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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 readers, or important in the respective research area. 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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10 pages, 1519 KiB  
Article
Complex Trophic Interactions in an Acidophilic Microbial Community
by Guntram Weithoff and Elanor M. Bell
Microorganisms 2022, 10(7), 1340; https://doi.org/10.3390/microorganisms10071340 - 2 Jul 2022
Cited by 5 | Viewed by 2478
Abstract
Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes [...] Read more.
Extreme habitats often harbor specific communities that differ substantially from non-extreme habitats. In many cases, these communities are characterized by archaea, bacteria and protists, whereas the number of species of metazoa and higher plants is relatively low. In extremely acidic habitats, mostly prokaryotes and protists thrive, and only very few metazoa thrive, for example, rotifers. Since many studies have investigated the physiology and ecology of individual species, there is still a gap in research on direct, trophic interactions among extremophiles. To fill this gap, we experimentally studied the trophic interactions between a predatory protist (Actinophrys sol, Heliozoa) and its prey, the rotifers Elosa woralli and Cephalodella sp., the ciliate Urosomoida sp. and the mixotrophic protist Chlamydomonas acidophila (a green phytoflagellate, Chlorophyta). We found substantial predation pressure on all animal prey. High densities of Chlamydomonas acidophila reduced the predation impact on the rotifers by interfering with the feeding behaviour of A. sol. These trophic relations represent a natural case of intraguild predation, with Chlamydomonas acidophila being the common prey and the rotifers/ciliate and A. sol being the intraguild prey and predator, respectively. We further studied this intraguild predation along a resource gradient using Cephalodella sp. as the intraguild prey. The interactions among the three species led to an increase in relative rotifer abundance with increasing resource (Chlamydomonas) densities. By applying a series of laboratory experiments, we revealed the complexity of trophic interactions within a natural extremophilic community. Full article
(This article belongs to the Special Issue Extremophilic Microorganisms and Their Communities)
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15 pages, 2915 KiB  
Article
Edwardsiella ictaluri T3SS Effector EseN Modulates Expression of Host Genes Involved in the Immune Response
by Lidiya P. Dubytska, Ranjan Koirala, Azhia Sanchez and Ronald Thune
Microorganisms 2022, 10(7), 1334; https://doi.org/10.3390/microorganisms10071334 - 1 Jul 2022
Cited by 6 | Viewed by 3469
Abstract
The type III secretion system (T3SS) effector EseN is encoded on the Edwardsiella ictaluri chromosome and is homologous to a family of T3SS effector proteins with phosphothreonine lyase activity. Previously we demonstrated that E. ictaluri invasion activates extracellular signal-regulated kinases 1 and 2 [...] Read more.
The type III secretion system (T3SS) effector EseN is encoded on the Edwardsiella ictaluri chromosome and is homologous to a family of T3SS effector proteins with phosphothreonine lyase activity. Previously we demonstrated that E. ictaluri invasion activates extracellular signal-regulated kinases 1 and 2 (ERK1/2) early in the infection, which are subsequently inactivated by EseN. Comparative transcriptomic analysis showed a total of 753 significant differentially expressed genes in head-kidney-derived macrophages (HKDM) infected with an EseN mutant (∆EseN) compared to HKDM infected with wild-type (WT) strains. This data strongly indicates classical activation of macrophages (the M1 phenotype) in response to E. ictaluri infection and a significant role for EseN in the manipulation of this process. Our data also indicates that E. ictaluri EseN is involved in the modulation of pathways involved in the immune response to infection and expression of several transcription factors, including NF-κβ (c-rel and relB), creb3L4, socs6 and foxo3a. Regulation of transcription factors leads to regulation of proinflammatory interleukins (IL-8, IL-12a, IL-15, IL-6) and cyclooxygenase-2 (COX-2) expression. Inhibition of COX-2 mRNA by WT E. ictaluri leads to decreased production of prostaglandin E2 (PGE2), which is the product of COX-2 activity. Collectively, our results indicate that E. ictaluri EseN is an important player in the modulation of host immune responses to E.ictaluri infection. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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16 pages, 1249 KiB  
Article
Ingenious Action of Vibrio cholerae Neuraminidase Recruiting Additional GM1 Cholera Toxin Receptors for Primary Human Colon Epithelial Cells
by Johanna Detzner, Charlotte Püttmann, Gottfried Pohlentz and Johannes Müthing
Microorganisms 2022, 10(6), 1255; https://doi.org/10.3390/microorganisms10061255 - 20 Jun 2022
Cited by 2 | Viewed by 2706
Abstract
For five decades it has been known that the pentamer of B subunits (choleragenoid) of the cholera toxin (CT) of Vibrio cholerae binds with high preference to the ganglioside GM1 (II3Neu5Ac-Gg4Cer). However, the exact structures of CT-binding GM1 lipoforms of primary [...] Read more.
For five decades it has been known that the pentamer of B subunits (choleragenoid) of the cholera toxin (CT) of Vibrio cholerae binds with high preference to the ganglioside GM1 (II3Neu5Ac-Gg4Cer). However, the exact structures of CT-binding GM1 lipoforms of primary human colon epithelial cells (pHCoEpiCs) have not yet been described in detail. The same holds true for generating further GM1 receptor molecules from higher sialylated gangliosides with a GM1 core through the neuraminidase of V. cholerae. To avoid the artificial incorporation of exogenous gangliosides from animal serum harboring GM1 and higher sialylated ganglio-series gangliosides, pHCoEpiCs were cultured in serum-free medium. Thin-layer chromatography overlay binding assays using a choleragenoid combined with electrospray ionization mass spectrometry revealed GM1 lipoforms with sphingosine (d18:1) as the sole sphingoid base linked to C14:0, C16:0, C18:0 or C20:0 fatty acyl chains forming the ceramide (Cer) moieties of the main choleragenoid-binding GM1 species. Desialylation of GD1a (IV3Neu5Ac,II3Neu5Ac-Gg4Cer) and GT1b (IV3Neu5Ac,II3(Neu5Ac)2-Gg4Cer) of pHCoEpiCs by V. cholerae neuraminidase was observed. GD1a-derived GM1 species with stable sphingosine (d18:1) and saturated fatty acyl chains varying in chain length from C16:0 up to C22:0 could be identified, indicating the ingenious interplay between CT and the neuraminidase of V. cholerae recruiting additional GM1 receptors of pHCoEpiCs. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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10 pages, 302 KiB  
Article
Mating Interactions between Schistosoma bovis and S. mansoni and Compatibility of Their F1 Progeny with Biomphalaria glabrata and Bulinus truncatus
by Amos Mathias Onyekwere, Alejandra De Elias-Escribano, Julien Kincaid-Smith, Sarah Dametto, Jean-François Allienne, Anne Rognon, Maria Dolores Bargues and Jérôme Boissier
Microorganisms 2022, 10(6), 1251; https://doi.org/10.3390/microorganisms10061251 - 19 Jun 2022
Cited by 4 | Viewed by 3443
Abstract
Contrary to the majority of other Trematoda, Schistosoma species are gonochoric. Consequently, in endemic areas where several schistosome species overlap and can co-infect the same definitive host, there may be frequent opportunities for interspecific pairing. Our experimental study provides novel insight on the [...] Read more.
Contrary to the majority of other Trematoda, Schistosoma species are gonochoric. Consequently, in endemic areas where several schistosome species overlap and can co-infect the same definitive host, there may be frequent opportunities for interspecific pairing. Our experimental study provides novel insight on the pairing behavior between Schistosoma bovis and S. mansoni in mixed infections in mice. We used six mate choice experiments to assess mating interactions between the two schistosome species. We show that mating between the two Schistosoma species is not random and that S. mansoni exhibits greater mate recognition compared to S. bovis. We also performed reciprocal crosses (male S. mansoni × female S. bovis) and (female S. mansoni × male S. bovis) that produce active swimming miracidia. These miracidia were genotyped by ITS2 sequencing and proposed for mollusc infection. Molecular analyses show that all the miracidia are parthenogenetically produced (i.e., their harbor the mother ITS2 genotype) and as a consequence can only infect the mollusc of the maternal species. Offspring produced by male S. mansoni × female S. bovis pairing can only infect Bulinus truncatus whereas offspring produced by female S. mansoni × male S. bovis can only infect Biomphalaria glabrata snails. Evolutionary and epidemiological consequences are discussed. Full article
(This article belongs to the Section Parasitology)
12 pages, 571 KiB  
Article
Influence on Soybean Aphid by the Tripartite Interaction between Soybean, a Rhizobium Bacterium, and an Arbuscular Mycorrhizal Fungus
by Élisée Emmanuel Dabré, Mohamed Hijri and Colin Favret
Microorganisms 2022, 10(6), 1196; https://doi.org/10.3390/microorganisms10061196 - 11 Jun 2022
Cited by 11 | Viewed by 3803
Abstract
The inoculation of arbuscular mycorrhizal (AM) fungi and rhizobia in legumes has been proven to increase plant growth and yield. To date, studies of the effects of these interactions on phytophagous insects have shown them to be context-dependent depending on the inoculant strain, [...] Read more.
The inoculation of arbuscular mycorrhizal (AM) fungi and rhizobia in legumes has been proven to increase plant growth and yield. To date, studies of the effects of these interactions on phytophagous insects have shown them to be context-dependent depending on the inoculant strain, the plant, and the insect species. Here, we document how a symbiosis involving an AM fungus, Rhizophagus irregularis; a rhizobium, Bradyrhizobium japonicum; and soybean, Glycine max, influences the soybean aphid, Aphis glycines. Soybean co-inoculated with the AM fungus–rhizobium pair increased the plant’s biomass, nodulation, mycorrhizal colonization, nitrogen, and carbon concentrations, but decreased phosphorus concentration. Similar effects were observed with rhizobium alone, with the exception that root biomass was unaffected. With AM fungus alone, we only observed an increase in mycorrhizal colonization and phosphorus concentration. The aphids experienced an increased reproductive rate with the double inoculation, followed by rhizobium alone, whereas no effect was observed with the AM fungus. The size of individual aphids was not affected. Furthermore, we found positive correlation between nitrogen concentration and aphid population density. Our results confirm that co-inoculation of two symbionts can enhance both plant and phytophagous insect performance beyond what either symbiont can contribute alone. Full article
(This article belongs to the Special Issue Microbial-Based Plant Biostimulants)
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19 pages, 7292 KiB  
Article
Complete Genome Analysis of Rhodococcus opacus S8 Capable of Degrading Alkanes and Producing Biosurfactant Reveals Its Genetic Adaptation for Crude Oil Decomposition
by Yanina Delegan, Kirill Petrikov, Ekaterina Frantsuzova, Natalia Rudenko, Viktor Solomentsev, Nataliya Suzina, Vasili Travkin and Inna P. Solyanikova
Microorganisms 2022, 10(6), 1172; https://doi.org/10.3390/microorganisms10061172 - 7 Jun 2022
Cited by 7 | Viewed by 4121
Abstract
Microorganisms capable of decomposing hydrophobic substrates in cold climates are of considerable interest both in terms of studying adaptive reactions to low temperatures and in terms of their application in biotechnologies for cleaning up oil spills in a crude-oil polluted soil. The aim [...] Read more.
Microorganisms capable of decomposing hydrophobic substrates in cold climates are of considerable interest both in terms of studying adaptive reactions to low temperatures and in terms of their application in biotechnologies for cleaning up oil spills in a crude-oil polluted soil. The aim of this work was to investigate the genome of Rhodococcus opacus S8 and explore behavior traits of this strain grown in the presence of hexadecane. The genome size of strain S8 is 8.78 Mb, of which the chromosome size is 7.75 Mb. The S8 strain contains 2 circular plasmids of 135 kb and 105 kb and a linear plasmid with a size of 788 kb. The analysis of the genome revealed the presence of genes responsible for the degradation of alkanes and synthesis of biosurfactants. The peculiarities of morphology of microbial cells when interacting with a hydrophobic substrate were revealed. An adaptive mechanism responsible in the absence of oxygen for maintaining the process of degradation of hexadecane is discussed. The data obtained show that the strain S8 has great potential to be used in biotechnologies. Full article
(This article belongs to the Section Environmental Microbiology)
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19 pages, 1579 KiB  
Article
Microbial Interrelationships across Sites of Breastfeeding Mothers and Infants at 6 Weeks Postpartum
by Erin C. Davis, Mei Wang and Sharon M. Donovan
Microorganisms 2022, 10(6), 1155; https://doi.org/10.3390/microorganisms10061155 - 2 Jun 2022
Cited by 8 | Viewed by 3198
Abstract
Infancy is a critical life stage for the establishment of the gut microbiome. Human milk contains a unique microbial ecosystem that serves as a continuous source of commensal bacteria for the infant. However, the origin of the human milk microbiota, how it is [...] Read more.
Infancy is a critical life stage for the establishment of the gut microbiome. Human milk contains a unique microbial ecosystem that serves as a continuous source of commensal bacteria for the infant. However, the origin of the human milk microbiota, how it is influenced by breastfeeding exclusivity, and its role in infant gut microbiota assembly are not clear. To interrogate these questions, we examined the relationships among fecal, oral, breast skin, and human milk microbiota of 33 exclusively breastfeeding (EBF) and mixed-feeding (MF; human milk + infant formula) mother–infant pairs at 6 weeks postpartum. Here, we show that MF infants have a significantly more diverse oral microbiome comprised of lower relative abundances of Streptococcus and Gemella and higher abundances of Veillonella. Using both SourceTracker2 and FEAST, we demonstrate breast skin and infant saliva as the principal contributing sources to the human milk microbiota. Of the sampled sites, human milk and maternal stool were predicted to contribute the largest fraction to the infant fecal microbiome, but the majority of the community was estimated to arise from unknown sources. Lastly, we identified twenty-one significant co-occurrence relationships between bacteria in human milk and on other maternal and infant body sites. These results demonstrate several unique microbial interrelationships between breastfeeding dyads, providing insight into potential mechanisms of microbial assembly in early life. Full article
(This article belongs to the Special Issue Novel Insights into the Infant Gut Microbiome and Host–Microbe Interactions)
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10 pages, 1043 KiB  
Article
Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase
by Jeferson M. Lourenco, Christina B. Welch, Taylor R. Krause, Michael A. Wieczorek, Francis L. Fluharty, Michael J. Rothrock, T. Dean Pringle and Todd R. Callaway
Microorganisms 2022, 10(6), 1128; https://doi.org/10.3390/microorganisms10061128 - 31 May 2022
Cited by 11 | Viewed by 3140
Abstract
The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 [...] Read more.
The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 days, had growth performance metrics evaluated. Steers were ranked based upon residual feed intake (RFI), and the 5 lowest RFI (most efficient) and 5 highest RFI (least efficient) steers were selected for evaluation. Fecal samples were collected on 0-d and 82-d of the finishing period and microbial DNA was extracted and evaluated by 16S rRNA gene sequencing. During the feedlot trial, inefficient steers had decreased (p = 0.02) Ruminococcaceae populations and increased (p = 0.01) Clostridiaceae populations. Conversely, efficient steers had increased Peptostreptococcaceae (p = 0.03) and Turicibacteraceae (p = 0.01), and a trend for decreased Proteobacteria abundance (p = 0.096). Efficient steers had increased microbial richness and diversity during the feedlot period, which likely resulted in increased fiber-degrading enzymes in their hindgut, allowing them to extract more energy from the feed. Results suggest that cattle with better feed efficiency have greater diversity of hindgut microorganisms, resulting in more enzymes available for digestion, and improving energy harvest in the gut of efficient cattle. Full article
(This article belongs to the Special Issue The Microbial Population of the Gastrointestinal Tract of Animals: Impacts on Host Physiology)
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17 pages, 13160 KiB  
Article
Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks
by Jakub Kubacki, Weihong Qi and Cornel Fraefel
Microorganisms 2022, 10(6), 1092; https://doi.org/10.3390/microorganisms10061092 - 25 May 2022
Cited by 13 | Viewed by 3076
Abstract
The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. [...] Read more.
The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by Next-Generation Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases. Full article
(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)
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17 pages, 1765 KiB  
Article
Fungal Diversity in Two Wastewater Treatment Plants in North Italy
by Simone Buratti, Carolina Elena Girometta, Rebecca Michela Baiguera, Barbara Barucco, Marco Bernardi, Giuseppe De Girolamo, Maura Malgaretti, Desdemona Oliva, Anna Maria Picco and Elena Savino
Microorganisms 2022, 10(6), 1096; https://doi.org/10.3390/microorganisms10061096 - 25 May 2022
Cited by 13 | Viewed by 3213
Abstract
In urban wastewater treatment plants, bacteria lead the biological component of the depuration process, but the microbial community is also rich in fungi (mainly molds, yeasts and pseudo-yeasts), whose taxonomical diversity and relative frequency depend on several factors, e.g., quality of wastewater input, [...] Read more.
In urban wastewater treatment plants, bacteria lead the biological component of the depuration process, but the microbial community is also rich in fungi (mainly molds, yeasts and pseudo-yeasts), whose taxonomical diversity and relative frequency depend on several factors, e.g., quality of wastewater input, climate, seasonality, and depuration stage. By joining morphological and molecular identification, we investigated the fungal diversity in two different plants for the urban wastewater treatment in the suburbs of the two major cities in Lombardia, the core of industrial and commercial activities in Italy. This study presents a comparison of the fungal diversity across the depuration stages by applying the concepts of α-, β- and ζ-diversity. Eurotiales (mainly with Aspergillus and Penicillium), Trichosporonales (Trichosporon sensu lato), Saccharomycetales (mainly with Geotrichum) and Hypocreales (mainly with Fusarium and Trichoderma) are the most represented fungal orders and genera in all the stages and both the plants. The two plants show different trends in α-, β- and ζ-diversity, despite the fact that they all share a crash during the secondary sedimentation and turnover across the depuration stages. This study provides an insight on which taxa potentially contribute to each depuration stage and/or keep viable propagules in sludges after the collection from the external environment. Full article
(This article belongs to the Special Issue Fungal Biodiversity for Bioremediation)
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16 pages, 1882 KiB  
Article
Enhanced Immunogenicity of Inactivated Dengue Vaccines by Novel Polysaccharide-Based Adjuvants in Mice
by Shuenn-Jue Wu, Dan Ewing, Appavu K. Sundaram, Hua-Wei Chen, Zhaodong Liang, Ying Cheng, Vihasi Jani, Peifang Sun, Gregory D. Gromowski, Rafael A. De La Barrera, Megan A. Schilling, Nikolai Petrovsky, Kevin R. Porter and Maya Williams
Microorganisms 2022, 10(5), 1034; https://doi.org/10.3390/microorganisms10051034 - 16 May 2022
Cited by 3 | Viewed by 4283
Abstract
Dengue fever, caused by any of four dengue viruses (DENV1-4), is a major global burden. Currently, there is no effective vaccine that prevents infection in dengue naïve populations. We tested the ability of two novel adjuvants (Advax-PEI and Advax-2), using aluminum hydroxide (alum) [...] Read more.
Dengue fever, caused by any of four dengue viruses (DENV1-4), is a major global burden. Currently, there is no effective vaccine that prevents infection in dengue naïve populations. We tested the ability of two novel adjuvants (Advax-PEI and Advax-2), using aluminum hydroxide (alum) as control, to enhance the immunogenicity of formalin- or psoralen-inactivated (PIV or PsIV) DENV2 vaccines in mice. Mice were vaccinated on days 0 and 30, and serum samples were collected on days 30, 60, 90, and 101. Neutralizing antibodies were determined by microneutralization (MN) assays, and the geometric mean 50% MN (MN50) titers were calculated. For the PIV groups, after one dose MN50 titers were higher in the novel adjuvant groups compared to the alum control, while MN50 titers were comparable between the adjuvant groups after the second dose. For the PsIV groups, both novel adjuvants induced higher MN50 titers than the alum control after the second dose. Spleen cells were collected on days 45 and 101 for enzyme-linked immunospot (ELISPOT) for IFNγ and IL4. Both PIV and PsIV groups elicited different degrees of IFNγ and IL4 responses. Overall, Advax-2 gave the best responses just ahead of Advax-PEI. Given Advax-2’s extensive human experience in other vaccine applications, it will be pursued for further development. Full article
(This article belongs to the Special Issue Arboviruses)
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15 pages, 1036 KiB  
Article
Fungi Can Be More Effective than Bacteria for the Bioremediation of Marine Sediments Highly Contaminated with Heavy Metals
by Filippo Dell’Anno, Eugenio Rastelli, Emanuela Buschi, Giulio Barone, Francesca Beolchini and Antonio Dell’Anno
Microorganisms 2022, 10(5), 993; https://doi.org/10.3390/microorganisms10050993 - 9 May 2022
Cited by 26 | Viewed by 5842
Abstract
The contamination of coastal marine sediments with heavy metals (HMs) is a widespread phenomenon that requires effective remediation actions. Bioremediation based on the use of bacteria is an economically and environmentally sustainable effective strategy for reducing HM contamination and/or toxicity in marine sediments. [...] Read more.
The contamination of coastal marine sediments with heavy metals (HMs) is a widespread phenomenon that requires effective remediation actions. Bioremediation based on the use of bacteria is an economically and environmentally sustainable effective strategy for reducing HM contamination and/or toxicity in marine sediments. However, information on the efficiency of marine-derived fungi for HM decontamination of marine sediments is still largely lacking, despite evidence of the performance of terrestrial fungal strains on other contaminated matrixes (e.g., soils, freshwater sediments, industrial wastes). Here, we carried out for the first time an array of parallel laboratory experiments by using different combinations of chemical and microbial amendments (including acidophilic autotrophic and heterotrophic bacteria, as well as filamentous marine fungi) for the bioremediation of highly HM-contaminated sediments of the Portman Bay (NW Mediterranean Sea), an area largely affected by long-term historical discharges of mine tailings. Our results indicate that the bioleaching performance of metals from the sediment is based on the addition of fungi (Aspergillus niger and Trichoderma sp.), either alone or in combination with autotrophic bacteria, was higher when compared to other treatments. In particular, fungal addition allowed obtaining bioleaching yields for As eight times higher than those by chemical treatments and double compared with the addition of bacteria alone. Moreover, in our study, the fungal addition was the only treatment allowing effective bioleaching of otherwise not mobile fractions of Zn and Cd, thus overtaking bacterial treatments. We found that the lower the sediment pH reached by the experimental conditions, as in the case of fungal addition, the higher the solubilization yield of metals, suggesting that the specific metabolic features of A. niger and Trichoderma sp. enable lowering sediment pH and enhance HM bioleaching. Overall, our findings indicate that fungi can be more effective than acidophilic autotrophic and heterotrophic bacteria in HM bioleaching, and as such, their use can represent a promising and efficient strategy for the bioremediation of marine sediments highly contaminated with heavy metals. Full article
(This article belongs to the Section Environmental Microbiology)
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9 pages, 1969 KiB  
Article
Changes in Invasive Neisseria meningitidis and Haemophilus influenzae Infections in France during the COVID-19 Pandemic
by Ala-Eddine Deghmane and Muhamed-Kheir Taha
Microorganisms 2022, 10(5), 907; https://doi.org/10.3390/microorganisms10050907 - 26 Apr 2022
Cited by 32 | Viewed by 5217
Abstract
BackgroundSince the appearance of COVID-19 in January 2020, invasive bacterial infections have decreased significantly worldwide. However, alterations in age and sex distributions, clinical forms, phenotypes, and genotypes of isolates have not been analyzed. Our goal is to present and discuss these data [...] Read more.
BackgroundSince the appearance of COVID-19 in January 2020, invasive bacterial infections have decreased significantly worldwide. However, alterations in age and sex distributions, clinical forms, phenotypes, and genotypes of isolates have not been analyzed. Our goal is to present and discuss these data considering the current COVID-19 pandemic situation. Methods: The data of the national reference center for meningococci and Haemophilus influenzae in France were mined to examine the above aspects of invasive bacterial infection before (2018–2019) and after (2020–2021) the COVID-19 pandemic. Detailed epidemiological, clinical, and microbiological data were collected, and whole genome sequencing was carried out on meningococcal isolates (n = 1466). Results: In addition to the overall decline in the number of cases, various changes in age, sex, and phenotypes of isolates were also noted. As for N. meningitidis, more cases were observed in adults, as well as more invasive pneumopathies. Furthermore, fewer hyperinvasive meningococcal genotypes have circulated since COVID-19 emerged. The situation has been different for H. influenzae, as the number of invasive cases among adults decreased due to a reduction in non-typeable isolates. In contrast, cases due to serotypeable isolates, particularly serotypes a and b, increased in children <5 years-old. Conclusions: It is possible that measures implemented to stop COVID-19 may have reduced the circulation of N. meningitidis and H. influenzae isolates, but to a variable extent. This may be due to differences in circulation between these two species according to age groups. Vaccination schedules against these two species may have also influenced the evolution of these invasive bacterial infections since the emergence of the COVID-19 pandemic. Full article
(This article belongs to the Special Issue The COVID-19 Pandemic and Bacterial Infections: Microbiological and Clinical Aspects)
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23 pages, 1114 KiB  
Article
Comparative Genomics Applied to Systematically Assess Pathogenicity Potential in Shiga Toxin-Producing Escherichia coli O145:H28
by Michelle Qiu Carter, Nicole Laniohan, Chien-Chi Lo and Patrick S. G. Chain
Microorganisms 2022, 10(5), 866; https://doi.org/10.3390/microorganisms10050866 - 21 Apr 2022
Cited by 7 | Viewed by 3333
Abstract
Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental [...] Read more.
Shiga toxin-producing Escherichia coli (STEC) O145:H28 can cause severe disease in humans and is a predominant serotype in STEC O145 environmental isolates. Here, comparative genomics was applied to a set of clinical and environmental strains to systematically evaluate the pathogenicity potential in environmental strains. While the core genes-based tree separated all O145:H28 strains from the non O145:H28 reference strains, it failed to segregate environmental strains from the clinical. In contrast, the accessory genes-based tree placed all clinical strains in the same clade regardless of their genotypes or serotypes, apart from the environmental strains. Loss-of-function mutations were common in the virulence genes examined, with a high frequency in genes related to adherence, autotransporters, and the type three secretion system. Distinct differences in pathogenicity islands LEE, OI-122, and OI-57, the acid fitness island, and the tellurite resistance island were detected between the O145:H28 and reference strains. A great amount of genetic variation was detected in O145:H28, which was mainly attributed to deletions, insertions, and gene acquisition at several chromosomal “hot spots”. Our study demonstrated a distinct virulence gene repertoire among the STEC O145:H28 strains originating from the same geographical region and revealed unforeseen contributions of loss-of-function mutations to virulence evolution and genetic diversification in STEC. Full article
(This article belongs to the Special Issue Know Your Enemy: Improved Understanding, Detection, Control, and Therapy for Shiga Toxin-Producing Escherichia coli Infection)
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12 pages, 763 KiB  
Article
Road Salt versus Urban Snow Effects on Lake Microbial Communities
by Isabelle B. Fournier, Connie Lovejoy and Warwick F. Vincent
Microorganisms 2022, 10(4), 803; https://doi.org/10.3390/microorganisms10040803 - 12 Apr 2022
Cited by 5 | Viewed by 2729
Abstract
Freshwater salinization is an ongoing concern for north temperate lakes; however, little is known about its impacts on microbial communities, particularly for bacteria. We tested the hypotheses that road de-icing salt induces changes in the microbial community structure of lake plankton, and that [...] Read more.
Freshwater salinization is an ongoing concern for north temperate lakes; however, little is known about its impacts on microbial communities, particularly for bacteria. We tested the hypotheses that road de-icing salt induces changes in the microbial community structure of lake plankton, and that changes due to chloride would differ from those due to urban snowmelt because of additional chemicals in the snowmelt. In a laboratory incubator experiment, an overwintering plankton community in lake water was exposed for two weeks to either NaCl or municipal road snow with the same level of chloride. Microbial community structure as determined by 16S (prokaryotes) and 18S (eukaryotes) rRNA transcript analysis showed changes in response to the chloride-only enrichment, with some rare taxa becoming more prominent. Consistent with our hypothesis, the salt and the snow treatments induced different community changes. These results indicate that ecotoxicology assays based on a single salt addition may not reflect the in situ effects of salt-contaminated urban snow, and that the combined chemical effects of urban snowmelt require direct testing. Full article
(This article belongs to the Section Environmental Microbiology)
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8 pages, 362 KiB  
Article
Outbreak of MRSA in a Gynecology/Obstetrics Department during the COVID-19 Pandemic: A Cautionary Tale
by Mareike Möllers, Marie-Kristin von Wahlde, Franziska Schuler, Alexander Mellmann, Christian Böing, Vera Schwierzeck, Julia Sophie Schneider and Stefanie Kampmeier
Microorganisms 2022, 10(4), 689; https://doi.org/10.3390/microorganisms10040689 - 23 Mar 2022
Cited by 10 | Viewed by 4788
Abstract
Since March 2020, the COVID-19 pandemic forced hospitals worldwide to intensify their infection control measures to prevent health care-associated transmission of SARS-CoV-2. The correct use of personal protective equipment, especially the application of masks, was quickly identified as priority to reduce transmission with [...] Read more.
Since March 2020, the COVID-19 pandemic forced hospitals worldwide to intensify their infection control measures to prevent health care-associated transmission of SARS-CoV-2. The correct use of personal protective equipment, especially the application of masks, was quickly identified as priority to reduce transmission with this pathogen. Here, we report a nosocomial cluster of methicillin-resistant Staphylococcus aureus (MRSA) that occurred during the COVID-19 pandemic in a gynecology/obstetrics department, despite these intensified contact precautions. Five MRSA originating from clinical samples after surgical intervention led to an outbreak investigation. Firstly, this included environmental sampling of the operation theatre (OT) and, secondly, a point prevalence screening of patients and health care workers (HCW). All detected MRSA were subjected to whole genome sequencing (WGS) and isolate relatedness was determined using core genome multilocus sequence typing (cgMLST). WGS revealed one MRSA cluster with genetically closely related five patient and two HCW isolates differing in a single cgMLST allele at maximum. The outbreak was terminated after implementation of infection control bundle strategies. Although contact precaution measures, which are also part of MRSA prevention bundle strategies, were intensified during the COVID-19 pandemic, this MRSA outbreak could take place. This illustrates the importance of adherence to classical infection prevention strategies. Full article
(This article belongs to the Special Issue Antimicrobial Resistance and Outbreaks Due to Multidrug-resistant Bacteria in Hospitalized COVID-19 Patients)
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15 pages, 1240 KiB  
Article
Colonization of Dogs and Their Owners with Staphylococcus aureus and Staphylococcus pseudintermedius in Households, Veterinary Practices, and Healthcare Facilities
by Christiane Cuny, Franziska Layer-Nicolaou, Robert Weber, Robin Köck and Wolfgang Witte
Microorganisms 2022, 10(4), 677; https://doi.org/10.3390/microorganisms10040677 - 22 Mar 2022
Cited by 30 | Viewed by 4666
Abstract
There are uncertainties with respect to the transmission of methicillin-susceptible and methicillin-resistant Staphylococcus aureus (MSSA and MRSA) and Staphylococcus pseudintermedius between dogs and humans. In this study, we investigated concomitant nasal colonization of dogs and humans in three cohorts. Cohort I, households owning [...] Read more.
There are uncertainties with respect to the transmission of methicillin-susceptible and methicillin-resistant Staphylococcus aureus (MSSA and MRSA) and Staphylococcus pseudintermedius between dogs and humans. In this study, we investigated concomitant nasal colonization of dogs and humans in three cohorts. Cohort I, households owning dogs: In 42 of 84 households, 66 humans (36.9%) and 10 dogs (8.9%) carried S. aureus. MRSA, attributed to sequence type (ST) 22 and ST130, were detected in two (1.1%) of the humans but in none of the dogs. Typing by means of spa-typing and whole-genome sequencing (WGS) indicated eight transmissions of S. aureus between humans and dogs in 8 of 42 (19.0%) households with human S. aureus carriers, whereas in 11 of 38 (29.0%) households with ≥two persons and S. aureus colonization of humans, 15 human-to-human transmissions were observed (p = 0.43). S. pseudintermedius was isolated from 42 dogs (37.5%), but from only one human (0.6%). In this case, WGS-based typing indicated strong relatedness of this isolate with a canine isolate from the same household. Cohort II, dogs and their owners visiting a veterinary practice: Among 17 humans and 17 dogs attending a veterinary practice, MSSA was detected in three humans and two dogs, and S. pseudintermedius in only six dogs. Cohort III, dogs used for animal-assisted interventions in human healthcare facilities and their owners: MSSA was obtained in 1 of 59 dogs (1.7%) and in 17 of 60 (28.3%) of the dog owners, while S. pseudintermedius was isolated from seven (12%) dogs and one (1.7%) human owner. We conclude that the risk of exchanging S. aureus/MRSA between humans and dogs is higher than that for S. pseudintermedius. Full article
(This article belongs to the Special Issue Multi-Drug Resistant (MDR) Gram-Positive Bacterial Infections)
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13 pages, 2502 KiB  
Article
Typing of the Gut Microbiota Community in Japanese Subjects
by Tomohisa Takagi, Ryo Inoue, Akira Oshima, Hiroshi Sakazume, Kenta Ogawa, Tomo Tominaga, Yoichi Mihara, Takeshi Sugaya, Katsura Mizushima, Kazuhiko Uchiyama, Yoshito Itoh and Yuji Naito
Microorganisms 2022, 10(3), 664; https://doi.org/10.3390/microorganisms10030664 - 20 Mar 2022
Cited by 22 | Viewed by 12013
Abstract
Gut microbiota are involved in both host health and disease and can be stratified based on bacteriological composition. However, gut microbiota clustering data are limited for Asians. In this study, fecal microbiota of 1803 Japanese subjects, including 283 healthy individuals, were analyzed by [...] Read more.
Gut microbiota are involved in both host health and disease and can be stratified based on bacteriological composition. However, gut microbiota clustering data are limited for Asians. In this study, fecal microbiota of 1803 Japanese subjects, including 283 healthy individuals, were analyzed by 16S rRNA sequencing and clustered using two models. The association of various diseases with each community type was also assessed. Five and fifteen communities were identified using partitioning around medoids (PAM) and the Dirichlet multinominal mixtures model, respectively. Bacteria exhibiting characteristically high abundance among the PAM-identified types were of the family Ruminococcaceae (Type A) and genera Bacteroides, Blautia, and Faecalibacterium (Type B); Bacteroides, Fusobacterium, and Proteus (Type C); and Bifidobacterium (Type D), and Prevotella (Type E). The most noteworthy community found in the Japanese subjects was the Bifidobacterium-rich community. The odds ratio based on type E, which had the largest population of healthy subjects, revealed that other types (especially types A, C, and D) were highly associated with various diseases, including inflammatory bowel disease, functional gastrointestinal disorder, and lifestyle-related diseases. Gut microbiota community typing reproducibly identified organisms that may represent enterotypes peculiar to Japanese individuals and that are partly different from those of indivuals from Western countries. Full article
(This article belongs to the Special Issue State-of-the-Art Gut Microbiota Research in Asia)
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15 pages, 15221 KiB  
Article
Localization of the Swainsonine-Producing Chaetothyriales Symbiont in the Seed and Shoot Apical Meristem in Its Host Ipomoea carnea
by Marwa Neyaz, Dale R. Gardner, Rebecca Creamer and Daniel Cook
Microorganisms 2022, 10(3), 545; https://doi.org/10.3390/microorganisms10030545 - 2 Mar 2022
Cited by 9 | Viewed by 3489
Abstract
Several species of fungi from the orders Chaetothyriales and Pleosporales have been reported to produce swainsonine and be associated as symbionts with plants of the Convolvulaceae and Fabaceae, respectively. An endosymbiont belonging to the Chaetothyriales produces swainsonine and grows as an epibiont on [...] Read more.
Several species of fungi from the orders Chaetothyriales and Pleosporales have been reported to produce swainsonine and be associated as symbionts with plants of the Convolvulaceae and Fabaceae, respectively. An endosymbiont belonging to the Chaetothyriales produces swainsonine and grows as an epibiont on the adaxial leaf surfaces of Ipomoea carnea, but how the symbiont passes through plant growth and development is unknown. Herein, different types of microscopy were used to localize the symbiont in seeds and in cross sections of plant parts. The symbiont was found in several tissues including the hilum, the sclereids, and the hypocotyl of seeds. In five-day old seedlings and mature plants, the symbiont was found in the shoot apical meristem (SAM) and the adaxial surface of immature folded leaves. The mycelia generally formed a close association with peltate glandular trichomes. This report provides further data explaining the relationship between the seed transmitted Chaetothyriales symbiont and Ipomoea carnea. These results provide a possible explanation for how this symbiont, and others like Periglandula may persist and are transmitted over time. Full article
(This article belongs to the Section Plant Microbe Interactions)
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17 pages, 2412 KiB  
Article
Persistent Cutaneous Leishmania major Infection Promotes Infection-Adapted Myelopoiesis
by Fabio Luiz Bandeira Ferreira, Olivier Séguin, Albert Descoteaux and Krista M. Heinonen
Microorganisms 2022, 10(3), 535; https://doi.org/10.3390/microorganisms10030535 - 28 Feb 2022
Cited by 6 | Viewed by 3855
Abstract
Hematopoietic stem/progenitor cells (HSPC) are responsible for the generation of most immune cells throughout the lifespan of the organism. Inflammation can activate bone marrow HSPCs, leading to enhanced myelopoiesis to replace cells, such as neutrophils, which are attracted to inflamed tissues. We have [...] Read more.
Hematopoietic stem/progenitor cells (HSPC) are responsible for the generation of most immune cells throughout the lifespan of the organism. Inflammation can activate bone marrow HSPCs, leading to enhanced myelopoiesis to replace cells, such as neutrophils, which are attracted to inflamed tissues. We have previously shown that HSPC activation promotes parasite persistence and expansion in experimental visceral leishmaniasis through the increased production of permissive monocytes. However, it is not clear if the presence of the parasite in the bone marrow was required for infection-adapted myelopoiesis. We therefore hypothesized that persistent forms of Leishmania major (cutaneous leishmaniasis) could also activate HSPCs and myeloid precursors in the C57Bl/6 mouse model of intradermal infection in the ear. The accrued influx of myeloid cells to the lesion site corresponded to an increase in myeloid-biased HSPCs in the bone marrow and spleen in mice infected with a persistent strain of L. major, together with an increase in monocytes and monocyte-derived myeloid cells in the spleen. Analysis of the bone marrow cytokine and chemokine environment revealed an attenuated type I and type II interferon response in the mice infected with the persistent strain compared to the self-healing strain, while both strains induced a rapid upregulation of myelopoietic cytokines, such as IL-1β and GM-CSF. These results demonstrate that an active infection in the bone marrow is not necessary for the induction of infection-adapted myelopoiesis, and underline the importance of considering alterations to the bone marrow output when analyzing in vivo host-pathogen interactions. Full article
(This article belongs to the Special Issue Leishmania and Leishmaniasis)
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14 pages, 5628 KiB  
Article
Unamplified, Long-Read Metagenomic Sequencing Approach to Close Endosymbiont Genomes of Low-Biomass Insect Populations
by Joseph R. Petrone, Alam Muñoz-Beristain, Paula Rios Glusberger, Jordan T. Russell and Eric W. Triplett
Microorganisms 2022, 10(3), 513; https://doi.org/10.3390/microorganisms10030513 - 26 Feb 2022
Cited by 5 | Viewed by 4965
Abstract
With the current advancements in DNA sequencing technology, the limiting factor in long-read metagenomic assemblies is now the quantity and quality of input DNA. Although these requirements can be met through the use of axenic bacterial cultures or large amounts of biological material, [...] Read more.
With the current advancements in DNA sequencing technology, the limiting factor in long-read metagenomic assemblies is now the quantity and quality of input DNA. Although these requirements can be met through the use of axenic bacterial cultures or large amounts of biological material, insect systems that contain unculturable bacteria or that contain a low amount of available DNA cannot fully utilize the benefits of third-generation sequencing. The citrus greening disease insect vector Diaphorina citri is an example that exhibits both of these limitations. Although endosymbiont genomes have mostly been closed after the short-read sequencing of amplified template DNA, creating de novo long-read genomes from the unamplified DNA of an insect population may benefit communities using bioinformatics to study insect pathosystems. Here all four genomes of the infected D. citri microbiome were sequenced to closure using unamplified template DNA and two long-read sequencing technologies. Avoiding amplification bias and using long reads to assemble the bacterial genomes allowed for the circularization of the Wolbachia endosymbiont of Diaphorina citri for the first time and paralleled the annotation context of all four reference genomes without utilizing a traditional hybrid assembly. The strategies detailed here are suitable for the sequencing of other insect systems for which the input DNA, time, and cost are an issue. Full article
(This article belongs to the Section Environmental Microbiology)
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24 pages, 7236 KiB  
Article
Ca2+/Calmodulin-Dependent Protein Kinase II Inhibits Hepatitis B Virus Replication from cccDNA via AMPK Activation and AKT/mTOR Suppression
by Jumi Kim, Hyeonjoong Kwon, Fadia Kalsoom, Muhammad Azhar Sajjad, Hyun Woong Lee, Jin Hong Lim, Jaesung Jung, Yong-Joon Chwae, Sun Park, Ho-Joon Shin and Kyongmin Kim
Microorganisms 2022, 10(3), 498; https://doi.org/10.3390/microorganisms10030498 - 23 Feb 2022
Cited by 8 | Viewed by 4221
Abstract
Ca2+/calmodulin-dependent protein kinase II (CaMKII), which is involved in the calcium signaling pathway, is an important regulator of cancer cell proliferation, motility, growth, and metastasis. The effects of CaMKII on hepatitis B virus (HBV) replication have never been evaluated. Here, we [...] Read more.
Ca2+/calmodulin-dependent protein kinase II (CaMKII), which is involved in the calcium signaling pathway, is an important regulator of cancer cell proliferation, motility, growth, and metastasis. The effects of CaMKII on hepatitis B virus (HBV) replication have never been evaluated. Here, we found that phosphorylated, active CaMKII is reduced during HBV replication. Similar to other members of the AMPK/AKT/mTOR signaling pathway associated with HBV replication, CaMKII, which is associated with this pathway, was found to be a novel regulator of HBV replication. Overexpression of CaMKII reduced the expression of covalently closed circular DNA (cccDNA), HBV RNAs, and replicative intermediate (RI) DNAs while activating AMPK and inhibiting the AKT/mTOR signaling pathway. Findings in HBx-deficient mutant-transfected HepG2 cells showed that the CaMKII-mediated AMPK/AKT/mTOR signaling pathway was independent of HBx. Moreover, AMPK overexpression reduced HBV cccDNA, RNAs, and RI DNAs through CaMKII activation. Although AMPK acts downstream of CaMKII, AMPK overexpression altered CaMKII phosphorylation, suggesting that CaMKII and AMPK form a positive feedback loop. These results demonstrate that HBV replication suppresses CaMKII activity, and that CaMKII upregulation suppresses HBV replication from cccDNA via AMPK and the AKT/mTOR signaling pathway. Thus, activation or overexpression of CaMKII may be a new therapeutic target against HBV infection. Full article
(This article belongs to the Section Virology)
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17 pages, 957 KiB  
Article
Spread of a Novel Indian Ocean Lineage Carrying E1-K211E/E2-V264A of Chikungunya Virus East/Central/South African Genotype across the Indian Subcontinent, Southeast Asia, and Eastern Africa
by Juthamas Phadungsombat, Hisham A. Imad, Emi E. Nakayama, Pornsawan Leaungwutiwong, Pongrama Ramasoota, Wang Nguitragool, Wasin Matsee, Watcharapong Piyaphanee and Tatsuo Shioda
Microorganisms 2022, 10(2), 354; https://doi.org/10.3390/microorganisms10020354 - 3 Feb 2022
Cited by 22 | Viewed by 4912
Abstract
The Indian Ocean Lineage (IOL) of the chikungunya virus (CHIKV) East/Central/South African (ECSA) genotype, which originated in Kenya, spread to the Indian ocean and the Indian subcontinent, and then expanded through Southeast Asia in the previous decade. It carried an adaptive mutation E1-A226V, [...] Read more.
The Indian Ocean Lineage (IOL) of the chikungunya virus (CHIKV) East/Central/South African (ECSA) genotype, which originated in Kenya, spread to the Indian ocean and the Indian subcontinent, and then expanded through Southeast Asia in the previous decade. It carried an adaptive mutation E1-A226V, which enhances CHIKV replication in Aedes albopictus. However, the IOL CHIKV of the most recent outbreaks during 2016–2020 in India, Pakistan, Bangladesh, the Maldives, Myanmar, Thailand, and Kenya lacked E1-A226V but carried E1-K211E and E2-V264A. Recent CHIKV genome sequences of the Maldives and Thailand were determined, and their phylogenetic relationships were further investigated together with IOL sequences reported in 2004–2020 in the database. The results showed that the ancestral IOLs diverged to a sub-lineage E1-K211E/E2-V264A, probably in India around 2008, and caused sporadic outbreaks in India during 2010–2015 and in Kenya in 2016. The massive expansion of this new sub-lineage occurred after the acquisition of E1-I317V in other neighboring and remote regions in 2014–2020. Additionally, the phylogenetic tree indicated that independent clades formed according to the geographical regions and introduction timing. The present results using all available partial or full sequences of the recent CHIKVs emphasized the dynamics of the IOL sub-lineages in the Indian subcontinent, Southeast Asia, and Eastern Africa. Full article
(This article belongs to the Special Issue Emerging Alphaviruses)
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24 pages, 6075 KiB  
Article
Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice
by Angela Peeb, Nga Phuong Dang, Marika Truu, Hiie Nõlvak, Chris Petrich and Jaak Truu
Microorganisms 2022, 10(2), 328; https://doi.org/10.3390/microorganisms10020328 - 1 Feb 2022
Cited by 18 | Viewed by 4608
Abstract
The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic [...] Read more.
The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 good- and high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification. Full article
(This article belongs to the Special Issue Oil Biodegradation and Bioremediation in Cold Marine Environment)
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21 pages, 5020 KiB  
Article
The nsp15 Nuclease as a Good Target to Combat SARS-CoV-2: Mechanism of Action and Its Inactivation with FDA-Approved Drugs
by Margarida Saramago, Vanessa G. Costa, Caio S. Souza, Cátia Bárria, Susana Domingues, Sandra C. Viegas, Diana Lousa, Cláudio M. Soares, Cecília M. Arraiano and Rute G. Matos
Microorganisms 2022, 10(2), 342; https://doi.org/10.3390/microorganisms10020342 - 1 Feb 2022
Cited by 18 | Viewed by 5207
Abstract
The pandemic caused by SARS-CoV-2 is not over yet, despite all the efforts from the scientific community. Vaccination is a crucial weapon to fight this virus; however, we still urge the development of antivirals to reduce the severity and progression of the COVID-19 [...] Read more.
The pandemic caused by SARS-CoV-2 is not over yet, despite all the efforts from the scientific community. Vaccination is a crucial weapon to fight this virus; however, we still urge the development of antivirals to reduce the severity and progression of the COVID-19 disease. For that, a deep understanding of the mechanisms involved in viral replication is necessary. nsp15 is an endoribonuclease critical for the degradation of viral polyuridine sequences that activate host immune sensors. This enzyme is known as one of the major interferon antagonists from SARS-CoV-2. In this work, a biochemical characterization of SARS-CoV-2 nsp15 was performed. We saw that nsp15 is active as a hexamer, and zinc can block its activity. The role of conserved residues from SARS-CoV-2 nsp15 was investigated, and N164 was found to be important for protein hexamerization and to contribute to the specificity to degrade uridines. Several chemical groups that impact the activity of this ribonuclease were also identified. Additionally, FDA-approved drugs with the capacity to inhibit the in vitro activity of nsp15 are reported in this work. This study is of utmost importance by adding highly valuable information that can be used for the development and rational design of therapeutic strategies. Full article
(This article belongs to the Special Issue Advances in RNA Biology in Pathogenic Microorganisms)
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15 pages, 2959 KiB  
Article
A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data
by Jinuk Jeong, Seyoung Mun, Yunseok Oh, Chun-Sung Cho, Kyeongeui Yun, Yongju Ahn, Won-Hyong Chung, Mi Young Lim, Kyung Eun Lee, Tae Soon Hwang and Kyudong Han
Microorganisms 2022, 10(2), 324; https://doi.org/10.3390/microorganisms10020324 - 30 Jan 2022
Cited by 15 | Viewed by 9225
Abstract
Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic [...] Read more.
Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries. Full article
(This article belongs to the Section Systems Microbiology)
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15 pages, 1891 KiB  
Article
RNase R, a New Virulence Determinant of Streptococcus pneumoniae
by Cátia Bárria, Dalila Mil-Homens, Sandra N. Pinto, Arsénio M. Fialho, Cecília M. Arraiano and Susana Domingues
Microorganisms 2022, 10(2), 317; https://doi.org/10.3390/microorganisms10020317 - 29 Jan 2022
Cited by 6 | Viewed by 4269
Abstract
Pneumococcal infections have increasingly high mortality rates despite the availability of vaccines and antibiotics. Therefore, the identification of new virulence determinants and the understanding of the molecular mechanisms behind pathogenesis have become of paramount importance in the search of new targets for drug [...] Read more.
Pneumococcal infections have increasingly high mortality rates despite the availability of vaccines and antibiotics. Therefore, the identification of new virulence determinants and the understanding of the molecular mechanisms behind pathogenesis have become of paramount importance in the search of new targets for drug development. The exoribonuclease RNase R has been involved in virulence in a growing number of pathogens. In this work, we used Galleria mellonella as an infection model to demonstrate that the presence of RNase R increases the pneumococcus virulence. Larvae infected with the RNase R mutant show an increased expression level of antimicrobial peptides. Furthermore, they have a lower bacterial load in the hemolymph in the later stages of infection, leading to a higher survival rate of the larvae. Interestingly, pneumococci expressing RNase R show a sudden drop in bacterial numbers immediately after infection, resembling the eclipse phase observed after intravenous inoculation in mice. Concomitantly, we observed a lower number of mutant bacteria inside larval hemocytes and a higher susceptibility to oxidative stress when compared to the wild type. Together, our results indicate that RNase R is involved in the ability of pneumococci to evade the host immune response, probably by interfering with internalization and/or replication inside the larval hemocytes. Full article
(This article belongs to the Special Issue Advances in RNA Biology in Pathogenic Microorganisms)
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17 pages, 13805 KiB  
Article
Toxocara canis- and Toxocara cati-Induced Neurotoxocarosis Is Associated with Comprehensive Brain Transcriptomic Alterations
by Patrick Waindok, Elisabeth Janecek-Erfurth, Dimitri L. Lindenwald, Esther Wilk, Klaus Schughart, Robert Geffers and Christina Strube
Microorganisms 2022, 10(1), 177; https://doi.org/10.3390/microorganisms10010177 - 14 Jan 2022
Cited by 9 | Viewed by 5037
Abstract
Toxocara canis and Toxocara cati are globally occurring zoonotic roundworms of dogs and cats. Migration and persistence of Toxocara larvae in the central nervous system of paratenic hosts including humans may cause clinical signs of neurotoxocarosis (NT). As pathomechanisms of NT and host [...] Read more.
Toxocara canis and Toxocara cati are globally occurring zoonotic roundworms of dogs and cats. Migration and persistence of Toxocara larvae in the central nervous system of paratenic hosts including humans may cause clinical signs of neurotoxocarosis (NT). As pathomechanisms of NT and host responses against Toxocara larvae are mostly unknown, whole-genome microarray transcription analysis was performed in cerebra and cerebella of experimentally infected C57Bl/6J mice as paratenic host model at days 14, 28, 70, 98, and 120 post-infection. Neuroinvasion of T. cati evoked 220 cerebral and 215 cerebellar differentially transcribed genes (DTGs), but no particular PANTHER (Protein ANalysis THrough Evolutionary Relationships) pathway was affected. In T. canis-infected mice, 1039 cerebral and 2073 cerebellar DTGs were identified. Statistically significant dysregulations occurred in various pathways, including cholesterol biosynthesis, apoptosis signaling, and the Slit/Robo mediated axon guidance as well as different pathways associated with the immune and defense response. Observed dysregulations of the cholesterol biosynthesis, as well as the Alzheimer disease-amyloid secretase pathway in conjunction with previous histopathological neurodegenerative findings, may promote the discussion of T. canis as a causative agent for dementia and/or Alzheimer’s disease. Furthermore, results contribute to a deeper understanding of the largely unknown pathogenesis and host-parasite interactions during NT, and may provide the basis for prospective investigations evaluating pathogenic mechanisms or designing novel diagnostic and therapeutic approaches. Full article
(This article belongs to the Special Issue Zoonotic Parasites: Toxoplasma gondii, Trichinella spp., and Toxocara spp.)
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17 pages, 1757 KiB  
Article
The Association of Toxoplasma gondii IgG Antibody and Chronic Kidney Disease Biomarkers
by Amani Babekir, Sayed Mostafa and Emmanuel Obeng-Gyasi
Microorganisms 2022, 10(1), 115; https://doi.org/10.3390/microorganisms10010115 - 6 Jan 2022
Cited by 9 | Viewed by 4278
Abstract
Background: Toxoplasma gondii (T. gondii) is a parasite that infects more than 40 million Americans and causes toxoplasmosis. Most cases of toxoplasmosis are asymptomatic; however, T. gondii is capable of invading organs like the kidney, causing chronic infections and cell destruction. [...] Read more.
Background: Toxoplasma gondii (T. gondii) is a parasite that infects more than 40 million Americans and causes toxoplasmosis. Most cases of toxoplasmosis are asymptomatic; however, T. gondii is capable of invading organs like the kidney, causing chronic infections and cell destruction. Methods: This study focused on evaluating the association between T. gondii exposure and chronic kidney disease (CKD) using data from the 2009–2010 National Health and Nutrition Examination Survey (NHANES). T. gondii exposure was assessed using Toxoplasma gondii IgG antibody status, and the status of CKD was assessed using the CKD biomarkers. The evaluation of risk rate and population prevalence was performed. In addition, multivariable regression models were used to further investigate this association after adjusting for sociodemographic, anthropometric, behavioral, and clinical covariates commonly associated with kidney dysfunction. Results: The positive T. gondii IgG antibody participants had significantly higher levels of CKD biomarkers, including second albumin-to-creatinine ratio (p = 0.0376), second albuminuria (p = 0.0005), and persistent albuminuria (p < 0.0001) compared to the negative participants. Furthermore, there were statistical associations between T. gondii exposure and the status of CKD (negative vs. positive) (p = 0.0001), and between T. gondii exposure and the CKD stage (negative, stage 1, …, stage 5) (p = 0.0004). Without adjusting for age, the positive T. gondii participants had a significantly higher risk (27% higher) of having CKD than the negative participants (RRcrude = 1.27, 95% CI: 1.09–1.49). The age-adjusted prevalence of CKD was higher among Toxoplasma-positive participants compared to the Toxoplasma-negative participants (10.45 vs. 8.99). T. gondii infection was significantly associated with CKD (OR = 1.40, 95% CI = 1.06–1.84, p = 0.00447) after adjusting for age, gender, race/ethnicity, and BMI. Age was positively associated with CKD (OR = 8.89, 95% CI = 6.31–12.51, p < 0.0001) with the participants 45+ years old being 8.89 times more likely to have CKD than those who are <45 years old, after adjusting for T. gondii infection, gender, race/ethnicity, and BMI. Moreover, positive T. gondii increased the odds of CKD progression (OR = 1.41, 95% CI = 1.07–1.86, p = 0.0424). Conclusions: Positive T. gondii IgG antibody is associated with CKD and the progression of CKD stages. This association is more apparent among older people. Further investigations are needed to examine these findings in different geographical locations and among differentially exposed populations. Full article
(This article belongs to the Section Public Health Microbiology)
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23 pages, 3392 KiB  
Article
A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor
by Joske Ruytinx, Shingo Miyauchi, Sebastian Hartmann-Wittulsky, Maíra de Freitas Pereira, Frédéric Guinet, Jean-Louis Churin, Carine Put, François Le Tacon, Claire Veneault-Fourrey, Francis Martin and Annegret Kohler
Microorganisms 2021, 9(12), 2612; https://doi.org/10.3390/microorganisms9122612 - 17 Dec 2021
Cited by 16 | Viewed by 6804
Abstract
Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and [...] Read more.
Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis. Full article
(This article belongs to the Special Issue Cellular and Molecular Basis of Plant-Fungal Interactions in Mycorrhizas)
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12 pages, 4366 KiB  
Article
Isolation of Lactococcus lactis from Whole Crop Rice and Determining Its Probiotic and Antimicrobial Properties towards Gastrointestinal Associated Bacteria
by Ilavenil Soundharrajan, Yong Hee Yoon, Karnan Muthusamy, Jeong-Sung Jung, Hyun Jeong Lee, Ouk-Kyu Han and Ki Choon Choi
Microorganisms 2021, 9(12), 2513; https://doi.org/10.3390/microorganisms9122513 - 3 Dec 2021
Cited by 10 | Viewed by 5276
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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12 pages, 1791 KiB  
Article
Characterization of the Biosynthetic Gene Cluster of Enterocin F4-9, a Glycosylated Bacteriocin
by Mohamed Abdelfattah Maky, Naoki Ishibashi, Jiro Nakayama and Takeshi Zendo
Microorganisms 2021, 9(11), 2276; https://doi.org/10.3390/microorganisms9112276 - 1 Nov 2021
Cited by 9 | Viewed by 3464
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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12 pages, 1864 KiB  
Article
Family SES Is Associated with the Gut Microbiome in Infants and Children
by Candace R. Lewis, Kevin S. Bonham, Shelley Hoeft McCann, Alexandra R. Volpe, Viren D’Sa, Marcus Naymik, Matt D. De Both, Matthew J. Huentelman, Kathryn Lemery-Chalfant, Sarah K. Highlander, Sean C. L. Deoni and Vanja Klepac-Ceraj
Microorganisms 2021, 9(8), 1608; https://doi.org/10.3390/microorganisms9081608 - 28 Jul 2021
Cited by 26 | Viewed by 7944
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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28 pages, 3734 KiB  
Article
Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
by Tim Piel, Giovanni Sandrini, Gerard Muyzer, Corina P. D. Brussaard, Pieter C. Slot, Maria J. van Herk, Jef Huisman and Petra M. Visser
Microorganisms 2021, 9(7), 1495; https://doi.org/10.3390/microorganisms9071495 - 13 Jul 2021
Cited by 27 | Viewed by 6769
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
(This article belongs to the Special Issue Global Intensification of Cyanobacterial Blooms: The Driving Forces and Mitigation Approaches)
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11 pages, 1367 KiB  
Article
Confounding Factors Influencing the Kinetics and Magnitude of Serological Response Following Administration of BNT162b2
by Jean-Louis Bayart, Laure Morimont, Mélanie Closset, Grégoire Wieërs, Tatiana Roy, Vincent Gerin, Marc Elsen, Christine Eucher, Sandrine Van Eeckhoudt, Nathalie Ausselet, Clara David, François Mullier, Jean-Michel Dogné, Julien Favresse and Jonathan Douxfils
Microorganisms 2021, 9(6), 1340; https://doi.org/10.3390/microorganisms9061340 - 21 Jun 2021
Cited by 33 | Viewed by 5351
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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12 pages, 1611 KiB  
Communication
SARS-CoV-2 Infects Hamster Testes
by Rafael K. Campos, Vidyleison N. Camargos, Sasha R. Azar, Clint A. Haines, Eduardo J. Eyzaguirre and Shannan L. Rossi
Microorganisms 2021, 9(6), 1318; https://doi.org/10.3390/microorganisms9061318 - 17 Jun 2021
Cited by 21 | Viewed by 15558
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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12 pages, 1527 KiB  
Article
Meropenem Pharmacokinetics and Target Attainment in Critically Ill Patients Are Not Affected by Extracorporeal Membrane Oxygenation: A Matched Cohort Analysis
by Matthias Gijsen, Erwin Dreesen, Pieter Annaert, Johan Nicolai, Yves Debaveye, Joost Wauters and Isabel Spriet
Microorganisms 2021, 9(6), 1310; https://doi.org/10.3390/microorganisms9061310 - 16 Jun 2021
Cited by 17 | Viewed by 4621
Abstract
Existing evidence is inconclusive whether meropenem dosing should be adjusted in patients receiving extracorporeal membrane oxygenation (ECMO). Therefore, the aim of this observational matched cohort study was to evaluate the effect of ECMO on pharmacokinetic (PK) variability and target attainment (TA) of meropenem. [...] Read more.
Existing evidence is inconclusive whether meropenem dosing should be adjusted in patients receiving extracorporeal membrane oxygenation (ECMO). Therefore, the aim of this observational matched cohort study was to evaluate the effect of ECMO on pharmacokinetic (PK) variability and target attainment (TA) of meropenem. Patients admitted to the intensive care unit (ICU) simultaneously treated with meropenem and ECMO were eligible. Patients were matched 1:1, based on renal function and body weight, with non-ECMO ICU patients. Meropenem blood sampling was performed over one or two dosing intervals. Population PK modelling was performed using NONMEM7.5. TA was defined as free meropenem concentrations >2 or 8 mg/L (i.e., 1 or 4× minimal inhibitory concentration, respectively) throughout the whole dosing interval. In total, 25 patients were included, contributing 27 dosing intervals. The overall TA was 56% and 26% for the 2 mg/L and 8 mg/L target, respectively. Population PK modelling identified estimated glomerular filtration rate according to the Chronic Kidney Disease Epidemiology equation and body weight, but not ECMO, as significant predictors. In conclusion, TA of meropenem was confirmed to be poor under standard dosing in critically ill patients but was not found to be influenced by ECMO. Future studies should focus on applying dose optimisation strategies for meropenem based on renal function, regardless of ECMO. Full article
(This article belongs to the Special Issue Complex Infectious Issues in Critically Ill Patients)
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21 pages, 11588 KiB  
Article
Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America
by Keisha Harrison and Chris Curtin
Microorganisms 2021, 9(5), 1060; https://doi.org/10.3390/microorganisms9051060 - 14 May 2021
Cited by 88 | Viewed by 18516
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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22 pages, 7778 KiB  
Article
Chemical Interactions at the Interface of Plant Root Hair Cells and Intracellular Bacteria
by Xiaoqian Chang, Kathryn L. Kingsley and James F. White
Microorganisms 2021, 9(5), 1041; https://doi.org/10.3390/microorganisms9051041 - 12 May 2021
Cited by 33 | Viewed by 11142
Abstract
In this research, we conducted histochemical, inhibitor and other experiments to evaluate the chemical interactions between intracellular bacteria and plant cells. As a result of these experiments, we hypothesize two chemical interactions between bacteria and plant cells. The first chemical interaction between endophyte [...] Read more.
In this research, we conducted histochemical, inhibitor and other experiments to evaluate the chemical interactions between intracellular bacteria and plant cells. As a result of these experiments, we hypothesize two chemical interactions between bacteria and plant cells. The first chemical interaction between endophyte and plant is initiated by microbe-produced ethylene that triggers plant cells to grow, release nutrients and produce superoxide. The superoxide combines with ethylene to form products hydrogen peroxide and carbon dioxide. In the second interaction between microbe and plant the microbe responds to plant-produced superoxide by secretion of nitric oxide to neutralize superoxide. Nitric oxide and superoxide combine to form peroxynitrite that is catalyzed by carbon dioxide to form nitrate. The two chemical interactions underlie hypothesized nutrient exchanges in which plant cells provide intracellular bacteria with fixed carbon, and bacteria provide plant cells with fixed nitrogen. As a consequence of these two interactions between endophytes and plants, plants grow and acquire nutrients from endophytes, and plants acquire enhanced oxidative stress tolerance, becoming more tolerant to abiotic and biotic stresses. Full article
(This article belongs to the Special Issue Plant Microbiome Augmentation and Stimulation: New Strategies to Grow Crops with Reduced Agrochemicals)
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21 pages, 2469 KiB  
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
by Jenny G. Maloney and Monica Santin
Microorganisms 2021, 9(5), 997; https://doi.org/10.3390/microorganisms9050997 - 5 May 2021
Cited by 70 | Viewed by 5792
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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15 pages, 3521 KiB  
Article
Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern
by Nariman Shahhosseini, George (Giorgi) Babuadze, Gary Wong and Gary P. Kobinger
Microorganisms 2021, 9(5), 926; https://doi.org/10.3390/microorganisms9050926 - 26 Apr 2021
Cited by 50 | Viewed by 7932
Abstract
One year since the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China, several variants of concern (VOC) have appeared around the world, with some variants seeming to pose a greater thread to public health due to enhanced transmissibility or [...] Read more.
One year since the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China, several variants of concern (VOC) have appeared around the world, with some variants seeming to pose a greater thread to public health due to enhanced transmissibility or infectivity. This study provides a framework for molecular characterization of novel VOC and investigates the effect of mutations on the binding affinity of the receptor-binding domain (RBD) to human angiotensin-converting enzyme 2 (hACE2) using in silico approach. Notable nonsynonymous mutations in RBD of VOC include the E484K and K417N/T that can be seen in South African and Brazilian variants, and N501Y and D614G that can be seen in all VOC. Phylogenetic analyses demonstrated that although the UK-VOC and the BR-VOC fell in the clade GR, they have different mutation signatures, implying an independent evolutionary pathway. The same is true about SA-VOC and COH-VOC felling in clade GH, but different mutation signatures. Combining molecular interaction modeling and the free energy of binding (FEB) calculations for VOC, it can be assumed that the mutation N501Y has the highest binding affinity in RBD for all VOC, followed by E484K (only for BR-VOC), which favors the formation of a stable complex. However, mutations at the residue K417N/T are shown to reduce the binding affinity. Once vaccination has started, there will be selective pressure that would be in favor of the emergence of novel variants capable of escaping the immune system. Therefore, genomic surveillance should be enhanced to find and monitor new emerging SARS-CoV-2 variants before they become a public health concern. Full article
(This article belongs to the Special Issue Discovery and Characterization of Novel/Emerging Viruses)
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28 pages, 1021 KiB  
Article
Global Landscape Review of Serotype-Specific Invasive Pneumococcal Disease Surveillance among Countries Using PCV10/13: The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) Project
by Maria Deloria Knoll, Julia C. Bennett, Maria Garcia Quesada, Eunice W. Kagucia, Meagan E. Peterson, Daniel R. Feikin, Adam L. Cohen, Marissa K. Hetrich, Yangyupei Yang, Jenna N. Sinkevitch, Krow Ampofo, Laurie Aukes, Sabrina Bacci, Godfrey Bigogo, Maria-Cristina C. Brandileone, Michael G. Bruce, Romina Camilli, Jesús Castilla, Guanhao Chan, Grettel Chanto Chacón, Pilar Ciruela, Heather Cook, Mary Corcoran, Ron Dagan, Kostas Danis, Sara de Miguel, Philippe De Wals, Stefanie Desmet, Yvonne Galloway, Theano Georgakopoulou, Laura L. Hammitt, Markus Hilty, Pak-Leung Ho, Sanjay Jayasinghe, James D. Kellner, Jackie Kleynhans, Mirjam J. Knol, Jana Kozakova, Karl Gústaf Kristinsson, Shamez N. Ladhani, Claudia S. Lara, Maria Eugenia León, Tiia Lepp, Grant A. Mackenzie, Lucia Mad’arová, Allison McGeer, Tuya Mungun, Jason M. Mwenda, J. Pekka Nuorti, Néhémie Nzoyikorera, Kazunori Oishi, Lucia Helena De Oliveira, Metka Paragi, Tamara Pilishvili, Rodrigo Puentes, Eric Rafai, Samir K. Saha, Larisa Savrasova, Camelia Savulescu, J. Anthony Scott, Kevin J. Scott, Fatima Serhan, Lena Petrova Setchanova, Nadja Sinkovec Zorko, Anna Skoczyńska, Todd D. Swarthout, Palle Valentiner-Branth, Mark van der Linden, Didrik F. Vestrheim, Anne von Gottberg, Inci Yildirim, Kyla Hayford and the PSERENADE Teamadd Show full author list remove Hide full author list
Microorganisms 2021, 9(4), 742; https://doi.org/10.3390/microorganisms9040742 - 2 Apr 2021
Cited by 39 | Viewed by 12028
Abstract
Serotype-specific surveillance for invasive pneumococcal disease (IPD) is essential for assessing the impact of 10- and 13-valent pneumococcal conjugate vaccines (PCV10/13). The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project aimed to evaluate the global evidence to estimate the impact of PCV10/13 by [...] Read more.
Serotype-specific surveillance for invasive pneumococcal disease (IPD) is essential for assessing the impact of 10- and 13-valent pneumococcal conjugate vaccines (PCV10/13). The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project aimed to evaluate the global evidence to estimate the impact of PCV10/13 by age, product, schedule, and syndrome. Here we systematically characterize and summarize the global landscape of routine serotype-specific IPD surveillance in PCV10/13-using countries and describe the subset that are included in PSERENADE. Of 138 countries using PCV10/13 as of 2018, we identified 109 with IPD surveillance systems, 76 of which met PSERENADE data collection eligibility criteria. PSERENADE received data from most (n = 63, 82.9%), yielding 240,639 post-PCV10/13 introduction IPD cases. Pediatric and adult surveillance was represented from all geographic regions but was limited from lower income and high-burden countries. In PSERENADE, 18 sites evaluated PCV10, 42 PCV13, and 17 both; 17 sites used a 3 + 0 schedule, 38 used 2 + 1, 13 used 3 + 1, and 9 used mixed schedules. With such a sizeable and generally representative dataset, PSERENADE will be able to conduct robust analyses to estimate PCV impact and inform policy at national and global levels regarding adult immunization, schedule, and product choice, including for higher valency PCVs on the horizon. Full article
(This article belongs to the Special Issue Bacterial Meningitis: Epidemiology and Vaccination)
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16 pages, 1218 KiB  
Article
Multi Locus Sequence Typing and spa Typing of Staphylococcus aureus Isolated from the Milk of Cows with Subclinical Mastitis in Croatia
by Luka Cvetnić, Marko Samardžija, Sanja Duvnjak, Boris Habrun, Marija Cvetnić, Vesna Jaki Tkalec, Dražen Đuričić and Miroslav Benić
Microorganisms 2021, 9(4), 725; https://doi.org/10.3390/microorganisms9040725 - 31 Mar 2021
Cited by 47 | Viewed by 4882
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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23 pages, 1767 KiB  
Article
Changes in Invasive Pneumococcal Disease Caused by Streptococcus pneumoniae Serotype 1 following Introduction of PCV10 and PCV13: Findings from the PSERENADE Project
by Julia C. Bennett, Marissa K. Hetrich, Maria Garcia Quesada, Jenna N. Sinkevitch, Maria Deloria Knoll, Daniel R. Feikin, Scott L. Zeger, Eunice W. Kagucia, Adam L. Cohen, Krow Ampofo, Maria-Cristina C. Brandileone, Dana Bruden, Romina Camilli, Jesús Castilla, Guanhao Chan, Heather Cook, Jennifer E. Cornick, Ron Dagan, Tine Dalby, Kostas Danis, Sara de Miguel, Philippe De Wals, Stefanie Desmet, Theano Georgakopoulou, Charlotte Gilkison, Marta Grgic-Vitek, Laura L. Hammitt, Markus Hilty, Pak-Leung Ho, Sanjay Jayasinghe, James D. Kellner, Jackie Kleynhans, Mirjam J. Knol, Jana Kozakova, Karl G. Kristinsson, Shamez N. Ladhani, Laura MacDonald, Grant A. Mackenzie, Lucia Mad’arová, Allison McGeer, Jolita Mereckiene, Eva Morfeldt, Tuya Mungun, Carmen Muñoz-Almagro, J. Pekka Nuorti, Metka Paragi, Tamara Pilishvili, Rodrigo Puentes, Samir K. Saha, Aalisha Sahu Khan, Larisa Savrasova, J. Anthony Scott, Anna Skoczyńska, Shigeru Suga, Mark van der Linden, Jennifer R. Verani, Anne von Gottberg, Brita A. Winje, Inci Yildirim, Khalid Zerouali, Kyla Hayford and the PSERENADE Teamadd Show full author list remove Hide full author list
Microorganisms 2021, 9(4), 696; https://doi.org/10.3390/microorganisms9040696 - 27 Mar 2021
Cited by 15 | Viewed by 8180
Abstract
Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally [...] Read more.
Streptococcus pneumoniae serotype 1 (ST1) was an important cause of invasive pneumococcal disease (IPD) globally before the introduction of pneumococcal conjugate vaccines (PCVs) containing ST1 antigen. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project gathered ST1 IPD surveillance data from sites globally and aimed to estimate PCV10/13 impact on ST1 IPD incidence. We estimated ST1 IPD incidence rate ratios (IRRs) comparing the pre-PCV10/13 period to each post-PCV10/13 year by site using a Bayesian multi-level, mixed-effects Poisson regression and all-site IRRs using a linear mixed-effects regression (N = 45 sites). Following PCV10/13 introduction, the incidence rate (IR) of ST1 IPD declined among all ages. After six years of PCV10/13 use, the all-site IRR was 0.05 (95% credibility interval 0.04–0.06) for all ages, 0.05 (0.04–0.05) for <5 years of age, 0.08 (0.06–0.09) for 5–17 years, 0.06 (0.05–0.08) for 18–49 years, 0.06 (0.05–0.07) for 50–64 years, and 0.05 (0.04–0.06) for ≥65 years. PCV10/13 use in infant immunization programs was followed by a 95% reduction in ST1 IPD in all ages after approximately 6 years. Limited data availability from the highest ST1 disease burden countries using a 3 + 0 schedule constrains generalizability and data from these settings are needed. Full article
(This article belongs to the Special Issue Bacterial Meningitis: Epidemiology and Vaccination)
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19 pages, 16344 KiB  
Article
Persistent Southern Tomato Virus (STV) Interacts with Cucumber Mosaic and/or Pepino Mosaic Virus in Mixed- Infections Modifying Plant Symptoms, Viral Titer and Small RNA Accumulation
by Laura Elvira González, Rosa Peiró, Luis Rubio and Luis Galipienso
Microorganisms 2021, 9(4), 689; https://doi.org/10.3390/microorganisms9040689 - 26 Mar 2021
Cited by 21 | Viewed by 5816
Abstract
Southern tomato virus (STV) is a persistent virus that was, at the beginning, associated with some tomato fruit disorders. Subsequent studies showed that the virus did not induce apparent symptoms in single infections. Accordingly, the reported symptoms could be induced by the interaction [...] Read more.
Southern tomato virus (STV) is a persistent virus that was, at the beginning, associated with some tomato fruit disorders. Subsequent studies showed that the virus did not induce apparent symptoms in single infections. Accordingly, the reported symptoms could be induced by the interaction of STV with other viruses, which frequently infect tomato. Here, we studied the effect of STV in co- and triple-infections with Cucumber mosaic virus (CMV) and Pepino mosaic virus (PepMV). Our results showed complex interactions among these viruses. Co-infections leaded to a synergism between STV and CMV or PepMV: STV increased CMV titer and plant symptoms at early infection stages, whereas PepMV only exacerbated the plant symptoms. CMV and PepMV co-infection showed an antagonistic interaction with a strong decrease of CMV titer and a modification of the plant symptoms with respect to the single infections. However, the presence of STV in a triple-infection abolished this antagonism, restoring the CMV titer and plant symptoms. The siRNAs analysis showed a total of 78 miRNAs, with 47 corresponding to novel miRNAs in tomato, which were expressed differentially in the plants that were infected with these viruses with respect to the control mock-inoculated plants. These miRNAs were involved in the regulation of important functions and their number and expression level varied, depending on the virus combination. The number of vsiRNAs in STV single-infected tomato plants was very small, but STV vsiRNAs increased with the presence of CMV and PepMV. Additionally, the rates of CMV and PepMV vsiRNAs varied depending on the virus combination. The frequencies of vsiRNAs in the viral genomes were not uniform, but they were not influenced by other viruses. Full article
(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)
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19 pages, 1064 KiB  
Article
Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli
by Katharina Juraschek, Maria Borowiak, Simon H. Tausch, Burkhard Malorny, Annemarie Käsbohrer, Saria Otani, Stefan Schwarz, Diana Meemken, Carlus Deneke and Jens Andre Hammerl
Microorganisms 2021, 9(3), 598; https://doi.org/10.3390/microorganisms9030598 - 14 Mar 2021
Cited by 35 | Viewed by 6130
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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15 pages, 769 KiB  
Article
The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors
by Jessica L. E. Wimmer, Andrey do Nascimento Vieira, Joana C. Xavier, Karl Kleinermanns, William F. Martin and Martina Preiner
Microorganisms 2021, 9(2), 458; https://doi.org/10.3390/microorganisms9020458 - 23 Feb 2021
Cited by 22 | Viewed by 7656
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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21 pages, 3267 KiB  
Article
Hypo- and Hyper-Virulent Listeria monocytogenes Clones Persisting in Two Different Food Processing Plants of Central Italy
by Fabrizia Guidi, Massimiliano Orsini, Alexandra Chiaverini, Marina Torresi, Patrizia Centorame, Vicdalia Aniela Acciari, Romolo Salini, Barbara Palombo, Giorgio Brandi, Giulia Amagliani, Giuditta Fiorella Schiavano, Francesca Romana Massacci, Stefano Fisichella, Marco Di Domenico, Massimo Ancora, Adriano Di Pasquale, Anna Duranti, Cesare Cammà, Francesco Pomilio and Giuliana Blasi
Microorganisms 2021, 9(2), 376; https://doi.org/10.3390/microorganisms9020376 - 13 Feb 2021
Cited by 29 | Viewed by 5815
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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13 pages, 1652 KiB  
Article
Performance of a Four-Antigen Staphylococcus aureus Vaccine in Preclinical Models of Invasive S. aureus Disease
by Ingrid L. Scully, Yekaterina Timofeyeva, Arthur Illenberger, Peimin Lu, Paul A. Liberator, Kathrin U. Jansen and Annaliesa S. Anderson
Microorganisms 2021, 9(1), 177; https://doi.org/10.3390/microorganisms9010177 - 15 Jan 2021
Cited by 20 | Viewed by 5622
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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13 pages, 2951 KiB  
Communication
Vibrio Colonization Is Highly Dynamic in Early Microplastic-Associated Biofilms as Well as on Field-Collected Microplastics
by Katharina Kesy, Matthias Labrenz, Brittan S. Scales, Bernd Kreikemeyer and Sonja Oberbeckmann
Microorganisms 2021, 9(1), 76; https://doi.org/10.3390/microorganisms9010076 - 30 Dec 2020
Cited by 65 | Viewed by 6156
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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