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1.
  • Kaden, Rene, 1975-, et al. (author)
  • How to Show the Real Microbial Biodiversity? A Comparison of Seven DNA Extraction Methods for Bacterial Population Analyses in Matrices Containing Highly Charged Natural Nanoparticles
  • 2015
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 3:4, s. 695-706
  • Journal article (peer-reviewed)abstract
    • A DNA extraction that comprises the DNA of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. Many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged DNA molecules after cell lysis within DNA extraction. Depending on the methodology of DNA extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possible misinterpretation of microbial interactions. With the aim to describe microbial interactions and the bio-geo-chemical reactions during a clay alteration experiment, several methods for the detection of a high number of microbial taxa were examined in this study. Altogether, 13 different methods of commercially available DNA extraction kits provided by seven companies as well as the classical phenol-chloroform DNA extraction were compared. The amount and the quality of nucleic acid extracts were determined and compared to the amplifiable amount of DNA. The 16S rRNA gene fragments of several taxa were separated using denaturing gradient gel electrophoresis (DGGE) to determine the number of different species and sequenced to get the information about what kind of species the microbial population consists of. A total number of 13 species was detected in the system. Up to nine taxa could be detected with commercially available DNA extraction kits while phenol-chloroform extraction lead to three detected species. In this paper, we describe how to combine several DNA extraction methods for the investigation of microbial community structures in clay.
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2.
  • Abdelfattah, Ahmed, et al. (author)
  • Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:6
  • Journal article (peer-reviewed)abstract
    • There is growing recognition of the role that the microbiome plays in the health and physiology of many plant species. However, considerably less research has been conducted on the postharvest microbiome of produce and the impact that postharvest processing may have on its composition. Here, amplicon sequencing was used to study the effect of washing, waxing, and low-temperature storage at 2 degrees C for six months on the bacterial and fungal communities of apple calyx-end, stem-end, and peel tissues. The results of the present work reveal that tissue-type is the main factor defining fungal and bacterial diversity and community composition on apple fruit. Both postharvest treatments and low temperature storage had a strong impact on the fungal and bacterial diversity and community composition of these tissue types. Distinct spatial and temporal changes in the composition and diversity of the microbiota were observed in response to various postharvest management practices. The greatest impact was attributed to sanitation practices with major differences among unwashed, washed and washed-waxed apples. The magnitude of the differences, however, was tissue-specific, with the greatest impact occurring on peel tissues. Temporally, the largest shift occurred during the first two months of low-temperature storage, although fungi were more affected by storage time than bacteria. In general, fungi and bacteria were impacted equally by sanitation practices, especially the epiphytic microflora of peel tissues. This research provides a foundation for understanding the impact of postharvest management practices on the microbiome of apple and its potential subsequent effects on postharvest disease management and food safety.
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3.
  • Agramont, J, et al. (author)
  • Fecal Pollution Drives Antibiotic Resistance and Class 1 Integron Abundance in Aquatic Environments of the Bolivian Andes Impacted by Mining and Wastewater
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:8
  • Journal article (peer-reviewed)abstract
    • An increased abundance of antibiotic resistance genes (ARGs) in aquatic environments has been linked to environmental pollution. Mining polluted sites with high concentration of metals could favor the in situ coselection of ARGs, whereas wastewater discharges release fecal antibiotic resistant bacteria in the environment. To study the effect of human fecal contamination and mining pollution, water and sediment samples affected by mining activities and sewage discharges were collected from three lakes in Bolivia, the pristine Andean lake Pata Khota, the Milluni Chico lake directly impacted by acid mine drainage, and the Uru-Uru lake located close to Oruro city and highly polluted by mining activities and human wastewater discharges. Physicochemical parameters, including metal composition, were analyzed in water and sediment samples. ARGs were screened for and verified by quantitative polymerase chain reaction (PCR) together with the mobile element class 1 integron (intl1), as well as crAssphage, a marker of human fecal pollution. The gene intl1 was positively correlated with sul1, sul2, tetA, and blaOXA-2. CrAssphage was only detected in the Uru-Uru lake, and its tributaries and significantly higher abundance of ARGs were found in these sites. Multivariate analysis showed that crAssphage abundance, electrical conductivity, and pH were positively correlated with higher levels of intl1 and ARGs. Taken together, our results suggest that fecal pollution is the major driver of higher levels of ARGs and intl1 in environments contaminated by wastewater and mining activities.
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4.
  • Ahle, Charlotte M., et al. (author)
  • Staphylococcus saccharolyticus : An Overlooked Human Skin Colonizer
  • 2020
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 8:8
  • Journal article (peer-reviewed)abstract
    • Coagulase-negative staphylococcal species constitute an important part of the human skin microbiota. In particular, facultative anaerobic species such as Staphylococcus epidermidis and Staphylococcus capitis can be found on the skin of virtually every human being. Here, we applied a culture-independent amplicon sequencing approach to identify staphylococcal species on the skin of healthy human individuals. While S. epidermidis and S. capitis were found as primary residents of back skin, surprisingly, the third most abundant member was Staphylococcus saccharolyticus, a relatively unstudied species. A search of skin metagenomic datasets detected sequences identical to the genome of S. saccharolyticus in diverse skin sites, including the back, forehead, and elbow pit. Although described as a slow-growing anaerobic species, a re-evaluation of its growth behavior showed that S. saccharolyticus can grow under oxic conditions, and, in particular, in a CO2-rich atmosphere. We argue here that S. saccharolyticus was largely overlooked in previous culture-dependent and -independent studies, due to its requirement for fastidious growth conditions and the lack of reference genome sequences, respectively. Future studies are needed to unravel the microbiology and host-interacting properties of S. saccharolyticus and its role as a prevalent skin colonizer.
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5.
  • Alao, John Patrick, 1973, et al. (author)
  • Caffeine stabilises fission yeast Wee1 in a Rad24-dependent manner but attenuates Its expression in response to DNA damage.
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:10
  • Journal article (peer-reviewed)abstract
    • The widely consumed neuroactive compound caffeine has generated much interest due to its ability to override the DNA damage and replication checkpoints. Previously Rad3 and its homologues was thought to be the target of caffeine's inhibitory activity. Later findings indicate that the Target of Rapamycin Complex 1 (TORC1) is the preferred target of caffeine. Effective Cdc2 inhibition requires both the activation of the Wee1 kinase and inhibition of the Cdc25 phosphatase. The TORC1, DNA damage, and environmental stress response pathways all converge on Cdc25 and Wee1. We previously demonstrated that caffeine overrides DNA damage checkpoints by modulating Cdc25 stability. The effect of caffeine on cell cycle progression resembles that of TORC1 inhibition. Furthermore, caffeine activates the Sty1 regulated environmental stress response. Caffeine may thus modulate multiple signalling pathways that regulate Cdc25 and Wee1 levels, localisation and activity. Here we show that the activity of caffeine stabilises both Cdc25 and Wee1. The stabilising effect of caffeine and genotoxic agents on Wee1 was dependent on the Rad24 chaperone. Interestingly, caffeine inhibited the accumulation of Wee1 in response to DNA damage. Caffeine may modulate cell cycle progression through increased Cdc25 activity and Wee1 repression following DNA damage via TORC1 inhibition, as TORC1 inhibition increased DNA damage sensitivity.
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6.
  • Bai, XN, et al. (author)
  • Characterization of Clinical Escherichia coli Strains Producing a Novel Shiga Toxin 2 Subtype in Sweden and Denmark
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:11
  • Journal article (peer-reviewed)abstract
    • Shiga toxin (Stx) is the key virulence factor in the Shiga Toxin-Producing Escherichia coli (STEC), which can cause diarrhea and hemorrhagic colitis with potential life-threatening complications. There are two major types of Stx: Stx1 and Stx2. Several Stx1/Stx2 subtypes have been identified in E. coli, varying in sequences, toxicity and host specificity. Here, we report a novel Stx2 subtype (designated Stx2m) from three clinical E. coli strains isolated from diarrheal patients and asymptomatic carriers in Sweden and Denmark. The Stx2m toxin was functional and exhibited cytotoxicity in vitro. The two Swedish Stx2m-producing strains belonged to the same serotype O148:H39 and Multilocus Sequencing Typing (MLST) Sequence Type (ST) 5825, while the Danish strain belonged to the O96:H19 serotype and ST99 type. Whole-genome sequencing (WGS) data analysis revealed that the three Stx2m-producing strains harbored additional virulence genes and the macrolide resistance gene mdf (A). Our findings expand the pool of Stx2 subtypes and highlight the clinical significance of emerging STEC variants. Given the clinical relevance of the Stx2m-producing strains, we propose to include Stx2m in epidemiological surveillance of STEC infections and clinical diagnosis.
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7.
  • Bergqvist, L, et al. (author)
  • Distribution of HPV Genotypes Differs Depending on Behavioural Factors among Young Women
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:4
  • Journal article (peer-reviewed)abstract
    • Risk factors for the different human papillomavirus (HPV) genotypes are not well understood, although the risk of cancer is known to vary among them. Our aim was to evaluate the association of diverse behavioral and reproductive factors with genotype-specific HPV prevalence among 879 unvaccinated women aged 18–75 years referred to the colposcopy clinic at Helsinki University Hospital in Finland. Cervical swabs for HPV genotyping were collected in the first visit and assessed for 34 high-risk (hr) and low-risk (lr) HPV genotypes. Participants completed a questionnaire on behavioral, reproductive, and lifestyle factors. Differences in genotype-specific HPV prevalence were analyzed overall and in age groups using binary logistic regression. Smoking was associated with higher prevalence in HPV16 compared with other hrHPV genotypes together with decreasing age, being highest among younger women <30 years old, odds ratio (OR) 3.74 (95% CI 1.42–9.88). The later the sexual debut, the more it seemed to protect from HPV16 infection. The best protection was achieved when the sexual debut took place at >20 years of age, with an OR of 0.43 (95% CI 0.23–0.83). This association was not seen with other hrHPV genotypes. Methods of contraception seemed not to have an effect on hrHPV positivity, regardless of the HPV genotype. The genotype specific hrHPV prevalence differs, depending on behavioral factors, especially among younger women referred to colposcopy.
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8.
  • Brezgin, S, et al. (author)
  • Replenishment of Hepatitis B Virus cccDNA Pool Is Restricted by Baseline Expression of Host Restriction Factors In Vitro
  • 2019
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 7:11
  • Journal article (peer-reviewed)abstract
    • Background: Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is the major cause of viral persistence in patients with chronic HBV infection. Understanding the mechanisms underlying stability and persistence of HBV cccDNA in hepatocytes is critical for developing novel therapeutics and managing chronic hepatitis B. In this study, we observed an unexpected increase in HBV cccDNA levels upon suppression of transcription by de novo DNA methyltransferase DNMT3A and uncovered additional mechanisms potentially involved in HBV cccDNA maintenance. Methods: HBV-expressing cell lines were transfected with a DNMT3A-expressing plasmid. Real-time PCR and HBsAg assays were used to assess the HBV replication rate. Cell cycling was analyzed by fluorescent cell sorting. CRISPR/Cas9 was utilized to abrogate expression of APOBEC3A and APOBEC3B. Alterations in the expression of target genes were measured by real-time PCR. Results: Similar to previous studies, HBV replication induced DNMT3A expression, which in turn, led to reduced HBV transcription but elevated HBV cccDNA levels (4- to 6-fold increase). Increased levels of HBV cccDNA were not related to cell cycling, as DNMT3A accelerated proliferation of infected cells and could not contribute to HBV cccDNA expansion by arresting cells in a quiescent state. At the same time, DNMT3A suppressed transcription of innate immunity factors including cytidine deaminases APOBEC3A and APOBEC3B. CRISPR/Cas9-mediated silencing of APOBEC3A and APOBEC3B transcription had minor effects on HBV transcription, but significantly increased HBV cccDNA levels, similar to DNMT3A. In an attempt to further analyze the detrimental effects of HBV and DNMT3A on infected cells, we visualized γ-H2AX foci and demonstrated that HBV inflicts and DNMT3A aggravates DNA damage, possibly by downregulating DNA damage response factors. Additionally, suppression of HBV replication by DNMT3A may be related to reduced ATM/ATR expression. Conclusion: Formation and maintenance of HBV cccDNA pools may be partially suppressed by the baseline expression of host inhibitory factors including APOBEC3A and APOBEC3B. HBV inflicts DNA damage both directly and by inducing DNMT3A expression.
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9.
  • Buckley, Scott, et al. (author)
  • Novel Microdialysis Technique Reveals a Dramatic Shift in Metabolite Secretion during the Early Stages of the Interaction between the Ectomycorrhizal Fungus Pisolithus microcarpus and Its Host Eucalyptus grandis
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9
  • Journal article (peer-reviewed)abstract
    • The colonisation of tree roots by ectomycorrhizal (ECM) fungi is the result of numerous signalling exchanges between organisms, many of which occur before physical contact. However, information is lacking about these exchanges and the compounds that are secreted by each organism before contact. This is in part due to a lack of low disturbance sampling methods with sufficient temporal and spatial resolution to capture these exchanges. Using a novel in situ microdialysis approach, we sampled metabolites released from Eucalyptus grandis and Pisolithus microcarpus independently and during indirect contact over a 48-h time-course using UPLC-MS. A total of 560 and 1530 molecular features (MFs; ESI- and ESI+ respectively) were identified with significant differential abundance from control treatments. We observed that indirect contact between organisms altered the secretion of MFs to produce a distinct metabolomic profile compared to either organism independently. Many of these MFs were produced within the first hour of contact and included several phenylpropanoids, fatty acids and organic acids. These findings show that the secreted metabolome, particularly of the ECM fungus, can rapidly shift during the early stages of pre-symbiotic contact and highlight the importance of observing these early interactions in greater detail. We present microdialysis as a useful tool for examining plant-fungal signalling with high temporal resolution and with minimal experimental disturbance.
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10.
  • Butler, Eile, et al. (author)
  • Lactobacillus reuteri DSM 17938 as a Novel Topical Cosmetic Ingredient : A Proof of Concept Clinical Study in Adults with Atopic Dermatitis
  • 2020
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 8:7
  • Journal article (peer-reviewed)abstract
    • Atopic Dermatitis (AD) is a chronically relapsing skin condition characterized by dry, itchy, and inflamed skin where sufferers can frequently be subject to infections. Probiotics are known to be potent immune-modulators, and liveLactobacillus reuteriDSM 17938 has shown to be anti-inflammatory but also to possess antimicrobial and barrier function properties. This study aimed to investigate and compare two investigational ointment products (topical probiotic and control) for cutaneous acceptability, safety, and efficacy under normal conditions of use, in adult subjects with atopic dermatitis. The products were applied twice daily for 8 weeks, and cutaneous acceptability, SCORAD index, local SCORAD, and adverse events were evaluated after 4 and 8 weeks of treatment. At the end of the observations, it was demonstrated that both the probiotic-containing and probiotic-free ointments were both cutaneously acceptable and safe. It importantly showed a statistically and clinically significant improvement of the SCORAD index and local SCORAD in adult subjects with AD after 4 and 8 weeks of continuous use. In conclusion, we show evidence that the probiotic product, containing liveL. reuteriDSM 17938 as an extra ingredient, is safe and promising as a novel topical cosmetic ointment and with further testing could be a standard topical product for the management of atopic dermatitis or other disorders associated with the skin.
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11.
  • Bösch, Yvonne (author)
  • Dynamics of the Apple Fruit Microbiome after Harvest and Implications for Fruit Quality
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9
  • Journal article (peer-reviewed)abstract
    • The contribution of the apple microbiome to the production chain of apple was so far largely unknown. Here, we describe the apple fruit microbiome and influences on its composition by parameters such as storage season, storage duration, storage technology, apple variety, and plant protection schemes. A combined culturing and metabarcoding approach revealed significant differences in the abundance, composition, and diversity of the apple fruit microbiome. We showed that relatively few genera contribute a large portion of the microbiome on fruit and that the fruit microbiome changes during the storage season depending on the storage conditions. In addition, we show that the plant protection regime has an influence on the diversity of the fruit microbiome and on the dynamics of pathogenic fungal genera during the storage season. For the genus Neofabraea, the quantitative results from the metabarcoding approach were validated with real-time PCR. In conclusion, we identified key parameters determining the composition and temporal changes of the apple fruit microbiome, and the main abiotic driving factors of microbiome diversity on apple fruit were characterized.
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12.
  • Calistri, A, et al. (author)
  • The New Generation hDHODH Inhibitor MEDS433 Hinders the In Vitro Replication of SARS-CoV-2 and Other Human Coronaviruses
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:8
  • Journal article (peer-reviewed)abstract
    • Although coronaviruses (CoVs) have long been predicted to cause zoonotic diseases and pandemics with high probability, the lack of effective anti-pan-CoVs drugs rapidly usable against the emerging SARS-CoV-2 actually prevented a promptly therapeutic intervention for COVID-19. Development of host-targeting antivirals could be an alternative strategy for the control of emerging CoVs infections, as they could be quickly repositioned from one pandemic event to another. To contribute to these pandemic preparedness efforts, here we report on the broad-spectrum CoVs antiviral activity of MEDS433, a new inhibitor of the human dihydroorotate dehydrogenase (hDHODH), a key cellular enzyme of the de novo pyrimidine biosynthesis pathway. MEDS433 inhibited the in vitro replication of hCoV-OC43 and hCoV-229E, as well as of SARS-CoV-2, at low nanomolar range. Notably, the anti-SARS-CoV-2 activity of MEDS433 against SARS-CoV-2 was also observed in kidney organoids generated from human embryonic stem cells. Then, the antiviral activity of MEDS433 was reversed by the addition of exogenous uridine or the product of hDHODH, the orotate, thus confirming hDHODH as the specific target of MEDS433 in hCoVs-infected cells. Taken together, these findings suggest MEDS433 as a potential candidate to develop novel drugs for COVID-19, as well as broad-spectrum antiviral agents exploitable for future CoVs threats.
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13.
  • Campos, Ana Carolina da Cruz, et al. (author)
  • Determining the virulence properties of Escherichia coli ST131 containing bacteriocin-encoding plasmids using short-and long-read sequencing and comparing them with those of other E. Coli lineages
  • 2019
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 7:11
  • Journal article (peer-reviewed)abstract
    • T. Escherichia coli ST131 is a clinical challenge due to its multidrug resistant profile and successful global spread. They are often associated with complicated infections, particularly urinary tract infections (UTIs). Bacteriocins play an important role to outcompete other microorganisms present in the human gut. Here, we characterized bacteriocin-encoding plasmids found in ST131 isolates of patients suffering from a UTI using both short-and long-read sequencing. Colicins Ia, Ib and E1, and microcin V, were identified among plasmids that also contained resistance and virulence genes. To investigate if the potential transmission range of the colicin E1 plasmid is influenced by the presence of a resistance gene, we constructed a strain containing a plasmid which had both the colicin E1 and blaCMY-2 genes. No difference in transmission range was found between transformant and wild-type strains. However, a statistically significantly difference was found in adhesion and invasion ability. Bacteriocin-producing isolates from both ST131 and non-ST131 lineages were able to inhibit the growth of other E. coli isolates, including other ST131. In summary, plasmids harboring bacteriocins give additional advantages for highly virulent and resistant ST131 isolates, improving the ability of these isolates to compete with other microbiota for a niche and thereby increasing the risk of infection.
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14.
  • Capo, Eric, et al. (author)
  • Landscape setting drives the microbial eukaryotic community structure in four Swedish mountain lakes over the holocene
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:2
  • Journal article (peer-reviewed)abstract
    • On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. How-ever, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co‐located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock‐dominated lakes—where the oldest DNA samples are dated to only a few hundred years after the lake formation—certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.
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15.
  • Centler, Florian, et al. (author)
  • Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule Mining
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:2
  • Journal article (peer-reviewed)abstract
    • Natural microbial communities in soils are highly diverse, allowing for rich networks of microbial interactions to unfold. Identifying key players in these networks is difficult as the distribution of microbial diversity at the local scale is typically non-uniform, and is the outcome of both abiotic environmental factors and microbial interactions. Here, using spatially resolved microbial presence-absence data along an aquifer transect contaminated with hydrocarbons, we combined co-occurrence analysis with association rule mining to identify potential keystone species along the hydrocarbon degradation process. Derived co-occurrence networks were found to be of a modular structure, with modules being associated with specific spatial locations and metabolic activity along the contamination plume. Association rules identify species that never occur without another, hence identifying potential one-sided cross-feeding relationships. We find that hub nodes in the rule network appearing in many rules as targets qualify as potential keystone species that catalyze critical transformation steps and are able to interact with varying partners. By contrasting analysis based on data derived from bulk samples and individual soil particles, we highlight the importance of spatial sample resolution. While individual inferred interactions are hypothetical in nature, requiring experimental verification, the observed global network patterns provide a unique first glimpse at the complex interaction networks at work in the microbial world.
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16.
  • Chepsergon, Jane, et al. (author)
  • Organize, Don't Agonize : Strategic Success of Phytophthora Species
  • 2020
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 8:6
  • Research review (peer-reviewed)abstract
    • Plants are constantly challenged by various environmental stressors ranging from abiotic—sunlight, elevated temperatures, drought, and nutrient deficits, to biotic factors—microbial pathogens and insect pests. These not only affect the quality of harvest but also the yield, leading to substantial annual crop losses, worldwide. Although plants have a multi-layered immune system, phytopathogens such as species of the oomycete genus Phytophthora, can employ elaborate mechanisms to breach this defense. For the last two decades, researchers have focused on the co-evolution between Phytophthora and interacting hosts to decouple the mechanisms governing their molecular associations. This has provided a comprehensive understanding of the pathobiology of plants affected by oomycetes. Ultimately, this is important for the development of strategies to sustainably improve agricultural production. Therefore, this paper discusses the present-day state of knowledge of the strategic mode of operation employed by species of Phytophthora for successful infection. Specifically, we consider motility, attachment, and host cell wall degradation used by these pathogenic species to obtain nutrients from their host. Also discussed is an array of effector types from apoplastic (hydrolytic proteins, protease inhibitors, elicitins) to cytoplastic (RxLRs, named after Arginine-any amino acid-Leucine-Arginine consensus sequence and CRNs, for CRinkling and Necrosis), which upon liberation can subvert the immune response and promote diseases in plants
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17.
  • Cojkic, Aleksandar, et al. (author)
  • Identification of bull semen microbiome by 16S sequencing and possible relationships with fertility
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9
  • Journal article (peer-reviewed)abstract
    • Reports on the use of 16S sequencing for the identification of bacteria in healthy animals are lacking. Bacterial contamination of bull semen can have a negative effect on the sperm quality. The aims of this study were threefold: to identify bacteria in the semen of healthy bulls using 16S sequencing; to investigate the differences in the bacterial community between individual bulls; and to establish if there was a relationship between the bacteria isolated and bull fertility. Semen from 18 bulls of known fertility was used for the DNA extraction and 16S sequencing; 107 bacterial genera were identified. The differences in the amplicon sequence variants (ASVs) and the numbers of genera between bulls were noted. Negative correlations (p < 0.05) between several bacterial genera with Curvibacter, Rikenellaceae RC9-gut-group and Dyella spp. were seen. Other negatively correlated bacteria were Cutibacterium, Ruminococcaceae UCG-005, Ruminococcaceae UCG-010 and Staphylococcus, all within the top 20 genera. Two genera, W5053 and Lawsonella, were enriched in bulls of low fertility; this is the first time that these bacteria have been reported in bull semen samples. The majority of the bacteria were environmental organisms or were species originating from the mucous membranes of animals and humans. The results of this study indicate that differences in the seminal microbiota of healthy bulls occur and might be correlated with fertility.
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18.
  • Daniel, Geoffrey, et al. (author)
  • Comparison of the decay behavior of two white‐rot fungi in relation to wood type and exposure conditions
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8
  • Journal article (peer-reviewed)abstract
    • Fungal wood decay strategies are influenced by several factors, such as wood species,moisture content, and temperature. This study aims to evaluate wood degradation characteristics ofspruce, beech, and oak after exposure to the white-rot fungi Pleurotus ostreatus and Trametes versicolor.Both fungi caused high mass losses in beech wood, while spruce and oak wood were more resistant todecay. The moisture content values of the decayed wood correlated with the mass losses for all threewood species and incubation periods. Combined microscopic and chemical studies indicated that thetwo fungi di ered in their decay behavior. While T. versicolor produced a decay pattern (cell wallerosion) typical of white-rot fungi in all wood species, P. ostreatus caused cell wall erosion in spruceand beech and soft-rot type I (cavity formation) decay in oak wood. These observations suggest thatP. ostreatus may have the capacity to produce a wider range of enzymes/radicals triggered by thechemical composition of wood cell walls and/or local compositional variability within the cell wall.
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19.
  • de Jesus, Hugo Emiliano, et al. (author)
  • Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:3
  • Journal article (peer-reviewed)abstract
    • The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 degrees C and (ii) a freeze-thaw cycle (FTC) alternating between -20 and 4 degrees C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.
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20.
  • Deka, Ram Pratim, et al. (author)
  • Seroprevalence and Risk Factors of Brucella Infection in Dairy Animals in Urban and Rural Areas of Bihar and Assam, India
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:4
  • Journal article (peer-reviewed)abstract
    • This study assessed seropositivity of Brucella infection in dairy animals and risk factors associated with it. The cross-sectional study used multi-stage, random sampling in the states of Bihar and Assam in India. In total, 740 dairy animals belonging to 534 households of 52 villages were covered under this study. Serological testing was conducted by indirect enzyme-linked immunosorbent assay (iELISA). Animal-level Brucella seropositivity was found to be 15.9% in Assam and 0.3% in Bihar. Seropositivity in urban areas (18.7%) of Assam was found to be higher than in rural areas (12.4%). Bihar was excluded from the risk factor analysis, as only one Brucella seropositive sample was detected in the state. A total of 30 variables were studied for assessing risk factors, of which 15 were selected for multivariable regression analyses following a systematic process. Finally, only three risk factors were identified as statistically significant. It was found that animals belonging to districts having smaller-sized herds were less likely (p < 0.001) to be Brucella seropositive than animals belonging to districts having larger-sized herds. Furthermore, the chance of being Brucella seropositive increased (p = 0.007) with the increase in age of dairy animals, but decreased (p = 0.072) with the adoption of artificial insemination (AI) for breeding. We speculated that the identified risk factors in Assam likely explained the reason behind lower Brucella seropositivity in Bihar, and therefore any future brucellosis control program should focus on addressing these risk factors.
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21.
  • Deprez, Marie Anne, et al. (author)
  • The role of Sch9 and the V-ATPase in the adaptation response to acetic acid and the consequences for growth and chronological lifespan
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:9
  • Journal article (peer-reviewed)abstract
    • Studies with Saccharomyces cerevisiae indicated that non-physiologically high levels of acetic acid promote cellular acidification, chronological aging, and programmed cell death. In the current study, we compared the cellular lipid composition, acetic acid uptake, intracellular pH, growth, and chronological lifespan of wild-type cells and mutants lacking the protein kinase Sch9 and/or a functional V-ATPase when grown in medium supplemented with different acetic acid concentrations. Our data show that strains lacking the V-ATPase are especially more susceptible to growth arrest in the presence of high acetic acid concentrations, which is due to a slower adaptation to the acid stress. These V-ATPase mutants also displayed changes in lipid homeostasis, including alterations in their membrane lipid composition that influences the acetic acid diffusion rate and changes in sphingolipid metabolism and the sphingolipid rheostat, which is known to regulate stress tolerance and longevity of yeast cells. However, we provide evidence that the supplementation of 20 mM acetic acid has a cytoprotective and presumable hormesis effect that extends the longevity of all strains tested, including the V-ATPase compromised mutants. We also demonstrate that the long-lived sch9∆ strain itself secretes significant amounts of acetic acid during stationary phase, which in addition to its enhanced accumulation of storage lipids may underlie its increased lifespan.
  •  
22.
  • Dimitriou, Ioannis (author)
  • Long-Term Effects of Soil Remediation with Willow Short Rotation Coppice on Biogeographic Pattern of Microbial Functional Genes
  • 2022
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 10
  • Journal article (peer-reviewed)abstract
    • Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees as compared to those under permanent grassland (C). GeoChip analysis showed a lower functional gene diversity in SRC than in C soil, whereas microbial ATP and respiration did not change. The SRC soil had lower relative abundances of microbial genes encoding for metal(-oid) resistance, antibiotic resistance and stress-related proteins. This indicates a more benign habitat under SRC for microbial communities after relieving heavy metal stress, consistent with the lower phytoavailability of some metals (i.e., As, Cd, Ni and Zn) and higher total organic carbon, NO3--N and P concentrations. The microbial taxa-area relationship was valid in both soils, but the space turnover rate was higher under SRC within 0.125 m(2), which was possibly linked to a more benign environment under SRC, whereas similar values were reached beyond thisarea. Overall, we concluded that SRC management can be considered as a phytotechnology that ameliorates the habitat for soil microorganisms, owing to TOC and nutrient enrichment on the long-term.
  •  
23.
  • Elbediwi, M, et al. (author)
  • Global Burden of Colistin-Resistant Bacteria: Mobilized Colistin Resistance Genes Study (1980-2018)
  • 2019
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 7:10
  • Journal article (peer-reviewed)abstract
    • Colistin is considered to be an antimicrobial of last-resort for the treatment of multidrug-resistant Gram-negative bacterial infections. The recent global dissemination of mobilized colistin resistance (mcr) genes is an urgent public health threat. An accurate estimate of the global prevalence of mcr genes, their reservoirs and the potential pathways for human transmission are required to implement control and prevention strategies, yet such data are lacking. Publications from four English (PubMed, Scopus, the Cochrane Database of Systematic Reviews and Web of Science) and two Chinese (CNKI and WANFANG) databases published between 18 November 2015 and 30 December 2018 were identified. In this systematic review and meta-analysis, the prevalence of mcr genes in bacteria isolated from humans, animals, the environment and food products were investigated. A total of 974 publications were identified. 202 observational studies were included in the systematic review and 71 in the meta-analysis. mcr genes were reported from 47 countries across six continents and the overall average prevalence was 4.7% (0.1–9.3%). China reported the highest number of mcr-positive strains. Pathogenic Escherichia coli (54%), isolated from animals (52%) and harboring an IncI2 plasmid (34%) were the bacteria with highest prevalence of mcr genes. The estimated prevalence of mcr-1 pathogenic E. coli was higher in food-animals than in humans and food products, which suggests a role for foodborne transmission. This study provides a comprehensive assessment of prevalence of the mcr gene by source, organism, genotype and type of plasmid.
  •  
24.
  • Esberg, Anders, et al. (author)
  • Corynebacterium matruchotii Demography and Adhesion Determinants in the Oral Cavity of Healthy Individuals
  • 2020
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 8:11
  • Journal article (peer-reviewed)abstract
    • Corynebacterium matruchotii may be key in tooth biofilm formation, but information about demographics, bacterial partners, and binding ligands is limited. The aims of this study were to explore C. matruchotii's demography by age and colonization site (plaque and saliva), in vitro bacterial-bacterial interactions in coaggregation and coadhesion assays, and glycolipids as potential binding ligands in thin-layer chromatogram binding assays. C. matruchotii prevalence increased from 3 months to 18 years old, with 90% and 100% prevalence in saliva and tooth biofilm, respectively. C. matruchotii aggregated in saliva in a dose-dependent manner but lacked the ability to bind to saliva-coated hydroxyapatite. In vivo, C. matruchotii abundance paralleled that of Actinomyces naeslundii, Capnocytophaga sp. HMT 326, Fusobacterium nucleatum subsp. polymorphum, and Tannerella sp. HMT 286. In vitro, C. matruchotii bound both planktonic and surface-bound A. naeslundii, Actinomyces odontolyticus, and F. nucleatum. In addition, C. matruchotii exhibited the ability to bind glycolipids isolated from human erythrocytes (blood group O), human granulocytes, rabbit intestine, human meconium, and rat intestine. Binding assays identified candidate carbohydrate ligands as isoglobotriaosylceramide, Gal alpha 3-isoglobotriaosylceramide, lactotriaosylceramide, lactotetraosylceramide, neolactotetraosylceramide, and neolactohexaosylceramide. Thus, C. matruchotii likely uses specific plaque bacteria to adhere to the biofilm and may interact with human tissues through carbohydrate interactions.
  •  
25.
  • Esberg, Anders, et al. (author)
  • Heritability of Oral Microbiota and Immune Responses to Oral Bacteria
  • 2020
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 8:8
  • Journal article (peer-reviewed)abstract
    • Maintaining a symbiotic oral microbiota is essential for oral and dental health, and host genetic factors may affect the composition or function of the oral microbiota through a range of possible mechanisms, including immune pathways. The study included 836 Swedish twins divided into separate groups of adolescents (n= 418) and unrelated adults (n= 418). Oral microbiota composition and functions of non-enzymatically lysed oral bacteria samples were evaluated using 16S rRNA gene sequencing and functional bioinformatics tools in the adolescents. Adaptive immune responses were assessed by testing for serum IgG antibodies against a panel of common oral bacteria in adults. In the adolescents, host genetic factors were associated with both the detection and abundance of microbial species, but with considerable variation between species. Host genetic factors were associated with predicted microbiota functions, including several functions related to bacterial sucrose, fructose, and carbohydrate metabolism. In adults, genetic factors were associated with serum antibodies against oral bacteria. In conclusion, host genetic factors affect the composition of the oral microbiota at a species level, and host-governed adaptive immune responses, and also affect the concerted functions of the oral microbiota as a whole. This may help explain why some people are genetically predisposed to the major dental diseases of caries and periodontitis.
  •  
26.
  • Esberg, Anders, et al. (author)
  • Oral microbiota identifies patients in early onset rheumatoid arthritis
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:8
  • Journal article (peer-reviewed)abstract
    • Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality register for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. The results support a deviating oral microbiota composition already in eRA patients compared with healthy controls and highlight a panel of oral bacteria that may be useful in eRA risk assessment in both periodontally healthy and diseased persons.
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27.
  • Fernández-Remolar, David C., et al. (author)
  • Preservation of underground microbial diversity in ancient subsurface deposits (>6 ma) of the rio tinto basement
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:8
  • Journal article (peer-reviewed)abstract
    • The drilling of the Rio Tinto basement has provided evidence of an underground microbial community primarily sustained by the Fe and S metabolism through the biooxidation of pyrite orebodies. Although the gossan is the microbial activity product, which dates back to the Oligocene (25 Ma), no molecular evidence of such activity in the past has been reported yet. A Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) molecular analysis of a subsurface sample in the Peña de Hierro basement has provided novel data of the ancient underground microbial community. It shows that the microbial remains are preserved in a mineral matrix composed of laminated Fe-oxysulfates and K-and Na-bearing sulfates alternating with secondary silica. In such a mineral substrate, the biomolecule traces are found in five different microstructure associations, (1) <15 micron-sized nodular microstructures composed of POn(2≤n≤4)−, (2) <30 micron-size mi-cronodules containing fatty acids, acylglycerides, and alkanol chains, (3) <20 micro-sized nodules containing NOn −(2≤n≤3) ions, (4) 40-micron size nodules with NH4+ and traces of peptides, and (5) >200-micron thick layer with N-bearing adducts, and sphingolipid and/or peptide traces. It suggests the mineralization of at least five microbial preserved entities with different metabolic ca-pabilities, including: (1) Acidiphilium/Tessaracoccus-like phosphate mineralizers, (2) microbial patches preserving phosphate-free acylglycerides bacteria, (3) nitrogen oxidizing bacteria (e.g., Acidovorax sp.), (4) traces of heterotrophic ammonifying bacteria, and (5) sphingolipid bearing bacteria (e.g., Sphin-gomonadales, and δ-Proteobacteria) and/or mineralized biofilms. The primary biooxidation process acted as a preservation mechanism to release the inorganic ions that ultimately mineralized the microbial structures.
  •  
28.
  • Fonseca, M. C., et al. (author)
  • Molecular Characterization of Coxsackievirus A24v from Feces and Conjunctiva Reveals Epidemiological Links
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:3
  • Journal article (peer-reviewed)abstract
    • Coxsackievirus A24 variant (CVA24v), the main causative agent of acute hemorrhagic conjunctivitis (AHC), can be isolated from both the eyes and lower alimentary tract. However, the molecular features of CVA24v in feces is not well-documented. In this study, we compared the VP1 and 3C sequences of CVA24v strains isolated from feces during AHC epidemics in Cuba in 1997, 2003, and 2008-2009 with those obtained from conjunctival swabs during the same epidemic period. The sequence analyses of the 3C and VP1 region of stool isolates from the three epidemics showed a high degree of nucleotide identity (ranging from 97.3-100%) to the corresponding conjunctival isolates. The phylogenetic analysis showed that fecal CVA24v isolates from the 1997 and 2003 Cuban outbreaks formed a clade with CVA24v strains isolated from conjunctival swabs in Cuba and other countries during the same period. There were three amino acid changes (3C region) and one amino acid change (VP1 region) in seven CVA24v strains isolated sequentially over 20 days from fecal samples of one patient, suggesting viral replication in the intestine. Despite these substitutions, the virus from the conjunctival swab and fecal samples were genetically very similar. Therefore, fecal samples should be considered as a reliable alternative sample type for the routine molecular diagnosis and molecular epidemiology of CVA24v, also during outbreaks of AHC.
  •  
29.
  • Garrigós, Víctor, et al. (author)
  • Wine yeast peroxiredoxin tsa1 plays a role in growth, stress response and trehalose metabolism in biomass propagation
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:10, s. 1-18
  • Journal article (peer-reviewed)abstract
    • Peroxiredoxins are a family of peroxide-degrading enzymes for challenging oxidative stress. They receive their reducing power from redox-controlling proteins called thioredoxins, and these, in turn, from thioredoxin reductase. The main cytosolic peroxiredoxin is Tsa1, a moonlighting protein that also acts as protein chaperone a redox switch controlling some metabolic events. Gene deletion of peroxiredoxins in wine yeasts indicate that TSA1, thioredoxins and thioredoxin reductase TRR1 are required for normal growth in medium with glucose and sucrose as carbon sources. TSA1 gene deletion also diminishes growth in molasses, both in flasks and bioreactors. The TSA1 mutation brings about an expected change in redox parameters but, interestingly, it also triggers a variety of metabolic changes. It influences trehalose accumulation, lowering it in first molasses growth stages, but increasing it at the end of batch growth, when respiratory metabolism is set up. Glycogen accumulation at the entry of the stationary phase also increases in the tsa1∆ mutant. The mutation reduces fermentative capacity in grape juice, but the vinification profile does not significantly change. However, acetic acid and acetaldehyde production decrease when TSA1 is absent. Hence, TSA1 plays a role in the regulation of metabolic reactions leading to the production of such relevant enological molecules.
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30.
  • Garriss, G, et al. (author)
  • Lysogeny in Streptococcus pneumoniae
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:10
  • Journal article (peer-reviewed)abstract
    • Bacterial viruses, or bacteriophages, are major contributors to the evolution, pathogenesis and overall biology of their host bacteria. During their life cycle, temperate bacteriophages form stable associations with their host by integrating into the chromosome, a process called lysogeny. Isolates of the human pathogen Streptococcus pneumoniae are frequently lysogenic, and genomic studies have allowed the classification of these phages into distinct phylogenetic groups. Here, we review the recent advances in the characterization of temperate pneumococcal phages, with a focus on their genetic features and chromosomal integration loci. We also discuss the contribution of phages, and specific phage-encoded features, to colonization and virulence. Finally, we discuss interesting research perspectives in this field.
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31.
  • Gilbert Temu, Stella, et al. (author)
  • Crustose Calicioid Lichens and Fungi in Mountain Cloud Forests of Tanzania
  • 2019
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 7:11
  • Journal article (peer-reviewed)abstract
    • A total of 26 crustose calicioid lichens and fungi were found in Tanzania. Most of them belong to a group of species with wide distributions in cool areas of both hemispheres and occasional occurrence in high mountains at low latitudes. In Tanzania calicioids mainly occur in the middle and upper forest zones and their niches are found on the bark of old trees and on lignum, most of them restricted to mountain cloud forests. Calicioids are rare and often red-listed, and are also bioindicators of long forest continuity. Consequently, they form an important biota in mountain cloud forests and deserve attention in the context of preserving biodiversity and developing conservation policies. One new species, Chaenothecopsis kilimanjaroensis, is described. Chaenotheca hispidula and Pyrgillus cambodiensis are reported as new to Africa and Calicium lenticulare and Chaenothecopsis debilis are reported as new to Tanzania.
  •  
32.
  • Goncalves dos Santos, Karen Cristine, et al. (author)
  • Unrelated Fungal Rust Candidate Effectors Act on Overlapping Plant Functions
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:5
  • Journal article (peer-reviewed)abstract
    • Rust fungi cause epidemics that threaten the production of important plant species, such as wheat and soy. Melampsora larici-populina (Mlp) causes the poplar rust and encodes at least 1184 candidate effectors (CEs) whose functions are poorly known. In this study, we sequenced the transcriptome and used mass spectrometry to analyze the metabolome of Arabidopsis plants constitutively expressing 14 Mlp CEs and of a control line to discover alterations leading to plant susceptibility. We found 2299 deregulated genes across the experiment. Genes involved in pattern-triggered immunity, such as FRK1, PR1, RBOHD, and WRKY33, as well as AUX/IAA genes were down-regulated. We further observed that 680 metabolites were deregulated in at least one CE-expressing transgenic line, with “highly unsaturated and phenolic compounds” and “peptides” enriched among down- and up-regulated metabolites. Interestingly, transgenic lines expressing unrelated CEs had correlated patterns of gene and metabolite deregulation, while expression of CEs belonging to the same family deregulated different genes and metabolites. Thus, our results uncouple effector sequence similarity and function. This supports that effector functional investigation in the context of their virulence activity and effect on plant susceptibility requires the investigation of the individual effector and precludes generalization based on sequence similarity.
  •  
33.
  • Grankvist, A., et al. (author)
  • Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:7
  • Journal article (peer-reviewed)abstract
    • Tick-borne 'Neoehrlichia (N.) mikurensis' is the cause of neoehrlichiosis, an infectious vasculitis of humans. This strict intracellular pathogen is a member of the family Anaplasmataceae and has been unculturable until recently. The only available genetic data on this new pathogen are six partially sequenced housekeeping genes. The aim of this study was to advance the knowledge regarding 'N. mikurensis' genomic relatedness with other Anaplasmataceae members, intra-species genotypic variability and potential virulence factors explaining its tropism for vascular endothelium. Here, we present the de novo whole-genome sequences of three 'N. mikurensis' strains derived from Swedish patients diagnosed with neoehrlichiosis. The genomes were obtained by extraction of DNA from patient plasma, library preparation using 10x Chromium technology, and sequencing by Illumina Hiseq-4500. 'N. mikurensis' was found to have the next smallest genome of the Anaplasmataceae family (1.1 Mbp with 27% GC contents) consisting of 845 protein-coding genes, every third of which with unknown function. Comparative genomic analyses revealed that 'N. mikurensis' was more closely related to Ehrlichia chaffeensis than to Ehrlichia ruminantium, the opposite of what 16SrRNA sequence-based phylogenetic analyses determined. The genetic variability of the three whole-genome-sequenced 'N. mikurensis' strains was extremely low, between 0.14 and 0.22 parts per thousand, a variation that was associated with geographic origin. No protein-coding genes exclusively shared by N. mikurensis and E. ruminantium were identified to explain their common tropism for vascular endothelium.
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34.
  • Hallang, Shirleen, et al. (author)
  • Healthy oral lifestyle behaviours are associated with favourable composition and function of the oral microbiota
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:8
  • Journal article (peer-reviewed)abstract
    • Modifiable lifestyle interventions may influence dental disease by shifting the composition of the oral microbiota. This study aimed to test whether lifestyle traits are associated with oral microbiota composition and function. Swedish volunteers, aged 16 to 79 years, completed a lifestyle traits questionnaire including lifestyle characteristics and oral health behaviours. Bacterial 16S rDNA amplicons were sequenced and classified into genera and species, using salivary DNA. Microbiota functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and the KO Database of Molecular Functions by ortholog annotation. Tests for association used partial least squares and linear regression analysis with correction for multiple testing. The main analysis included 401 participants and 229 common bacterial species (found in ≥10% of the participants). The overall microbiota composition was strongly associated with questions “do you think caries is a disease?” and “do you use floss or a toothpick?”. Enriched relative abundance of Actinomyces, Campylobacter, Dialister, Fusobacterium, Peptidophaga and Scardovia genera (all p < 0.05 after adjustment for multiple testing), and functional profiles showing enrichment of carbohydrate related functions, were found in participants who answered “no” to these questions. Socio-demographic traits and other oral hygiene behaviours were also associated. Healthier oral microbiota composition and predicted functions are found in those with favourable oral health behaviours. Modifiable risk factors could be prioritized for possible interventions.
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35.
  • Hankaniemi, MM, et al. (author)
  • Structural Insight into CVB3-VLP Non-Adjuvanted Vaccine
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:9
  • Journal article (peer-reviewed)abstract
    • Coxsackievirus B (CVB) enteroviruses are common pathogens that can cause acute and chronic myocarditis, dilated cardiomyopathy, aseptic meningitis, and they are hypothesized to be a causal factor in type 1 diabetes. The licensed enterovirus vaccines and those currently in clinical development are traditional inactivated or live attenuated vaccines. Even though these vaccines work well in the prevention of enterovirus diseases, new vaccine technologies, like virus-like particles (VLPs), can offer important advantages in the manufacturing and epitope engineering. We have previously produced VLPs for CVB3 and CVB1 in insect cells. Here, we describe the production of CVB3-VLPs with enhanced production yield and purity using an improved purification method consisting of tangential flow filtration and ion exchange chromatography, which is compatible with industrial scale production. We also resolved the CVB3-VLP structure by Cryo-Electron Microscopy imaging and single particle reconstruction. The VLP diameter is 30.9 nm on average, and it is similar to Coxsackievirus A VLPs and the expanded enterovirus cell-entry intermediate (the 135s particle), which is ~2 nm larger than the mature virion. High neutralizing and total IgG antibody levels, the latter being a predominantly Th2 type (IgG1) phenotype, were detected in C57BL/6J mice immunized with non-adjuvanted CVB3-VLP vaccine. The structural and immunogenic data presented here indicate the potential of this improved methodology to produce highly immunogenic enterovirus VLP-vaccines in the future.
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36.
  • Hartlaub, J, et al. (author)
  • Sheep and Cattle Are Not Susceptible to Experimental Inoculation with Hazara Orthonairovirus, a Tick-Borne Arbovirus Closely Related to CCHFV
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:12
  • Journal article (peer-reviewed)abstract
    • Hazara orthonairovirus (HAZV) is a tick-borne arbovirus closely related to Crimean–Congo hemorrhagic fever orthonairovirus (CCHFV). Whereas CCHFV is a biosafety level (BSL) 4 agent, HAZV is classified as BSL 2, as it is not known to cause any disease in humans. Belonging to the same serogroup as CCHFV, HAZV might act as a model which can provide a better understanding of this important zoonosis. Furthermore, the serological relatedness may cause diagnostic problems if antibodies against HAZV interfere with current CCHFV serological assays. Therefore, sheep and cattle—important natural hosts for CCHFV—were experimentally infected with HAZV to prove their susceptibility and evaluate potential antibody cross-reactivities. According to this study, neither sheep nor cattle are susceptible to experimental HAZV infections. Consequently, the HAZV infection in ruminants is clearly distinct from CCHFV infections. Sera of immunized animals weakly cross-reacted between HAZV and CCHFV in immunofluorescence and immunoblot assays, but not in commercial CCHFV ELISAs commonly used for field studies.
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37.
  • Hokynar, Kati, et al. (author)
  • The Finnish New Variant of Chlamydia trachomatis with a Single Nucleotide Polymorphism in the 23S rRNA Target Escapes Detection by the Aptima Combo 2 Test
  • 2019
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 7:8
  • Journal article (peer-reviewed)abstract
    • In 2019, more than 200 cases of Chlamydia trachomatis negative/equivocal by the Aptima Combo 2 assay (AC2, target: 23S rRNA) with slightly elevated relative light units (RLUs), but positive by the Aptima Chlamydia trachomatis assay (ACT, target: 16S rRNA) have been detected in Finland To identify the cause of the AC2 CT false-negative specimens, we sequenced parts of the CT 23S rRNA gene in 40 specimens that were AC2 negative/equivocal but ACT positive. A single nucleotide polymorphism (SNP; C1515T in the C. trachomatis 23S rRNA gene) was revealed in 39 AC2/ACT discordant specimens. No decrease in the number of mandatorily notified C. trachomatis cases was observed nationally in Finland in 2010-2019. When RLUs obtained for AC2 negative specimens were retrospectively evaluated in 2011-2019, a continuous increase in the proportion of samples with RLUs 10-19 was observed since 2014, and a slight increase in the proportion of samples with RLUs 20-84 in 2017-2019, indicating that the Finnish new variant of C. trachomatis might have been spreading nationally for several years. This emphasizes that careful surveillance of epidemiology, positivity rate and test performance are mandatory to detect any changes affecting detection of infections.
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38.
  • Hull, Rodney, et al. (author)
  • Microbiomics in Collusion with the Nervous System in Carcinogenesis : Diagnosis, Pathogenesis and Treatment
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:10
  • Research review (peer-reviewed)abstract
    • The influence of the naturally occurring population of microbes on various human diseases has been a topic of much recent interest. Not surprisingly, continuously growing attention is devoted to the existence of a gut brain axis, where the microbiota present in the gut can affect the nervous system through the release of metabolites, stimulation of the immune system, changing the permeability of the blood-brain barrier or activating the vagus nerves. Many of the methods that stimulate the nervous system can also lead to the development of cancer by manipulating pathways associated with the hallmarks of cancer. Moreover, neurogenesis or the creation of new nervous tissue, is associated with the development and progression of cancer in a similar manner as the blood and lymphatic systems. Finally, microbes can secrete neurotransmitters, which can stimulate cancer growth and development. In this review we discuss the latest evidence that support the importance of microbiota and peripheral nerves in cancer development and dissemination.
  •  
39.
  • Hurtado, Pilar, et al. (author)
  • Contrasting Environmental Drivers Determine Biodiversity Patterns in Epiphytic Lichen Communities along a European Gradient
  • 2020
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 8:12
  • Journal article (peer-reviewed)abstract
    • Assessing the ecological impacts of environmental change on biological communities requires knowledge of the factors driving the spatial patterns of the three diversity facets along extensive environmental gradients. We quantified the taxonomic (TD), functional (FD), and phylogenetic diversity (PD) of lichen epiphytic communities in 23 beech forests along Europe to examine their response to environmental variation (climate, habitat quality, spatial predictors) at a continental geographic scale. We selected six traits related to the climatic conditions in forest ecosystems, the water-use strategy and the nutrient uptake, and we built a phylogenetic tree based on four molecular markers. FD and climate determined TD and PD, with spatial variables also affecting PD. The three diversity facets were primarily shaped by distinct critical predictors, with the temperature diurnal range affecting FD and PD, and precipitation of the wettest month determining TD. Our results emphasize the value of FD for explaining part of TD and PD variation in lichen communities at a broad geographic scale, while highlighting that these diversity facets provide complementary information about the communities' response under changing environmental conditions. Furthermore, traits such as growth form, photobiont type, and reproductive strategy mediated the response of lichen communities to abiotic factors emerging as useful indicators of macroclimatic variations.
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40.
  • Hutchinson, Ashley, 1984-, et al. (author)
  • The Effect of Probiotics on Health Outcomes in the Elderly : A Systematic Review of Randomized, Placebo-Controlled Studies
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:6
  • Research review (peer-reviewed)abstract
    • Increasing evidence suggests that probiotic supplementation may be efficacious in counteracting age-related shifts in gut microbiota composition and diversity, thereby impacting health outcomes and promoting healthy aging. However, randomized controlled trials (RCTs) with probiotics in healthy older adults have utilized a wide variety of strains and focused on several different outcomes with conflicting results. Therefore, a systematic review was conducted to determine which outcomes have been investigated in randomized controlled trials with probiotic supplementation in healthy older adults and what has been the effect of these interventions. For inclusion, studies reporting on randomized controlled trials with probiotic and synbiotic supplements in healthy older adults (defined as minimum age of 60 years) were considered. Studies reporting clinical trials in specific patient groups or unhealthy participants were excluded. In addition to assessment of eligibility and data extraction, each study was examined for risk of bias and quality assessment was performed by two independent reviewers. Due to the heterogeneity of outcomes, strains, study design, duration, and methodology, we did not perform any meta-analyses and instead provided a narrative overview of the outcomes examined. Of 1997 potentially eligible publications, 17 studies were included in this review. The risk of bias was low, although several studies failed to adequately describe random sequence generation, allocation concealment, and blinding. The overall study quality was high; however, many studies did not include sample calculations, and the majority of studies had a small sample size. The main outcomes examined in the trials included microbiota composition, immune-related measurements, digestive health, general well-being, cognitive function, and lipid and other biomarkers. The most commonly assessed outcome with the most consistent effect was microbiota composition; all but one study with this outcome showed significant effects on gut microbiota composition in healthy older adults. Overall, probiotic supplementation had modest effects on markers of humoral immunity, immune cell population levels and activity, as well as the incidence and duration of the common cold and other infections with some conflicting results. Digestive health, general-well-being, cognitive function, and lipid and other biomarkers were investigated in a very small number of studies; therefore, the impact on these outcomes remains inconclusive. Probiotics appear to be efficacious in modifying gut microbiota composition in healthy older adults and have moderate effects on immune function. However, the effect of probiotic supplementation on other health outcomes remains inconclusive, highlighting the need for more well-designed, sufficiently-powered studies to investigate if and the mechanisms by which probiotics impact healthy aging.
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41.
  • Isaguliants, M, et al. (author)
  • Cellular Immune Response Induced by DNA Immunization of Mice with Drug Resistant Integrases of HIV-1 Clade A Offers Partial Protection against Growth and Metastatic Activity of Integrase-Expressing Adenocarcinoma Cells
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:6
  • Journal article (peer-reviewed)abstract
    • Therapeutic DNA-vaccination against drug-resistant HIV-1 may hinder emergence and spread of drug-resistant HIV-1, allowing for longer successful antiretroviral treatment (ART) up-to relief of ART. We designed DNA-vaccines against drug-resistant HIV-1 based on consensus clade A integrase (IN) resistant to raltegravir: IN_in_r1 (L74M/E92Q/V151I/N155H/G163R) or IN_in_r2 (E138K/G140S/Q148K) carrying D64V abrogating IN activity. INs, overexpressed in mammalian cells from synthetic genes, were assessed for stability, route of proteolytic degradation, and ability to induce oxidative stress. Both were found safe in immunotoxicity tests in mice, with no inherent carcinogenicity: their expression did not enhance tumorigenic or metastatic potential of adenocarcinoma 4T1 cells. DNA-immunization of mice with INs induced potent multicytokine T-cell response mainly against aa 209–239, and moderate IgG response cross-recognizing diverse IN variants. DNA-immunization with IN_in_r1 protected 60% of mice from challenge with 4Tlluc2 cells expressing non-mutated IN, while DNA-immunization with IN_in_r2 protected only 20% of mice, although tumor cells expressed IN matching the immunogen. Tumor size inversely correlated with IN-specific IFN-γ/IL-2 T-cell response. IN-expressing tumors displayed compromised metastatic activity restricted to lungs with reduced metastases size. Protective potential of IN immunogens relied on their immunogenicity for CD8+ T-cells, dependent on proteasomal processing and low level of oxidative stress.
  •  
42.
  • Jaen-Luchoro, Daniel, et al. (author)
  • Genomic and Proteomic Characterization of the Extended-Spectrum beta-Lactamase (ESBL)-Producing Escherichia coli Strain CCUG 73778: A Virulent, Nosocomial Outbreak Strain
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:6
  • Journal article (peer-reviewed)abstract
    • Escherichia colistrain CCUG 78773 is a virulent extended-spectrum beta-lactamase (ESBL)-producing ST131-O25b type strain isolated during an outbreak at a regional university hospital. The complete and closed genome sequence, comprising one chromosome (5,076,638 bp) and six plasmids (1718-161,372 bp), is presented. Characterization of the genomic features detected the presence of 59 potential antibiotic resistance factors, including three prevalent beta-lactamases. Several virulence associated elements were determined, mainly related with adherence, invasion, biofilm formation and antiphagocytosis. Twenty-eight putative type II toxin-antitoxin systems were found. The plasmids were characterized, through in silico analyses, confirming the two beta-lactamase-encoding plasmids to be conjugative, while the remaining plasmids were mobilizable. BLAST analysis of the plasmid sequences showed high similarity with plasmids inE. colifrom around the world. Expression of many of the described virulence and AMR factors was confirmed by proteomic analyses, using bottom-up, liquid chromatography-tandem mass spectrometry (LC-MS/MS). The detailed characterization ofE. colistrain CCUG 78773 provides a reference for the relevance of genetic elements, as well as the characterization of antibiotic resistance and the spread of bacteria harboring ESBL genes in the hospital environment.
  •  
43.
  • Jaenson, Thomas G. T., 1948-, et al. (author)
  • First Record of a Suspected Human-Pathogenic Borrelia Species in Populations of the Bat Tick Carios vespertilionis in Sweden
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:5
  • Journal article (peer-reviewed)abstract
    • The bat tick Carios vespertilionis has been reported from Sweden to occasionally feed on humans resulting in disease symptoms. The aim of this study was to investigate C. vespertilionis as a potential vector and reservoir of Borrelia species. In 2015 and 2018 in south-central Sweden, C. vespertilionis ticks were collected from a wooden bat box harboring Soprano pipistrelle bats, Pipistrellus pygmaeus. In addition, one C. vespertilionis tick found inside a house in southern Sweden in 2019 was collected. Ticks were screened for Borrelia spp. using a genus-specific quantitative PCR assay. The Borrelia species of the positive specimens were determined by conventional PCR followed by DNA sequencing and phylogenetic analyses. A total of 24% (22 of 92) of the analyzed C. vespertilionis ticks were Borrelia-positive. Phylogenetic analyses indicate that the bacteria belong to the relapsing fever group of borreliae; some of them appear to be identical with Borrelia sp. CPB1, a spirochete only found twice before-in the United Kingdom and in France. Our results also indicate a temporal and spatial distribution of this Borrelia species. Since C. vespertilionis occasionally bites humans, and since it exhibits a high prevalence of Borrelia bacteria, it is possible that it presents a risk of human disease. Further studies are needed to characterize Borrelia sp. CPB1 to determine if it is human-pathogenic and to determine if C. vespertilionis is a vector and/or reservoir of this agent.
  •  
44.
  • Jansons, J, et al. (author)
  • Reciprocal Inhibition of Immunogenic Performance in Mice of Two Potent DNA Immunogens Targeting HCV-Related Liver Cancer
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:5
  • Journal article (peer-reviewed)abstract
    • Chronic HCV infection and associated liver cancer impose a heavy burden on the healthcare system. Direct acting antivirals eliminate HCV, unless it is drug resistant, and partially reverse liver disease, but they cannot cure HCV-related cancer. A possible remedy could be a multi-component immunotherapeutic vaccine targeting both HCV-infected and malignant cells, but also those not infected with HCV. To meet this need we developed a two-component DNA vaccine based on the highly conserved core protein of HCV to target HCV-infected cells, and a renowned tumor-associated antigen telomerase reverse transcriptase (TERT) based on the rat TERT, to target malignant cells. Their synthetic genes were expression-optimized, and HCV core was truncated after aa 152 (Core152opt) to delete the domain interfering with immunogenicity. Core152opt and TERT DNA were highly immunogenic in BALB/c mice, inducing IFN-γ/IL-2/TNF-α response of CD4+ and CD8+ T cells. Additionally, DNA-immunization with TERT enhanced cellular immune response against luciferase encoded by a co-delivered plasmid (Luc DNA). However, DNA-immunization with Core152opt and TERT mix resulted in abrogation of immune response against both components. A loss of bioluminescence signal after co-delivery of TERT and Luc DNA into mice indicated that TERT affects the in vivo expression of luciferase directed by the immediate early cytomegalovirus and interferon-β promoters. Panel of mutant TERT variants was created and tested for their expression effects. TERT with deleted N-terminal nucleoli localization signal and mutations abrogating telomerase activity still suppressed the IFN-β driven Luc expression, while the inactivated reverse transcriptase domain of TERT and its analogue, enzymatically active HIV-1 reverse transcriptase, exerted only weak suppressive effects, implying that suppression relied on the presence of the full-length/nearly full-length TERT, but not its enzymatic activity. The effect(s) could be due to interference of the ectopically expressed xenogeneic rat TERT with biogenesis of mRNA, ribosomes and protein translation in murine cells, affecting the expression of immunogens. HCV core can aggravate this effect, leading to early apoptosis of co-expressing cells, preventing the induction of immune response.
  •  
45.
  • Johansson, Cecilia, et al. (author)
  • Genomic and Phenotypic Characteristics in Geographically Separated Clinical Campylobacter jejuni ST353CC Isolates
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:12
  • Journal article (peer-reviewed)abstract
    • Campylobacter jejuni fecal isolates of eight international travelers, 5 of which had traveled to Ecuador and 3 to Bangladesh, were characterized, and the possible relationship between bacterial traits and clinical symptoms was further analyzed. All eight isolates belonged to the same Multi-Locus Sequence Type clonal complex (ST353CC). The three isolates from Bangladesh were all of the same sequence type (ST-9438), and when compared to isolates of various other sequence types, they had a larger quantity of unique genetic content, higher expression levels of some putative virulence genes involved in adhesion and invasion (flpA, ciaB and iamA), and showed higher adhesion levels to human HT-29 colon cancer cells in an in vitro infection model. However, in contrast to the seemingly higher pathogenic potential of these bacterial isolates, travelers infected with the ST-9438 isolates had no or only very mild symptoms, whereas the other individuals, whose bacterial isolates seemed to have less pathogenic potential, generally reported severe symptoms. When studying the 16S rRNA gene-based fecal microbiota in samples collected prior to travel, there was an individual variation in the relative abundance of the three major bacterial phyla Actinobacteria, Bacteroidetes and Firmicutes, but there were no associations between composition and diversity of microbiota and development of severe symptoms from the infection. It remains to be confirmed by larger studies whether an individual's characteristics such as gut microbiota, might be related to the severity of symptoms in Campylobacter infections.
  •  
46.
  • Kaasalainen, Ulla, et al. (author)
  • Diversity of Leptogium (Collemataceae, Ascomycota) in East African Montane Ecosystems
  • 2021
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 9:2
  • Journal article (peer-reviewed)abstract
    • Tropical mountains and especially their forests are hot spots of biodiversity threatened by human population pressure and climate change. The diversity of lichens in tropical Africa is especially poorly known. Here we use the mtSSU and nuITS molecular markers together with morphology and ecology to assess Leptogium (Peltigerales, Ascomycota) diversity in the tropical mountains of Taita Hills and Mt. Kasigau in Kenya and Mt. Kilimanjaro in Tanzania. The sampled habitats cover a wide range of ecosystems from savanna to alpine heath vegetation and from relatively natural forests to agricultural environments and plantation forests. We demonstrate that Leptogium diversity in Africa is much higher than previously known and provide preliminary data on over 70 putative species, including nine established species previously known from the area and over 60 phylogenetically, morphologically, and/or ecologically defined Operational Taxonomic Units (OTUs). Many traditional species concepts are shown to represent morphotypes comprised of several taxa. Many of the species were only found from specific ecosystems and/or restricted habitats and are thus threatened by ongoing habitat fragmentation and degradation of the natural environment. Our results emphasize the importance of molecular markers in species inventories of highly diverse organism groups and geographical areas.
  •  
47.
  • Kang, Dingrong, et al. (author)
  • Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:5
  • Journal article (peer-reviewed)abstract
    • A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.
  •  
48.
  • Karami, Nahid, 1959, et al. (author)
  • Identity of bla ctx-m carrying plasmids in sequential esbl-e. Coli isolates from patients with recurrent urinary tract infections
  • 2021
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 9:6
  • Journal article (peer-reviewed)abstract
    • Plasmid-mediated multidrug resistance in E. coli is becoming increasingly prevalent. Considering this global threat to human health, it is important to understand how plasmid-mediated resistance spreads. From a cohort of 123 patients with recurrent urinary tract infections (RUTI) due to extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (ESBL E. coli), only five events with a change of ESBL E. coli strain between RUTI episodes were identified. Their blaCTX-M encoding plasmids were compared within each pair of isolates using optical DNA mapping (ODM) and PCR-based replicon typing. Despite similar blaCTX-M genes and replicon types, ODM detected only one case with identical plasmids in the sequential ESBL E. coli strains, indicating that plasmid transfer could have occurred. For comparison, plasmids from seven patients with the same ESBL E. coli strain reoccurring in both episodes were analyzed. These plasmids (encoding blaCTX-M-3, blaCTX-M-14, and blaCTX-M-15 ) were unaltered for up to six months between recurrent infections. Thus, transmission of blaCTX-M plasmids appears to be a rare event during the course of RUTI. Despite the limited number (n = 23) of plasmids investigated, similar blaCTX-M-15 plasmids in unrelated isolates from different patients were detected, suggesting that some successful plasmids could be associated with specific strains, or are more easily transmitted.
  •  
49.
  • Kelava, Ina, et al. (author)
  • Atg5-Deficient Mice Infected with Francisella tularensis LVS Demonstrate Increased Survival and Less Severe Pathology in Internal Organs
  • 2020
  • In: Microorganisms. - : MDPI. - 2076-2607. ; 8:10
  • Journal article (peer-reviewed)abstract
    • Francisella tularensis is a highly virulent intracellular pathogen that proliferates within various cell types and can infect a multitude of animal species. Francisella escapes the phagosome rapidly after infection and reaches the host cell cytosol where bacteria undergo extensive replication. Once cytosolic, Francisella becomes a target of an autophagy-mediated process. The mechanisms by which autophagy plays a role in replication of this cytosolic pathogen have not been fully elucidated. In vitro, F. tularensis avoids degradation via autophagy and the autophagy process provides nutrients that support its intracellular replication, but the role of autophagy in vivo is unknown. Here, we investigated the role of autophagy in the pathogenesis of tularemia by using transgenic mice deficient in Atg5 in the myeloid lineage. The infection of Atg5-deficient mice with Francisella tularensis subsp. holarctica live vaccine strain (LVS) resulted in increased survival, significantly reduced bacterial burden in the mouse organs, and less severe histopathological changes in the spleen, liver and lung tissues. The data highlight the contribution of Atg5 in the pathogenesis of tularemia in vivo.
  •  
50.
  • Kõljalg, U., et al. (author)
  • The taxon hypothesis paradigm—On the unambiguous detection and communication of taxa
  • 2020
  • In: Microorganisms. - : MDPI AG. - 2076-2607. ; 8:12
  • Journal article (peer-reviewed)abstract
    • Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
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