequently dominating methane production in high-ammonia biogas systems, while also revealing notable variation in this trait among its subspecies.

The scientific and technological change at the recent speed and scale, and the vast amount of information available at everyone's fingertips, can be overwhelming. Thus, scientists and educators need to support everyone in becoming and being able to judge scientific expertise and the credibility of a source and the information provided; and need to facilitate developing or strengthening trust in science. Papers from around the globe, addressing current educational approaches that drive the development of science literacy, were published in the FEMS Microbiology Letters virtual Thematic Issue 'Learning together for our future' in October 2025. The paper's themes of timely education practice range from public engagement with microbiology, active and authentic learning that prepares for professional and civic contributions, to citizen science and service learning. Its content is reviewed and contextualized here to facilitate discussions within the professional community. Crucially, we need to offer and create inclusive opportunities for learning and developing science literacy, so we can truly learn together for our future.

The microbial communities in anaerobic ammonium oxidation (anammox) bioreactors have been extensively studied to unveil their diversity and roles in nitrogen removal. Yet, the viruses infecting the key functional microorganisms in these systems remain unexplored. Here, we utilize genome-resolved metagenomics to systematically assess viral diversity, functions and interaction with microbial hosts in granular sludges of different sizes from three laboratory-scale (LS) and full-scale (FS) anammox reactors. Analysis of the 190 microbial genomes recovered through bulk metagenomics revealed the predominance (FS 29%-54% and LS 31%-45%) of anammox species exclusively from the Brocadiae in all sludges examined. Viral metagenomics identified 5210 candidate viral species, 61.1∼97.3% of which were novel. Members of six genera from the Caudovirales order constitute the majority of the taxonomically assigned viral species. Between-group variance analysis revealed that both environment (reactor type) and granule size had a significant influence on the metabolic potential of viruses. In silico predictions showed that many of the important functional microbes were frequent targets of previously unrecognized viruses, including six viral populations infecting the anammox bacteria. Our results suggest that viruses actively infect microbial hosts and thus may have a major impact on the microbial metabolic processes and biogeochemical cycling in the anammox reactors.

This review focuses on the role of C-type lectin receptors (CLRs) in inflammatory bowel disease (IBD). It outlines their classification, structural features, and functional mechanisms within intestinal immunity. The article comprehensively examines recent advances in understanding the contributions of specific CLRs-including Dectin-1, Mincle, Dectin-3, and the mannose receptor (MR/CD206)-to IBD pathogenesis, particularly their functions in microbial recognition, immune cell activation, and the regulation of inflammatory responses. Finally, the review addresses current research challenges and future directions, with the aim of providing deeper insights into disease mechanisms and facilitating the development of novel CLR-targeted therapies.

Trichoderma fungi are colonizers of plant substrates and rhizosphere and are valued for their antagonism against phytopathogens and ability to promote plant health. We investigated Trichoderma diversity in coffee-growing soils in Caranavi region of Yungas-La Paz, Bolivia, where high humidity and fungal diseases threaten yield, and evaluated their potential as biocontrol agents against coffee pathogens. A total of 440 Trichoderma were isolated from coffee rhizosphere, fallow lands, and forest ecosystems across an altitudinal gradient in Caranavi. DNA barcode analyses using ITS, rpb2, and tef1 loci identified only four species. However, 47 taxa comprising 344 isolates were ambiguous, and 41 isolates were previously unrecognised species. The diversity of Trichoderma spp. was significantly affected by ecosystem type and altitude, with more species isolated from coffee rhizosphere than fallow lands and forest ecosystems, and from lower altitudes than higher ones. Evaluation of 100 isolates against a native coffee wilt pathogen Fusarium oxysporum identified 70 potent antagonists, with 30 achieving 90-100% disease control. This is the first comprehensive study of Trichoderma diversity in Yungas, identifying indigenous Trichoderma for biocontrol applications against coffee diseases. It also emphasizes the need to refine the Trichoderma species concept and improve the taxonomic resolution within the genus.

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.

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.

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.