Frontiers in Microbiology最新文献

The introduced rhizobial inoculum M. ciceri USDA 3378 demonstrates a significant competitive advantage over the indigenous M. muleiense CCBAU 83963 for nodulating chickpea in newly established planting areas in China. Previous genomic analyses revealed that USDA 3378 possesses a greater number of genes related to cell movement and flagella production compared to CCBAU 83963. Transcriptomic analysis indicated that the expression of the flagella-associated gene motA (flagellar motor protein) significantly changed under symbiotic conditions. Although the genome of M. ciceri USDA 3378 contains the motA gene, its biological function within this strain has not been previously reported. In this study, we constructed a motA mutant (ΔmotA-3378) in USDA 3378 using homologous recombination and biparental conjugation methods to assess the differences in bacterial structure, growth, motility, exopolysaccharide synthesis, biofilm formation, and competitive nodulation ability between the wild type and the mutant. Experimental results showed that the ΔmotA-3378 mutant was unable to produce flagella, leading to reduced motility, diminished biofilm formation, and lower exopolysaccharide production. In competitive nodulation with wild-type USDA 3378, the ΔmotA-3378 mutant's nodule occupancy was 40.43 %. Furthermore, its competitive nodulation advantage against CCBAU 83963 decreased from 100 % (achieved by wild-type USDA 3378) to 94.6 %. These findings indicate that the motA gene plays a crucial role in the motility, exopolysaccharide synthesis, biofilm formation, and competitive nodulation ability of M. ciceri USDA 3378.

Introduction: Algal-microbiome interactions are considered pivotal for host health and development. Current understanding of the diversity and function of algal-associated microorganisms in aquaculture settings remains limited, preventing the development of microbiome-based solutions for sustainable algal growth.

Methods: We employed cultivation-dependent and -independent approaches to determine the structure of bacterial communities associated with farmed Atlantic Nori (Porphyra dioica and Porphyra umbilicalis) at early developmental stages. 16S rRNA gene amplicon sequencing and cultivation of bacterial symbionts were performed for algal and culturing water samples harvested from indoor photobioreactors at stages S1 (conchocelis cultures growing vegetatively), S2 (conchosporangia), and S3 (young blades).

Results: The phyla Pseudomonadota (Alpha- and Gammaproteobacteria classes) and Bacteroidota were dominant in algal samples, followed by Planctomycetota, Actinobacteriota, and Verrucomicrobiota. At the phylotype level, these communities were highly structured throughout the host's life cycle. Uncultivated lineages Sva0996 (Actinomycetota), OM190 (Planctomycetota), Pir4 (Planctomycetota), and the genera Blastopirellula, Algoriphagus, Hyphomonas, and Marinobacter, among others, were enriched in algal samples and presented significantly different abundances across developmental stages. In some cases (e.g., genera Aquimarina, Sulfitobacter, Maribacter, and Nonlabens), those changes were also observed in culturing water. Moreover, the genera Ensifer (Rhizobiaceae), Paraglaciecola (Alteromonadaceae), and the uncultivated lineages DEV007 (Verrucomicrobiota) and Pir4 (Planctomycetota) were consistently present in P. dioica and P. umbilicalis samples at multiple developmental stages. Several Porphyra-associated bacterial genera and putative novel species, mostly belonging to the families Roseobacteraceae, Flavobacteriaceae, and Alteromonadaceae were identified via cultivation. Many cultured members of the Porphyra microbiome produced the growth-promoting hormone auxin, particularly those belonging to the genera Alteromonas, Marinobacter, Sulfitobacter, Leucothrix, and Roseovarius.

Discussion: This study unveils complex, phylogenetically distinct, and temporally structured bacterial communities possessing algal morphogenesis-inducing capacities during early developmental stages of Porphyra spp., highlighting the potential of microbiome-based interventions for sustainable growth of marine algae in aquaculture.

Background: Fusarium proliferatum, a globally distributed phytopathogen causing destructive root rot in economically vital crops, employs epigenetic mechanisms to adapt to environmental conditions.

Results: Our genome-wide characterization identified eight histone deacetylase (FpHDACs) genes phylogenetically classified into RPD3/HDA1 and Sirtuin subfamilies. Comprehensive genomic characterization revealed two distinctive features: expanded domain architectures exemplified by the Arb2domain within Fp_HDA1, and subcellular localization prediction indicates-where most FpHDACs reside cytoplasmically under neutral pH, but undergo nuclear translocation in alkaline environments. Evolutionary diversification occurred principally via subfunctionalization rather than gene duplication, evidenced by non-clustered chromosomal distribution (8 genes across 5 chromosomes), divergent gene architectures in intron-exon organization and CDS lengths, and promoter cis-element enrichment featuring combinatorial stress-responsive signatures, most notably the dehydration-responsive DRE motifs exclusive to Fp_HOS3. Expression profiling analysis reveals a conserved global suppression of FpHDACs under abiotic stress, which is markedly potentiated by histone deacetylase inhibitor treatment. Crucially, the observed suppression was counterbalanced by a context-dependent induction of Fp_HOS3-specifically triggered under oxidative and cell wall stress, but not by other stressors. This specialized isoform functions as a compensatory epigenetic modulator, fine-tuning stress responses through targeted histone modification.

Conclusion: This study provides the first systematic elucidation of the HDAC gene family's core structural and functional characteristics in F. proliferatum, yielding novel insights into the adaptive strategies-both conserved and innovative-that underpin fungal stress epigenetics.

Portugal has one of the highest incidence rates of tuberculosis (TB) in Western Europe and, historically, multidrug-resistant (MDR) cases have been strongly associated with Mycobacterium tuberculosis strains pertaining to the endemic Q1 and Lisboa3 clades. Notwithstanding, the contribution of drug resistance-associated allelic configurations in these clades to differing levels of drug resistance and their relationship with drug efficacy has yet to be uncovered. A representative sample of the drug-resistant M. tuberculosis population in Portugal, comprised of 40 clinical strains were subjected to whole genome sequencing for characterization of allelic combinations of drug resistance-associated mutations and their minimum inhibitory concentrations for 12 anti-TB drugs was determined. Pharmacokinetic (PK) models were generated to ascertain the maximum concentration to which each drug remains efficacious. Drug resistance levels were determined and compared between different allelic configurations. Double inhA and embA/B mutation genotypes contributed with increased isoniazid and ethambutol resistance levels compared with single mutation configurations, respectively. Significant differences in drug resistance levels were observed between phylogenetic groups for rifamycin, streptomycin and ethionamide, largely explained by the presence/absence of unique high-level resistance-associated genotypes. The PK models for isoniazid and moxifloxacin suggest an increase in dosage to be ineffective against strains harboring high-level resistance-conferring double inhA mutations and gyrA/B mutations. Cycloserine and para-aminosalicylic acid are the only drugs predicted to remain efficacious against the majority of tested strains, while the effectiveness of newer drugs like bedaquiline, pretomanid and delamanid have yet to be uncovered. Proper diagnosis of drug resistance-associated mutations provides invaluable insights into the treatment of TB, as different allelic configurations lead to differing drug resistance levels, often rendering drugs ineffective.

Introduction: Severe fever with thrombocytopenia syndrome virus (SFTSV), first identified in Henan Province, China (2009), has since been detected in 26 Chinese provinces and remains a significant public health threat. Despite its spread, key aspects of its molecular evolution, particularly the genetic characterization and codon usage bias, remain understudied.

Methods: In this study, we analyzed blood samples collected in 2022 from six suspected SFTS cases in Jinan, Shandong Province. This was complemented by a comprehensive analysis of whole-genome sequences obtained from the ViPR and GenBank databases, updated through July 2023. Phylogenetic analysis was employed for genotype classification. Potential recombination events were identified using RDP4. Codon usage patterns were investigated through multiple analyses, including ENC-plot, parity rule 2 (PR2) analysis, and neutral evolution analysis.

Results: Phylogenetic analysis revealed that the detected viral strains belonged to genotypes C3 and C1. Recombination analysis identified 99 potential recombination events among 89 viral strains. Codon usage analyses demonstrated a weak codon usage bias in SFTSV. Further evaluation indicated that both natural selection and mutational pressure shape its codon usage patterns, with natural selection being the predominant force in four SFTSV genes.

Discussion: Our findings highlight the expanding evolutionary diversity of SFTSV, evidenced by recombination events and distinct genotypes. The elucidation of its codon usage characteristics, primarily driven by natural selection, provides critical insights for advancing SFTSV surveillance, improving disease control strategies, and informing targeted vaccine development.

Antimicrobial resistance to cephalosporins in Enterobacterales is commonly mediated by extended-spectrum β-lactamases (ESBL). The ESBL-encoding gene most frequently detected in Salmonella isolates from livestock and the second most frequently detected in Salmonella isolates in humans in Germany is the bla _CTX-M-1 gene. In this study, we characterize ESBL-producing Salmonella enterica collected from non-human sources in Germany, with a particular focus on bla _CTX-M-1 harboring IncI1 plasmids. Therefore, a total of 95 bla _CTX-M-1 positive isolates (S. Derby, S. Infantis, and S. Typhimurium/1,4,[5],12:i:-) from food and animal origin were investigated using short and long-read Whole-Genome Sequencing (WGS) with subsequent in-depth characterization and phylogenetic analysis of the samples and associated mobile genetic elements. WGS revealed a diverse population of bla _CTX-M-1-producing S. enterica isolates in German food and animal samples. In 66 of the 95 isolates, an IncI1 plasmid could be detected. A total of 38 IncI1 positive isolates were selected for long-read sequencing to confirm the location of bla _CTX-M-1 on the IncI plasmid. Additionally, to our 38 bla _CTX-M-1 harboring IncI plasmids, further bla _CTX-M-1 harboring IncI plasmids (n = 103) from the Plasmid Library Search Database (PLSDB), derived from different host bacteria, isolation sources, and geographical locations, were analyzed in detail to gain a deeper insight into IncI1 plasmid evolution. Results revealed that the bla _CTX-M-1 gene was associated with the ISEcp1 transposable element in all but two cases. A total of six distinct integration sites (ISts) were detected across 141 IncI1 plasmids studied here. The integration sites correlated with the plasmid ST and the plasmid phylogeny, regardless of the sample origin, host bacterium, or Salmonella serovar. In conclusion, the emergence of serovar-specific or geographically restricted CTX-M-1 encoding IncI1 plasmids appears to play a minor role. In contrast, evidence suggests that a few successful IncI1 plasmid lineages/plasmid ST types are the primary vehicles for bla _CTX-M-1 gene transmission in Salmonella isolates from diverse geographical origins and sources along the food production chain in Germany.

The feeding rhythm is a major temporal regulator of metabolic physiology, yet its impact on microbiome-derived functional traits relevant to cardiometabolic disease remains insufficiently understood. Our previous work demonstrated that ad libitum, daytime-restricted, and nighttime-restricted feeding produce markedly different atherosclerotic outcomes in Apoe^-/^- mice, indicating that the feeding rhythm acts as a modifiable determinant of atherogenic susceptibility. Here, we used shotgun metagenomics to profile risk-associated microbial functional modules-including Type III and Type VI secretion systems (T3SS/T6SS), siderophore-based iron acquisition pathways, quorum-sensing (QS) regulators, and antimicrobial resistance determinants-across feeding regimens. The feeding rhythm induced pronounced functional segregation independent of α-diversity, which was consistent with selective functional reprogramming rather than taxonomic restructuring. Daytime feeding, which is misaligned with the murine active phase, is associated with coordinated enrichment of the T3SS/T6SS, iron uptake, and QS pathways, forming a tightly interconnected "virulence-iron-QS-ARG" functional consortium. In contrast, circadian-aligned nighttime feeding resulted in attenuated virulence orientation and enhanced metabolic-cooperative signatures. Network inference further revealed strong coactivation of virulence secretion, iron mobilization, and QS modules under circadian misalignment. These findings show that the feeding rhythm modulates atherogenic susceptibility not only through host metabolism but also by remodeling gut microbial functional capacities, highlighting microbial functional ecology as an integral component of diet-host interactions.

The lack of a full automation and control of environmental parameters might result in potential risk of microbial contamination in small-scale production plants such as artisanal cheese and salami Italian productions. In a previous study, genomes of 33 E. coli isolates were sequenced. In the present study, the pathogenicity potential of E. coli strains was investigated by: (1) phylogenomic comparison with 202 public genomes of human, animal and environmental Italian origin; (2) pathogenicity assessment of strains with virulence patterns predicting specific E. coli pathotypes by using larvae of Galleria mellonella as in vivo infection model. Phylogenetic reconstruction revealed raw material and not the processing environment as source of salami contamination. Moreover, close proximity of some strains isolated from salami production with wild boar and extraintestinal human public strains was observed suggesting pigs and wild boar as potential reservoirs of pathogenic E. coli. The virulome of salami strains revealed the presence of genes already described as gene markers of atypical enteropathogenic E. coli (aEPEC; bfp-, eae+). Interestingly the analysis of virulence genes pointed toward additional genomes which showed genetic markers previously described as strongly associated to and/or extraintestinal pathogenic E. coli (ExPEC). In vivo experiments, confirmed the higher pathogenicity of strain 5STM5 with genetic pattern corresponding to hybrid aEPEC/ExPEC and two strains 3CP1522 and 6MB5 of cheese and salami production, respectively, with virulence genes previously associated to ExPEC pathotype. The combined approach pointed toward two genes espC for aEPEC, as well as malX for ExPEC which were significantly enriched in clinical genomes in comparison to genomes of other origins. These genes are worth of future investigations which could help to assess the risk for consumers after the consumption of contaminated artisanal food.

Background: Nosocomial outbreaks of fluconazole-resistant Candida parapsilosis are concerning. Here we characterised a cluster of fluconazole-resistant C. parapsilosis utilising whole-genome sequencing (WGS) and correlate phenotypic azole resistance with resistome-based WGS analysis of azole resistance-conferring mutations.

Materials and methods: Seventeen C. parapsilosis isolates were studied. Group 1: seven fluconazole-resistant isolates from a hospital intensive care unit (ICU) outbreak (2023-2024), Group 2: six isolates from a historical case cluster, Group 3: four additional unrelated isolates. Minimum inhibitory concentrations (MICs) were determined using SENSITITRE AUSNMRC1 (TREK Diagnostics). Single nucleotide polymorphism (SNP)-based phylogenomic analysis was undertaken using two (MycoSNP and custom-based) bioinformatic pipelines to assess relatedness. Target-gene mutations for azole resistance were evaluated.

Results: ICU patient risks for fluconazole-resistant C. parapsilosis included presence of intravascular device and recent broad-spectrum antimicrobial use. Core SNP-based analysis showed clustering of Group 1, and separately, of Group 2 isolates. With greater genetic similarity (range <2-9 SNP difference) between isolates within Group 1, than between these and Group 2 and 3 isolates (1700-3,000 SNPs); the in-house pipeline yielded the same phylogenetic pattern with isolates within both Group 1 and 2 clusters separated by ≅100 SNPs (range 47-124). The eight fluconazole-resistant (MIC >64 mg/L) isolates had ERG11 Y132F and TAC1 D444Y mutations which were absent in fluconazole-susceptible isolates. The mutation ERG11 R398I was present in azole-resistant and azole-susceptible strains.

Conclusion: Genomic relatedness amongst clustered isolates was confirmed in this first fluconazole-resistant C. parapsilosis outbreak in Australia. Fluconazole-resistant isolates harboured ERG11 Y132F and TAC1 D444Y mutations. The protracted outbreak underscores the need to prioritise enhanced surveillance.