Canadian journal of microbiology最新文献

Specialized metabolites produced by microorganisms found in ocean sediments display a wide range of clinically relevant bioactivities, including antimicrobial, anticancer, antiviral, and anti-inflammatory. Due to limitations in our ability to culture many benthic microorganisms under laboratory conditions, their potential to produce bioactive compounds remains underexplored. However, the advent of modern mass spectrometry technologies and data analysis methods for chemical structure prediction has aided in the discovery of such metabolites from complex mixtures. In this study, ocean sediments were collected from Baffin Bay (Canadian Arctic) and the Gulf of Maine for untargeted metabolomics using mass spectrometry. A direct examination of prepared organic extracts identified 1468 spectra, of which ∼45% could be annotated using in silico analysis methods. A comparable number of spectral features were detected in sediments collected from both locations, but 16S rRNA gene sequencing revealed a significantly more diverse bacterial community in samples from Baffin Bay. Based on spectral abundance, 12 specialized metabolites known to be associated with bacteria were selected for discussion. The application of metabolomics directly on marine sediments provides an avenue for culture-independent detection of metabolites produced under natural settings. The strategy can help prioritize samples for novel bioactive metabolite discovery using traditional workflows.

Daqu is the natural starter for Nong-flavor Baijiu brewing. The effects of Daqu properties on the microbial community succession and their metabolites in fermented grains (FG) during Baijiu brewing were determined. These results showed that the effect of Daqu on the bacterial communities was stronger than that of the fungal communities. Compared with the conventional Daqu (DZ), Taikong (TK), and Qianghua (QH), Daqu significantly enhanced the content of volatile metabolites (especially esters) and ethanol when they were used, respectively, for FG fermentation. In the second round of fermentation, the relative abundance of Lactobacillus decreased, the content of lactic acid decreased, and that of caproic acid increased. In particular, the abundance of Lactobacillus was also reduced by 20% in FGs of the second round when TK Daqu was used than that in the respective first round. Partial least squares structural equation model analysis also showed that physicochemical parameters and Daqu properties significantly affected FG community structure and metabolism. This study provides a theoretical basis for further study on the effect of high-quality Daqu on the quality of fresh Baijiu and lays an important theoretical foundation for the stabilization of the Baijiu fermentation system based on Daqu.

The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.

This study explored the effects of Lactiplantibacillus plantarum (previously Lactobacillus plantarum) BW2013 on mucosal integrity and gut microbiota of mice with dextran sulfate sodium (DSS)-induced colitis. The results show that the clinical symptoms in DSS-modelled ulcerative colitis (UC) were improved by L. plantarum BW2013 via decreasing disease activity index scores and suppressing inflammatory cell infiltration. Furthermore, L. plantarum BW2013 decreased the levels of diamine oxidase activity, myeloperoxidase, and D-lactic acid. The mRNA expression of ZO-1, occludin, and claudin-1 was upregulated by L. plantarum BW2013, which also increased IL-10 and reduced TNF-α, IL-1β, and IL-6 in the colon. 16S rDNA sequencing showed that L. plantarum BW2013 enhanced α-diversity. L. plantarum BW2013 upregulated significantly the abundance of unidentfied Lachnospiraceae, Lactococcus, Rikenella, Lactobacillus, and Odoribacter, which had an inhibitory effect on inflammation and a protective effect on the integrity of the mucosa. These results demonstrate that L. plantarum BW2013 alleviates DSS-modelled UC by protecting mucosal integrity and ameliorating the composition of gut microbiota.

The GeneXpert^® Xpert^® Xpress SARS-CoV-2/Flu/RSV PLUS combination test (PLUS assay) received Health Canada approval in January 2022. The PLUS assay is similar to the SARS-CoV-2/Flu/RSV combination test, with modifications to improve assay robustness against circulating and emerging variants. The performance characteristics of the PLUS assay were assessed at the Lakeridge Health Oshawa Hospital Centre and the National Microbiology Laboratory of Canada. The PLUS assay was directly compared to the SARS-CoV-2/Flu/RSV combination test using SARS-CoV-2 culture from five variants and remnant clinical specimens collected across the coronavirus disease 2019 pandemic. This included 50 clinical specimens negative for all pathogens, 110 clinical specimens positive for SARS-CoV-2, influenza A, influenza B, RSVA, and(or) RSVB and an additional 11 mixed samples to screen for target interactions. The PLUS assay showed a high % agreement with the widely used SARS-CoV-2/Flu/RSV combination test. Based on these findings, the PLUS assay and the Xpert SARS-CoV-2/Flu/RSV combination test results are largely consistent with no observed difference in sensitivity, specificity, or time to result when challenged with various SARS-CoV-2 variants. The reported cycle threshold (Ct) values provided by the new PLUS assay were also unchanged, with the exception of a possible 1-2 decrease reported in Ct for RSVA across a limited sample size.

Integrative and conjugative elements (ICEs) are self-transferable mobile genetic elements that play a significant role in disseminating antimicrobial resistance between bacteria via horizontal gene transfer. A recently identified ICE in a clinical isolate of Histophilus somni (ICEHs02) is 72 914 base pairs in length and harbours seven predicted antimicrobial resistance genes conferring resistance to tetracycline (tetR-tet(H)), florfenicol (floR), sulfonamide (Sul2), aminoglycosides (APH(3″)-Ib, APH(6)-Id, APH(3')-Ia), and copper (mco). This study investigated ICEHs02 host range, assessed effects of antimicrobial stressors on transfer frequency, and examined effects of ICEHs02 acquisition on hosts. Conjugation assays examined transfer frequency of ICEHs02 to H. somni and Pasteurella multocida strains. Polymerase chain reaction assays confirmed the presence of a circular intermediate, ICE-associated core genes, and cargo genes in recipient strains. Susceptibility testing examined ICEHs02-associated resistance phenotypes in recipient strains. Tetracycline and ciprofloxacin induction significantly increased the transfer rates of ICEHs02 in vitro. The copy numbers of the circular intermediate of ICEHs02 per chromosome exhibited significant increases of ∼37-fold after tetracycline exposure and ∼4-fold after ciprofloxacin treatment. The acquisition of ICEHs02 reduced the relative fitness of H. somni transconjugants (TG) by 28% (w = 0.72 ± 0.04) and the relative fitness of P. multocida TG was decreased by 15% (w = 0.85 ± 0.01).

Cordyceps farinosa, an entomopathogenic fungus, infects and leads to high mortality of Thitarodes armoricanus larvae, which die soon after the infection of C. farinose, usually before the colonization of Ophiocordyceps sinensis owing to competitive inhibition and fruiting body formation. Therefore, monitoring C. farinosa in the O. sinensis cultivation environment is critical for minimizing the C. farinosa infection-induced losses. In this study, we initially designed a PCR primer pair (Tar-1F/Tar-1R) through open reading frame prediction and homology comparison of the C. farinosa genome sequence. This primer pair can detect both C. farinosa and Samsoniella hepiali. To further distinguish, primers (ITS5-172/ITS4-95) were then designed to selectively amplify the large ribosomal subunit sequences in the C. farinosa genome. All these primers were applied in combination for detection of C. farinosa in soil samples. The sensitivity reached a detection limit of 1 × 10⁶ spores/g soil. In addition, these primers can detect the presence of C. farinosa in dead T. armoricanus larval samples. This newly established rapid detection method provides important information for C. farinosa control during O. sinensis cultivation.

Lactoferrin is an innate glycoprotein with broad antibacterial and antibiofilm properties. The autonomous antibiofilm activity of lactoferrin against Gram-positive bacteria is postulated to involve the cell wall and biofilm components. Thus, the prevention of biomass formation and eradication of preformed biofilms by lactoferrin was investigated using a methicillin-resistant Staphylococcus epidermidis (MRSE) strain. Additionally, the ability of lactoferrin to modulate the expression of the biofilm-associated protein gene (bap) was studied. The bap gene regulates the production of biofilm-associated proteins responsible for bacterial adhesion and aggregation. In the in vitro biofilm assays, lactoferrin prevented biofilm formation and eradicated established biofilms for up to 24 and 72 h, respectively. Extensive eradication of MRSE biofilm biomass was accompanied by the significant upregulation of bap gene expression. These data suggest the interaction of lactoferrin with the biofilm components and cell wall of MRSE, including the biofilm-associated protein.

Chemical weed control is an effective method, but has proved hazardous for humans, environment, and soil biodiversity. Use of allelopathic bacteria may be more efficient and sustainable weed control measure. The bacterial inoculants have never been studied in context of their interaction with weed root exudates and precursor-dependent production of the natural phytotoxins (cyanide, cytolytic enzymes and auxin) by these strains to understand their weed suppression and wheat growth promotion abilities. Therefore, root exudates of Avena fatua, Phalaris minor, Rumex dentatus, and wheat were quantified and their role in microbial root colonization and secondary metabolite production, i.e., cyanide, cytolytic enzymes, phenolics, and elevated auxin concentration, was studied. The results depicted l-tryptophan and glycine as major contributors of elevated cyanide and elevated levels in weed rhizosphere by the studied Pseudomonas strains, through their higher root colonization ability in weeds as compared with wheat. Furthermore, the higher root colonization also enhanced p-coumaric acid (photosynthesis inhibitor by impairing cytochrome c oxidase activity in plants) and cytolytic enzyme (root cell wall degradation) concentration in weed rhizosphere. In conclusion, the differential root colonization of wheat and weeds by these strains is responsible for enhancing weed suppression (enhancing phytotoxic effect) and wheat growth promotion (lowering phytotoxic effect).

In the present study, we report the in vitro interactions between Frankia sp. ACN10a and non-Frankia nodular endophytes (NFNE) isolated from alder. The supernatant of NFNE grown in nitrogen-replete medium had neutral or negative effects on Frankia growth; none had a stimulatory effect. Inhibitory effects were observed for supernatants of some NFNE, notably Micromonospora, Pseudomonas, Serratia and Stenotrophomonas isolates. However, some NFNE-Frankia coculture supernatants could stimulate Frankia growth when used as a culture medium supplement. This was observed for supernatants of Frankia cocultured with Microvirga and Streptomyces isolates. In nitrogen-limited conditions, cocultures of Frankia with some NFNE, including some rhizobia and Cytobacillus, resulted in higher total biomass than Frankia-only cultures, suggesting cooperation, while other NFNE were strongly antagonistic. Microscopic observation of cocultures also revealed compromised Frankia membrane integrity, and some differentiation into stress resistance-associated morphotypes such as sporangia and reproductive torulose hyphae (RTH). Furthermore, the coculture of Frankia with Serratia sp. isolates resulted in higher concentrations of the auxinic plant hormone indole-3-acetic acid and related indolic compounds in the culture supernatant. This study sheds new light on the breadth of microbial interactions that occur amongst bacteria that inhabit the understudied ecological niche of the alder nodule.