Canadian journal of microbiology最新文献

{"title":"BEVA2.0: Modular Assembly of Golden Gate-Compatible Vectors with Expanded Utility for Genetic Engineering.","authors":"Barney Geddes, Riley Williamson, Jake D D Schumacher, Ahmad Ardi, Garrett Levin, Emily Červenka, Rui Huang, George C diCenzo","doi":"10.1139/cjm-2024-0246","DOIUrl":"https://doi.org/10.1139/cjm-2024-0246","url":null,"abstract":"<p><p>This expansion for the modular vector assembly platform BEVA (Bacterial Expression Vector Archive) introduces 11 new BEVA parts including two new cloning site variants, two new antibiotic resistance modules, three new origins of replication, and four new accessary modules. As a result, the modular system is now doubled in size and expanded in its capacity to produce diverse replicating plasmids. Furthermore, it is now amenable to genetic engineering methods involving genome-manipulation of target strains through deletions or integrations. In addition to introducing the new modules, we provide several BEVA-derived Golden Gate cloning plasmids that are used to validate parts and that may be useful for genetic engineering of proteobacteria and other bacteria. We also introduce new parts to allow compatibility with the CIDAR MoClo parts libraries.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The application of shrub willow chip organic amendments impacts soil microbial community dynamics.","authors":"Yvonne Uwituze, Judith Nyiraneza, Kyra Dougherty, Cameron Wagg, Yefang Jiang, Jacynthe Dessureault-Rompre, Fatima Mitterboeck, Tandra Fraser","doi":"10.1139/cjm-2024-0110","DOIUrl":"https://doi.org/10.1139/cjm-2024-0110","url":null,"abstract":"<p><p>Incorporating shrub willow chips into soil may improve the chemical, physical and biological properties of soils with low organic matter but the impact on soil microbial communities and their dynamics is not known. We assessed changes in the soil microbial communities in response to willow chip applied at increasing rates (0, 20, 40 and 60 Mg ha-1) in a potato-barley cropping system. Bacterial and fungal community diversity, relative abundance, and potential functions were assessed using amplicon sequencing of 16S and ITS rRNA genes at six time points. High rates (40 and 60 Mg ha-1) of willow chips had no effect on bacterial alpha diversity but significantly decreased fungal alpha diversity (Shannon) while increasing fungal richness (Chao-1). At rates of 40 Mg ha⁻¹ and higher, the relative abundance of copiotrophic bacterial groups increased, while that of copiotrophic fungal groups decreased. The relative abundance of the most dominant microbial phyla and genera varied over time, with copiotrophic groups declining and oligotrophic groups increasing. High willow chip application rates increased bacterial molecular markers related to carbon fixation and degradation, nitrogen fixation, and phosphorus solubilization, while decreasing markers related to cellobiose transport and denitrification. This study demonstrates the ability of willow chips to influence the microbial community composition and potential function over time.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143122298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of viable Enterobacteriaceae and Enterococcus spp. across the agro-ecosystem of an antibiotic-free swine farm.","authors":"Alexandra Langlois, Antony T Vincent, Renée M Petri, Karoline Lauzon, Dominic Poulin-Laprade","doi":"10.1139/cjm-2024-0173","DOIUrl":"https://doi.org/10.1139/cjm-2024-0173","url":null,"abstract":"<p><p>Agricultural practices, specifically the use of antibiotics and other biocides, have repercussions on human, animal and plant health. The aim of this study was to evaluate the levels of Enterobacteriaceae and Enterococcus, as antibiotic resistant marker bacteria, in various matrices across the agro-ecosystem of an antibiotic-free swine farm in Quebec (Canada), namely pig feed, feces, manure, agricultural soil, water and sediment from a crossing stream, and soil from nearby forests. Samples were collected in fall 2022, spring and fall 2023 and spring 2024. All samples were subjected to counts of total, cefotaxime- and ciprofloxacin-resistant Enterobacteriaceae as well as total and vancomycin-resistant Enterococcus spp. The frequency of total and cefotaxime-resistant Enterobacteriaceae along with the vancomycin-resistant Enterococcus decreased with age in pig feces, from weaning to the end of the fattening period. High proportions of the Enterobacteriaceae recovered from feces and environmental samples were resistant to cefotaxime. Application of manure on fields contributed a significant input of Enterococcus, but those resistant to vancomycin were under the detection limit. This study shows the prevalence of antibiotic-resistant bacteria in a farm agro-ecosystem even without the administration of antibiotics to the animals, and highlights the complexity of components influencing antimicrobial resistance in the environment.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial communities in Hudson Strait amidst rapid environmental changes.","authors":"Samantha Jane Tanlimco Loutet, Alia Sanger, Kallie Strong, Eric Collins, Nagissa Mahmoudi","doi":"10.1139/cjm-2024-0154","DOIUrl":"https://doi.org/10.1139/cjm-2024-0154","url":null,"abstract":"<p><p>Climate change is rapidly altering Arctic marine environments, leading to warmer waters, increased river discharge, and accelerated sea ice melt. The Hudson Bay Marine System (HBMS) experiences the fastest rate of sea ice loss in the Canadian North resulting in a prolonged open water season during the summer months. We examined microbial communities in the Hudson Strait using high throughput 16s rRNA gene sequencing during the peak of summer, in which the bay was almost completely ice-free, and air temperatures were high. We found that salinity and temperature significantly affected the taxonomic composition among microbial communities across sites. We observed a higher relative abundance of specific Polaribacter sp. ASVs at more saline sites. Shannon diversity was not significantly impacted by salinity or temperature. These results contribute to our understanding of surface water microbial community composition in the Hudson Strait and shed light on how future salinity and temperature conditions may favour certain microbial populations.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A pilot study on the effects of in-feed probiotic <i>Lactobacillus rhamnosus</i> ATCC 53103 (LGG) on vaccinated Atlantic salmon (<i>Salmo salar</i>): microbiomes and <i>Aeromonas salmonicida</i> challenge resilience.","authors":"Natalia Lorenc, Steven Leadbeater, Josh Wang, Jennifer Ronholm, Xiaoji Liu","doi":"10.1139/cjm-2024-0130","DOIUrl":"https://doi.org/10.1139/cjm-2024-0130","url":null,"abstract":"<p><p>The use of probiotics is an alternative approach to mitigate the proliferation of antimicrobial resistance in aquaculture. In our study, we examined the effects of <i>Lactobacillus rhamnosus</i> GG (ATCC 53103, LGG) delivered in-feed on the weight, length, skin mucus, and faecal microbiomes of Atlantic salmon. We also challenged the salmon with <i>Aeromonas salmonicida</i> 2004-05MF26 (Asal2004) and assessed the mortality. Our results showed no significant change (<i>P</i> > 0.05) in weight or length of Atlantic salmon or their resilience to Asal2004 infection after LGG feeding. Infection changed significantly the skin mucus and faecal microbiomes: <i>Clostridium sensu stricto</i> increased from 3.14% to 9.20% in skin mucus and 1.39% to 3.74% in faeces (<i>P</i> < 0.05). <i>Aeromonas</i> increased from 0.02% to 0.60% in faeces (<i>P</i> < 0.05). <i>Photobacterium</i> increased from not detected (0%) to 52.16% (<i>P</i> < 0.01) and <i>Aliivibrio</i> decreased from 67.21% to 0.71% in faeces (<i>P</i> < 0.01). After infection, <i>Lactococcus</i> (9.93%) and <i>Lactobacillus</i> (2.11%) in skin mucus of the LGG group were significantly higher (<i>P</i> < 0.05) than in the skin mucus from the rest of the groups (4.14% and 1.08%, respectively). In conclusion, LGG feeding did not further increase the resilience of vaccinated Atlantic salmon. Asal2004 infection had much greater impact on skin mucus and faecal microbiomes than LGG feeding.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic characterization of pathotype diversity and drug resistance among generic Escherichia coli isolated from broiler chickens in Canada.","authors":"Rhiannon Louise Wallace, Shawn Hoogstra, David Mahoney, Mark Lubberts, Richard Reid-Smith, Tara Signorelli, James Robertson, Shannon H C Eagle, Emil Jurga, John Nash, Edward Topp, Catherine D Carrillo","doi":"10.1139/cjm-2024-0209","DOIUrl":"https://doi.org/10.1139/cjm-2024-0209","url":null,"abstract":"<p><p>Escherichia coli is a Gram-negative bacterium that is ubiquitous in animals and humans, with some strains capable of causing disease. The aim of this study was to perform a comparative genomic analysis of 2,732 generic E. coli isolates that were recovered from poultry samples collected from six regions in Canada as part of the National Microbiological Baseline study in Broiler Chicken. Isolates were subjected to whole genome sequencing and a subset (1,122/2,732) were tested for phenotypic resistance to fifteen antimicrobials. These E. coli isolates were highly diverse, representing 376 serotypes, 236 Sequence Types and twenty-one pathotypes, of which 19 were hybrid pathotypes. A high concordance (>85%) between resistance phenotype and the presence of antimicrobial resistance genes and point mutations (resistance determinants) was observed for 13/15 antimicrobials. Over 95% of the β-lactam, fluoroquinolone, and phenicol resistance genes were predicted to be plasmid-borne. The number of resistance determinants per genome was highest in Quebec, while resistance genes associated with β-lactam resistance were more frequently detected in isolates from British Columbia. Generic E. coli in Canadian poultry are highly diverse, can carry pathotype-associated virulence factors and resistance determinants of clinical significance with a risk of emerging into pathogenic strains.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Characterization and whole-genome sequencing of an extreme arsenic tolerant <i>Citrobacter freundii</i> SRS1 strain isolated from Savar area in Bangladesh.","authors":"Mohammed Jafar Uddin, Farhana Haque, Ishrat Jabeen, Sabbir R Shuvo","doi":"10.1139/cjm-2024-0195","DOIUrl":"10.1139/cjm-2024-0195","url":null,"abstract":"","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variation in plasmid conjugation among nontyphoidal <i>Salmonella enterica</i> serovars.","authors":"Anna Laidlaw, Madeleine Blondin-Brosseau, Julie A Shay, Forest Dussault, Mary Rao, Nicholas Petronella, Sandeep Tamber","doi":"10.1139/cjm-2024-0164","DOIUrl":"10.1139/cjm-2024-0164","url":null,"abstract":"<p><p>Conjugation is a complex phenomenon involving multiple plasmid, bacterial, and environmental factors. Here we describe an IncI1 plasmid encoding multidrug antibiotic resistance to aminoglycosides, sulfonamides, and third-generation cephalosporins. This plasmid is widespread geographically among animal, human, and environmental sectors. We present data on the transmissibility of this plasmid from <i>Salmonella</i> <i>enterica</i> ser. Kentucky into 40 strains of <i>S. enterica</i> (10 strains each from serovars Enteritidis, Heidelberg, Infantis, and Typhimurium). Thirty seven out of 40 strains were able to take up the plasmid. Rates of conjugation were variable between strains ranging from 10^-8 to 10^-4. Overall, serovars Enteritidis and Typhimurium demonstrated the highest rates of conjugation, followed by Heidelberg, and then Infantis. No relationships were observed between the recipient cell surface and rate of conjugation. Recipient cell numbers correlated positively with conjugation rate and strains with high conjugation rates had marginally but significantly higher growth parameters compared to strains that took up the plasmid at lower frequencies. Environmental conditions known to impact cell growth, such as temperature, nutrient availability, and the presence of antibiotics, had a modulating effect on conjugation. Collectively, these results will further understanding of plasmid transmission dynamics in <i>Salmonella</i>, which is a critical first step towards the development of mitigation strategies.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-14"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crossing the streams: improving data quality and integration across the One Health genomics continuum with data standards and implementation strategies.","authors":"Emma J Griffiths, Emil Jurga, Gabriel Wajnberg, Julie A Shay, Rhiannon Cameron, Charlie Barclay, Anoosha Sehar, Damion Dooley, Nithu Sara John, Andrew Scott, Lisa A Johnson, James Robertson, Justin Schonfeld, D Patrick Bastedo, Joshua Tang, Xianhua Yin, Attiq Rehman, Rhiannon L Wallace, Krysty Thomas, Shannon H C Eagle, Tim McAllister, Moussa S Diarra, John H E Nash, Ed Topp, Gary Van Domselaar, Eduardo Taboada, Sandeep Tamber, Tony Kess, Jordyn Broadbent, Dominic Poulin-Laprade, Derek D N Smith, Richard Reid-Smith, Rahat Zaheer, Chad R Laing, Catherine D Carrillo, William W L Hsiao","doi":"10.1139/cjm-2024-0203","DOIUrl":"10.1139/cjm-2024-0203","url":null,"abstract":"<p><p>The Canadian Genomics Research and Development Initiative for Antimicrobial Resistance (GRDI-AMR) uses a genomics-based approach to understand how health care, food production and the environment contribute to the development of antimicrobial resistance. Integrating genomics contextual data streams across the One Health continuum is challenging because of the diversity in data scope, content and structure. To better enable data harmonization for analyses, a contextual data standard was developed. However, development of standards does not guarantee their use. Implementation strategies are critical for putting standards into practice. This work focuses on the development of implementation strategies to better operationalize data standards across the Canadian federal genomics ecosystem. Results include improved understanding of complex data models that can create challenges for existing systems. Technical implementation strategies included spreadsheet-based solutions, new exchange formats, and direct standards integration into new databases. Data curation exercises highlighted common data collection and sharing issues, which informed improved practices and evaluation procedures. These new practices are contributing to improved data quality and sharing within the GRDI-AMR consortium as evidenced by publicly available datasets. The implementation strategies and lessons learned described in this work are generalizable for other standards and can be applied more broadly within other initiatives.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-14"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of cannabidiol (CBD), a cannabis plant derivative, against <i>Candida albicans</i> growth and biofilm formation.","authors":"Maryam Bahraminia, Shujun Cui, Ze Zhang, Abdelhabib Semlali, Étienne Le Roux, Kelly-Anne Giroux, Camille Lajoie, François Béland, Mahmoud Rouabhia","doi":"10.1139/cjm-2024-0034","DOIUrl":"10.1139/cjm-2024-0034","url":null,"abstract":"<p><strong>Highlights: </strong>Cannabidiol (CBD) decreases the growth of <i>C. albicans</i>. CBD inhibits the yeast-to-hyphae transition. CBD reduces biofilm formation by <i>C. albicans</i>. CBD induces <i>C. albicans</i> death through necrosis.</p>","PeriodicalId":9381,"journal":{"name":"Canadian journal of microbiology","volume":" ","pages":"1-13"},"PeriodicalIF":1.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142458629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}