Journal Description
Microorganisms
Microorganisms
is a scientific, peer-reviewed, open access journal of microbiology, published monthly online by MDPI. The Hellenic Society Mikrobiokosmos (MBK), the Spanish Society for Nitrogen Fixation (SEFIN) and the Society for Microbial Ecology and Disease (SOMED) are affiliated with the Microorganisms, and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Microbiology) / CiteScore - Q2 (Microbiology (medical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 15.1 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
- Testimonials: See what our editors and authors say about the Microorganisms.
- Companion journal: Applied Microbiology.
Impact Factor:
4.5 (2022);
5-Year Impact Factor:
4.8 (2022)
Latest Articles
Abundance, Characterization and Diversity of Culturable Anoxygenic Phototrophic Bacteria in Manitoban Marshlands
Microorganisms 2024, 12(5), 1007; https://doi.org/10.3390/microorganisms12051007 (registering DOI) - 17 May 2024
Abstract
Marshes are an important ecosystem, acting as a biodiversity hotspot, a carbon sink and a bioremediation site, breaking down anthropogenic waste such as antibiotics, metals and fertilizers. Due to their participation in these metabolic activities and their capability to contribute to primary productivity,
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Marshes are an important ecosystem, acting as a biodiversity hotspot, a carbon sink and a bioremediation site, breaking down anthropogenic waste such as antibiotics, metals and fertilizers. Due to their participation in these metabolic activities and their capability to contribute to primary productivity, the microorganisms in such habitats have become of interest to investigate. Since Proteobacteria were previously found to be abundant and the waters are well aerated and organic-rich, this study on the presence of anoxygenic phototrophic bacteria, purple non-sulfur bacteria and aerobic anoxygenic phototrophs in marshes was initiated. One sample was collected at each of the seven Manitoban sites, and anoxygenic phototrophs were cultivated and enumerated. A group of 14 strains, which represented the phylogenetic diversity of the isolates, was physiologically investigated further. Aerobic anoxygenic phototrophs and purple non-sulfur bacteria were present at each location, and they belonged to the α- and β-Proteobacteria subphyla. Some were closely related to known heavy metal reducers (Brevundimonas) and xenobiotic decomposers (Novosphingobium and Sphingomonas). All were able to synthesize the photosynthetic complexes aerobically. This research highlights the diversity of and the potential contributions that anoxygenic phototrophs make to the essential functions taking place in wetlands.
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(This article belongs to the Section Environmental Microbiology)
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Ticks and Tick-Borne Pathogens Circulating in Peri-Domestic Areas in Mainland Portugal
by
Leonardo Moerbeck, Ricardo Parreira, Magdalena Szczotko, Gonçalo Seixas, Rita Velez, Małgorzata Dmitryjuk, Ana Sofia Santos, Ana Domingos and Sandra Antunes
Microorganisms 2024, 12(5), 1006; https://doi.org/10.3390/microorganisms12051006 - 16 May 2024
Abstract
Over the years, tick-borne pathogens (TBPs) have garnered significant interest due to their medical, veterinary and economic importance. Additionally, TBPs have drawn attention to how these microorganisms interact with their own vectors, increasing the risk to human and animal infection of emerging and
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Over the years, tick-borne pathogens (TBPs) have garnered significant interest due to their medical, veterinary and economic importance. Additionally, TBPs have drawn attention to how these microorganisms interact with their own vectors, increasing the risk to human and animal infection of emerging and reemerging zoonoses. In this sense, ticks, which are obligate hematophagous ectoparasites, have a key role in maintaining and transmitting TBPs among humans and animals. The aim of this study was to assess the prevalence of neglected TBPs in mainland Portugal, namely Anaplasma spp., Babesia spp., Ehrlichia spp. and Neoehrlichia mikurensis. DNA fragments were detected in questing ticks collected from five different ecological areas under investigation. To the best of the authors’ knowledge, this study reports new worldwide findings, including B. bigemina infecting Ixodes frontalis, Ixodes ricinus and Rhipicephalus sanguineus sensu lato. Additionally, it presents new findings in Portugal of N. mikurensis infecting I. ricinus and of presumably Wolbachia endosymbionts being detected in I. ricinus. Overall, there were 208 tick samples that were negative for all screened TBPs. The results herein obtained raise concerns about the circulation of neglected TBPs in mainland Portugal, especially in anthropophilic ticks, highlighting the importance of adopting a One Health perspective.
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(This article belongs to the Special Issue The One Health Challenge: Zoonotic Parasites)
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Open AccessArticle
Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions
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Laís F. O. Lima, Amanda T. Alker, Megan M. Morris, Robert A. Edwards, Samantha J. de Putron and Elizabeth A. Dinsdale
Microorganisms 2024, 12(5), 1005; https://doi.org/10.3390/microorganisms12051005 - 16 May 2024
Abstract
Coral reef health is tightly connected to the coral holobiont, which is the association between the coral animal and a diverse microbiome functioning as a unit. The coral holobiont depends on key services such as nitrogen and sulfur cycling mediated by the associated
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Coral reef health is tightly connected to the coral holobiont, which is the association between the coral animal and a diverse microbiome functioning as a unit. The coral holobiont depends on key services such as nitrogen and sulfur cycling mediated by the associated bacteria. However, these microbial services may be impaired in response to environmental changes, such as thermal stress. A perturbed microbiome may lead to coral bleaching and disease outbreaks, which have caused an unprecedented loss in coral cover worldwide, particularly correlated to a warming ocean. The response mechanisms of the coral holobiont under high temperatures are not completely understood, but the associated microbial community is a potential source of acquired heat-tolerance. Here we investigate the effects of increased temperature on the taxonomic and functional profiles of coral surface mucous layer (SML) microbiomes in relationship to coral–algal physiology. We used shotgun metagenomics in an experimental setting to understand the dynamics of microbial taxa and genes in the SML microbiome of the coral Pseudodiploria strigosa under heat treatment. The metagenomes of corals exposed to heat showed high similarity at the level of bacterial genera and functional genes related to nitrogen and sulfur metabolism and stress response. The coral SML microbiome responded to heat with an increase in the relative abundance of taxa with probiotic potential, and functional genes for nitrogen and sulfur acquisition. Coral–algal physiology significantly explained the variation in the microbiome at taxonomic and functional levels. These consistent and specific microbial taxa and gene functions that significantly increased in proportional abundance in corals exposed to heat are potentially beneficial to coral health and thermal resistance.
Full article
(This article belongs to the Special Issue Marine Microbial Diversity: Focus on Corals)
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Open AccessReview
Exploring the Toxin-Mediated Mechanisms in Clostridioides difficile Infection
by
Evdokia Pourliotopoulou, Theodoros Karampatakis and Melania Kachrimanidou
Microorganisms 2024, 12(5), 1004; https://doi.org/10.3390/microorganisms12051004 - 16 May 2024
Abstract
Clostridioides difficile infection (CDI) is the leading cause of nosocomial antibiotic-associated diarrhea, and colitis, with increasing incidence and healthcare costs. Its pathogenesis is primarily driven by toxins produced by the bacterium C. difficile, Toxin A (TcdA) and Toxin B (TcdB). Certain strains
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Clostridioides difficile infection (CDI) is the leading cause of nosocomial antibiotic-associated diarrhea, and colitis, with increasing incidence and healthcare costs. Its pathogenesis is primarily driven by toxins produced by the bacterium C. difficile, Toxin A (TcdA) and Toxin B (TcdB). Certain strains produce an additional toxin, the C. difficile transferase (CDT), which further enhances the virulence and pathogenicity of C. difficile. These toxins disrupt colonic epithelial barrier integrity, and induce inflammation and cellular damage, leading to CDI symptoms. Significant progress has been made in the past decade in elucidating the molecular mechanisms of TcdA, TcdB, and CDT, which provide insights into the management of CDI and the future development of novel treatment strategies based on anti-toxin therapies. While antibiotics are common treatments, high recurrence rates necessitate alternative therapies. Bezlotoxumab, targeting TcdB, is the only available anti-toxin, yet limitations persist, prompting ongoing research. This review highlights the current knowledge of the structure and mechanism of action of C. difficile toxins and their role in disease. By comprehensively describing the toxin-mediated mechanisms, this review provides insights for the future development of novel treatment strategies and the management of CDI.
Full article
(This article belongs to the Special Issue Recent Advances in Clostridioides difficile Infection)
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Open AccessArticle
Whole Genome Sequence Analysis of Listeria monocytogenes Isolates Obtained from the Beef Production Chain in Gauteng Province, South Africa
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James Gana, Nomakorinte Gcebe, Rian Edward Pierneef, Yi Chen, Rebone Moerane and Abiodun Adewale Adesiyun
Microorganisms 2024, 12(5), 1003; https://doi.org/10.3390/microorganisms12051003 - 16 May 2024
Abstract
The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes obtained from the beef production chain (cattle farms, abattoirs, and retail outlets) in Gauteng province, South Africa. The sequence types (STs), clonal complexes (CCs),
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The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes obtained from the beef production chain (cattle farms, abattoirs, and retail outlets) in Gauteng province, South Africa. The sequence types (STs), clonal complexes (CCs), and the lineages of the isolates were determined using in silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence and antimicrobial genes, plasmids, proviruses/prophages, and the CRISPR-Cas system. The study investigated any association of the detected genes to the origin in the beef production chain of the L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were seven STs, six CCs, forty-four putative virulence factors, two resistance genes, one plasmid with AMR genes, and three with conjugative genes, one CRISPR gene, and all 60 isolates were positive for proviruses/prophages. Among the seven STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST frequency varying significantly (p < 0.001). The predominant CC detected were CC2 (21.7%) and CC204 (46.7%) in lineages I and II, respectively. Of the 44 virulence factors detected, 26 (across Listeria Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency varied significantly (p < 0.001). The two AMR genes (fosX and vga(G)) detected were present in all 60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in three (5%) isolates. A CRISPR-Cas system was detected in six (10%), and all the isolates carried proviruses/prophages. The source and sample type significantly affected the frequencies of STs and virulence factors in the isolates of L. monocytogenes. The presence of fosX and vga(G) genes in all L. monocytogenes isolates obtained from the three industries of the beef production chain can potentially cause therapeutic implications. Our study, which characterized L. monocytogenes recovered from the three levels in the beef production chain, is the first time genomics was performed on this type of data set in the country, and this provides insights into the health implications of Listeria.
Full article
(This article belongs to the Special Issue Foodborne Pathogens: Detection Methods, Food Safety, and Public Health 2.0)
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Open AccessArticle
Real-Time PCR (qtPCR) to Discover the Fate of Plant Growth-Promoting Rhizobacteria (PGPR) in Agricultural Soils
by
Ilenia Iosa, Caterina Agrimonti and Nelson Marmiroli
Microorganisms 2024, 12(5), 1002; https://doi.org/10.3390/microorganisms12051002 - 16 May 2024
Abstract
To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time
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To optimize the application of plant growth-promoting rhizobacteria (PGPR) in field trials, tracking methods are needed to assess their shelf life and to determine the elements affecting their effectiveness and their interactions with plants and native soil microbiota. This work developed a real-time PCR (qtPCR) method which traces and quantifies bacteria when added as microbial consortia, including five PGPR species: Burkholderia ambifaria, Bacillus amyloliquefaciens, Azotobacter chroococcum, Pseudomonas fluorescens, and Rahnella aquatilis. Through a literature search and in silico sequence analyses, a set of primer pairs which selectively tag three bacterial species (B. ambifaria, B. amyloliquefaciens and R. aquatilis) was retrieved. The primers were used to trace these microbial species in a field trial in which the consortium was tested as a biostimulant on two wheat varieties, in combination with biochar and the mycorrhizal fungus Rhizophagus intraradices. The qtPCR assay demonstrated that the targeted bacteria had colonized and grown into the soil, reaching a maximum of growth between 15 and 20 days after inoculum. The results also showed biochar had a positive effect on PGPR growth. In conclusion, qtPCR was once more an effective method to trace the fate of supplied bacterial species in the consortium when used as a cargo system for their delivery.
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(This article belongs to the Special Issue Microbial Ecology of Soil Microorganisms, Networks with Plants and Ecosystem Services)
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Open AccessCommunication
Differential Epigenetic Regulation in Uninfected and Tuberculosis–Human Immunodeficiency Virus Co-Infected Patients
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Katlego Mamabolo, Reubina Wadee, Yvonne Perner, Pumza Magangane, Sanelisiwe Thinasonke Duze and Musa Marimani
Microorganisms 2024, 12(5), 1001; https://doi.org/10.3390/microorganisms12051001 - 16 May 2024
Abstract
This study aimed to compare the degree of epigenetic modifications between a TB-HIV co-infected cohort and uninfected subjects. Formalin-fixed paraffin-embedded (FFPE) tissues were retrieved from 45 TB-HIV co-infected and 45 control individuals. Real-time PCR was applied to compare the level of expression of
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This study aimed to compare the degree of epigenetic modifications between a TB-HIV co-infected cohort and uninfected subjects. Formalin-fixed paraffin-embedded (FFPE) tissues were retrieved from 45 TB-HIV co-infected and 45 control individuals. Real-time PCR was applied to compare the level of expression of genes involved in epigenetic regulation. The protein multiplex assay was used to assess the degree of protein modification. DNA sequencing was used to determine the evolutionary relationships between the infecting HIV and Mtb strains. Our results indicated a significant increase in the expression of the five candidate genes in the patients with TB-HIV relative to the control cohort. A sharp increase in the degree of histone methylation, acetylation and phosphorylation was observed in TB-HIV co-infected patients. The phylogenetic analysis classified the strains into three distinct HIV clusters and five Mtb clusters. The disparities in the expression profiles of our candidate genes between the TB-HIV cohort and non-TB-HIV group highlights the important role played by various TB and HIV strains in regulating the host gene expression landscape.
Full article
(This article belongs to the Special Issue Understanding the Interactions between HIV and Other Infections and Their Impact on Immune Function)
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Open AccessArticle
The Application of Probiotic Bacteria from Strawberry (Fragaria ananassa × Duch.) in the Fermentation of Strawberry Tree Fruit (Arbutus unedo L.) Extract
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Deni Kostelac, Filip Dolenec, Anica Bebek Markovinović, Ksenija Markov, Danijela Bursać Kovačević and Jadranka Frece
Microorganisms 2024, 12(5), 1000; https://doi.org/10.3390/microorganisms12051000 - 15 May 2024
Abstract
The search for unexplored plant resources that would provide a good basis for the development of novel probiotic functional foods is rapidly increasing. In this context, the strawberry tree fruit (Arbutus unedo L.) is particularly interesting, as it is rich in numerous
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The search for unexplored plant resources that would provide a good basis for the development of novel probiotic functional foods is rapidly increasing. In this context, the strawberry tree fruit (Arbutus unedo L.) is particularly interesting, as it is rich in numerous antioxidant bioactive compounds that have been shown to be beneficial to health, but have not yet found industrial applications. In this work, the probiotic characterization of lactic acid bacteria strain Lactiplantibacillus plantarum DB2, isolated from strawberries (Fragaria ananassa × Duch.), was performed. The tested strain proved to be safe to use, displaying no antibiotic resistance or hemolytic activity. Due to its proven probiotic potential during simulated gastrointestinal transit, its antimicrobial activity, and its coaggregation with pathogens, it was selected for fermentation of an aqueous Arbutus unedo L. extract, which was subsequently microencapsulated and freeze-dried to extend its shelf life and preserve its functional properties. The antioxidant activity of the ferment obtained was maintained (80%), while after microencapsulation and freeze-drying, about 50% and 20% of the antioxidant activity was retained, respectively. In conclusion, this study demonstrates for the first time the application of probiotics isolated from strawberries in the fermentation of strawberry tree extract and monitors the antioxidant activity during post-fermentation formulation, paving the way for a potential industrial application of this underutilized plant.
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(This article belongs to the Special Issue Microorganisms in Functional Foods)
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Open AccessBrief Report
Specific Mycobacterium tuberculosis Strain Circulating in Prison Revealed by Cost-Effective Amplicon Sequencing
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Joaquín Hurtado, María Noel Bentancor, Paula Laserra, Cecilia Coitinho and Gonzalo Greif
Microorganisms 2024, 12(5), 999; https://doi.org/10.3390/microorganisms12050999 - 15 May 2024
Abstract
This scientific study focuses on tuberculosis (TB) within prison settings, where persons deprived of liberty (PDL) face significantly higher rates of the disease compared to the general population. The research employs the low-cost amplicon sequencing of Mycobacterium tuberculosis strains, aiming first to identify
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This scientific study focuses on tuberculosis (TB) within prison settings, where persons deprived of liberty (PDL) face significantly higher rates of the disease compared to the general population. The research employs the low-cost amplicon sequencing of Mycobacterium tuberculosis strains, aiming first to identify specific lineages and also to detect mutations associated with drug resistance. The method involves multiplex amplification, DNA extraction, and sequencing, providing valuable insights into TB dynamics and resistance-mutation profiles within the prison system at an affordable cost. The study identifies a characteristic lineage (X) circulating among PDLs in the penitentiary system in Uruguay, absent in the general population, and notes its prevalence at prison entry. No high-confidence mutations associated with drug resistance were found. The findings underscore the importance of molecular epidemiology in TB control, emphasizing the potential for intra-prison transmissions and the need for broader studies to understand strain dynamics.
Full article
(This article belongs to the Special Issue Mycobacterial Tuberculosis Pathogenesis and Vaccine Development)
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Open AccessArticle
Improving Surfactin Production in Bacillus subtilis 168 by Metabolic Engineering
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Zihao Guo, Jiuyu Sun, Qinyuan Ma, Mengqi Li, Yamin Dou, Shaomei Yang and Xiuzhen Gao
Microorganisms 2024, 12(5), 998; https://doi.org/10.3390/microorganisms12050998 - 15 May 2024
Abstract
Surfactin is widely used in the petroleum extraction, cosmetics, biopharmaceuticals and agriculture industries. It possesses antibacterial and antiviral activities and can reduce interfacial tension. Bacillus are commonly used as production chassis, but wild-type Bacillus subtilis 168 cannot synthesise surfactin. In this study, the
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Surfactin is widely used in the petroleum extraction, cosmetics, biopharmaceuticals and agriculture industries. It possesses antibacterial and antiviral activities and can reduce interfacial tension. Bacillus are commonly used as production chassis, but wild-type Bacillus subtilis 168 cannot synthesise surfactin. In this study, the phosphopantetheinyl transferase (PPTase) gene sfp* (with a T base removed) was overexpressed and enzyme activity was restored, enabling B. subtilis 168 to synthesise surfactin with a yield of 747.5 ± 6.5 mg/L. Knocking out ppsD and yvkC did not enhance surfactin synthesis. Overexpression of predicted surfactin transporter gene yfiS increased its titre to 1060.7 ± 89.4 mg/L, while overexpression of yerP, ycxA and ycxA-efp had little or negative effects on surfactin synthesis, suggesting YfiS is involved in surfactin efflux. By replacing the native promoter of the srfA operon encoding surfactin synthase with three promoters, surfactin synthesis was significantly reduced. However, knockout of the global transcriptional regulator gene codY enhanced the surfactin titre to 1601.8 ± 91.9 mg/L. The highest surfactin titre reached 3.89 ± 0.07 g/L, with the yield of 0.63 ± 0.02 g/g DCW, after 36 h of fed-batch fermentation in 5 L fermenter. This study provides a reference for further understanding surfactin synthesis and constructing microbial cell factories.
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(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)
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Open AccessArticle
Study of the Impact of the Parasitic Microalgae Coccomyxa parasitica on the Health of Bivalve Modiolus kurilensis
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Ayna V. Tumas, Veronika A. Slatvinskaya, Vadim V. Kumeiko and Yulia N. Sokolnikova
Microorganisms 2024, 12(5), 997; https://doi.org/10.3390/microorganisms12050997 - 15 May 2024
Abstract
The invasion of bivalves by parasitic microalgae Coccomyxa is widespread and causes pathologies and dysfunctions of the organs, especially in the most valuable products: the mantle and the muscle. The pathogenesis of the disease remains completely unknown. In this study, based on a
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The invasion of bivalves by parasitic microalgae Coccomyxa is widespread and causes pathologies and dysfunctions of the organs, especially in the most valuable products: the mantle and the muscle. The pathogenesis of the disease remains completely unknown. In this study, based on a macroscopic examination of Modiolus kurilensis and microalgae count in each infected individual, four stages of disease development with characteristic pathognomonic symptoms were described. During the progression of the disease, the concentration of alkaline phosphatase, glucose, calcium, hemolytic and agglutinating activities, number of basophils, eosinophils, phagocytes, and cells with reactive oxygen species increased in the hemolymph, while number of agranulocytes, cells with lysosomes, dead hemocytes, total protein concentration, as well as the weight of mollusks decreased. In the nephridia and digestive gland, necrosis, invasion of Nematopsis sp., hemocyte infiltration, and fibrosis increased. The ratio of changed tubules and occurrence of granulocytomas increased in the digestive gland, while the base membrane, nephrocytes and concretions changed in the nephridia. This study helps establish the variability of these parameters under normal conditions and their alteration during the disease. Moreover, these findings can be used for veterinary monitoring of the state of bivalves in natural and aquaculture populations.
Full article
(This article belongs to the Special Issue Microorganisms and Diseases Associated with Aquatic Animals 2.0)
Open AccessArticle
Comparative In Vitro Killing by Pradofloxacin in Comparison to Ceftiofur, Enrofloxacin, Florfenicol, Marbofloxacin, Tildipirosin, Tilmicosin and Tulathromycin against Bovine Respiratory Bacterial Pathogens
by
Joseph M. Blondeau and Shantelle D. Fitch
Microorganisms 2024, 12(5), 996; https://doi.org/10.3390/microorganisms12050996 - 15 May 2024
Abstract
Pradofloxacin is the newest of the veterinary fluoroquinolones to be approved for use in animals—initially companion animals and most recently food animals. It has a broad spectrum of in vitro activity, working actively against Gram-positive/negative, atypical and some anaerobic microorganisms. It simultaneously targets
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Pradofloxacin is the newest of the veterinary fluoroquinolones to be approved for use in animals—initially companion animals and most recently food animals. It has a broad spectrum of in vitro activity, working actively against Gram-positive/negative, atypical and some anaerobic microorganisms. It simultaneously targets DNA gyrase (topoisomerase type II) and topoisomerase type IV, suggesting a lower propensity to select for antimicrobial resistance. The purpose of this study was to determine the rate and extent of bacterial killing by pradofloxacin against bovine strains of Mannheimia haemolytica and Pasteurella multocida, in comparison with several other agents (ceftiofur, enrofloxacin, florfenicol, marbofloxacin, tildipirosin, tilmicosin and tulathromycin) using four clinically relevant drug concentrations: minimum inhibitory and mutant prevention drug concentration, maximum serum and maximum tissue drug concentrations. At the maximum serum and tissue drug concentrations, pradofloxacin killed 99.99% of M. haemolytica cells following 5 min of drug exposure (versus growth to 76% kill rate for the other agents) and 94.-1−98.6% of P. multocida following 60−120 min of drug exposure (versus growth to 98.6% kill rate for the other agents). Statistically significant differences in kill rates were seen between the various drugs tested depending on drug concentration and time of sampling after drug exposure.
Full article
(This article belongs to the Special Issue Bacterial Infections and Antibiotic Resistance in Veterinary Medicine)
Open AccessArticle
Increasing Rate of Fatal Streptococcus pyogenes Bacteriemia—A Challenge for Prompt Diagnosis and Appropriate Therapy in Real Praxis
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Vaclava Adamkova, Vanda Gabriela Adamkova, Gabriela Kroneislova, Jan Zavora, Marie Kroneislova, Michal Huptych and Helena Lahoda Brodska
Microorganisms 2024, 12(5), 995; https://doi.org/10.3390/microorganisms12050995 - 15 May 2024
Abstract
Streptococcus pyogenes, group A streptococci (GAS) bacteriaemia, is a life-threatening infection with high mortality, requiring fast diagnosis together with the use of appropriate antibiotic therapy as soon as possible. Our study analysed data from 93 patients with GAS bacteraemia at the General
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Streptococcus pyogenes, group A streptococci (GAS) bacteriaemia, is a life-threatening infection with high mortality, requiring fast diagnosis together with the use of appropriate antibiotic therapy as soon as possible. Our study analysed data from 93 patients with GAS bacteraemia at the General University Hospital in Prague between January 2006 and March 2024. In the years 2016–2019 there was an increase in GAS bacteraemia. Mortality in the period 2006–2019 was 21.9%; in the period 2020–2024, the mortality increased to 41.4%, p = 0.08. At the same time, in the post-2020 period, the time from hospital admission to death was reduced from 9.5 days to 3 days. A significant predictor of worse outcome in this period was high levels of procalcitonin, >35.1 µg/L (100% sensitivity and 82.35% specificity), and lactate, >5 mmol/L (90.91% sensitivity and 91.67% specificity). Myoglobin was a significant predictor in both compared periods, the AUC was 0.771, p = 0.044, and the AUC was an even 0.889, p ≤ 0.001, respectively. All isolates of S. pyogenes were susceptible to penicillin, and resistance to clindamycin was 20.3% from 2006–2019 and 10.3% in 2020–2024. Appropriate therapy was initiated in 89.1%. and 96.6%, respectively. We hypothesise that the increase in mortality after 2020 might be due to a decrease in the immune status of the population.
Full article
(This article belongs to the Special Issue Bacteremia and Sepsis)
Open AccessArticle
Assessment of the Safety and Probiotic Properties of Enterococcus faecium B13 Isolated from Fermented Chili
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Jingmin Xiao, Cai Chen, Zhuxian Fu, Shumin Wang and Fan Luo
Microorganisms 2024, 12(5), 994; https://doi.org/10.3390/microorganisms12050994 - 15 May 2024
Abstract
Enterococcus faecium B13, selected from fermentation chili, has been proven to promote animal growth by previous studies, but it belongs to opportunistic pathogens, so a comprehensive evaluation of its probiotic properties and safety is necessary. In this study, the probiotic properties and safety
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Enterococcus faecium B13, selected from fermentation chili, has been proven to promote animal growth by previous studies, but it belongs to opportunistic pathogens, so a comprehensive evaluation of its probiotic properties and safety is necessary. In this study, the probiotic properties and safety of B13 were evaluated at the genetic and phenotype levels in vitro and then confirmed in vivo. The genome of B13 contains one chromosome and two plasmids. The average nucleotide identity indicated that B13 was most closely related to the fermentation-plant-derived strain. The strain does not carry the major virulence genes of the clinical E. faecium strains but contains aac(6′)-Ii, ant (6)-Ia, msrC genes. The strain had a higher tolerance to acid at pH 3.0, 4.0, and 0.3% bile salt and a 32.83% free radical DPPH clearance rate. It can adhere to Caco-2 cells and reduce the adhesion of E. coli to Caco-2 cells. The safety assessment revealed that the strain showed no hemolysis and did not exhibit gelatinase, ornithine decarboxylase, lysine decarboxylase, or tryptophanase activity. It was sensitive to twelve antibiotics but was resistant to erythromycin, rifampicin, tetracycline, doxycycline, and minocycline. Experiments in vivo have shown that B13 can be located in the ileum and colon and has no adverse effects on experiment animals. After 28 days of feeding, B13 did not remarkable change the α-diversity of the gut flora or increase the virulence genes. Our study demonstrated that E. faecium B13 may be used as a probiotic candidate.
Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
Open AccessArticle
The Role of Bacteria in Acute Oak Decline in South-West Poland
by
Miłosz Tkaczyk and Katarzyna Sikora
Microorganisms 2024, 12(5), 993; https://doi.org/10.3390/microorganisms12050993 - 15 May 2024
Abstract
The process of multifactorial oak disease has been of interest to scientists from all over the world for many years. Recently, a new phenomenon has been added to the model related to oak decline, acute oak dieback, which causes oak decline and was
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The process of multifactorial oak disease has been of interest to scientists from all over the world for many years. Recently, a new phenomenon has been added to the model related to oak decline, acute oak dieback, which causes oak decline and was first described in the UK. This study presents research on this phenomenon in the area of the largest oak stand complex in Poland, the so-called Krotoszyn Plateau. This work was carried out in two stages. In the first stage, 54 trees were tested for the presence of bacteria using molecular biology (real-time PCR). Subsequently, a tissue fragment was taken for inoculation from the trees in which the presence of B. goodwinii and G. quercinecans bacteria was confirmed. The isolates obtained were used to test Koch’s postulates and for biochemical analyses for Polish strains. In addition, the results obtained were also compared with the presence of A. biguttatus, which is considered a bacterial vector, which, in turn, confirmed that the bacteria responsible for the AOD phenomenon can also be present in trees not inhabited by this insect. The results obtained confirmed the presence of bacteria and their potential to cause necrosis in oaks, which fits into the model of the spiral disease that has been causing mass mortality of oaks in this naturally and economically valuable area since the 1980s.
Full article
(This article belongs to the Special Issue Phytopathogens: Detection and Control)
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Open AccessArticle
Impact of Plant Oil Supplementation on Lipid Production and Fatty Acid Composition in Cunninghamella elegans TISTR 3370
by
Surasak Khankhum, Karnjana Khamkaew, Hua Li, Chuenjit Prakitchaiwattana and Sirithon Siriamornpun
Microorganisms 2024, 12(5), 992; https://doi.org/10.3390/microorganisms12050992 - 15 May 2024
Abstract
The Cunninghamella genus has been utilized for the production of PUFA-rich lipids. Therefore, we investigate the impact of plant oil supplementation in the culture medium (soybean oil, rice bran oil, and perilla oil), selected based on their different fatty acid predominant, on lipid
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The Cunninghamella genus has been utilized for the production of PUFA-rich lipids. Therefore, we investigate the impact of plant oil supplementation in the culture medium (soybean oil, rice bran oil, and perilla oil), selected based on their different fatty acid predominant, on lipid production and fatty acid composition in C. elegans (TISTR 3370). All oils significantly boosted fungal growth, each influencing distinct patterns of lipid accumulation within the cells. The cells exhibited distinct patterns of lipid accumulation, forming intracellular lipid bodies, influenced by the different oils. Monounsaturated fatty acids (MUFAs) were found to be the most abundant, followed by polyunsaturated fatty acids (PUFAs) and saturated fatty acids (SFAs) in the fungal lipid cultures. Oleic acid was identified as the primary MUFA, while palmitic acid was the predominant SFA in perilla oil supplements. Remarkably, perilla oil supplement provided the highest total lipid production with arachidonic acid being exclusively detected. The percentage of PUFAs ranged from 12% in the control to 33% in soybean oil, 32% in rice bran oil, and 61% in perilla oil supplements. These findings offer valuable opportunities for advancing biotechnological applications in lipid production and customization, with implications for food and nutrition as well as pharmaceuticals and cosmetics.
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(This article belongs to the Section Food Microbiology)
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Open AccessArticle
Secreted Metabolites from Pseudomonas, Staphylococcus, and Borrelia Biofilm: Modulation of Immunogenicity by a Nutraceutical Enzyme and Botanical Blend
by
Dina Cruickshank, Debby E. Hamilton, Ifeanyi Iloba and Gitte S. Jensen
Microorganisms 2024, 12(5), 991; https://doi.org/10.3390/microorganisms12050991 - 15 May 2024
Abstract
Bacterial biofilms are hardy, adaptable colonies, evading immune recognition while triggering and sustaining inflammation. The goals for this study were to present a method for testing the immunogenicity of secreted metabolites from pathogenic biofilm and to document whether biofilm treated with a nutraceutical
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Bacterial biofilms are hardy, adaptable colonies, evading immune recognition while triggering and sustaining inflammation. The goals for this study were to present a method for testing the immunogenicity of secreted metabolites from pathogenic biofilm and to document whether biofilm treated with a nutraceutical enzyme and botanical blend (NEBB) showed evidence of reprogrammed bacterial metabolism, potentially becoming more recognizable to the immune system. We screened immune-modulating properties of metabolites from established biofilm from Pseudomonas aeruginosa (Pa), Stapholycoccus simulans (Ss), and Borrelia burgdorferi (Bb). Secreted metabolites significantly increased the cytokine production by human peripheral blood mononuclear cells, including Interleukin-1-beta (IL-1β), Interleukin-6 (IL-6), macrophage inflammatory protein-1-alpha (MIP-1α), tumor necrosis factor-alpha (TNF-α), interleukin-1 receptor antagonist (IL-1ra), and interleukin-10 (IL-10). Pa metabolites triggered the most robust increase in IL-1β, whereas Bb metabolites triggered the most robust increase in IL-10. NEBB-disrupted biofilm produced metabolites triggering altered immune modulation compared to metabolites from untreated biofilm. Metabolites from NEBB-disrupted biofilm triggered increased MIP-1α levels and reduced IL-10 levels, suggesting a reduced ability to suppress the recruitment of phagocytes compared to untreated biofilm. The results suggest that nutraceutical biofilm disruption offers strategies for inflammation management in chronic infectious illnesses. Further clinical studies are warranted to evaluate clinical correlations in infected human hosts.
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(This article belongs to the Special Issue Research on Natural Products against Pathogens)
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Epidemiological Investigation of Goose Astrovirus in Hebei Province, China, 2019–2021
by
Ligong Chen, Huan Cui, Jiaqi Li, Yuxin Zhang, Heng Wang, Yejin Yang, Xuejing Wang, Cheng Zhang and Juxiang Liu
Microorganisms 2024, 12(5), 990; https://doi.org/10.3390/microorganisms12050990 - 14 May 2024
Abstract
The goose astrovirus (GAstV), a key pathogen causing visceral gout and high mortality in geese, has spread widely in China, with frequent outbreaks in recent years. Outbreaks and transmissions of this virus have been reported across China, causing considerable economic losses to the
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The goose astrovirus (GAstV), a key pathogen causing visceral gout and high mortality in geese, has spread widely in China, with frequent outbreaks in recent years. Outbreaks and transmissions of this virus have been reported across China, causing considerable economic losses to the goose industry worldwide, with losses exceeding tens of billions in China alone. However, there is still no effective prevention strategy against this virus. Therefore, continuous monitoring of the genetic diversity of dominant GAstV strains is crucial for developing targeted vaccines and appropriate therapeutics. As a crucial region for goose breeding in China, Hebei Province has previously lacked reports on the epidemiology of GAstV. Hence, investigating the epidemiology of GAstV in Hebei Province is highly important. From January 2019 to December 2021, 474 samples suspected of having a GAstV infection were collected in Hebei Province in this study. Through detailed histological observations, pathological examinations, virus isolation and identification, and genetic diversity analysis, we found that GAstV-2 has become the predominant circulating genotype. However, the presence of GAstV-1 and mixed infections cannot be ignored and should receive increased attention. The findings of this study not only deepened our understanding of GAstV in waterfowl in China but also provided scientific evidence for developing effective prevention and control measures, thereby promoting the healthy development of the goose industry in China.
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(This article belongs to the Section Veterinary Microbiology)
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Open AccessArticle
Distinct Gastrointestinal and Reproductive Microbial Patterns in Female Holobiont of Infertility
by
Ana T. Marcos, Maria J. Rus, Victoria Areal-Quecuty, Aurea Simon-Soro and José Manuel Navarro-Pando
Microorganisms 2024, 12(5), 989; https://doi.org/10.3390/microorganisms12050989 - 14 May 2024
Abstract
The microbiota is in symbiosis with the human body as a holobiont. Infertility conditions affect the female reproductive tract (FRT) and its resident microbiota. However, a disturbance in homeostasis could influence the FRT and other distal body sites, such as the gastrointestinal tract
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The microbiota is in symbiosis with the human body as a holobiont. Infertility conditions affect the female reproductive tract (FRT) and its resident microbiota. However, a disturbance in homeostasis could influence the FRT and other distal body sites, such as the gastrointestinal tract (GIT). We included 21 patients with endometriosis and other infertility-associated diseases with clinical profiles and biological samples from the FRT (endometrium, endometrial fluid, and vagina), and GIT samples (oral and feces). We performed a 16S rRNA analysis of site-specific microbial communities and estimated diversity metrics. The study found body site-specific microbial patterns in the FRT–GIT. In both study groups, Lactobacillus was the most shared Amplicon Sequence Variant (ASV), a precise identifier of microbial sequences, between endometrial and vagina samples. However, shared Gardnerella and Enterobacteriaceae ASVs were linked to other conditions but not endometriosis. Remarkably, Haemophilus was a specific GIT-shared taxon in endometriosis cases. In conclusion, infertility influences distinctly the FRT and GIT microbiomes, with endometriosis showing unique microbial characteristics. We proposed the concept of ‘female holobiont’ as a community that comprises the host and microbes that must maintain overall homeostasis across all body sites to ensure a woman’s health. Insights into these microbial patterns not only advance our understanding of the pathophysiology of infertility but also open new avenues for developing microbe-based therapeutic interventions aimed at restoring microbial balance, thereby enhancing fertility prospects.
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(This article belongs to the Special Issue Gut Microbiota in Disease—Third Edition)
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Forensic Microbiology: When, Where and How
by
Riccardo Nodari, Milena Arghittu, Paolo Bailo, Cristina Cattaneo, Roberta Creti, Francesco D’Aleo, Veroniek Saegeman, Lorenzo Franceschetti, Stefano Novati, Amparo Fernández-Rodríguez, Andrea Verzeletti, Claudio Farina and Claudio Bandi
Microorganisms 2024, 12(5), 988; https://doi.org/10.3390/microorganisms12050988 - 14 May 2024
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application
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Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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(This article belongs to the Special Issue Forensic and Post-Mortem Microbiology)
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