Microorganisms

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ISSN / EISSN : 2076-2607 / 2076-2607
Published by: MDPI (10.3390)
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Published: 26 January 2022
by MDPI
Abstract:
Recurrent infection by Clostridioides difficile has recently been treated by fecal microbiota transplantation (FMT). As viable SARS-CoV-2 was recovered from stool of asymptomatic individuals, the FMT procedure could be a potential risk of SARS-CoV-2 transmission, thus underlying the need to reliably detect SARS-CoV-2 in stool. Here, we performed a multicentric study to explore performances of two commercially available assays for detection of SARS-CoV-2 RNA in stool of potential FMT donors. In three hospitals, 180 stool samples were spiked with serial 10-fold dilutions of a SARS-CoV-2 inactivated lysate to evaluate the Seegene Allplex™ SARS-CoV-2 (SC2) and SARS-CoV-2/FluA/FluB/RSV (SC2FABR) Assays for the detection of viral RNA in stool of FMT donors. The results revealed that both assays detected down to 2 TCID50/mL with comparable limit of detection values, SC2 showing more consistent target positivity rate than SC2FABR. Beyond high amplification efficiency, correlation between CT values and log concentrations of inactivated viral lysates showed R2 values ranging from 0.88 to 0.90 and from 0.87 to 0.91 for the SC2 and SC2FABR assay, respectively. The present results demonstrate that both methods are highly reproducible, sensitive, and accurate for SARS-CoV-2 RNA detection in stool, suggesting a potential use in FMT-donor screening.
Published: 26 January 2022
by MDPI
Abstract:
Whole genome sequencing (WGS) of Salmonella supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in Salmonella enterica (n = 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard. To facilitate high-throughput prediction of AMR from genome assemblies, we created a tool called Staramr, which incorporates the ResFinder and PointFinder databases and a custom gene-drug key for antibiogram prediction. Overall, there was 99% concordance between phenotypic and genotypic detection of categorical resistance for 14 antimicrobials in 1321 isolates (18,305 of 18,494 results in agreement). We observed an average sensitivity of 91.2% (range 80.5–100%), a specificity of 99.7% (98.6–100%), a positive predictive value of 95.4% (68.2–100%), and a negative predictive value of 99.1% (95.6–100%). The positive predictive value of gentamicin was 68%, due to seven isolates that carried aac(3)-IVa, which conferred MICs just below the breakpoint of resistance. Genetic mechanisms of resistance in these 1321 isolates included 64 unique acquired alleles and mutations in three chromosomal genes. In general, in silico prediction of AMR in Salmonella was reliable compared to the gold standard of broth microdilution. WGS can provide higher-resolution data on the epidemiology of resistance mechanisms and the emergence of new resistance alleles.
Published: 26 January 2022
by MDPI
Abstract:
Faecalibacterium prausnitzii is prevalent in the human gut and is a potential candidate for next-generation probiotics (NGPs) or biotherapeutics. However, the biodiversity and physiological characteristics of Faecalibacterium prausnitzii remain unclear. This study isolated 26 novel F. prausnitzii strains from human feces using a combination of negative screening and prime-specific PCR amplification (NSPA). Based on a 16S rRNA gene analysis, F. prausnitzii strains can be classified into two main phylogroups (phylogroups I and II), which were further clustered into five subgroups (I-A, II-B, II-C, II-D, and II-E). The ultrastructure, colony morphology, growth performance, and short-chain fatty acids (SCFAs)-producing ability were found to be variable among these F. prausnitzii isolates. The optimal pH for the isolates growth ranged between 6.0 and 7.0, while most isolates were inhibited by 0.1% of bile salts. Antimicrobial resistance profiles showed that all F. prausnitzii isolates were susceptible to vancomycin, whereas >80% were kanamycin and gentamicin resistant. Additionally, all strains can utilize maltose, cellulose, and fructose but not xylose, sorbose, and 2′-FL. Overall, our work provides new insights into the biodiversity and physiological characteristics of F. prausnitzii, as well as the choices of strains suitable for NGPs.
Published: 26 January 2022
by MDPI
Abstract:
Sourdough is one of the oldest starters traditionally used for making baked goods, offering several advantages to the sensory, rheology, and shelf life of final products. The present study investigated, for the first time, the microbiota of spontaneously fermented Maiorca dough samples collected from bakeries located in Sicily (Italy). Four sourdough samples (M1, M2, M3, and M4), were produced using Triticum vulgare Host. var. albidum Koern (Maiorca grain) were subjected to LAB and yeasts isolation and identification at the species level. The in-depth characterization of the lactobacilli population revealed that Lactiplantibacillus plantarum and Levilactobacillus brevis unquestionably dominated the Maiorca sourdough ecosystem. Concerning the yeasts community, high species diversity was found. Saccharomyces cerevisiae and Wickerhamomyces anomalus were the most frequently isolated species. In addition, Torulaspora delbrueckii, Pichia kluyveri, Candida boidinii, and Candida diddensiae were also detected. Investigations on both pro-technological and functional traits of the isolated strains could lead to the selection of starters for the production of baked goods.
Published: 26 January 2022
by MDPI
Abstract:
To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO’s capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.
Published: 26 January 2022
by MDPI
Abstract:
Over the past decade, scientific evidence for the properties, functions, and beneficial effects of probiotics for humans has continued to accumulate. Interest in the use of probiotics for humans has increased tremendously. Among various microorganisms, probiotics using bacteria have been widely studied and commercialized, and, among them, Lactobacillus is representative. This genus contains about 300 species of bacteria (recently differentiated into 23 genera) and countless strains have been reported. They improved a wide range of diseases including liver disease, gastrointestinal diseases, respiratory diseases, and autoimmune diseases. Here, we intend to discuss in depth the genus Lactobacillus as a representative probiotic for chronic liver diseases.
Published: 26 January 2022
by MDPI
Abstract:
Trypanosomes belonging to Trypanosoma theileri group are mammalian blood parasites with keds and horse fly vectors. Our aim is to study to vector specificity of T. theileri trypanosomes. During our bloodsucking Diptera survey, we found a surprisingly high prevalence of T. theileri trypanosomes in mosquitoes (154/4051). Using PCR and gut dissections, we detected trypanosomes of T. theileri group mainly in Aedes mosquitoes, with the highest prevalence in Ae. excrucians (22%), Ae. punctor (21%), and Ae. cantans/annulipes (10%). Moreover, T. theileri group were found in keds and blackflies, which were reported as potential vectors for the first time. The vectorial capacity was confirmed by experimental infections of Ae. aegypti using our isolates from mosquitoes; sand fly Phlebotomus perniciosus supported the development of trypanosomes as well. Infection rates were high in both vectors (47–91% in mosquitoes, 65% in sandflies). Furthermore, metacyclic stages of T. theileri trypanosomes were observed in the gut of infected vectors; these putative infectious forms were found in the urine of Ae. aegypti after a second bloodmeal. On the contrary, Culex pipiens quinquefasciatus was refractory to experimental infections. According to a phylogenetic analysis of the 18S rRNA gene, our trypanosomes belong into three lineages, TthI, ThII, and a lineage referred to as here a putative lineage TthIII. The TthI lineage is transmitted by Brachycera, while TthII and ThIII include trypanosomes from Nematocera. In conclusion, we show that T. theileri trypanosomes have a wide range of potential dipteran vectors, and mosquitoes and, possibly, sandflies serve as important vectors.
Published: 26 January 2022
by MDPI
Abstract:
The objective of this study was to provide information on Trypanosoma cruzi genetic diversity among isolates obtained from different biological sources circulating in endemic areas of Panama. Initial discrete typing units (DTUs) assignment was performed evaluating three single locus molecular markers (mini-exon, heat shock protein 60 and glucose-6-phosphate isomerase genes). Further diversity within TcI lineages was explored using a multi-locus sequence typing approach with six maxicircle genes. Haplotype network analysis and evolutionary divergency estimations were conducted to investigate the genetic relatedness between Panamanian TcI isolates and isolates from different endemic regions in the Americas. Our molecular approach validated that TcI is the predominant DTU circulating in Panama across different hosts and vector species, but also confirmed the presence of TcIII and TcVI circulating in the country. The phylogenetic tree topography for most Panamanian TcI isolates displayed a high level of genetic homogeneity between them. The haplotype network analysis inferred a higher genetic diversity within Panamanian TcI isolates, displaying eight different haplotypes circulating in endemic regions of the country, and revealed geographical structuring among TcI from different endemic regions in the Americas. This study adds novelty on the genetic diversity of T. cruzi circulating in Panama and complements regional phylogeographic studies regarding intra-TcI variations.
Published: 26 January 2022
by MDPI
Abstract:
Isolated from desert, the nitrogen-fixing bacterium Ensifer aridi LMR001 is capable of survival under particularly harsh environmental conditions. To obtain insights in molecular mechanisms involved in stress adaptation, a recent study using RNAseq revealed that the RpoE2-mediated general stress response was activated under mild saline stress but appeared non-essential for the bacterium to thrive under stress and develop the symbiosis. Functions associated with the stress response included the metabolisms of trehalose, methionine, and inositol. To explore the roles of these metabolisms in stress adaptation and symbiosis development, and the possible regulatory mechanisms involved, mutants were generated notably in regulators and their transcriptions were studied in various mutant backgrounds. We found that mutations in regulatory genes nesR and sahR of the methionine cycle generating S-adenosylmethionine negatively impacted symbiosis, tolerance to salt, and motility in the presence of NaCl. When both regulators were mutated, an increased tolerance to detergent, oxidative, and acid stresses was found, suggesting a modification of the cell wall components which may explain these phenotypes and support a major role of the fine-tuning methylation for symbiosis and stress adaptation of the bacterium. In contrast, we also found that mutations in the predicted trehalose transport and utilization regulator ThuR and the trehalose phosphate phosphatase OtsB-encoding genes improved symbiosis and growth in liquid medium containing 0.4 M of NaCl of LMR001ΔotsB, suggesting that trehalose metabolism control and possibly trehalose-6 phosphate cellular status may be biotechnologically engineered for improved symbiosis under stress. Finally, transcriptional fusions of gfp to promoters of selected genes and expression studies in the various mutant backgrounds suggest complex regulatory interplay between inositol, methionine, and trehalose metabolic pathways.
Xin Yee Ang, Uma Mageswary Mageswaran, Yi Li Fiona Chung, Boon Kiat Lee, Siti Nur Afiqah Azhar, Nurhanis Syazni Roslan, Ili Farhana Binti Saufian, Nor Sheila Mustaffa, Ermadina Mohamad Kalam, Aini Farhah Ibrahim, et al.
Published: 26 January 2022
by MDPI
Abstract:
We previously reported on the effects of a lactobacilli probiotic (SynForU-HerCare; two capsules/day of 9.5 log CFU/capsule) in improving symptoms of vaginal irritation, discharge and burning in pregnant women with vaginal candidiasis upon administration for 8 weeks, accompanied by improved emotional and social quality of life parameters. Thus, the present study aimed to analyse vaginal microbiota and inflammatory changes in hope to better understand the improved clinical symptoms as observed previously. Patients in the probiotic group showed a decreased abundance of Candida glabrata after 8 weeks (p = 0.009) in the lower vaginal region, while patients in the placebo group did not show any changes over time. In the higher vaginal and cervicovaginal regions, patients in the placebo group showed a decreased abundance of Candida albicans only within 4 weeks (p< 0.05) but no changes in abundance of C. glabrata over time, while patients in the probiotic group showed a continuous decreased abundance of C. albicans and C. glabrata over 8 weeks (p< 0.05). Patients in the placebo group also had a decreased abundance of Lactobacillus crispatus over 4 weeks (p = 0.023) in the lower vaginal region and a decreased abundance of L. jensenii over 8 weeks in the cervicovaginal region (p = 0.001). Meanwhile, patients in the probiotic group had an increased abundance of L. crispatus in the lower vaginal region after 8 weeks (p = 0.012) and Lactobacillus jensenii over 4 weeks in the cervicovaginal region (p< 0.001). Inflammation may have occurred in both low and high vaginal regions, predominantly observed by the increased concentration of pro-inflammatory cytokine TNF-alpha in patients from the placebo group (p< 0.05), while the administration of probiotics has shortened the period of inflammation as observed from the reduced need for anti-inflammatory cytokine IL-4 and IL-10 over time (p< 0.05). Taken together, our present new data further support previous findings that probiotic SynForU-HerCare had a beneficial effect against vaginal candidiasis in pregnant women via modulation of the vaginal microbiota and microenvironment.
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