Canadian journal of microbiology最新文献

Although Citrus aurantium has enormous medicinal and ecological value in southern China, little research has been conducted into the composition and functions of endophytic fungi in it. To better explore the characteristics of the endophytic fungal community in C. aurantium, ITS rRNA gene analyses were used to characterize the endophytic fungal microbiome across three plant compartments and three regions. The results showed that a total of 12 109 OTUs were obtained and further divided into 15 phyla and 768 genera. Ascomycota was the dominant phylum. Fusarium, Alternaria, Mortierella, Plectosphaerella, Cladosporium, Colletotrichum, Trichomerium, Botryotrichum, and Aspergillus were the dominant genera. The endemic and dominant genera of endophytic fungi in C. aurantium exhibited plant compartment specificity. The assembly of endophytic fungal communities was dominated by homogeneous selection of deterministic processes. The endophytic fungal genera of C. aurantium predominantly exhibited positive interactions (with a proportion > 99%). The dominant functions of endophytic fungi in C. aurantium were pathotroph and saprotroph. The composition (niche: R² = 0.09, P = 0.001; site: R² = 0.06, P = 0.021) and functional components (niche: R² = 0.117, P = 0.002; site: R² = 0.122, P = 0.006) exhibited significant plant compartment and region specificity. The results of this study reveal the characteristics of the endophytic fungal community of C. aurantium, and provide a theoretical reference for the further development and utilization of endophytic fungal resources.

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.

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.

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.

Antimicrobial resistance (AMR) poses a significant threat to global health, demanding a collaborative and multi-sectoral approach to mitigate its impact. The Canadian Genomics Research and Development Initiative for Antimicrobial Resistance (GRDI-AMR) project exemplifies this approach by uniting a diverse team of experts from various Canadian science-based departments and agencies (SBDAs). This highly effective and collaborative team leverages the existing expertise within SBDAs, fostering innovation and driving advancements in AMR research. By integrating genomics and One Health principles, GRDI-AMR is generating critical knowledge and developing impactful solutions to combat AMR in Canada and beyond. This special issue provides a glimpse into the impactful outcomes generated by this collaborative network.

Antimicrobial resistance (AMR) is a growing public health threat in Canada. In 2022, rising resistance was reported among key pathogens, yet national coordination remains inconsistent, with strategies varying widely by province and territory. This study explored AMR-related challenges in healthcare and the impact of the COVID-19 pandemic on AMR efforts in Canada. Using a qualitative design, researchers conducted semi-structured interviews with 59 experts from fields such as microbiology, public health, and industry. Participants were identified through environmental scanning and snowball sampling. Thematic analysis of transcripts revealed major barriers to a unified AMR response, including inconsistent surveillance, fragmented stewardship efforts, and decentralized health systems. According to participating AMR experts, COVID-19 disrupted AMR control by diverting resources and potentially increasing resistance but also led to improvements in infection prevention, public awareness, and health infrastructure. Participants emphasized the need for stronger political commitment, improved surveillance, a One Health approach, and better funded, coordinated stewardship programs. With the publication of the Pan-Canadian Action Plan in 2023, the Canadian federal government has announced changes. However, effectively addressing AMR will require a unified, multisectoral strategy that bridges political, health, and societal efforts across jurisdictions.

Botrytis cinerea is a pathogen infecting Cannabis sativa L. plants, causing economic losses, and can develop resistance to chemical fungicides, the use of which is restricted in cannabis production. Thus, developing biocontrol methods is imperative. Seven bacterial strains were isolated from hemp seed oil, characterized, and examined for the potential to control a Botrytis cinerea isolate from cannabis. Three isolates, Bacillus mojavensis HOB3, Paenibacillus sp. HOB6, and Bacillus subtilis HOB7 exhibited significant inhibition of Botrytis cinerea. These isolates were further evaluated for their biosurfactant activity using two liquid media, Lysogeny Broth (LB) and hydrocarbon-amended Bushnell and Haas (BH). The oil-spreading and drop-collapse assays revealed growth-medium-dependent variation in surface activity associated with biosurfactant presence. The BH cell-free extract (BH-CFE) of Bacillus subtilis HOB7 showed the highest estimated biosurfactant presence and antifungal activity against Botrytis cinerea, but both activities were absent when using the LB cell-free extract (LB-CFE) of Bacillus subtilis HOB7. Thus, a potential relationship between antifungal activity and biosurfactant production was suggested. Genome mining of the strains identified gene clusters encoding compounds with antifungal activity, including the biosurfactants polymyxin B, fusaricidin B, fengycin, and surfactin. To our knowledge, this is the first report of the isolation of hemp seed oil bacteria with potential biocontrol properties against fungal phytopathogens.

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 processed, segregated, and stored eggs from an infected premises that were laid by uninfected flocks to market. 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.

In 2022, highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b was detected in United States (US) poultry, quickly escalating into an outbreak that surpassed the 2014/15 HPAI US event in scale and impact. Unlike in 2014/15, the 2022/3/4/5 outbreak has included numerous HPAI detections in previously infrequently affected commodities such as broilers and commercially-raised upland game birds. Here, we describe H5 HPAIV detections that occurred between December 2023 and January 2024 in a multi-premises upland game bird system located in the Midwestern US. We used an approximate Bayesian computation algorithm and stochastic within-flock HPAI transmission model to estimate the following: 1) times of HPAI introduction onto each affected premises, 2) number of days between estimate time of introduction and time of detection, and 3) the adequate contact rates and basic reproduction numbers within individual barns. Clinical signs and mortality observed in the infected pheasant flocks were largely consistent with other pheasant H5 clade 2.3.4.4b outbreaks. Across the system, the estimated transmission metrics were noticeably lower than those calculated from outbreaks in other poultry species. However, time to detection was similar to HPAI outbreaks that have occurred in other commodities.

Highly pathogenic avian influenza (HPAI) virus H5N1 clade 2.3.4.4b was introduced into North America in 2021. In 2022, clade 2.3.4.4b spilled into domestic poultry in the United States (U.S.), resulting in the largest HPAI outbreak in U.S. history. In December 2023, H5N1 2.3.4.4b was detected on an upland game bird farm in Pennsylvania. History, clinical signs, and gross lesions were suggestive of marble spleen disease. However, HPAI was identified by real-time reverse-transcriptase polymerase chain reaction; gene sequencing confirmed genotype C2.1 with phylodynamic analyses providing evidence of a wild bird introduction. Predictive mathematical modeling estimated the time of virus introduction onto the farm (15 days [95% C.I., 11 - 23] before the date of confirmed detection) being similar or longer than previously described for domestic poultry. Although bioexclusion measures were unable to prevent the initial exposure due to industry rearing practices, biocontainment procedures appeared to prevent spread. The lessons learned from this case may be important for other animal agriculture commodities, especially those species that are infrequently handled or observed and may have inaccurately calculated mortality levels. This well characterized outbreak and other experiences with natural infection should be taken as opportunities to better understand the field dynamics of this virus.