Editor's Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to authors, or important in this field. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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Article
Isolation of Lactococcus lactis from Whole Crop Rice and Determining Its Probiotic and Antimicrobial Properties towards Gastrointestinal Associated Bacteria
Microorganisms 2021, 9(12), 2513; https://doi.org/10.3390/microorganisms9122513 - 03 Dec 2021
Abstract
Antimicrobial resistance is an emerging condition that increases the risk of spreading and prolonging infectious diseases globally. Therefore, a new alternative strategy for antibiotics is required urgently to control pathogens spreading. Probiotics are considered as an alternative for antibiotics that inhibit pathogens. In [...] Read more.
Antimicrobial resistance is an emerging condition that increases the risk of spreading and prolonging infectious diseases globally. Therefore, a new alternative strategy for antibiotics is required urgently to control pathogens spreading. Probiotics are considered as an alternative for antibiotics that inhibit pathogens. In the present study, potent lactic acid bacteria (LAB) were isolated and screened for their probiotic characteristics and antagonistic activity against intestinal pathogens by agar well diffusion, Time and Dose-dependent killing assay, minimum inhibitor, and minimum bactericidal concentration (MIC/MBC), and co-culture methods. The Lactococcus lactis RWP-3 and RWP-7 fermented the different carbohydrate substrates and produced different extracellular enzymes. Both isolates showed significant tolerant capability in the gastric, duodenal, and intestinal juices. In addition, RWP-3 and RWP-7 had hydrophobicity and aggregation properties in a time-dependent manner. Furthermore, the cell-free secondary metabolites (CFS) of RWP-3 and RWP-7 showed strong antibacterial activity against Escherichia coli,Staphylococcus aureus, Pseudomonas aeruginosa and Enterococcus faecalis. A co-culture study revealed that the RWP-3 and RWP-7 strongly compete with pathogen growths. RWP-3 and RWP-7 showed strong antagonistic activities against tested pathogens with significant probiotic characteristics, suggesting that these strains obtained could be used as an alternative strategy for the antibiotic to control infectious pathogens. Full article
(This article belongs to the Special Issue Antimicrobial Impact of Probiotic Bacteria)
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Article
Characterization of the Biosynthetic Gene Cluster of Enterocin F4-9, a Glycosylated Bacteriocin
Microorganisms 2021, 9(11), 2276; https://doi.org/10.3390/microorganisms9112276 - 01 Nov 2021
Cited by 1
Abstract
Enterocin F4-9 belongs to the glycocin family having post-translational modifications by two molecules of N-acetylglucosamine β-O-linked to Ser37 and Thr46. In this study, the biosynthetic gene cluster of enterocin F4-9 was cloned and expressed in Enterococcus faecalis JH2-2. Production of [...] Read more.
Enterocin F4-9 belongs to the glycocin family having post-translational modifications by two molecules of N-acetylglucosamine β-O-linked to Ser37 and Thr46. In this study, the biosynthetic gene cluster of enterocin F4-9 was cloned and expressed in Enterococcus faecalis JH2-2. Production of glycocin by the JH2-2 expression strain was confirmed by expression of the five genes. The molecular weight was greater than glycocin secreted by the wild strain, E. faecalis F4-9, because eight amino acids from the N-terminal leader sequence remained attached. This N-terminal extension was eliminated after treatment with the culture supernatant of strain F4-9, implying an extracellular protease from E. faecalis F4-9 cleaves the N-terminal sequence. Thus, leader sequences cleavage requires two steps: the first via the EnfT protease domain and the second via extracellular proteases. Interestingly, the long peptide, with N-terminal extension, demonstrated advanced antimicrobial activity against Gram-positive and Gram-negative bacteria. Furthermore, enfC was responsible for glycosylation, a necessary step prior to secretion and cleavage of the leader peptide. In addition, enfI was found to grant self-immunity to producer cells against enterocin F4-9. This report demonstrates specifications of the minimal gene set responsible for production of enterocin F4-9, as well as a new biosynthetic mechanism of glycocins. Full article
(This article belongs to the Special Issue Genus Enterococcus and Bacteriocins)
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Article
Family SES Is Associated with the Gut Microbiome in Infants and Children
Microorganisms 2021, 9(8), 1608; https://doi.org/10.3390/microorganisms9081608 - 28 Jul 2021
Cited by 4
Abstract
Background: While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic [...] Read more.
Background: While early life exposures such as mode of birth, breastfeeding, and antibiotic use are established regulators of microbiome composition in early childhood, recent research suggests that the social environment may also exert influence. Two recent studies in adults demonstrated associations between socioeconomic factors and microbiome composition. This study expands on this prior work by examining the association between family socioeconomic status (SES) and host genetics with microbiome composition in infants and children. Methods: Family SES was used to predict a latent variable representing six genera abundances generated from whole-genome shotgun sequencing. A polygenic score derived from a microbiome genome-wide association study was included to control for potential genetic associations. Associations between family SES and microbiome diversity were assessed. Results: Anaerostipes, Bacteroides, Eubacterium, Faecalibacterium, and Lachnospiraceae spp. significantly loaded onto a latent factor, which was significantly predicted by SES (p < 0.05) but not the polygenic score (p > 0.05). Our results indicate that SES did not predict alpha diversity but did predict beta diversity (p < 0.001). Conclusions: Our results demonstrate that modifiable environmental factors influence gut microbiome composition at an early age. These results are important as our understanding of gut microbiome influences on health continue to expand. Full article
(This article belongs to the Section Gut Microbiota)
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Article
Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
Microorganisms 2021, 9(7), 1495; https://doi.org/10.3390/microorganisms9071495 - 13 Jul 2021
Cited by 5
Abstract
Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2 [...] Read more.
Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little is known about the impacts of these H2O2 treatments on other members of the microbial community. In this study, we investigated changes in microbial community composition during two lake treatments with low H2O2 concentrations (target: 2.5 mg L−1) and in two series of controlled lake incubations. The results show that the H2O2 treatments effectively suppressed the dominant cyanobacteria Aphanizomenon klebahnii, Dolichospermum sp. and, to a lesser extent, Planktothrix agardhii. Microbial community analysis revealed that several Proteobacteria (e.g., Alteromonadales, Pseudomonadales, Rhodobacterales) profited from the treatments, whereas some bacterial taxa declined (e.g., Verrucomicrobia). In particular, the taxa known to be resistant to oxidative stress (e.g., Rheinheimera) strongly increased in relative abundance during the first 24 h after H2O2 addition, but subsequently declined again. Alpha and beta diversity showed a temporary decline but recovered within a few days, demonstrating resilience of the microbial community. The predicted functionality of the microbial community revealed a temporary increase of anti-ROS defenses and glycoside hydrolases but otherwise remained stable throughout the treatments. We conclude that the use of low concentrations of H2O2 to suppress cyanobacterial blooms provides a short-term pulse disturbance but is not detrimental to lake microbial communities and their ecosystem functioning. Full article
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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
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
Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America
Microorganisms 2021, 9(5), 1060; https://doi.org/10.3390/microorganisms9051060 - 14 May 2021
Cited by 13
Abstract
Kombucha fermentation is initiated by transferring a solid-phase cellulosic pellicle into sweetened tea and allowing the microbes that it contains to initiate the fermentation. This pellicle, commonly referred to as a symbiotic culture of bacteria and yeast (SCOBY), floats to the surface of [...] Read more.
Kombucha fermentation is initiated by transferring a solid-phase cellulosic pellicle into sweetened tea and allowing the microbes that it contains to initiate the fermentation. This pellicle, commonly referred to as a symbiotic culture of bacteria and yeast (SCOBY), floats to the surface of the fermenting tea and represents an interphase environment, where embedded microbes gain access to oxygen as well as nutrients in the tea. To date, various yeast and bacteria have been reported to exist within the SCOBY, with little consensus as to which species are essential and which are incidental to Kombucha production. In this study, we used high-throughput sequencing approaches to evaluate spatial homogeneity within a single commercial SCOBY and taxonomic diversity across a large number (n = 103) of SCOBY used by Kombucha brewers, predominantly in North America. Our results show that the most prevalent and abundant SCOBY taxa were the yeast genus Brettanomyces and the bacterial genus Komagataeibacter, through careful sampling of upper and lower SCOBY layers. This sampling procedure is critical to avoid over-representation of lactic acid bacteria. K-means clustering was used on metabarcoding data of all 103 SCOBY, delineating four SCOBY archetypes based upon differences in their microbial community structures. Fungal genera Zygosaccharomyces, Lachancea and Starmerella were identified as the major compensatory taxa for SCOBY with lower relative abundance of Brettanomyces. Interestingly, while Lactobacillacae was the major compensatory taxa where Komagataeibacter abundance was lower, phylogenic heat-tree analysis infers a possible antagonistic relationship between Starmerella and the acetic acid bacterium. Our results provide the basis for further investigation of how SCOBY archetype affects Kombucha fermentation, and fundamental studies of microbial community assembly in an interphase environment. Full article
(This article belongs to the Special Issue Food Microbial Diversity)
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Article
Mind the Gap: New Full-Length Sequences of Blastocystis Subtypes Generated via Oxford Nanopore Minion Sequencing Allow for Comparisons between Full-Length and Partial Sequences of the Small Subunit of the Ribosomal RNA Gene
Microorganisms 2021, 9(5), 997; https://doi.org/10.3390/microorganisms9050997 - 05 May 2021
Cited by 24
Abstract
Blastocystis is a common food- and water-borne intestinal protist parasite of humans and many other animals. Blastocystis comprises multiple subtypes (STs) based on variability within the small subunit ribosomal (SSU rRNA) RNA gene. Though full-length reference sequences of the SSU rRNA gene [...] Read more.
Blastocystis is a common food- and water-borne intestinal protist parasite of humans and many other animals. Blastocystis comprises multiple subtypes (STs) based on variability within the small subunit ribosomal (SSU rRNA) RNA gene. Though full-length reference sequences of the SSU rRNA gene are a current requirement to name a novel Blastocystis subtype, full-length reference sequences are not currently available for all subtypes. In the present study, Oxford Nanopore MinION long-read sequencing was employed to generate full-length SSU rRNA sequences for seven new Blastocystis subtypes for which no full-length references currently exist: ST21, ST23, ST24, ST25, ST26, ST27, and ST28. Phylogenetic analyses and pairwise distance matrixes were used to compare full-length and partial sequences of the two regions that are most commonly used for subtyping. Analyses included Blastocystis nucleotide sequences obtained in this study (ST21 and ST23–ST28) and existing subtypes for which full-length reference sequences were available (ST1–ST17 and ST29). The relationships and sequence variance between new and existing subtypes observed in analyses of different portions of the SSU rRNA gene are discussed. The full-length SSU rRNA reference sequences generated in this study provide essential new data to study and understand the relationships between the genetic complexity of Blastocystis and its host specificity, pathogenicity, and epidemiology. Full article
(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)
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Article
Multi Locus Sequence Typing and spa Typing of Staphylococcus aureus Isolated from the Milk of Cows with Subclinical Mastitis in Croatia
Microorganisms 2021, 9(4), 725; https://doi.org/10.3390/microorganisms9040725 - 31 Mar 2021
Cited by 15
Abstract
Background: The bacterial species S. aureus is the most common causative agent of mastitis in cows in most countries with a dairy industry. The prevalence of infection caused by S. aureus ranges from 2% to more than 50%, and it causes 10–12% of [...] Read more.
Background: The bacterial species S. aureus is the most common causative agent of mastitis in cows in most countries with a dairy industry. The prevalence of infection caused by S. aureus ranges from 2% to more than 50%, and it causes 10–12% of all cases of clinical mastitis. Aim: The objective was to analyze 237 strains of S. aureus isolated from the milk of cows with subclinical mastitis regarding the spa, mecA, mecC and pvl genes and to perform spa and multi-locus sequence typing (MLST). Methods: Sequencing amplified gene sequences was conducted at Macrogen Europe. Ridom StaphType and BioNumerics software was used to analyze obtained sequences of spa and seven housekeeping genes. Results: The spa fragment was present in 204 (86.1%) of strains, while mecA and mecC gene were detected in 10 strains, and the pvl gene was not detected. Spa typing successfully analyzed 153 tested isolates (64.3%), confirming 53 spa types, four of which were new types. The most frequent spa type was t2678 (14%). MLST typed 198 (83.5%) tested strains and defined 32 different allele profiles, of which three were new. The most frequent allele profile was ST133 (20.7%). Six groups (G) and 15 singletons were defined. Conclusion: Taking the number of confirmed spa types and sequence types (STs) into account, it can be concluded that the strains of S. aureus isolated from the milk of cows with subclinical mastitis form a heterogenous group. To check the possible zoonotic potential of isolates it would be necessary to test the persons and other livestock on the farms. Full article
(This article belongs to the Section Food Microbiology)
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Article
Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli
Microorganisms 2021, 9(3), 598; https://doi.org/10.3390/microorganisms9030598 - 14 Mar 2021
Cited by 13
Abstract
Antimicrobial resistance (AMR) is a major threat to public health worldwide. Currently, AMR typing changes from phenotypic testing to whole-genome sequence (WGS)-based detection of resistance determinants for a better understanding of the isolate diversity and elements involved in gene transmission (e.g., plasmids, bacteriophages, [...] Read more.
Antimicrobial resistance (AMR) is a major threat to public health worldwide. Currently, AMR typing changes from phenotypic testing to whole-genome sequence (WGS)-based detection of resistance determinants for a better understanding of the isolate diversity and elements involved in gene transmission (e.g., plasmids, bacteriophages, transposons). However, the use of WGS data in monitoring purposes requires suitable techniques, standardized parameters and approved guidelines for reliable AMR gene detection and prediction of their association with mobile genetic elements (plasmids). In this study, different sequencing and assembly strategies were tested for their suitability in AMR monitoring in Escherichia coli in the routines of the German National Reference Laboratory for Antimicrobial Resistances. To assess the outcomes of the different approaches, results from in silico predictions were compared with conventional phenotypic- and genotypic-typing data. With the focus on (fluoro)quinolone-resistant E.coli, five qnrS-positive isolates with multiple extrachromosomal elements were subjected to WGS with NextSeq (Illumina), PacBio (Pacific BioSciences) and ONT (Oxford Nanopore) for in depth characterization of the qnrS1-carrying plasmids. Raw reads from short- and long-read sequencing were assembled individually by Unicycler or Flye or a combination of both (hybrid assembly). The generated contigs were subjected to bioinformatics analysis. Based on the generated data, assembly of long-read sequences are error prone and can yield in a loss of small plasmid genomes. In contrast, short-read sequencing was shown to be insufficient for the prediction of a linkage of AMR genes (e.g., qnrS1) to specific plasmid sequences. Furthermore, short-read sequencing failed to detect certain duplications and was unsuitable for genome finishing. Overall, the hybrid assembly led to the most comprehensive typing results, especially in predicting associations of AMR genes and mobile genetic elements. Thus, the use of different sequencing technologies and hybrid assemblies currently represents the best approach for reliable AMR typing and risk assessment. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Molecular Tracing of Foodborne Pathogens)
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Article
The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors
Microorganisms 2021, 9(2), 458; https://doi.org/10.3390/microorganisms9020458 - 23 Feb 2021
Cited by 7
Abstract
The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) [...] Read more.
The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO2 is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO2, and the circumstance that the core’s main products are far more reduced than CO2 indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H2, inorganic carbon, and NH3 in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. Such conditions are very similar to those found in serpentinizing hydrothermal systems. Full article
(This article belongs to the Special Issue Microbial One-Carbon Metabolism of Natural and Engineered Systems)
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Article
Hypo- and Hyper-Virulent Listeria monocytogenes Clones Persisting in Two Different Food Processing Plants of Central Italy
Microorganisms 2021, 9(2), 376; https://doi.org/10.3390/microorganisms9020376 - 13 Feb 2021
Cited by 11
Abstract
A total of 66 Listeria monocytogenes (Lm) isolated from 2013 to 2018 in a small-scale meat processing plant and a dairy facility of Central Italy were studied. Whole Genome Sequencing and bioinformatics analysis were used to assess the genetic relationships between [...] Read more.
A total of 66 Listeria monocytogenes (Lm) isolated from 2013 to 2018 in a small-scale meat processing plant and a dairy facility of Central Italy were studied. Whole Genome Sequencing and bioinformatics analysis were used to assess the genetic relationships between the strains and investigate persistence and virulence abilities. The biofilm forming-ability was assessed in vitro. Cluster analysis grouped the Lm from the meat plant into three main clusters: two of them, both belonging to CC9, persisted for years in the plant and one (CC121) was isolated in the last year of sampling. In the dairy facility, all the strains grouped in a CC2 four-year persistent cluster. All the studied strains carried multidrug efflux-pumps genetic determinants (sugE, mdrl, lde, norM, mepA). CC121 also harbored the Tn6188 specific for tolerance to Benzalkonium Chloride. Only CC9 and CC121 carried a Stress Survival Islet and presented high-level cadmium resistance genes (cadA1C1) carried by different plasmids. They showed a greater biofilm production when compared with CC2. All the CC2 carried a full-length inlA while CC9 and CC121 presented a Premature Stop Codon mutation correlated with less virulence. The hypo-virulent clones CC9 and CC121 appeared the most adapted to food-processing environments; however, even the hyper-virulent clone CC2 warningly persisted for a long time. The identification of the main mechanisms promoting Lm persistence in a specific food processing plant is important to provide recommendations to Food Business Operators (FBOs) in order to remove or reduce resident Lm. Full article
(This article belongs to the Special Issue An Update on Listeria monocytogenes)
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Article
Performance of a Four-Antigen Staphylococcus aureus Vaccine in Preclinical Models of Invasive S. aureus Disease
Microorganisms 2021, 9(1), 177; https://doi.org/10.3390/microorganisms9010177 - 15 Jan 2021
Cited by 10
Abstract
A Staphylococcus aureus four-antigen vaccine (SA4Ag) was designed for the prevention of invasive disease in surgical patients. The vaccine is composed of capsular polysaccharide type 5 and type 8 CRM197 conjugates, a clumping factor A mutant (Y338A-ClfA) and manganese transporter subunit C [...] Read more.
A Staphylococcus aureus four-antigen vaccine (SA4Ag) was designed for the prevention of invasive disease in surgical patients. The vaccine is composed of capsular polysaccharide type 5 and type 8 CRM197 conjugates, a clumping factor A mutant (Y338A-ClfA) and manganese transporter subunit C (MntC). S. aureus pathogenicity is characterized by an ability to rapidly adapt to the host environment during infection, which can progress from a local infection to sepsis and invasion of distant organs. To test the protective capacity of the SA4Ag vaccine against progressive disease stages of an invasive S. aureus infection, a deep tissue infection mouse model, a bacteremia mouse model, a pyelonephritis model, and a rat model of infectious endocarditis were utilized. SA4Ag vaccination significantly reduced the bacterial burden in deep tissue infection, in bacteremia, and in the pyelonephritis model. Complete prevention of infection was demonstrated in a clinically relevant endocarditis model. Unfortunately, these positive preclinical findings with SA4Ag did not prove the clinical utility of SA4Ag in the prevention of surgery-associated invasive S. aureus infection. Full article
(This article belongs to the Special Issue Staphylococcal Infections (Host and Pathogenic Factors))
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Communication
Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics
Microorganisms 2021, 9(1), 76; https://doi.org/10.3390/microorganisms9010076 - 30 Dec 2020
Cited by 12
Abstract
Microplastics are ubiquitous in aquatic ecosystems and provide a habitat for biofilm-forming bacteria. The genus Vibrio, which includes potential pathogens, was detected irregularly on microplastics. Since then, the potential of microplastics to enrich (and serve as a vector for) Vibrio has been [...] Read more.
Microplastics are ubiquitous in aquatic ecosystems and provide a habitat for biofilm-forming bacteria. The genus Vibrio, which includes potential pathogens, was detected irregularly on microplastics. Since then, the potential of microplastics to enrich (and serve as a vector for) Vibrio has been widely discussed. We investigated Vibrio abundance and operational taxonomic unit (OTU) composition on polyethylene and polystyrene within the first 10 h of colonization during an in situ incubation experiment, along with those found on particles collected from the Baltic Sea. We used 16S rRNA gene amplicon sequencing and co-occurrence networks to elaborate the role of Vibrio within biofilms. Colonization of plastics with Vibrio was detectable after one hour of incubation; however, Vibrio numbers and composition were very dynamic, with a more stable population at the site with highest nutrients and lowest salinity. Likewise, Vibrio abundances on field-collected particles were variable but correlated with proximity to major cities. Vibrio was poorly connected within biofilm networks. Taken together, this indicates that Vibrio is an early colonizer of plastics, but that the process is undirected and independent of the specific surface. Still, higher nutrients could enhance a faster establishment of Vibrio populations. These parameters should be considered when planning studies investigating Vibrio on microplastics. Full article
(This article belongs to the Special Issue Microbes on Plastics, Close Encounters of the Fourth Kind)
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Article
Probiotic Alternative to Chlorhexidine in Periodontal Therapy: Evaluation of Clinical and Microbiological Parameters
Microorganisms 2021, 9(1), 69; https://doi.org/10.3390/microorganisms9010069 - 29 Dec 2020
Cited by 53
Abstract
Periodontitis consists of a progressive destruction of tooth-supporting tissues. Considering that probiotics are being proposed as a support to the gold standard treatment Scaling-and-Root-Planing (SRP), this study aims to assess two new formulations (toothpaste and chewing-gum). 60 patients were randomly assigned to three [...] Read more.
Periodontitis consists of a progressive destruction of tooth-supporting tissues. Considering that probiotics are being proposed as a support to the gold standard treatment Scaling-and-Root-Planing (SRP), this study aims to assess two new formulations (toothpaste and chewing-gum). 60 patients were randomly assigned to three domiciliary hygiene treatments: Group 1 (SRP + chlorhexidine-based toothpaste) (control), Group 2 (SRP + probiotics-based toothpaste) and Group 3 (SRP + probiotics-based toothpaste + probiotics-based chewing-gum). At baseline (T0) and after 3 and 6 months (T1–T2), periodontal clinical parameters were recorded, along with microbiological ones by means of a commercial kit. As to the former, no significant differences were shown at T1 or T2, neither in controls for any index, nor in the experimental groups for adherent gingiva and gingival recession. Conversely, some significant differences were found in Group 2 and 3 for the other clinical indexes tested. Considering microbiological parameters, no significant differences were detected compared to baseline values for any group, except in Group 2 and 3 at T2 only for the percentage of the orange complex pathogens and for the copies/microliter of Prevotella intermedia and Fusobacterium nucleatum. Accordingly, although colonization of probiotic bacteria has not been assessed in this study, the probiotics tested represent a valid support to SRP with a benefit on several clinical indexes and on specific periodontopathogens. Despite this promising action, the relationship between the use of probiotics and improvement in clinical parameters is still unclear and deserves to be further explored. Full article
(This article belongs to the Special Issue Oral Biofilms)
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Article
Anti–SARS-CoV-2 Antibody Responses in Convalescent Plasma Donors Are Increased in Hospitalized Patients; Subanalyses of a Phase 2 Clinical Study
Microorganisms 2020, 8(12), 1885; https://doi.org/10.3390/microorganisms8121885 - 28 Nov 2020
Cited by 30
Abstract
We evaluated the antibody responses in 259 potential convalescent plasma donors for Covid-19 patients. Different assays were used: a commercial ELISA detecting antibodies against the recombinant spike protein (S1); a multiplex assay detecting total and specific antibody isotypes against three SARS-CoV-2 antigens (S1, [...] Read more.
We evaluated the antibody responses in 259 potential convalescent plasma donors for Covid-19 patients. Different assays were used: a commercial ELISA detecting antibodies against the recombinant spike protein (S1); a multiplex assay detecting total and specific antibody isotypes against three SARS-CoV-2 antigens (S1, basic nucleocapsid (N) protein and receptor-binding domain (RBD)); and an in-house ELISA detecting antibodies to complete spike, RBD and N in 60 of these donors. Neutralizing antibodies (NAb) were also evaluated in these 60 donors. Analyzed samples were collected at a median time of 62 (14–104) days from the day of first symptoms or positive PCR (for asymptomatic patients). Anti-SARS-CoV-2 antibodies were detected in 88% and 87.8% of donors using the ELISA and the multiplex assay, respectively. The multivariate analysis showed that age ≥50 years (p < 0.001) and need for hospitalization (p < 0.001) correlated with higher antibody titers, while asymptomatic status (p < 0.001) and testing >60 days after symptom onset (p = 0.001) correlated with lower titers. Interestingly, pseudotype virus-neutralizing antibodies (PsNAbs) significantly correlated with spike and with RBD antibodies by ELISA. Sera with high PsNAb also showed a strong ability to neutralize active SARS-CoV-2 virus, with hospitalized patients showing higher titers. Therefore, convalescent plasma donors can be selected based on the presence of high RBD antibody titers. Full article
(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)
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Communication
Spill-Over from Public Health? First Detection of an OXA-48-Producing Escherichia coli in a German Pig Farm
Microorganisms 2020, 8(6), 855; https://doi.org/10.3390/microorganisms8060855 - 05 Jun 2020
Cited by 12
Abstract
Resistance to carbapenems is a severe threat to human health. These last resort antimicrobials are indispensable for the treatment of severe human infections with multidrug-resistant Gram-negative bacteria. In accordance with their increasing medical impact, carbapenemase-producing Enterobacteriaceae (CPE) might be disseminated from colonized humans [...] Read more.
Resistance to carbapenems is a severe threat to human health. These last resort antimicrobials are indispensable for the treatment of severe human infections with multidrug-resistant Gram-negative bacteria. In accordance with their increasing medical impact, carbapenemase-producing Enterobacteriaceae (CPE) might be disseminated from colonized humans to non-human reservoirs (i.e., environment, animals, food). In Germany, the occurrence of CPE in livestock and food has been systematically monitored since 2016. In the 2019 monitoring, an OXA-48-producing E. coli (19-AB01443) was recovered from a fecal sample of a fattening pig. Phenotypic resistance was confirmed by broth microdilution and further characterized by PFGE, conjugation, and combined short-/long-read whole genome sequencing. This is the first detection of this resistance determinant in samples from German meat production. Molecular characterization and whole-genome sequencing revealed that the blaOXA-48 gene was located on a common pOXA-48 plasmid-prototype. This plasmid-type seems to be globally distributed among various bacterial species, but it was frequently associated with clinical Klebsiella spp. isolates. Currently, the route of introduction of this plasmid/isolate combination into the German pig production is unknown. We speculate that due to its strong correlation with human isolates a transmission from humans to livestock has occurred. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in the Food Production Chain )
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Article
Effect of Co-Inoculation of Candida zemplinina, Saccharomyces cerevisiae and Lactobacillus plantarum for the Industrial Production of Negroamaro Wine in Apulia (Southern Italy)
Microorganisms 2020, 8(5), 726; https://doi.org/10.3390/microorganisms8050726 - 13 May 2020
Cited by 13
Abstract
The employment of multi-species starter cultures has growing importance in modern winemaking for improving the complexity and wine attributes. The assessment of compatibility for selected species/strains at the industrial-scale is crucial to assure the quality and the safety associated with fermentations. An aspect [...] Read more.
The employment of multi-species starter cultures has growing importance in modern winemaking for improving the complexity and wine attributes. The assessment of compatibility for selected species/strains at the industrial-scale is crucial to assure the quality and the safety associated with fermentations. An aspect particularly relevant when the species belong to non-Saccharomyces, Saccharomyces spp. and malolactic bacteria, three categories with different biological characteristics and oenological significance. To the best of our knowledge, the present report is the first study regarding the utilization of a combined starter culture composed of three strains of non-Saccharomyces, Saccharomyces cerevisiae and Lactobacillus plantarum for production of wine at the industrial scale. More in-depth, this work investigated the oenological potential of the autochthonous characterized strains from the Apulian region (Southern Italy), Candida zemplinina (syn. Starmerella bacillaris) 35NC1, S. cerevisiae (NP103), and L. plantarum (LP44), in co-inoculation following a complete scale-up scheme. Microbial dynamics, fermentative profiles and production of volatile secondary compounds were assessed in lab-scale micro-vinification tests and then the performances of the mixed starter formulation were further evaluated by pilot-scale wine production. The above results were finally validated by performing an industrial-scale vinification on 100HL of Negroamaro cultivar grape must. The multi-starter formulation was able to rule the different stages of the fermentation processes effectively, and the different microbial combinations enhanced the organoleptic wine features to different extents. The findings indicated that the simultaneous inoculation of the three species affect the quality and quantity of several volatile compounds, confirming that the complexity of the wine can reflect the complexity of the starter cultures. Moreover, the results underlined that the same mixed culture could differently influence wine quality when tested at the lab-, pilot- and industrial-scale. Finally, we highlighted the significance of employment non-Saccharomyces and L. plantarum, together with S. cerevisiae, autochthonous strains in the design of custom-made starter culture formulation for typical regional wine production with pronounced unique quality. Full article
(This article belongs to the Special Issue Microbial Dynamics in Wine Production)
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Article
Microbial Community and Fermentation Dynamics of Corn Silage Prepared with Heat-Resistant Lactic Acid Bacteria in a Hot Environment
Microorganisms 2020, 8(5), 719; https://doi.org/10.3390/microorganisms8050719 - 12 May 2020
Cited by 25
Abstract
To develop a silage fermentation technique to adapt to global climate changes, the microbiome and fermentation dynamics of corn silage inoculated with heat-resistant lactic acid bacteria (LAB) under high-temperature conditions were studied. Corn was ensiled in laboratory silo, with and without two selected [...] Read more.
To develop a silage fermentation technique to adapt to global climate changes, the microbiome and fermentation dynamics of corn silage inoculated with heat-resistant lactic acid bacteria (LAB) under high-temperature conditions were studied. Corn was ensiled in laboratory silo, with and without two selected strains, Lactobacillus salivarius LS358 and L. rhamnosus LR753, two type strains L. salivarius ATCC 11741T and L. rhamnosus ATCC 7469T. The ensiling temperatures were designed at 30 °C and 45 °C, and the sampling took place after 0, 3, 7, 14, and 60 days of fermentation. The higher pH and dry matter losses were observed in the silages stored at 45 °C compared to those stored at 30 °C. Silages inoculated with strains LS358 and LR753 at 30 °C had a lower ratio of lactic acid/acetic acid. The dominant bacterial genera gradually changed from Pediococcus and Lactobacillus to Lactobacillus in silages during ensiling at 30 °C, while the bacterial community became more complex and fragmented after 7 d of ensiling at 45 °C. The high temperatures significantly led to a transformation of the LAB population from homo-fermentation to hetero-fermentation. This study is the first to describe microbial population dynamics response to high temperature during corn ensiling, and the results indicate that L. rhamnosus 753 shows potential ability to improve silage fermentation in tropics and subtropics. Full article
(This article belongs to the Special Issue Lactic Acid Bacteria and Bifidobacteria and Their Application)
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Article
Tocilizumab for Treatment of Severe COVID-19 Patients: Preliminary Results from SMAtteo COvid19 REgistry (SMACORE)
Microorganisms 2020, 8(5), 695; https://doi.org/10.3390/microorganisms8050695 - 09 May 2020
Cited by 147
Abstract
Objective: This study aimed to assess the role of Tocilizumab therapy (TCZ) in terms of ICU admission and mortality rate of critically ill patients with severe COVID-19 pneumonia. Design: Patients with COVID-19 pneumonia were prospectively enrolled in SMAtteo COvid19 REgistry (SMACORE). A retrospective [...] Read more.
Objective: This study aimed to assess the role of Tocilizumab therapy (TCZ) in terms of ICU admission and mortality rate of critically ill patients with severe COVID-19 pneumonia. Design: Patients with COVID-19 pneumonia were prospectively enrolled in SMAtteo COvid19 REgistry (SMACORE). A retrospective analysis of patients treated with TCZ matched using propensity score to patients treated with Standard Of Care (SOC) was conducted. Setting: The study was conducted at IRCCS Policlinico San Matteo Hospital, Pavia, Italy, from March 14, 2020 to March 27, 2020. Participants: Patients with a confirmed diagnosis of COVID-19 hospitalized in our institution at the time of TCZ availability. Interventions: TCZ was administered to 21 patients. The first administration was 8 mg/kg (up to a maximum 800 mg per dose) of Tocilizumab intravenously, repeated after 12 h if no side effects were reported after the first dose. Main Outcomes and Measures: ICU admission and 7-day mortality rate. Secondary outcomes included clinical and laboratory data. Results: There were 112 patients evaluated (82 were male and 30 were female, with a median age of 63.55 years). Using propensity scores, the 21 patients who received TCZ were matched to 21 patients who received SOC (a combination of hydroxychloroquine, azithromycin and prophylactic dose of low weight heparin). No adverse event was detected following TCZ administration. This study found that treatment with TCZ did not significantly affect ICU admission (OR 0.11; 95% CI between 0.00 and 3.38; p = 0.22) or 7-day mortality rate (OR 0.78; 95% CI between 0.06 and 9.34; p = 0.84) when compared with SOC. Analysis of laboratory measures showed significant interactions between time and treatment regarding C-Reactive Protein (CRP), alanine aminotransferase (ALT), platelets and international normalized ratio (INR) levels. Variation in lymphocytes count was observed over time, irrespective of treatment. Conclusions: TCZ administration did not reduce ICU admission or mortality rate in a cohort of 21 patients. Additional data are needed to understand the effect(s) of TCZ in treating patients diagnosed with COVID-19. Full article
(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)
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Article
Microbial Resource Management for Ex Situ Biomethanation of Hydrogen at Alkaline pH
Microorganisms 2020, 8(4), 614; https://doi.org/10.3390/microorganisms8040614 - 24 Apr 2020
Cited by 21
Abstract
Biomethanation is a promising solution to convert H2 (produced from surplus electricity) and CO2 to CH4 by using hydrogenotrophic methanogens. In ex situ biomethanation with mixed cultures, homoacetogens and methanogens compete for H2/CO2. We enriched a [...] Read more.
Biomethanation is a promising solution to convert H2 (produced from surplus electricity) and CO2 to CH4 by using hydrogenotrophic methanogens. In ex situ biomethanation with mixed cultures, homoacetogens and methanogens compete for H2/CO2. We enriched a hydrogenotrophic microbiota on CO2 and H2 as sole carbon and energy sources, respectively, to investigate these competing reactions. The microbial community structure and dynamics of bacteria and methanogenic archaea were evaluated through 16S rRNA and mcrA gene amplicon sequencing, respectively. Hydrogenotrophic methanogens and homoacetogens were enriched, as acetate was concomitantly produced alongside CH4. By controlling the media composition, especially changing the reducing agent, the formation of acetate was lowered and grid quality CH4 (≥97%) was obtained. Formate was identified as an intermediate that was produced and consumed during the bioprocess. Stirring intensities ≥ 1000 rpm were detrimental, probably due to shear force stress. The predominating methanogens belonged to the genera Methanobacterium and Methanoculleus. The bacterial community was dominated by Lutispora. The methanogenic community was stable, whereas the bacterial community was more dynamic. Our results suggest that hydrogenotrophic communities can be steered towards the selective production of CH4 from H2/CO2 by adapting the media composition, the reducing agent and the stirring intensity. Full article
(This article belongs to the Special Issue Anaerobic Digestion)
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Article
Antimicrobial and Fermentation Potential of Himanthalia elongata in Food Applications
Microorganisms 2020, 8(2), 248; https://doi.org/10.3390/microorganisms8020248 - 13 Feb 2020
Cited by 13
Abstract
Himanthalia elongata is a brown oceanic seaweed rich in bioactive compounds. It could play an important role in food production because of its antimicrobial and antioxidant properties. Three strains belonging to the Lactobacillus casei group (Lactobacillus casei, Lactobacillus paracasei, and [...] Read more.
Himanthalia elongata is a brown oceanic seaweed rich in bioactive compounds. It could play an important role in food production because of its antimicrobial and antioxidant properties. Three strains belonging to the Lactobacillus casei group (Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus) and a Bacillus subtilis strain were used for the solid-state fermentation of commercial seaweeds, and bacterial growth was monitored using the plate count method. High-pressure processing (HPP) was also employed (6000 bar, 5 min, 5 °C) before extraction. The antimicrobial activity of the extracts was tested in terms of the main food pathogenic bacteria (Salmonella spp., Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, and Bacillus cereus), and the phenolic content was estimated using the Folin–Ciocalteau method. In addition, targeted UHPLC-MS2 methods were used to unravel the profile of phlorotannins. H. elongata allowed the growth of the L. casei group strains and B. subtilis, showing the fermentability of this substrate. Significant antimicrobial activity toward L. monocytogenes was observed in the extracts obtained from unfermented samples, but neither fermentation nor HPP enhanced the natural antimicrobial activity of this seaweed species. The content in the phenolic compounds decreased because of the fermentation process, and the amount of phenolics in both the unfermented and fermented H. elongata extracts was very low. Despite phlorotannins being related to the natural antimicrobial activity of this brown seaweed, these results did not support this association. Even if fermentation and HPP were not proven to be effective tools for enhancing the useful compounds of H. elongata, the seaweed was shown to be a suitable substrate for L. casei group strains as well as for B. subtilis growth, and its extracts exhibited antimicrobial activity toward foodborne pathogens. Full article
(This article belongs to the Special Issue Biocontrol of Food Borne Pathogens)
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Article
The Impact of Primer Design on Amplicon-Based Metagenomic Profiling Accuracy: Detailed Insights into Bifidobacterial Community Structure
Microorganisms 2020, 8(1), 131; https://doi.org/10.3390/microorganisms8010131 - 17 Jan 2020
Cited by 20
Abstract
Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological [...] Read more.
Next Generation Sequencing (NGS) technologies have overcome the limitations of cultivation-dependent approaches and allowed detailed study of bacterial populations that inhabit the human body. The consortium of bacteria residing in the human intestinal tract, also known as the gut microbiota, impacts several physiological processes important for preservation of the health status of the host. The most widespread microbiota profiling method is based on amplification and sequencing of a variable portion of the 16S rRNA gene as a universal taxonomic marker among members of the Bacteria domain. Despite its popularity and obvious advantages, this 16S rRNA gene-based approach comes with some important limitations. In particular, the choice of the primer pair for amplification plays a major role in defining the accuracy of the reconstructed bacterial profiles. In the current study, we performed an in silico PCR using all currently described 16S rRNA gene-targeting primer pairs (PP) in order to assess their efficiency. Our results show that V3, V4, V5, and V6 were the optimal regions on which to design 16S rRNA metagenomic primers. In detail, PP39 (Probio_Uni/Probio_Rev), PP41 (341F/534R), and PP72 (970F/1050R) were the most suitable primer pairs with an amplification efficiency of >98.5%. Furthermore, the Bifidobacterium genus was examined as a test case for accurate evaluation of intra-genus performances at subspecies level. Intriguingly, the in silico analysis revealed that primer pair PP55 (527f/1406r) was unable to amplify the targeted region of any member of this bacterial genus, while several other primer pairs seem to rather inefficiently amplify the target region of the main bifidobacterial taxa. These results highlight that selection of a 16S rRNA gene-based PP should be done with utmost care in order to avoid biases in microbiota profiling results. Full article
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