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Microorganisms, Volume 9, Issue 6 (June 2021) – 235 articles

Cover Story (view full-size image): Pseudomonas syringae are plant pathogenic bacteria that use a type III secretion system (T3SS) to establish growth within host tissues. In P. syringae, multiple regulatory systems positively control deployment of the T3SS in response to plant metabolic signals. Other host signals and regulatory systems suppress the T3SS (e.g., the GacS/GacA system, pictured), potentially enabling fine-tuning of T3SS production over the course of infection. In this review, we summarize the current knowledge on how P. syringae regulates T3SS deployment in response to host environmental stimuli. View this paper
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Review
The Effect of Probiotics on Health Outcomes in the Elderly: A Systematic Review of Randomized, Placebo-Controlled Studies
Microorganisms 2021, 9(6), 1344; https://doi.org/10.3390/microorganisms9061344 - 21 Jun 2021
Cited by 4 | Viewed by 1596
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Probiotics for Next Generations)
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Article
Wide Genetic Diversity of Blastocystis in White-Tailed Deer (Odocoileus virginianus) from Maryland, USA
Microorganisms 2021, 9(6), 1343; https://doi.org/10.3390/microorganisms9061343 - 21 Jun 2021
Cited by 21 | Viewed by 996
Abstract
Blastocystis is a gastrointestinal protist frequently reported in humans and animals worldwide. Wildlife populations, including deer, may serve as reservoirs of parasitic diseases for both humans and domestic animals, either through direct contact or through contamination of food or water resources. However, no [...] Read more.
Blastocystis is a gastrointestinal protist frequently reported in humans and animals worldwide. Wildlife populations, including deer, may serve as reservoirs of parasitic diseases for both humans and domestic animals, either through direct contact or through contamination of food or water resources. However, no studies of the occurrence and subtype distribution of Blastocystis in wildlife populations have been conducted in the United States. PCR and next generation amplicon sequencing were used to determine the occurrence and subtypes of Blastocystis in white-tailed deer (Odocoileus virginianus). Blastocystis was common, with 88.8% (71/80) of samples found to be positive. Twelve subtypes were identified, ten previously reported (ST1, ST3, ST4, ST10, ST14, ST21, and ST23–ST26) and two novel subtypes (ST30 and ST31). To confirm the validity of ST30 and ST31, MinION sequencing was used to obtain full-length SSU rRNA gene sequences, and phylogenetic and pairwise distance analyses were performed. ST10, ST14, and ST24 were the most commonly observed subtypes. Potentially zoonotic subtypes ST1, ST3, or ST4 were present in 8.5% of Blastocystis-positives. Mixed subtype infections were common (90.1% of Blastocystis-positives). This study is the first to subtype Blastocystis in white-tailed deer. White-tailed deer were found to be commonly infected/colonized with a wide diversity of subtypes, including two novel subtypes, zoonotic subtypes, and subtypes frequently reported in domestic animals. More studies in wildlife are needed to better understand their role in the transmission of Blastocystis. Full article
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Article
Encapsulated Mixture of Methyl Salicylate and Tributyrin Modulates Intestinal Microbiota and Improves Growth Performance of Weaned Piglets
Microorganisms 2021, 9(6), 1342; https://doi.org/10.3390/microorganisms9061342 - 21 Jun 2021
Viewed by 1070
Abstract
Tributyrin and essential oils have been used as alternatives to antimicrobials to improve gut health and growth performance in piglets. This study was to evaluate the effects of a dietary supplement with two encapsulated products containing different combinations of tributyrin with oregano or [...] Read more.
Tributyrin and essential oils have been used as alternatives to antimicrobials to improve gut health and growth performance in piglets. This study was to evaluate the effects of a dietary supplement with two encapsulated products containing different combinations of tributyrin with oregano or with methyl salicylate on growth performance, serum biochemical parameters related to the physiological status, intestinal microbiota and metabolites of piglets. A total of 108 weaned crossbred piglets (Yorkshire × Landrace, 21 ± 1 d, 8.21 ± 0.04 kg) were randomly divided into three groups. Piglets were fed with one of the following diets for 5 weeks: a basal diet as the control (CON); the control diet supplemented with an encapsulated mixture containing 30% of methyl salicylate and tributyrin at a dosage of 3 kg/t (CMT); and the control diet supplemented with an encapsulated mixture containing 30% of oregano oil and tributyrin at a dosage of 3 kg/t (COT). At the end of the feeding trial, six piglets from each group were slaughtered to collect blood and gut samples for physiological status and gut microbiological analysis. The study found that the CMT group was larger in feed intake (FI) (p < 0.05), average daily gain (ADG) (p = 0.09), total protein (TP), albumin (ALB), glutathione peroxidase (GSH-PX) (p < 0.05), blood total antioxidant capacity (T-AOC) (p < 0.05), and crypt depth in the ileum (p < 0.05) compared with the CON group. The genus abundance of Tissierella and Campylobacter in the CMT group was significantly decreased compared with the CON group. The CMT group also resulted in significantly higher activity in amino acid metabolism and arginine biosynthesis compared with the CON group. The COT group was larger in T-AOC, and the genus abundance of Streptophyta and Chlamydia was significantly increased in the ileum compared with the CON group. Data analysis found a significantly high correlation between the genus abundance of Chlamydia and that of Campylobacter in the ileum. The genus abundance of Campylobacter was also positively correlated with the sorbitol level. In general, the results indicated that the supplementation of both encapsulated mixtures in diet of weaned piglets could improve the animal blood antioxidant capacity. Additionally, the encapsulated mixture of methyl salicylate plus tributyrin improved the growth performance and resulted in certain corresponding changes in nutrient metabolism and in the genus abundance of ileum microbial community. Full article
(This article belongs to the Special Issue Gut Microbiota Development in Farm Animals)
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Article
Effects of Lactobacillus reuteri and Streptomyces coelicolor on Growth Performance of Broiler Chickens
Microorganisms 2021, 9(6), 1341; https://doi.org/10.3390/microorganisms9061341 - 21 Jun 2021
Cited by 2 | Viewed by 1015
Abstract
There are well documented complications associated with the continuous use of antibiotics in the poultry industry. Over the past few decades, probiotics have emerged as viable alternatives to antibiotics; however, most of these candidate probiotic microorganisms have not been fully evaluated for their [...] Read more.
There are well documented complications associated with the continuous use of antibiotics in the poultry industry. Over the past few decades, probiotics have emerged as viable alternatives to antibiotics; however, most of these candidate probiotic microorganisms have not been fully evaluated for their effectiveness as potential probiotics for poultry. Recent evaluation of a metagenome of broiler chickens in our laboratory revealed a prevalence of Lactobacillus reuteri (L. reuteri) and Actinobacteria class of bacteria in their gastrointestinal tract. In this study Lactobacillus reuteri and Streptomyces coelicolor (S. coelicolor) were selected as probiotic bacteria, encapsulated, and added into broiler feed at a concentration of 100 mg/kg of feed. In an 8-week study, 240 one day-old chicks were randomly assigned to four dietary treatments. Three dietary treatments contained two probiotic bacteria in three different proportions (L. reuteri and S. coelicolor individually at 100 ppm, and mixture of L. reuteri and S. coelicolor at 50 ppm each). The fourth treatment had no probiotic bacteria and it functioned as the control diet. L. reuteri and S. coelicolor were added to the feed by using wheat middlings as a carrier at a concentration of 100 ppm (100 mg/kg). Chickens fed diets containing L. reuteri and S. coelicolor mixture showed 2% improvement in body weight gain, 7% decrease in feed consumption, and 6–7% decrease in feed conversion ratios. This research suggests that L. reuteri and S. coelicolor have the potential to constitute probiotics in chickens combined or separately, depending on the desired selection of performance index. Full article
(This article belongs to the Section Gut Microbiota)
Article
Confounding Factors Influencing the Kinetics and Magnitude of Serological Response Following Administration of BNT162b2
Microorganisms 2021, 9(6), 1340; https://doi.org/10.3390/microorganisms9061340 - 21 Jun 2021
Cited by 15 | Viewed by 1487
Abstract
Background: Little is known about potential confounding factors influencing the humoral response in individuals having received the BNT162b2 vaccine. Methods: Blood samples from 231 subjects were collected before and 14, 28, and 42 days following coronavirus disease 2019 (COVID-19) vaccination with BNT162b2. Anti-spike [...] Read more.
Background: Little is known about potential confounding factors influencing the humoral response in individuals having received the BNT162b2 vaccine. Methods: Blood samples from 231 subjects were collected before and 14, 28, and 42 days following coronavirus disease 2019 (COVID-19) vaccination with BNT162b2. Anti-spike receptor-binding-domain protein (anti-Spike/RBD) immunoglobulin G (IgG) antibodies were measured at each time-point. Impact of age, sex, childbearing age status, hormonal therapy, blood group, body mass index and past-history of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection were assessed by multivariable analyses. Results and Conclusions: In naïve subjects, the level of anti-Spike/RBD antibodies gradually increased following administration of the first dose to reach the maximal response at day 28 and then plateauing at day 42. In vaccinated subjects with previous SARS-CoV-2 infection, the plateau was reached sooner (i.e., at day 14). In the naïve population, age had a significant negative impact on anti-Spike/RBD titers at days 14 and 28 while lower levels were observed for males at day 42, when corrected for other confounding factors. Body mass index (BMI) as well as B and AB blood groups had a significant impact in various subgroups on the early response at day 14 but no longer after. No significant confounding factors were highlighted in the previously infected group. Full article
(This article belongs to the Special Issue COVID-19: Antivirals and Vaccines)
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Article
Epigenetic Silencing of MicroRNA-126 Promotes Cell Growth in Marek’s Disease
Microorganisms 2021, 9(6), 1339; https://doi.org/10.3390/microorganisms9061339 - 21 Jun 2021
Cited by 1 | Viewed by 895
Abstract
During latency, herpesvirus infection results in the establishment of a dormant state in which a restricted set of viral genes are expressed. Together with alterations of the viral genome, several host genes undergo epigenetic silencing during latency. These epigenetic dysregulations of cellular genes [...] Read more.
During latency, herpesvirus infection results in the establishment of a dormant state in which a restricted set of viral genes are expressed. Together with alterations of the viral genome, several host genes undergo epigenetic silencing during latency. These epigenetic dysregulations of cellular genes might be involved in the development of cancer. In this context, Gallid alphaherpesvirus 2 (GaHV-2), causing Marek’s disease (MD) in susceptible chicken, was shown to impair the expression of several cellular microRNAs (miRNAs). We decided to focus on gga-miR-126, a host miRNA considered a tumor suppressor through signaling pathways controlling cell proliferation. Our objectives were to analyze the cause and the impact of miR-126 silencing during GaHV-2 infection. This cellular miRNA was found to be repressed at crucial steps of the viral infection. In order to determine whether miR-126 low expression level was associated with specific epigenetic signatures, DNA methylation patterns were established in the miR-126 gene promoter. Repression was associated with hypermethylation at a CpG island located in the miR-126 host gene epidermal growth factor like-7 (EGFL-7). A strategy was developed to conditionally overexpress miR-126 and control miRNAs in transformed CD4+ T cells propagated from Marek’s disease (MD) lymphoma. This functional assay showed that miR-126 restoration specifically diminishes cell proliferation. We identified CT10 regulator of kinase (CRK), an adaptor protein dysregulated in several human malignancies, as a candidate target gene. Indeed, CRK protein levels were markedly reduced by the miR-126 restoration. Full article
(This article belongs to the Special Issue Marek’s Disease Virus)
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Article
Two Lysine Sites That Can Be Malonylated Are Important for LuxS Regulatory Roles in Bacillus velezensis
Microorganisms 2021, 9(6), 1338; https://doi.org/10.3390/microorganisms9061338 - 21 Jun 2021
Viewed by 812
Abstract
S-ribosylhomocysteine lyase (LuxS) has been shown to regulate bacterial multicellular behaviors, typically biofilm formation. However, the mechanisms for the regulation are still mysterious. We previously identified a malonylation modification on K124 and K130 of the LuxS in the plant growth-promoting rhizobacterium B.  [...] Read more.
S-ribosylhomocysteine lyase (LuxS) has been shown to regulate bacterial multicellular behaviors, typically biofilm formation. However, the mechanisms for the regulation are still mysterious. We previously identified a malonylation modification on K124 and K130 of the LuxS in the plant growth-promoting rhizobacterium B. velezensis (FZB42). In this work, we investigated the effects of the two malonylation sites on biofilm formation and other biological characteristics of FZB42. The results showed that the K124R mutation could severely impair biofilm formation, swarming, and sporulation but promote AI-2 production, suggesting inhibitory effects of high-level AI-2 on the features. All mutations (K124R, K124E, K130R, and K130E) suppressed FZB42 sporulation but increased its antibiotic production. The double mutations generally had a synergistic effect or at least equal to the effects of the single mutations. The mutation of K130 but not of K124 decreased the in vitro enzymatic activity of LuxS, corresponding to the conservation of K130 among various Bacillus LuxS proteins. From the results, we deduce that an alternative regulatory circuit may exist to compensate for the roles of LuxS upon its disruption. This study broadens the understanding of the biological function of LuxS in bacilli and underlines the importance of the two post-translational modification sites. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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Article
An Internal Promoter Drives the Expression of a Truncated Form of CCC1 Capable of Protecting Yeast from Iron Toxicity
Microorganisms 2021, 9(6), 1337; https://doi.org/10.3390/microorganisms9061337 - 20 Jun 2021
Viewed by 871
Abstract
In yeast, iron storage and detoxification depend on the Ccc1 transporter that mediates iron accumulation in vacuoles. While deletion of the CCC1 gene renders cells unable to survive under iron overload conditions, the deletion of its previously identified regulators only partially affects survival, [...] Read more.
In yeast, iron storage and detoxification depend on the Ccc1 transporter that mediates iron accumulation in vacuoles. While deletion of the CCC1 gene renders cells unable to survive under iron overload conditions, the deletion of its previously identified regulators only partially affects survival, indicating that the mechanisms controlling iron storage and detoxification in yeast are still far from well understood. This work reveals that CCC1 is equipped with a complex transcriptional structure comprising several regulatory regions. One of these is located inside the coding sequence of the gene and drives the expression of a short transcript encoding an N-terminally truncated protein, designated as s-Ccc1. s-Ccc1, though less efficiently than Ccc1, is able to promote metal accumulation in the vacuole, protecting cells against iron toxicity. While the expression of the s-Ccc1 appears to be repressed in the normal genomic context, our current data clearly demonstrates that it is functional and has the capacity to play a role under iron overload conditions. Full article
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Article
Carboxy-Terminal Processing Protease Controls Production of Outer Membrane Vesicles and Biofilm in Acinetobacter baumannii
Microorganisms 2021, 9(6), 1336; https://doi.org/10.3390/microorganisms9061336 - 20 Jun 2021
Cited by 1 | Viewed by 1456
Abstract
Carboxy-terminal processing protease (Ctp) is a serine protease that controls multiple cellular processes through posttranslational modification of proteins. Acinetobacter baumannii ATCC 17978 ctp mutant, namely MR14, is known to cause cell wall defects and autolysis. The objective of this study was to investigate [...] Read more.
Carboxy-terminal processing protease (Ctp) is a serine protease that controls multiple cellular processes through posttranslational modification of proteins. Acinetobacter baumannii ATCC 17978 ctp mutant, namely MR14, is known to cause cell wall defects and autolysis. The objective of this study was to investigate the role of ctp mutation–driven autolysis in regulating biofilms in A. baumannii and to evaluate the vesiculation caused by cell wall defects. We found that in A. baumannii, Ctp is localized in the cytoplasmic membrane, and loss of Ctp function enhances the biofilm-forming ability of A. baumannii. Quantification of the matrix components revealed that extracellular DNA (eDNA) and proteins were the chief constituents of MR14 biofilm, and the transmission electron microscopy further indicated the presence of numerous dead cells compared with ATCC 17978. The large number of MR14 dead cells is potentially the result of compromised outer membrane integrity, as demonstrated by its high sensitivity to sodium dodecyl sulfate (SDS) and ethylenediaminetetraacetic acid (EDTA). MR14 also exhibited the hypervesiculation phenotype, producing outer-membrane vesicles (OMVs) of large mean size. The MR14 OMVs were more cytotoxic toward A549 cells than ATCC 17978 OMVs. Our overall results indicate that A. baumanniictp negatively controls pathogenic traits through autolysis and OMV biogenesis. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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Communication
Comparative Genomics of Prophages Sato and Sole Expands the Genetic Diversity Found in the Genus Betatectivirus
Microorganisms 2021, 9(6), 1335; https://doi.org/10.3390/microorganisms9061335 - 19 Jun 2021
Viewed by 981
Abstract
Tectiviruses infecting the Bacillus cereus group represent part of the bacterial “plasmid repertoire” as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze [...] Read more.
Tectiviruses infecting the Bacillus cereus group represent part of the bacterial “plasmid repertoire” as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze the complete genome sequences of phages Sato and Sole. The linear dsDNA genome of Sato spans 14,852 bp with 32 coding DNA sequences (CDSs), whereas the one of Sole has 14,444 bp comprising 30 CDSs. Both phage genomes contain inverted terminal repeats and no tRNAs. Genomic comparisons and phylogenetic analyses placed these two phages within the genus Betatectivirus in the family Tectiviridae. Additional comparative genomic analyses indicated that the “gene regulation-genome replication” module of phages Sato and Sole is more diverse than previously observed among other fully sequenced betatectiviruses, displaying very low sequence similarities and containing some ORFans. Interestingly, the ssDNA binding protein encoded in this genomic module in phages Sato and Sole has very little amino acid similarity with those of reference betatectiviruses. Phylogenetic analyses showed that both Sato and Sole represent novel tectivirus species, thus we propose to include them as two novel species in the genus Betatectivirus. Full article
(This article belongs to the Special Issue Bacteriophage Genomics)
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Article
Antibiotic Resistant and Biofilm-Associated Escherichia coli Isolates from Diarrheic and Healthy Dogs
Microorganisms 2021, 9(6), 1334; https://doi.org/10.3390/microorganisms9061334 - 19 Jun 2021
Viewed by 926
Abstract
Bacteria isolated from companion animals are attracting concerns in a view of public health including antimicrobial resistance and biofilm development, both contributing to difficult-to-treat infections. The purpose of this study was to evaluate the minimum inhibitory concentrations (MIC) of 18 antibiotics in Escherichia [...] Read more.
Bacteria isolated from companion animals are attracting concerns in a view of public health including antimicrobial resistance and biofilm development, both contributing to difficult-to-treat infections. The purpose of this study was to evaluate the minimum inhibitory concentrations (MIC) of 18 antibiotics in Escherichia coli isolated from two groups of dogs (healthy and diarrheic). Isolates were classified into phylogroups, examined for the presence of resistance genes and biofilm-formation capacity. In healthy dogs, phylogenetic analysis showed that 47.37% and 34.22% of E. coli isolates belonged to commensal groups (A; B1) in contrast to diarrheic dogs; 42.2% of isolates were identified as the B2 phylogroup, and these E. coli bacteria formed a stronger biofilm. The results of healthy dogs showed higher MIC levels for tetracycline (32 mg/L), ampicillin (64 mg/L), ciprofloxacin (8 mg/L) and trimethoprim-sulphonamide (8 mg/L) compared to clinical breakpoints. The most detected gene encoding plasmid-mediated resistance to quinolones in the healthy group was qnrB, and in dogs with diarrhea, qnrS. The resistance genes were more frequently detected in healthy dogs. The presence of the integron int1 and the transposon tn3 increases the possibility of transfer of many different cassette-associated antibiotic-resistance genes. These results suggest that dogs could be a potential reservoir of resistance genes. Full article
(This article belongs to the Special Issue Virulence Factors and Antibiotic Resistance of Enterobacterales)
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Article
Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil
Microorganisms 2021, 9(6), 1333; https://doi.org/10.3390/microorganisms9061333 - 19 Jun 2021
Cited by 1 | Viewed by 917
Abstract
Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in [...] Read more.
Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil. Full article
(This article belongs to the Special Issue Fungal Biodiversity for Bioremediation)
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Article
Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter
Microorganisms 2021, 9(6), 1332; https://doi.org/10.3390/microorganisms9061332 - 19 Jun 2021
Cited by 1 | Viewed by 953
Abstract
Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and [...] Read more.
Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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Article
Assessment of the Degradation Potential and Genomic Insights towards Phenanthrene by Dietzia psychralcaliphila JI1D
Microorganisms 2021, 9(6), 1327; https://doi.org/10.3390/microorganisms9061327 - 19 Jun 2021
Cited by 3 | Viewed by 1122
Abstract
Extreme marine environments are potential sources of novel microbial isolations with dynamic metabolic activity. Dietzia psychralcaliphila J1ID was isolated from sediments originated from Deception Island, Antarctica, grown over phenanthrene. This strain was also assessed for its emulsifying activity. In liquid media, Dietzia psychralcaliphila [...] Read more.
Extreme marine environments are potential sources of novel microbial isolations with dynamic metabolic activity. Dietzia psychralcaliphila J1ID was isolated from sediments originated from Deception Island, Antarctica, grown over phenanthrene. This strain was also assessed for its emulsifying activity. In liquid media, Dietzia psychralcaliphila J1ID showed 84.66% degradation of phenanthrene examined with HPLC-PDA. The identification of metabolites by GC-MS combined with its whole genome analysis provided the pathway involved in the degradation process. Whole genome sequencing indicated a genome size of 4,216,480 bp with 3961 annotated genes. The presence of a wide range of monooxygenase and dioxygenase, as well as dehydrogenase catabolic genes provided the genomic basis for the biodegradation. The strain possesses the genetic compartments for a wide range of toxic aromatic compounds, which includes the benABCD and catABC clusters. COG2146, COG4638, and COG0654 through COG analysis confirmed the genes involved in the oxygenation reaction of the hydrocarbons by the strain. Insights into assessing the depletion of phenanthrene throughout the incubation process and the genetic components involved were obtained. This study indicates the degradation potential of the strain, which can also be further expanded to other model polyaromatic hydrocarbons. Full article
(This article belongs to the Special Issue Oil Biodegradation and Bioremediation in Cold Marine Environment)
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Article
Temperature Sensitivity and Composition of Nitrate-Reducing Microbiomes from a Full-Scale Woodchip Bioreactor Treating Agricultural Drainage Water
Microorganisms 2021, 9(6), 1331; https://doi.org/10.3390/microorganisms9061331 - 18 Jun 2021
Cited by 7 | Viewed by 1153
Abstract
Denitrifying woodchip bioreactors (WBR), which aim to reduce nitrate (NO3) pollution from agricultural drainage water, are less efficient when cold temperatures slow down the microbial transformation processes. Conducting bioaugmentation could potentially increase the NO3 removal efficiency during these [...] Read more.
Denitrifying woodchip bioreactors (WBR), which aim to reduce nitrate (NO3) pollution from agricultural drainage water, are less efficient when cold temperatures slow down the microbial transformation processes. Conducting bioaugmentation could potentially increase the NO3 removal efficiency during these specific periods. First, it is necessary to investigate denitrifying microbial populations in these facilities and understand their temperature responses. We hypothesized that seasonal changes and subsequent adaptations of microbial populations would allow for enrichment of cold-adapted denitrifying bacterial populations with potential use for bioaugmentation. Woodchip material was sampled from an operating WBR during spring, fall, and winter and used for enrichments of denitrifiers that were characterized by studies of metagenomics and temperature dependence of NO3 depletion. The successful enrichment of psychrotolerant denitrifiers was supported by the differences in temperature response, with the apparent domination of the phylum Proteobacteria and the genus Pseudomonas. The enrichments were found to have different microbiomes’ composition and they mainly differed with native woodchip microbiomes by a lower abundance of the genus Flavobacterium. Overall, the performance and composition of the enriched denitrifying population from the WBR microbiome indicated a potential for efficient NO3 removal at cold temperatures that could be stimulated by the addition of selected cold-adapted denitrifying bacteria. Full article
(This article belongs to the Section Environmental Microbiology)
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Article
Dental Biofilm and Saliva Microbiome and Its Interplay with Pediatric Allergies
Microorganisms 2021, 9(6), 1330; https://doi.org/10.3390/microorganisms9061330 - 18 Jun 2021
Cited by 3 | Viewed by 1460
Abstract
Little is known about the interplay and contribution of oral microorganisms to allergic diseases, especially in children. The aim of the clinical study was to associate saliva and dental biofilm microbiome with allergic disease, in particular with allergic asthma. In a single-center study, [...] Read more.
Little is known about the interplay and contribution of oral microorganisms to allergic diseases, especially in children. The aim of the clinical study was to associate saliva and dental biofilm microbiome with allergic disease, in particular with allergic asthma. In a single-center study, allergic/asthmatic children (n = 15; AA-Chd; age 10.7 ± 2.9), atopic/allergic children (n = 16; AT/AL-Chd; 11.3 ± 2.9), and healthy controls (n = 15; CON-Chd; age 9.9 ± 2.2) were recruited. After removing adhering biofilms from teeth and collecting saliva, microbiome was analyzed by using a 16s-rRNA gene-based next-generation sequencing in these two mediums. Microbiome structure differed significantly between saliva and dental biofilms (β-diversity). Within the groups, the dental biofilm microbiome of AA-Chd and AT/AL-Chd showed a similar microbial fingerprint characterized by only a small number of taxa that were enriched or depleted (4) compared to the CON-Chd, while both diseased groups showed a stronger microbial shift compared to CON-Chd, revealing 14 taxa in AA-Chd and 15 taxa in AT/AL-Chd that were different. This could be the first note to the contribution of dental biofilm and its metabolic activity to allergic health or disease. Full article
(This article belongs to the Special Issue Microbial Films-the Interplay of Physics and Biology)
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Article
Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities
Microorganisms 2021, 9(6), 1329; https://doi.org/10.3390/microorganisms9061329 - 18 Jun 2021
Cited by 2 | Viewed by 1029
Abstract
The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of [...] Read more.
The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress. Full article
(This article belongs to the Special Issue Microbial Interactions in Soil)
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Article
Transposon Mutagenesis of Pseudomonas syringae Pathovars syringae and morsprunorum to Identify Genes Involved in Bacterial Canker Disease of Cherry
Microorganisms 2021, 9(6), 1328; https://doi.org/10.3390/microorganisms9061328 - 18 Jun 2021
Cited by 1 | Viewed by 1275
Abstract
Bacterial canker of Prunus, affecting economically important stone fruit crops including cherry, peach, apricot and plum, is caused by the plant pathogen Pseudomonas syringae (P.s.). Strains from two pathovars—P.s. pv. syringae (Pss) and P.s. pv. morsprunorum [...] Read more.
Bacterial canker of Prunus, affecting economically important stone fruit crops including cherry, peach, apricot and plum, is caused by the plant pathogen Pseudomonas syringae (P.s.). Strains from two pathovars—P.s. pv. syringae (Pss) and P.s. pv. morsprunorum race 1 (PsmR1) and 2 (PsmR2)—in three phylogenetically distant clades have convergently evolved to infect Prunus. The bacteria enter woody tissues through wounds and leaf scars, causing black necrotic cankers. Symptoms are also produced on blossom, fruit and leaves. Little is known about the mechanisms P.s. uses to colonise tree hosts such as Prunus. Here, we created transposon (Tn) mutant libraries in one strain of P.s. from each of the three clades and screened the mutants on immature cherry fruit to look for changes in virulence. Mutants (242) with either reduced or enhanced virulence were detected and further characterised by in vitro screens for biofilm formation, swarming ability, and pathogenicity on leaves and cut shoots. In total, 18 genes affecting virulence were selected, and these were involved in diverse functions including motility, type III secretion, membrane transport, amino acid synthesis, DNA repair and primary metabolism. Interestingly, mutation of the effector gene, hopAU1, led to an increase in virulence of Psm R2. Full article
(This article belongs to the Special Issue Plant-Associated Pseudomonads)
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Article
Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer
Microorganisms 2021, 9(6), 1326; https://doi.org/10.3390/microorganisms9061326 - 18 Jun 2021
Cited by 2 | Viewed by 1541
Abstract
Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This [...] Read more.
Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO3/NH4+ ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions. Full article
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Review
Preventing Colorectal Cancer through Prebiotics
Microorganisms 2021, 9(6), 1325; https://doi.org/10.3390/microorganisms9061325 - 18 Jun 2021
Cited by 1 | Viewed by 1558
Abstract
Colorectal cancer (CRC), the third most common cancer in the world, has been recently rising in emerging countries due to environmental and lifestyle factors. Many of these factors are brought up by industrialization, which includes lack of physical activity, poor diet, circadian rhythm [...] Read more.
Colorectal cancer (CRC), the third most common cancer in the world, has been recently rising in emerging countries due to environmental and lifestyle factors. Many of these factors are brought up by industrialization, which includes lack of physical activity, poor diet, circadian rhythm disruption, and increase in alcohol consumption. They can increase the risk of CRC by changing the colonic environment and by altering gut microbiota composition, a state referred to as gut dysbiosis. Prebiotics, which are nutrients that can help maintain intestinal microbial homeostasis and mitigate dysbiosis, could be beneficial in preventing inflammation and CRC. These nutrients can hinder the effects of dysbiosis by encouraging the growth of beneficial bacteria involved in short-chain fatty acids (SCFA) production, anti-inflammatory immunity, maintenance of the intestinal epithelial barrier, pro-apoptotic mechanisms, and other cellular mechanisms. This review aims to summarize recent reports about the implication of prebiotics, and probable mechanisms, in the prevention and treatment of CRC. Various experimental studies, specifically in gut microbiome, have effectively demonstrated the protective effect of prebiotics in the progress of CRC. Hence, comprehensive knowledge is urgent to understand the clinical applications of prebiotics in the prevention or treatment of CRC. Full article
(This article belongs to the Special Issue Gut Microbiota and Nutrients)
Article
The Respiratory Commensal Bacterium Dolosigranulum pigrum 040417 Improves the Innate Immune Response to Streptococcus pneumoniae
Microorganisms 2021, 9(6), 1324; https://doi.org/10.3390/microorganisms9061324 - 18 Jun 2021
Viewed by 985
Abstract
Previously, we demonstrated that the nasal administration of Dolosigranulum pigrum 040417 differentially modulated the respiratory innate immune response triggered by the activation of Toll-like receptor 2 in infant mice. In this work, we aimed to evaluate the beneficial effects of D. pigrum 040417 [...] Read more.
Previously, we demonstrated that the nasal administration of Dolosigranulum pigrum 040417 differentially modulated the respiratory innate immune response triggered by the activation of Toll-like receptor 2 in infant mice. In this work, we aimed to evaluate the beneficial effects of D. pigrum 040417 in the context of Streptococcus pneumoniae infection and characterize the role of alveolar macrophages (AMs) in the immunomodulatory properties of this respiratory commensal bacterium. The nasal administration of D. pigrum 040417 to infant mice significantly increased their resistance to pneumococcal infection, differentially modulated respiratory cytokines production, and reduced lung injuries. These effects were associated to the ability of the 040417 strain to modulate AMs function. Depletion of AMs significantly reduced the capacity of the 040417 strain to improve both the reduction of pathogen loads and the protection against lung tissue damage. We also demonstrated that the immunomodulatory properties of D. pigrum are strain-specific, as D. pigrum 030918 was not able to modulate respiratory immunity or to increase the resistance of mice to an S. pneumoniae infection. These findings enhanced our knowledge regarding the immunological mechanisms involved in modulation of respiratory immunity induced by beneficial respiratory commensal bacteria and suggested that particular strains could be used as next-generation probiotics. Full article
(This article belongs to the Special Issue Probiotics for Next Generations)
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Article
A Metzincin and TIMP-Like Protein Pair of a Phage Origin Sensitize Listeria monocytogenes to Phage Lysins and Other Cell Wall Targeting Agents
Microorganisms 2021, 9(6), 1323; https://doi.org/10.3390/microorganisms9061323 - 18 Jun 2021
Cited by 1 | Viewed by 883
Abstract
Infection of mammalian cells by Listeria monocytogenes (Lm) was shown to be facilitated by its phage elements. In a search for additional phage remnants that play a role in Lm’s lifecycle, we identified a conserved locus containing two XRE regulators [...] Read more.
Infection of mammalian cells by Listeria monocytogenes (Lm) was shown to be facilitated by its phage elements. In a search for additional phage remnants that play a role in Lm’s lifecycle, we identified a conserved locus containing two XRE regulators and a pair of genes encoding a secreted metzincin protease and a lipoprotein structurally similar to a TIMP-family metzincin inhibitor. We found that the XRE regulators act as a classic CI/Cro regulatory switch that regulates the expression of the metzincin and TIMP-like genes under intracellular growth conditions. We established that when these genes are expressed, their products alter Lm morphology and increase its sensitivity to phage mediated lysis, thereby enhancing virion release. Expression of these proteins also sensitized the bacteria to cell wall targeting compounds, implying that they modulate the cell wall structure. Our data indicate that these effects are mediated by the cleavage of the TIMP-like protein by the metzincin, and its subsequent release to the extracellular milieu. While the importance of this locus to Lm pathogenicity remains unclear, the observation that this phage-associated protein pair act upon the bacterial cell wall may hold promise in the field of antibiotic potentiation to combat antibiotic resistant bacterial pathogens. Full article
(This article belongs to the Special Issue Temperate Phages)
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Article
First Emergence of Resistance to Macrolides and Tetracycline Identified in Mannheimia haemolytica and Pasteurella multocida Isolates from Beef Feedlots in Australia
Microorganisms 2021, 9(6), 1322; https://doi.org/10.3390/microorganisms9061322 - 17 Jun 2021
Cited by 3 | Viewed by 1291 | Correction
Abstract
Bovine respiratory disease (BRD) causes high morbidity and mortality in beef cattle worldwide. Antimicrobial resistance (AMR) monitoring of BRD pathogens is critical to promote appropriate antimicrobial stewardship in veterinary medicine for optimal treatment and control. Here, the susceptibility of Mannheimia haemolytica and Pasteurella [...] Read more.
Bovine respiratory disease (BRD) causes high morbidity and mortality in beef cattle worldwide. Antimicrobial resistance (AMR) monitoring of BRD pathogens is critical to promote appropriate antimicrobial stewardship in veterinary medicine for optimal treatment and control. Here, the susceptibility of Mannheimia haemolytica and Pasteurella multicoda isolates obtained from BRD clinical cases (deep lung swabs at post-mortem) among feedlots in four Australian states (2014–2019) was determined for 19 antimicrobial agents. The M. haemolytica isolates were pan-susceptible to all tested agents apart from a single macrolide-resistant isolate (1/88; 1.1%) from New South Wales (NSW). Much higher frequencies of P. multocida isolates were resistant to tetracycline (18/140; 12.9%), tilmicosin (19/140; 13.6%), tulathromycin/gamithromycin (17/140; 12.1%), and ampicillin/penicillin (6/140; 4.6%). Five P. multocida isolates (3.6%), all obtained from NSW in 2019, exhibited dual resistance to macrolides and tetracycline, and a further two Queensland isolates from 2019 (1.4%) exhibited a multidrug-resistant phenotype to ampicillin/penicillin, tetracycline, and tilmicosin. Random-amplified polymorphic DNA (RAPD) typing identified a high degree of genetic homogeneity among the M. haemolytica isolates, whereas P. multocida isolates were more heterogeneous. Illumina whole genome sequencing identified the genes msr(E) and mph(E)encoding macrolide resistance, tet(R)-tet(H) or tet(Y) encoding tetracycline resistance, and blaROB-1 encoding ampicillin/penicillin resistance in all isolates exhibiting a corresponding resistant phenotype. The exception was the tilmicosin-resistant, tulathromycin/gamithromycin-susceptible phenotype identified in two Queensland isolates, the genetic basis of which could not be determined. These results confirm the first emergence of AMR in M. haemolytica and P. multocida from BRD cases in Australia, which should be closely monitored. Full article
(This article belongs to the Special Issue Breaking the Code of Antibiotic Resistance)
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Article
Predictive Modeling and Validation on Growth, Production of Asexual Spores and Ochratoxin A of Aspergillus Ochraceus Group under Abiotic Climatic Variables
Microorganisms 2021, 9(6), 1321; https://doi.org/10.3390/microorganisms9061321 - 17 Jun 2021
Viewed by 743
Abstract
This study aimed to generate predictive models for growth, sporulation, and ochratoxin A (OTA) production under abiotic climatic variables, including temperatures (15–35 °C) and water activity levels (0.99–0.90 aw) by Aspergillus ochraceus group. The data were divided into three sets: one [...] Read more.
This study aimed to generate predictive models for growth, sporulation, and ochratoxin A (OTA) production under abiotic climatic variables, including temperatures (15–35 °C) and water activity levels (0.99–0.90 aw) by Aspergillus ochraceus group. The data were divided into three sets: one for training, one for testing, and the third one for model validation. Optimum growth occurred at 0.95 aw and 25 °C and 0.95 aw and 30 °C for A. westerdijkiae and A. steynii, respectively. Significantly improved A. westerdijkiae and A. steynii spore production occurred at 0.95 aw and 20 °C and 0.90 aw and 35 °C, respectively. A. steynii and A. westerdijkiae produced the majority of OTA at 35 °C and 0.95 aw and 25–30 °C at 0.95–0.99 aw, respectively. The accuracy of the third-order polynomial regression model reached 96% in growth cases, 94.7% in sporulation cases, and 90.9% in OTA production cases; the regression coefficients (R2) ranged from 0.8819 to 0.9978 for the Aspergillus ochraceus group. A reliable agreement was reached between the predicted and observed growth, sporulation, and OTA production. The effects of abiotic climatic variables on growth, sporulation, and OTA production of A. ochraceus group have been effectively defined, and the models generated were responsible for adequately predicted and validated models against data from other strains within A. ochraceus group that had been published in the literature under the current treatments. These models could be successfully implemented to predict fungal growth and OTA contamination on food matrices for these strains under these conditions. Full article
(This article belongs to the Section Environmental Microbiology)
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Article
Characterisation of the Antibiotic Profile of Lysobacter capsici AZ78, an Effective Biological Control Agent of Plant Pathogenic Microorganisms
Microorganisms 2021, 9(6), 1320; https://doi.org/10.3390/microorganisms9061320 - 17 Jun 2021
Cited by 3 | Viewed by 1219
Abstract
Determining the mode of action of microbial biocontrol agents plays a key role in their development and registration as commercial biopesticides. The biocontrol rhizobacterium Lysobacter capsici AZ78 (AZ78) is able to inhibit a vast array of plant pathogenic oomycetes and Gram-positive bacteria due [...] Read more.
Determining the mode of action of microbial biocontrol agents plays a key role in their development and registration as commercial biopesticides. The biocontrol rhizobacterium Lysobacter capsici AZ78 (AZ78) is able to inhibit a vast array of plant pathogenic oomycetes and Gram-positive bacteria due to the release of antimicrobial secondary metabolites. A combination of MALDI-qTOF-MSI and UHPLC-HRMS/M was applied to finely dissect the AZ78 metabolome and identify the main secondary metabolites involved in the inhibition of plant pathogenic microorganisms. Under nutritionally limited conditions, MALDI-qTOF-MSI revealed that AZ78 is able to release a relevant number of antimicrobial secondary metabolites belonging to the families of 2,5-diketopiperazines, cyclic lipodepsipeptides, macrolactones and macrolides. In vitro tests confirmed the presence of secondary metabolites toxic against Pythium ultimum and Rhodococcus fascians in AZ78 cell-free extracts. Subsequently, UHPLC-HRMS/MS was used to confirm the results achieved with MALDI-qTOF-MSI and investigate for further putative antimicrobial secondary metabolites known to be produced by Lysobacter spp. This technique confirmed the presence of several 2,5-diketopiperazines in AZ78 cell-free extracts and provided the first evidence of the production of the cyclic depsipeptide WAP-8294A2 in a member of L. capsici species. Moreover, UHPLC-HRMS/MS confirmed the presence of dihydromaltophilin/Heat Stable Antifungal Factor (HSAF) in AZ78 cell-free extracts. Due to the production of HSAF by AZ78, cell-free supernatants were effective in controlling Plasmopara viticola on grapevine leaf disks after exposure to high temperatures. Overall, our work determined the main secondary metabolites involved in the biocontrol activity of AZ78 against plant pathogenic oomycetes and Gram-positive bacteria. These results might be useful for the future development of this bacterial strain as the active ingredient of a microbial biopesticide that might contribute to a reduction in the chemical input in agriculture. Full article
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Article
Determination of Antimicrobial Resistance Patterns in Salmonella from Commercial Poultry as Influenced by Microbiological Culture and Antimicrobial Susceptibility Testing Methods
Microorganisms 2021, 9(6), 1319; https://doi.org/10.3390/microorganisms9061319 - 17 Jun 2021
Viewed by 956
Abstract
Monitoring antimicrobial resistance of foodborne pathogens in poultry is critical for food safety. We aimed to compare antimicrobial resistance phenotypes in Salmonella isolated from poultry samples as influenced by isolation and antimicrobial susceptibility testing methods. Salmonella isolates were cultured from a convenience sample [...] Read more.
Monitoring antimicrobial resistance of foodborne pathogens in poultry is critical for food safety. We aimed to compare antimicrobial resistance phenotypes in Salmonella isolated from poultry samples as influenced by isolation and antimicrobial susceptibility testing methods. Salmonella isolates were cultured from a convenience sample of commercial broiler ceca with and without selective broth enrichment, and resistance phenotypes were determined for 14 antimicrobials using the Sensititre® platform and a qualitative broth breakpoint assay. The broth breakpoint method reported higher resistance to chloramphenicol, sulfisoxazole, and the combination of trimethoprim and sulfamethoxazole, and lower resistance to streptomycin as compared to the Sensititre® assay in trial one. Selective enrichment of samples containing Salmonella in Rappaport-Vassiliadis broth reported lowered detectable resistance to amoxicillin/clavulanic acid, ampicillin, azithromycin, cefoxitin, ceftriaxone, nalidixic acid, and meropenem, and increased resistance to streptomycin and tetracycline than direct-plating samples in trial one. Using matched isolates in trial two, the Sensititre® assay reported higher resistance to chloramphenicol and gentamicin, and lower resistance to nalidixic acid as compared to the broth breakpoint method. These results suggest methodology is a critical consideration in the detection and surveillance of antimicrobial resistance phenotypes in Salmonella isolates from poultry samples and could affect the accuracy of population or industry surveillance insights and intervention strategies. Full article
(This article belongs to the Special Issue Antimicrobial Stewardship in Food-Producing Animals)
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Communication
SARS-CoV-2 Infects Hamster Testes
Microorganisms 2021, 9(6), 1318; https://doi.org/10.3390/microorganisms9061318 - 17 Jun 2021
Cited by 8 | Viewed by 7061
Abstract
The COVID-19 pandemic continues to affect millions of people worldwide. Although SARS-CoV-2 is a respiratory virus, there is growing concern that the disease could cause damage and pathology outside the lungs, including in the genital tract. Studies suggest that SARS-CoV-2 infection can damage [...] Read more.
The COVID-19 pandemic continues to affect millions of people worldwide. Although SARS-CoV-2 is a respiratory virus, there is growing concern that the disease could cause damage and pathology outside the lungs, including in the genital tract. Studies suggest that SARS-CoV-2 infection can damage the testes and reduce testosterone levels, but the underlying mechanisms are unknown and evidence of virus replication in testicular cells is lacking. We infected golden Syrian hamsters intranasally, a model for mild human COVID-19, and detected viral RNA in testes samples without histopathological changes up to one month post-infection. Using an ex vivo infection model, we detected SARS-CoV-2 replication in hamster testicular cells. Taken together, our data raise the possibility that testes damage observed in severe cases of COVID-19 could be partly explained by direct SARS-CoV-2 infection of the testicular cells. Full article
(This article belongs to the Special Issue SARS-CoV-2 Systemic Effects: New Clues)
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Article
Klebsiella pneumoniae Lipopolysaccharides Serotype O2afg Induce Poor Inflammatory Immune Responses Ex Vivo
Microorganisms 2021, 9(6), 1317; https://doi.org/10.3390/microorganisms9061317 - 17 Jun 2021
Cited by 5 | Viewed by 882
Abstract
Currently, Klebsiella pneumoniae is a pathogen of clinical relevance due to its plastic ability of acquiring resistance genes to multiple antibiotics. During K. pneumoniae infections, lipopolysaccharides (LPS) play an ambiguous role as they both activate immune responses but can also play a role [...] Read more.
Currently, Klebsiella pneumoniae is a pathogen of clinical relevance due to its plastic ability of acquiring resistance genes to multiple antibiotics. During K. pneumoniae infections, lipopolysaccharides (LPS) play an ambiguous role as they both activate immune responses but can also play a role in immune evasion. The LPS O2a and LPS O2afg serotypes are prevalent in most multidrug resistant K. pneumoniae strains. Thus, we sought to understand if those two particular LPS serotypes were involved in a mechanism of immune evasion. We have extracted LPS (serotypes O1, O2a and O2afg) from K. pneumoniae strains and, using human monocytes ex vivo, we assessed the ability of those LPS antigens to induce the production of pro-inflammatory cytokines and chemokines. We observed that, when human monocytes are incubated with LPS serotypes O1, O2a or O2afg strains, O2afg and, to a lesser extent, O2a but not O1 failed to elicit the production of pro-inflammatory cytokines and chemokines, which suggests a role in immune evasion. Our preliminary data also shows that nuclear translocation of NF-κB, a process which regulates an immune response against infections, occurs in monocytes incubated with LPS O1 and, to a smaller extent, with LPS O2a, but not with the LPS serotype O2afg. Our results indicate that multidrug resistant K. pneumoniae expressing LPS O2afg serotypes avoid an initial inflammatory immune response and, consequently, are able to systematically spread inside the host unharmed, which results in the several pathologies associated with this bacterium. Full article
(This article belongs to the Section Medical Microbiology)
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Article
In Vitro Selection of Probiotics, Prebiotics, and Antioxidants to Develop an Innovative Synbiotic (NatuREN G) and Testing Its Effect in Reducing Uremic Toxins in Fecal Batches from CKD Patients
Microorganisms 2021, 9(6), 1316; https://doi.org/10.3390/microorganisms9061316 - 17 Jun 2021
Cited by 2 | Viewed by 1158
Abstract
We aimed to develop an innovative synbiotic formulation for use in reducing dysbiosis, uremic toxins (e.g., p-cresol and indoxyl sulfate), and, consequently, the pathognomonic features of patients with chronic kidney disease (CKD). Twenty-five probiotic strains, belonging to lactobacilli and Bifidobacterium, were [...] Read more.
We aimed to develop an innovative synbiotic formulation for use in reducing dysbiosis, uremic toxins (e.g., p-cresol and indoxyl sulfate), and, consequently, the pathognomonic features of patients with chronic kidney disease (CKD). Twenty-five probiotic strains, belonging to lactobacilli and Bifidobacterium, were tested for their ability to grow in co-culture with different vegetable (pomegranate, tomato, and grapes) sources of antioxidants and prebiotics (inulin, fructo-oligosaccharides, and β-glucans). Probiotics were selected based on the acidification rates and viable cell counts. Inulin and fructo-oligosaccharides reported the best prebiotic activity, while a pomegranate seed extract was initially chosen as antioxidant source. The investigation was also conducted in fecal batches from healthy and CKD subjects, on which metabolomic analyses (profiling volatile organic compounds and total free amino acids) were conducted. Two out of twenty-five probiotics were finally selected. After the stability tests, the selective innovative synbiotic formulation (named NatuREN G) comprised Bifidobacterium animalis BLC1, Lacticaseibacillus casei LC4P1, fructo-oligosaccharides, inulin, quercetin, resveratrol, and proanthocyanidins. Finally, NatuREN G was evaluated on fecal batches collected from CKD in which modified the viable cell densities of some cultivable bacterial patterns, increased the concentration of acetic acid and decane, while reduced the concentration of nonanoic acid, dimethyl trisulfide, and indoxyl sulfate. Full article
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Brief Report
Coordinate Induction of Humoral and Spike Specific T-Cell Response in a Cohort of Italian Health Care Workers Receiving BNT162b2 mRNA Vaccine
Microorganisms 2021, 9(6), 1315; https://doi.org/10.3390/microorganisms9061315 - 16 Jun 2021
Cited by 24 | Viewed by 1500
Abstract
Vaccination is the main public health measure to reduce SARS-CoV-2 transmission and hospitalization, and a massive worldwide scientific effort resulted in the rapid development of effective vaccines. This work aimed to define the dynamics of humoral and cell-mediated immune response in a cohort [...] Read more.
Vaccination is the main public health measure to reduce SARS-CoV-2 transmission and hospitalization, and a massive worldwide scientific effort resulted in the rapid development of effective vaccines. This work aimed to define the dynamics of humoral and cell-mediated immune response in a cohort of health care workers (HCWs) who received a two-dose BNT162b2-mRNA vaccination. The serological response was evaluated by quantifying the anti-RBD and neutralizing antibodies. The cell-mediated response was performed by a whole blood test quantifying Th1 cytokines (IFN-γ, TNF-α, IL-2), produced in response to spike peptides. The BNT162b2-mRNA vaccine induced both humoral and cell-mediated immune responses against spike peptides in virtually all HCWs without previous SARS-CoV-2 infection, with a moderate inverse relation with age in the anti-RBD response. Spike-specific T cells produced several Th1 cytokines (IFN-γ, TNF-α, and IL-2), which correlated with the specific-serological response. Overall, our study describes the ability of the BNT162b2 mRNA vaccine to elicit a coordinated neutralizing humoral and spike-specific T cell response in HCWs. Assessing the dynamics of these parameters by an easy immune monitoring protocol can allow for the evaluation of the persistence of the vaccine response in order to define the optimal vaccination strategy. Full article
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