Canadian journal of microbiology最新文献

The interferon response is a signalling pathway unique to vertebrates that links the innate and adaptive immune responses. Interferons signal through a cascade of factors including the JAK-STAT pathway to induce the transcription of hundreds of interferon-stimulated genes (ISGs). Although the main interferon signal transduction pathways and ISGs have been elucidated, translational regulation of ISG transcripts is not fully understood. Prior work demonstrated that ribosomal protein RPL28 negatively regulates a subset of ISGs; however, we find that this effect may be due to a reduction in overall ribosome abundance. Multi-omics analysis of RNA-seq and LC-MS/MS data reveal proteins, including several ISGs, that are translationally up-regulated in IFN-β-stimulated cells depleted of ribosome biogenesis factor BOP1. Analysis of codon usage demonstrates a significant reduction in codon optimality for proteins that are translationally up-regulated during BOP1 knockdown and IFN-β stimulation. Using reporter constructs, we demonstrate that codon nonoptimal reporters are translated more than codon-optimized reporters in BOP1-depleted IFN-β cells. We propose that ribosome biogenesis may in part regulate the translational fine-tuning of integral ISG protein production to ensure optimal interferon responses, with potential effects extending beyond this pathway.

We reported phage cocktails of AHP24 (T1), wV7 (T4), AKFV33 (T5), and AHP24S (rV5) had superior efficacy against STEC O157:H7 strains in broth culture and beef matrices, but it is unknown if they can lyse the pathogens in the context of intestinal epithelial cells, which may reduce Shiga toxin-producing Escherichia coli (STEC) attachment, an initial step for STEC invasion. The objective of this study was to compare efficacy of lytic phages T1, T4, T5, and rV5 as individuals or cocktails in preventing STEC attachment to human intestinal epithelial cells. Two intestinal epithelial cell lines, Caco2 and T84, that are susceptible to STEC attachment were used. There were ∼2-3 log₁₀ colony forming units/mL reductions (P < 0.0001) in STEC attachment when these epithelial cells were exposed to individual or cocktails of phages 1 h before inoculation. The phage cocktail (T5 + T1 + rV5 + T4) significantly reduced STEC attachment onto T84 cells when compared to individual phage treatments T4 and T1 (P < 0.0001). Notably, applying three- (excluding T5) or four-phage cocktails concurrent with STEC inoculation did not significantly different from phage pre-exposure. Phages may be a viable approach for preventing and treating STEC infection in human.

There is a great divide between the microbes active in natural environments and the organisms that may be grown in a laboratory setting. In this work we set out to cultivate representatives of the marine myxobacterial clade, a highly diverse, largely uncultured group of Gram-negative bacteria believed to have extensive biosynthetic potential. Sediment samples were collected from the St. Lawrence Estuary and Gulf and the presence of active marine myxobacteria was established through qPCR analysis of 16S rRNA gene and transcript abundances. In the expectation that the marine myxobacteria would exhibit predatory behaviour like their terrestrial counterparts, the sediment samples were then streaked on agar plates that contained common marine bacteria as the sole carbon source. Unexpectedly, in place of myxobacteria we isolated Pseudomonas, Bacillus, and Stenotropomonas spp., among others, revealing a generalized ability for these strains to break down living organic matter and suggesting that "bait" bacteria may be an effective approach for the cultivation of novel marine saprophytes.

Phallus rubrovolvatus is a valuable edible fungus extensively cultivated in Guizhou Province, China. However, the changes in the soil microbiome throughout its growth cycle remain poorly understood. In this study, we collected 35 casing soil samples across five growth stages covering the entire 120-day cultivation cycle of Phallus rubrovolvatus and conducted metagenomic sequencing to examine alterations in soil microbial composition, diversity, key biomarkers, and functional potential. Our analyses revealed significant stage-dependent shifts in microbial community structure, with alpha diversity reaching its lowest at the primordium stage (Shannon of 5.12) and network complexity peaking at harvest stage (1.8-fold increase in connectivity). Through LEfSe analysis, we identified 37 stage-specific microbial biomarkers primarily affiliated with Actinomycetota and Acidobacteriota. Notably, Acidobacteriota biomarkers dominated at the primordium stage, while Nitrospirota enrichment characterized the harvest stage. Functional analyses revealed that membrane transport and energy metabolism pathways were enriched during early mycelial colonization, whereas secondary metabolite biosynthesis and signaling pathways became prominent during fruiting body maturation. Correlation analyses identified available nitrogen as the primary soil variable associated with microbial community composition. These findings provide foundational knowledge of microbiome dynamics during Phallus rubrovolvatus cultivation and suggest that microbiome-based management strategies may benefit from stage-specific interventions synchronized with fungal developmental transitions.

RNA extraction demands careful sample handling and processing due to the lack of stability of RNA in the environment. However, these conditions are sometimes challenging to achieve when working with free-ranging animals. The main objective of this study was to evaluate the efficiency of three commercial RNA extraction kits for biological samples obtained from six wild bird species (black-headed gull, griffon vulture, house sparrow, mallard, song thrush, and common starling). We extracted 24 samples (faeces, oropharyngeal swabs, and cloacal swabs) using RNeasy PowerMicrobiome Kit, RNeasy PowerFecal Pro Kit, and RNeasy Mini Kit (Qiagen). The extraction performance was assessed based on total RNA yield, RNA integrity, and purity ratios (260/280 and 260/230). Moreover, an analysis to determine the inhibitory effect of the extracted samples and a multiple linear regression model were performed. RNA extraction performance varied considerably among species, sample types, and extraction kits. Overall, the RNeasy PowerFecal Pro Kit yielded higher RNA integrity and purity values and showed lower quantitative reverse transcription polymerase chain reaction inhibition than the other kits, particularly in faecal samples. Our findings highlight the importance of selecting extraction methods according to both species and sample type when working with wildlife samples.

The chicken intestine presents a complex environment for microbial survival due to high interbacterial competition, high bile salt concentrations, a low pH, and microaerophilic conditions. While most probiotics contain members of the Bacillota phylum, members of the Pseudomonadota phylum are known to be more important in competitive exclusion-which may be an important consideration in the formulation of future probiotics. Little is known about commensal Pseudomonadota in healthy chickens, or what benefits members of this phylum may offer the host; most studies on Pseudomonadota focus on aspects of opportunistic pathogenesis and dysbiosis. In this study, we use an in silico approach to evaluate the pathogenic potential, competition strategies, and potential host benefits of Pseudomonadota isolates from healthy chickens. We analyzed the draft genomes of 29 representative isolates of Pseudomonadota using Bagle4, AntiSMash, SeCreT6, KEGG mapper, and Virsorter2 to identify key interbacterial competition strategies including secondary metabolite biosynthesis, secretion systems, quorum sensing, and prophages. Our results revealed that each isolate exhibits distinct interbacterial competitive strategies, often independent of their taxonomic affiliation. Including Pseudomonadota in future poultry probiotics may be critical to improving colonization resistance in industrially raised poultry.

Clade 2.3.4.4b A/goose/Guangdong/1/1996 (Gs/GD) H5N1 highly pathogenic (HP) influenza A virus (IAV) (HP H5N1) infection in Blue-winged Teal in the Mississippi Flyway in the United States during the 2022/2023 and 2023/2024 migratory seasons followed a seasonal pattern similar to low pathogenic IAV, with infection peaks in late summer and fall. To determine if this seasonal pattern persisted during the 2024/2025 migration season, we repeated testing of Blue-winged Teal from September 2024 to April 2025 in the Mississippi Flyway. Results from other dabbling duck species sampled concurrently with Blue-winged Teal during the 2023/2024 and 2024/2025 migratory seasons in the Mississippi and Central Flyways also were compared. For Blue-winged Teal in the Mississippi Flyway, a seasonal peak in infection was detected during late fall (November/December 2024) on wintering grounds in Louisiana and Texas corresponding to low H5 and N1 antibody prevalence in juvenile birds. Estimated antibody prevalence increased rapidly following this detection, and from January to April 2025, HP H5N1 infections were not detected. Virologic and serologic results in Mallard, Northern Pintail, American Wigeon, Northern Shoveler, and Green-winged Teal mirrored virologic and serologic results observed in Blue-winged Teal and were consistent between flyways.

A novel mechanism of balancing selection, a type of natural selection, in root pathogen Plasmodiophora brassicae, is presented. Recent studies have demonstrated that Plasmodiophora brassicae retains entire genomes in its population over time. The proposed mechanism for this retention is suppression of host resistance during infection by a virulent genotype (pathotype). This suppression of resistance provides an opportunity for infection by avirulent pathotypes, which would otherwise not be able to infect and reproduce in the resistant host cultivar. In this novel mechanism, which we propose to name as beta retention, a virulent genotype (alpha genotype) opens the door for infection by avirulent genotype (beta genotypes). Under other conditions, such as a different resistant cultivar or host, the alpha genotype could function as a beta genotype and vice versa. This novel mechanism of balancing selection is distinct from existing mechanisms in that entire genomes are retained in the population; other mechanisms maintain single genes or gene clusters. Retention of whole genomes has not previously been reported, probably because it occurs only in microbial plant pathogens and the beta genotypes could only be identified using whole-genome sequences. Beta retention is proposed as a separate mechanism of balancing selection.

During highly pathogenic avian influenza (HPAI) outbreaks, the United States Department of Agriculture response requires infected egg production premises to discard on-site poultry products, including eggs that have been processed and stored prior to infection of the site. The disposal of these eggs contributes to global food insecurity through market disruptions, industry revenue loss, and federal indemnity paid. Further, rural farming communities are economically destabilized and farmer health and well-being challenged. To support continuity of business movement decisions during HPAI outbreaks, the Secure Poultry Supply team at the University of Minnesota along with an egg sector stakeholder workgroup has been examining the risk of moving to market processed, segregated, and stored eggs from an infected premises that were laid by uninfected flocks (i.e., a group of egg-laying hens kept in one house/barn during their entire lay cycle). Three important criteria for achieving both acceptable risk and confidence for movement were identified: identification and removal of potentially contaminated eggs from the cooler; protection of cooler eggs from recontamination; and science-assessed egg truck disinfection protocols for exiting an infected premises. The science behind biosecurity and biocontainment practices and risk determination for moving eggs off infected premises are discussed. Confidence in movements determined to be low risk may provide a means for farm and food-protein sustainability.

Pseudomonas aeruginosa is a major opportunistic pathogen responsible for severe human infections and is increasingly associated with multidrug resistance and limited treatment options. In this study, we isolated and characterized bacteriophages targeting drug-resistant P. aeruginosa strains and evaluated their capacity to disrupt biofilms and modulate biofilm-associated gene expression. Phages recovered from sewage showed broad lytic activity against P. aeruginosa and were classified morphologically into the families Podoviridae and Myoviridae. Two phages, A2 and A4, exhibited the highest lytic activity against the resistant strains examined. Both phages significantly degraded preformed biofilms, with phage A4 showing comparatively stronger antibiofilm activity. In addition, phage exposure altered the expression of several biofilm-associated genes, including pelA, htpB, bifA, psl, fimW, and wspA. A notable finding was the reversal of bifA expression from downregulation at 12 h to upregulation at 24 h following treatment with phage A4. Collectively, these results demonstrate that phages A2 and A4 possess strong lytic and antibiofilm activities and are capable of modulating biofilm-associated transcriptional responses in drug-resistant P. aeruginosa. The findings support the potential application of bacteriophages as alternative therapeutic agents against drug-resistant biofilm-associated infections.