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
Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering
Microorganisms 2024, 12(5), 858; https://doi.org/10.3390/microorganisms12050858 (registering DOI) - 25 Apr 2024
Abstract
Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its
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Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.
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(This article belongs to the Section Plant Microbe Interactions)
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Open AccessCase Report
From Investigating a Case of Cellulitis to Exploring Nosocomial Infection Control of ST1 Legionella pneumophila Using Genomic Approaches
by
Charlotte Michel, Fedoua Echahidi, Sammy Place, Lorenzo Filippin, Vincent Colombie, Nicolas Yin, Delphine Martiny, Olivier Vandenberg, Denis Piérard and Marie Hallin
Microorganisms 2024, 12(5), 857; https://doi.org/10.3390/microorganisms12050857 (registering DOI) - 25 Apr 2024
Abstract
Legionella pneumophila can cause a large panel of symptoms besides the classic pneumonia presentation. Here we present a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a second case of Legionnaires’ disease in the same ward. While
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Legionella pneumophila can cause a large panel of symptoms besides the classic pneumonia presentation. Here we present a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a second case of Legionnaires’ disease in the same ward. While the first case was easily assumed as nosocomial based on the date of symptom onset, the second case required clear typing results to be assigned either as nosocomial and related to the same environmental source as the first case, or community acquired. To untangle this specific question, we applied core-genome multilocus typing (MLST), whole-genome single nucleotide polymorphism and whole-genome MLST methods to a collection of 36 Belgian and 41 international sequence-type 1 (ST1) isolates using both thresholds recommended in the literature and tailored threshold based on local epidemiological data. Based on the thresholds applied to cluster isolates together, the three methods gave different results and no firm conclusion about the nosocomial setting of the second case could been drawn. Our data highlight that despite promising results in the study of outbreaks and for large-scale epidemiological investigations, next-generation sequencing typing methods applied to ST1 outbreak investigation still need standardization regarding both wet-lab protocols and bioinformatics. A deeper evaluation of the L. pneumophila evolutionary clock is also required to increase our understanding of genomic differences between isolates sampled during a clinical infection and in the environment.
Full article
(This article belongs to the Special Issue Clinical and Environmental Surveillance for the Prevention of Legionellosis 2.0)
Open AccessCommunication
Trichinella spiralis Infecting Wild Boars in West, Southwest, and Northwest of Romania: Evidence of an Underrated Risk
by
Ana-Maria Marin, Tudor Rareș Olariu, Dan-Cornel Popovici, Gianluca Marucci, Sorin Morariu, Daian Popa and Narcisa Mederle
Microorganisms 2024, 12(5), 856; https://doi.org/10.3390/microorganisms12050856 (registering DOI) - 25 Apr 2024
Abstract
The species of the genus Trichinella are etiological agents distributed all over the world and are able to infect mammals, birds, and reptiles. Trichinella spiralis is the species most adapted to domestic and wild pigs and is also the most important etiological agent
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The species of the genus Trichinella are etiological agents distributed all over the world and are able to infect mammals, birds, and reptiles. Trichinella spiralis is the species most adapted to domestic and wild pigs and is also the most important etiological agent of trichinellosis. The wild boar (Sus scrofa) is a nocturnal omnivorous mammal belonging to the Suidae family. S. scrofa has a great appetite and its diet includes a variety of small prey such as mice, rats, and other rodents, as well as carcasses of larger animals. The aim of this study was the identification and the molecular characterization of Trichinella larvae isolated from the muscle tissue of S. scrofa specimens collected in different counties of Romania. The muscle samples were examined by artificial digestion and the larvae identified at the species level by multiplex PCR. T. spiralis, a species that is able to infect a considerable number of different host species including humans, was identified. In Romania, S. scrofa is an important reservoir species for T. spiralis and plays an important role in linking the domestic and the wild cycle of Trichinella, with serious repercussions for human health.
Full article
(This article belongs to the Section Parasitology)
Open AccessReview
The Impact of Artificial Restoration of Alpine Grasslands in the Qilian Mountains on Vegetation, Soil Bacteria, and Soil Fungal Community Diversity
by
Xiaomei Yang, Qi Feng, Meng Zhu, Jutao Zhang, Linshan Yang and Ruolin Li
Microorganisms 2024, 12(5), 854; https://doi.org/10.3390/microorganisms12050854 (registering DOI) - 25 Apr 2024
Abstract
To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed
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To understand how the soil microbial community structure responds to vegetation restoration in alpine mining areas, this study specifically examines the grassland ecosystem in the Qianmalong mining area of the Qilian Mountains after five years of artificial restoration. High-throughput sequencing methods were employed to analyze soil bacteria and fungi microbial characteristics in diverse grassland communities. Combined with modifications in vegetation diversity as well as soil physicochemical properties, the impact of vegetation restoration on soil microbiome diversity in this alpine mining area was investigated. The findings indicated that the dominant plants were Cyperus rotundus, Carex spp., and Elymus nutans. As the extent of the grassland’s restoration increased, the number of plant species, importance values, and plant community diversity showed an increasing trend. The plant functional groups were mainly dominated by Cyperaceae, followed by Poaceae. Plant height, density, plant cover, frequency, and aboveground biomass showed an increasing trend, and soil water content (SWC) increased. While soil pH and soil electrical conductivity (EC) exhibited a declining trend, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), soil organic carbon (SOC), and soil water content (SWC) showed an increasing trend. The dominant bacterial communities were Actinobacteriota, Proteobacteria, Acidobacteriota, Chloroflexi, Firmicutes, and Gemmatimonadota, while the dominant fungal communities were Ascomycota, Mortierellomycota, Basidiomycota, unclassified_k_Fungi, and Glomeromycota. Significant differences were detected within soil microbial community composition among different degrees of restoration grasslands, with bacteria generally dominating over fungi. SWC, TP, and TN were found to be the main soil physicochemical factors affecting the distribution of soil bacterial communities’ structure; however, SOC, TN, and NO3-N were the primary factors influencing the soil distribution of fungal communities. The results of this study indicate that different degrees of vegetation restoration in alpine mining areas can significantly affect soil bacterial and fungal communities, and the degree of restoration has varying effects on the soil bacteria and fungi community structure in alpine mining areas.
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(This article belongs to the Section Environmental Microbiology)
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Open AccessArticle
Fodinisporobacter ferrooxydans gen. nov., sp. nov.—A Spore-Forming Ferrous-Oxidizing Bacterium Isolated from a Polymetallic Mine
by
Zhen Jiang, Xiutong Li, Zonglin Liang, Zebao Tan, Nan Zhou, Ying Liu, Zhenghua Liu, Huaqun Yin, Kun Luo, Supawadee Ingsriswang, Shuangjiang Liu and Chengying Jiang
Microorganisms 2024, 12(5), 853; https://doi.org/10.3390/microorganisms12050853 (registering DOI) - 25 Apr 2024
Abstract
A novel acidophilic, aerobic bacterium strain, MYW30-H2T, was isolated from a heap of polymetallic mine. Cells of strain MYW30-H2T were Gram-stain-positive, endospore-forming, motile, and rod-shaped. Strain MYW30-H2T grew at a temperature range of 30–45 °C (optimum 40 °C) and
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A novel acidophilic, aerobic bacterium strain, MYW30-H2T, was isolated from a heap of polymetallic mine. Cells of strain MYW30-H2T were Gram-stain-positive, endospore-forming, motile, and rod-shaped. Strain MYW30-H2T grew at a temperature range of 30–45 °C (optimum 40 °C) and a pH range of 3.5–6.0 (optimum 4.0) in the presence of 0–0.5% (w/v) NaCl. Strain MYW30-H2T could grow heterotrophically on yeast extract and glucose, and grow mixotrophically using ferrous iron as an electron donor with yeast extract. Menaquinone-7 (MK-7) was the sole respiratory quinone of the strain. Iso-C15:0 and anteiso-C15:0 were the major cellular fatty acids. The 16S rRNA gene sequence analysis showed that MYW30-H2T was phylogenetically affiliated with the family Alicyclobacillaceae, and the sequence similarity with other Alicyclobacillaceae genera species was below 91.51%. The average amino acid identity value of the strain with its phylogenetically related species was 52.3–62.1%, which fell into the genus boundary range. The DNA G+C content of the strain was 44.2%. Based on physiological and phylogenetic analyses, strain MYW30-H2T represents a novel species of a new genus of the family Alicyclobacillaceae, for which the name Fodinisporobacter ferrooxydans gen. nov., sp. nov. is proposed. The type strain is MYW30-H2T (=CGMCC 1.17422T = KCTC 43278T).
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(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)
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Open AccessReview
Developing the Common Marmoset as a Translational Geroscience Model to Study the Microbiome and Healthy Aging
by
Kelly R. Reveles, Alexana J. Hickmott, Kelsey A. Strey, Aaryn C. Mustoe, Juan Pablo Arroyo, Michael L. Power, Benjamin J. Ridenhour, Katherine R. Amato and Corinna N. Ross
Microorganisms 2024, 12(5), 852; https://doi.org/10.3390/microorganisms12050852 (registering DOI) - 25 Apr 2024
Abstract
Emerging data support associations between the depletion of the healthy gut microbiome and aging-related physiological decline and disease. In humans, fecal microbiota transplantation (FMT) has been used successfully to restore gut microbiome structure and function and to treat C. difficile infections, but its
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Emerging data support associations between the depletion of the healthy gut microbiome and aging-related physiological decline and disease. In humans, fecal microbiota transplantation (FMT) has been used successfully to restore gut microbiome structure and function and to treat C. difficile infections, but its application to healthy aging has been scarcely investigated. The marmoset is an excellent model for evaluating microbiome-mediated changes with age and interventional treatments due to their relatively shorter lifespan and many social, behavioral, and physiological functions that mimic human aging. Prior work indicates that FMT is safe in marmosets and may successfully mediate gut microbiome function and host health. This narrative review (1) provides an overview of the rationale for FMT to support healthy aging using the marmoset as a translational geroscience model, (2) summarizes the prior use of FMT in marmosets, (3) outlines a protocol synthesized from prior literature for studying FMT in aging marmosets, and (4) describes limitations, knowledge gaps, and future research needs in this field.
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(This article belongs to the Special Issue Fecal Microbiota Transplantation in Animals)
Open AccessReview
Advances in Gut Microbiota-Targeted Therapeutics for Metabolic Syndrome
by
Yu Gao, Wujuan Li, Xiaoyu Huang, Yuhong Lyu and Changwu Yue
Microorganisms 2024, 12(5), 851; https://doi.org/10.3390/microorganisms12050851 (registering DOI) - 24 Apr 2024
Abstract
Previous investigations have illuminated the significant association between the gut microbiome and a broad spectrum of health conditions, including obesity, diabetes, cardiovascular diseases, and psychiatric disorders. Evidence from certain studies suggests that dysbiosis of the gut microbiota may play a role in the
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Previous investigations have illuminated the significant association between the gut microbiome and a broad spectrum of health conditions, including obesity, diabetes, cardiovascular diseases, and psychiatric disorders. Evidence from certain studies suggests that dysbiosis of the gut microbiota may play a role in the etiology of obesity and diabetes. Moreover, it is acknowledged that dietary habits, pharmacological interventions, psychological stress, and other exogenous factors can substantially influence the gut microbial composition. For instance, a diet rich in fiber has been demonstrated to increase the population of beneficial bacteria, whereas the consumption of antibiotics can reduce these advantageous microbial communities. In light of the established correlation between the gut microbiome and various pathologies, strategically altering the gut microbial profile represents an emerging therapeutic approach. This can be accomplished through the administration of probiotics or prebiotics, which aim to refine the gut microbiota and, consequently, mitigate the manifestations of associated diseases. The present manuscript evaluates the recent literature on the relationship between gut microbiota and metabolic syndrome published over the past three years and anticipates future directions in this evolving field.
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(This article belongs to the Section Gut Microbiota)
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Open AccessArticle
Type I Cystatin Derived from Cysticercus pisiformis—Stefins, Suppresses LPS-Mediated Inflammatory Response in RAW264.7 Cells
by
Qianqian Yang, Jia Li, Lilan Zhang, Ningning Zhao, Xiaolin Sun and Zexiang Wang
Microorganisms 2024, 12(5), 850; https://doi.org/10.3390/microorganisms12050850 - 24 Apr 2024
Abstract
Cysticercus pisiformis is a kind of tapeworm larvae of Taenia pisiformis, which parasitizes the liver envelope, omentum, mesentery, and rectum of rodents such as rabbits. Cysteine protease inhibitors derived from helminth were immunoregulatory molecules of intermediate hosts and had an immunomodulatory function
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Cysticercus pisiformis is a kind of tapeworm larvae of Taenia pisiformis, which parasitizes the liver envelope, omentum, mesentery, and rectum of rodents such as rabbits. Cysteine protease inhibitors derived from helminth were immunoregulatory molecules of intermediate hosts and had an immunomodulatory function that regulates the production of inflammatory factors. Thus, in the present research, the recombinant Stefin of C. pisiformis was confirmed to have the potential to fight inflammation in LPS-Mediated RAW264.7 murine macrophages. CCK8 test showed that rCpStefin below 50 μg/mL concentration did not affect cellular viability. Moreover, the NO production level determined by the Griess test was decreased. In addition, the secretion levels of IL-1β, IL-6, and TNF-α as measured by ELISA were decreased. Furthermore, it exerted anti-inflammatory activity by decreasing the production of proinflammatory cytokines and proinflammatory mediators, including IL-1β, IL-6, TNF-α, iNOS, and COX-2 at the gene transcription level, as measured by qRT-PCR. Therefore, Type I cystatin derived from C. pisiformis suppresses the LPS-Mediated inflammatory response of the intermediate host and is a potential candidate for the treatment of inflammatory diseases.
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(This article belongs to the Section Parasitology)
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Open AccessArticle
Prosthetic Joint Infections Caused by Mycobacterium tuberculosis Complex—An ESGIAI–ESGMYC Multicenter, Retrospective Study and Literature Review
by
Alvaro Auñon, Llanos Salar-Vidal, Ignacio Mahillo-Fernandez, Francisco Almeida, Pedro Pereira, Jaime Lora-Tamayo, Tristan Ferry, Sarah Souèges, Aurélien Dinh, Rosa Escudero, Candela Menéndez Fernández-Miranda, Alicia Rico, Nicolo Rossi and Jaime Esteban
Microorganisms 2024, 12(5), 849; https://doi.org/10.3390/microorganisms12050849 - 24 Apr 2024
Abstract
Purpose: While tuberculosis remains a significant global health concern, prosthetic joint infections (PJIs) caused by members of the Mycobacterium tuberculosis complex are exceptionally rare. Our objective is to perform a retrospective search of new cases of this disease and analyze all cases available
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Purpose: While tuberculosis remains a significant global health concern, prosthetic joint infections (PJIs) caused by members of the Mycobacterium tuberculosis complex are exceptionally rare. Our objective is to perform a retrospective search of new cases of this disease and analyze all cases available in the literature of tuberculous PJIs, aiming to detect factors that may influence patient outcomes. Methods: The ESGIAI and ESGMYC study groups were used to collect information on non-published cases of tuberculous prosthetic joint infections (PJIs). Additionally, a literature review of all published cases of tuberculous PJIs was conducted. All identified cases in the retrospective study and in the literature review were merged and included in the statistical analysis, involving both univariate and multivariate analyses. Results: Fifteen previously unreported cases of tuberculous prosthetic joint infections (PJIs) from four countries were detailed. Among them, ten patients were female, with a median age of 76 years. The hip was affected in 13 cases. Seven patients experienced co-infection with another microorganism. Treatment approaches varied, with 13 patients undergoing implant removal, one treated with DAIR (debridement, antibiotics, and implant retention), and one case was treated with an unknown treatment method. All patients received antibiotic therapy and achieved a cure. The literature review that was conducted detected 155 published cases. Univariate analysis revealed a statistical significance for previous tuberculosis, joint, and no importance of surgery for cure. Conclusions: Tuberculous prosthetic joint infection (PJI) is a rare condition, typically presenting as a localized chronic infection. Antibiotic treatment is essential for the management of these patients, but neither surgical treatment nor duration of treatment seems to have importance in the outcome.
Full article
(This article belongs to the Special Issue Device-Related Infections and Bacterial Biofilms)
Open AccessArticle
Evaluation of the Increased Genetic Resolution and Utility for Source Tracking of a Recently Developed Method for Genotyping Cyclospora cayetanensis
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Susan R. Leonard, Mark K. Mammel, Sonia Almeria, Solomon T. Gebru, David K. Jacobson, Anna C. Peterson, Joel L. N. Barratt and Steven M. Musser
Microorganisms 2024, 12(5), 848; https://doi.org/10.3390/microorganisms12050848 - 24 Apr 2024
Abstract
Cyclospora cayetanensis is a foodborne parasite that causes cyclosporiasis, an enteric illness in humans. Genotyping methods are used to genetically discriminate between specimens from cyclosporiasis cases and can complement source attribution investigations if the method is sufficiently sensitive for application to food items.
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Cyclospora cayetanensis is a foodborne parasite that causes cyclosporiasis, an enteric illness in humans. Genotyping methods are used to genetically discriminate between specimens from cyclosporiasis cases and can complement source attribution investigations if the method is sufficiently sensitive for application to food items. A very sensitive targeted amplicon sequencing (TAS) assay for genotyping C. cayetanensis encompassing 52 loci was recently designed. In this study, we analyzed 66 genetically diverse clinical specimens to assess the change in phylogenetic resolution between the TAS assay and a currently employed eight-marker scheme. Of the 52 markers, ≥50 were successfully haplotyped for all specimens, and these results were used to generate a hierarchical cluster dendrogram. Using a previously described statistical approach to dissect hierarchical trees, the 66 specimens resolved into 24 and 27 distinct genetic clusters for the TAS and an 8-loci scheme, respectively. Although the specimen composition of 15 clusters was identical, there were substantial differences between the two dendrograms, highlighting the importance of both inclusion of additional genome coverage and choice of loci to target for genotyping. To evaluate the ability to genetically link contaminated food samples with clinical specimens, C. cayetanensis was genotyped from DNA extracted from raspberries inoculated with fecal specimens. The contaminated raspberry samples were assigned to clusters with the corresponding clinical specimen, demonstrating the utility of the TAS assay for traceback efforts.
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(This article belongs to the Section Food Microbiology)
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Open AccessSystematic Review
Evidence for Immunity against Tetanus, Diphtheria, and Pertussis through Natural Infection or Vaccination in Adult Solid Organ Transplant Recipients: A Systematic Review
by
Emil Lenzing, Zitta Barrella Harboe, Søren Schwartz Sørensen, Allan Rasmussen, Susanne Dam Nielsen and Omid Rezahosseini
Microorganisms 2024, 12(5), 847; https://doi.org/10.3390/microorganisms12050847 - 24 Apr 2024
Abstract
(1) Background: We aim to systematically review the current evidence on immunity against tetanus, diphtheria, and pertussis in adult solid organ transplantation (SOT) recipients, either through natural infection or vaccination. (2) Methods: This systematic review was conducted per PRISMA guidelines. We assessed the
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(1) Background: We aim to systematically review the current evidence on immunity against tetanus, diphtheria, and pertussis in adult solid organ transplantation (SOT) recipients, either through natural infection or vaccination. (2) Methods: This systematic review was conducted per PRISMA guidelines. We assessed the risk of bias using the Cochrane RoB 2 and ROBINS-I and summarized the findings narratively due to the heterogeneity of the studies. (3) Results: Of the 315 screened articles, 11 were included. Tetanus immunity varied between 55% and 86%, diphtheria immunity from 23% to 75%, and pertussis immunity was between 46% and 82%. Post-vaccination immunity showed variation across the studies, with some indicating reductions and others no change, with antibody responses influenced by transplanted organs, gender, age, and immunosuppressive regimens. The single randomized study exhibited a low risk of bias, while of the ten non-randomized studies, six showed moderate and four serious risks of bias, necessitating cautious interpretation of results. (4) Conclusions: SOT recipients exhibit considerable immunity against tetanus and diphtheria at transplantation, but this immunity decreases over time. Although vaccination can enhance this immunity, the response may be suboptimal, and the increased antibody levels may not persist, underscoring the need for tailored vaccination strategies in this vulnerable population.
Full article
(This article belongs to the Special Issue Infections in Solid Organ Transplant Recipients)
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Open AccessArticle
Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy
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Emil Tonon, Riccardo Cecchetto, Erica Diani, Nicoletta Medaina, Giona Turri, Anna Lagni, Virginia Lotti and Davide Gibellini
Microorganisms 2024, 12(5), 846; https://doi.org/10.3390/microorganisms12050846 - 24 Apr 2024
Abstract
The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time.
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The availability of new technologies for deep sequencing, including next-generation sequencing (NGS), allows for the detection of viral genome variations. The epidemiological determination of SARS-CoV-2 viral genome changes during the pandemic waves displayed the genome evolution and subsequent onset of variants over time. These variants were often associated with a different impact on viral transmission and disease severity. We investigated, in a retrospective study, the trend of SARS-CoV-2-positive samples collected from the start of the Italian pandemic (January 2020) to June 2023. In addition, viral RNAs extracted from 938 nasopharyngeal swab samples were analyzed using NGS between February 2022 and June 2023. Sequences were analyzed with bioinformatic tools to identify lineages and mutations and for phylogenetic studies. Six pandemic waves were detected. In our samples, we predominantly detected BA.2, BQ.1, BA.5.1, BA.5.2, and, more recently, XBB.1 and its subvariants. The data describe the SARS-CoV-2 genome evolution involved in viral interactions with the host and the dynamics of specific genome mutations and deletions.
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(This article belongs to the Section Virology)
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Open AccessArticle
Comparative Genomics Reveals Genetic Diversity and Variation in Metabolic Traits in Fructilactobacillus sanfranciscensis Strains
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Xiaxia He, Yujuan Yu, Rober Kemperman, Luciana Jimenez, Faizan Ahmed Sadiq and Guohua Zhang
Microorganisms 2024, 12(5), 845; https://doi.org/10.3390/microorganisms12050845 - 23 Apr 2024
Abstract
Fructilactobacillus sanfranciscensis is a significant and dominant bacterial species of sourdough microbiota from ecological and functional perspectives. Despite the remarkable prevalence of different strains of this species in sourdoughs worldwide, the drivers behind the genetic diversity of this species needed to be clarified.
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Fructilactobacillus sanfranciscensis is a significant and dominant bacterial species of sourdough microbiota from ecological and functional perspectives. Despite the remarkable prevalence of different strains of this species in sourdoughs worldwide, the drivers behind the genetic diversity of this species needed to be clarified. In this research, 14 F. sanfranciscensis strains were isolated from sourdough samples to evaluate the genetic diversity and variation in metabolic traits. These 14 and 31 other strains (obtained from the NCBI database) genomes were compared. The values for genome size and GC content, on average, turned out to 1.31 Mbp and 34.25%, respectively. In 45 F. sanfranciscensis strains, there were 162 core genes and 0 to 51 unique genes present in each strain. The primary functions of core genes were related to nucleotide, lipid transport, and amino acid, as well as carbohydrate metabolism. The size of core genes accounted for 41.18% of the pan-genome size in 14 F. sanfranciscensis strains, i.e., 0.70 Mbp of 1.70 Mbp. There were genetic variations among the 14 strains involved in carbohydrate utilization and antibiotic resistance. Moreover, exopolysaccharides biosynthesis-related genes were annotated, including epsABD, wxz, wzy. The Type IIA & IE CRISPR-Cas systems, pediocin PA-1 and Lacticin_3147_A1 bacteriocins operons were also discovered in F. sanfranciscensis. These findings can help to select desirable F. sanfranciscensis strains to develop standardized starter culture for sourdough fermentation, and expect to provide traditional fermented pasta with a higher quality and nutritional value for the consumers.
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(This article belongs to the Special Issue Food Microorganisms and Genomics)
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Open AccessArticle
Genomic Characterization and Molecular Detection of Rehmannia Allexivirus Virus, a Novel Allexivirus Infecting Rehmannia glutinosa
by
Yanhong Qin, Shuhao Lu, Yi Wen, Shaojian Li, Suxia Gao, Yuxia Liu, Xuemeng Li, Jin Yang, Fengli Wang, Fei Wang and Chuantao Lu
Microorganisms 2024, 12(5), 844; https://doi.org/10.3390/microorganisms12050844 - 23 Apr 2024
Abstract
Rehmannia glutinosa is one of the most important medicinal plants in China and is affected by viral diseases. In this study, a new virus tentatively named Rehmannia Allexivirus virus (ReAV) was identified through high-throughput sequencing, reverse-transcription polymerase chain reaction (RT-PCR), and Sanger sequencing.
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Rehmannia glutinosa is one of the most important medicinal plants in China and is affected by viral diseases. In this study, a new virus tentatively named Rehmannia Allexivirus virus (ReAV) was identified through high-throughput sequencing, reverse-transcription polymerase chain reaction (RT-PCR), and Sanger sequencing. The complete genome length was 7297 nt and it contained five open reading frames (ORFs) encoding replicase, triple gene block 1(TGB1), TGB2, TGB3, and coat protein (CP). The replicase and CP presented nucleotide homology ranges of 59.9–65.2% and 47.5–55.5% between the nine ReAV isolates and the other 12 species of the genus Allexivirus. In the nine isolates, ReAV-20 and ReAV-31 isolates showed breakpoints in the replicase and CP regions, respectively. The other isolates shared 87.2–96.5% nt with the whole genome nucleotide identity. The phylogenetic tree showed that seven ReAV isolates based on replicase, CP, and whole genome sequences were clustered in the same branch and were related to the genus Allexivirus. The ReAV detection rates for 60 R. glutinosa samples were 73.3–81.7% through RT-PCR using primers targeting the replicase or CP genes. These results demonstrate that ReAV is the dominant virus in R. glutinosa. This study provides important evidence for understanding viruses infecting R. glutinosa and for establishing efficient strategies to prevent viral spread.
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(This article belongs to the Section Microbial Biotechnology)
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Open AccessArticle
Chemical Characterization and Effect of a Lactobacilli-Postbiotic on Streptococcus mutans Biofilm In Vitro
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Guilherme Bandeira Santana, Patrick Veras Quelemes, Enedina Rodrigues da Silva Neta, Sidney Gonçalo de Lima and Gláuber Campos Vale
Microorganisms 2024, 12(5), 843; https://doi.org/10.3390/microorganisms12050843 - 23 Apr 2024
Abstract
Postbiotic is the term used to define the soluble factors, metabolic products, or byproducts released by live probiotic bacteria or after its lysis. The objective of this study was to carry out the chemical characterization of the postbiotic of Lacticaseibacillus rhamnosus LR-32 and
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Postbiotic is the term used to define the soluble factors, metabolic products, or byproducts released by live probiotic bacteria or after its lysis. The objective of this study was to carry out the chemical characterization of the postbiotic of Lacticaseibacillus rhamnosus LR-32 and to evaluate its in vitro effect on the development of the Streptococcus mutans biofilm. After the cultivation of the probiotic strain, the postbiotic was extracted by centrifuging the culture and filtering the supernatant. This postbiotic was characterized by using gas chromatography coupled with mass spectrometry (GC–MS), and then it was used to determine the growth inhibition of S. mutans in its planktonic form; additionally, its effects on the following parameters in 48 h biofilm were evaluated: viable bacteria, dry weight, and gene expression of glucosyltransferases and VicR gene. The control group consisted of the biofilm without any treatment. A paired t-test was performed for statistical analysis, with the p-value set at 5%. Seventeen compounds of various chemical classes were identified in the postbiotic, including sugars, amino acids, vitamins, and acids. The treatment with the postbiotic led to an inhibition of the growth of S. mutans in its planktonic form, as well as a decrease in the number of viable bacteria, reduction in dry weight, and a negative regulation of the gene expression of gtfB, gtfC, gtfD, and vicR in its biofilm state, compared with the nontreated group (p < 0.05). The postbiotic of L. rhamnosus impaired the development of S. mutans biofilm.
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(This article belongs to the Special Issue A Contemporary Look at Oral Microbe Management)
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Open AccessReview
Tackling the Antimicrobial Resistance “Pandemic” with Machine Learning Tools: A Summary of Available Evidence
by
Doris Rusic, Marko Kumric, Ana Seselja Perisin, Dario Leskur, Josipa Bukic, Darko Modun, Marino Vilovic, Josip Vrdoljak, Dinko Martinovic, Marko Grahovac and Josko Bozic
Microorganisms 2024, 12(5), 842; https://doi.org/10.3390/microorganisms12050842 - 23 Apr 2024
Abstract
Antimicrobial resistance is recognised as one of the top threats healthcare is bound to face in the future. There have been various attempts to preserve the efficacy of existing antimicrobials, develop new and efficient antimicrobials, manage infections with multi-drug resistant strains, and improve
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Antimicrobial resistance is recognised as one of the top threats healthcare is bound to face in the future. There have been various attempts to preserve the efficacy of existing antimicrobials, develop new and efficient antimicrobials, manage infections with multi-drug resistant strains, and improve patient outcomes, resulting in a growing mass of routinely available data, including electronic health records and microbiological information that can be employed to develop individualised antimicrobial stewardship. Machine learning methods have been developed to predict antimicrobial resistance from whole-genome sequencing data, forecast medication susceptibility, recognise epidemic patterns for surveillance purposes, or propose new antibacterial treatments and accelerate scientific discovery. Unfortunately, there is an evident gap between the number of machine learning applications in science and the effective implementation of these systems. This narrative review highlights some of the outstanding opportunities that machine learning offers when applied in research related to antimicrobial resistance. In the future, machine learning tools may prove to be superbugs’ kryptonite. This review aims to provide an overview of available publications to aid researchers that are looking to expand their work with new approaches and to acquaint them with the current application of machine learning techniques in this field.
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(This article belongs to the Special Issue Latest Review Papers in Antimicrobial Agents and Resistance 2024)
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Open AccessArticle
A Comparative Transcriptome Analysis Unveils the Mechanisms of Response in Feather Degradation by Pseudomonas aeruginosa Gxun-7
by
Chaodong Song, Rui Liu, Doudou Yin, Chenjie Xie, Ying Liang, Dengfeng Yang, Mingguo Jiang, Hongyan Zhang and Naikun Shen
Microorganisms 2024, 12(4), 841; https://doi.org/10.3390/microorganisms12040841 - 22 Apr 2024
Abstract
Microbial degradation of feathers offers potential for bioremediation, yet the microbial response mechanisms warrant additional investigation. In prior work, Pseudomonas aeruginosa Gxun-7, which demonstrated robust degradation of feathers at elevated concentrations, was isolated. However, the molecular mechanism of this degradation remains only partially
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Microbial degradation of feathers offers potential for bioremediation, yet the microbial response mechanisms warrant additional investigation. In prior work, Pseudomonas aeruginosa Gxun-7, which demonstrated robust degradation of feathers at elevated concentrations, was isolated. However, the molecular mechanism of this degradation remains only partially understood. To investigate this, we used RNA sequencing (RNA-seq) to examine the genes that were expressed differentially in P. aeruginosa Gxun-7 when exposed to 25 g/L of feather substrate. The RNA-seq analysis identified 5571 differentially expressed genes; of these, 795 were upregulated and 603 were downregulated. Upregulated genes primarily participated in proteolysis, amino acid, and pyruvate metabolism. Genes encoding proteases, as well as those involved in sulfur metabolism, phenazine synthesis, and type VI secretion systems, were notably elevated, highlighting their crucial function in feather decomposition. Integration of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) taxonomies, combined with a review of the literature, led us to propose that metabolic feather degradation involves environmental activation, reducing agent secretion, protease release, peptide/amino acid uptake, and metabolic processes. Sulfite has emerged as a critical activator of keratinase catalysis, while cysteine serves as a regulatory mediator. qRT–PCR assay results for 11 selected gene subset corroborated the RNA-seq findings. This study enhances our understanding of the transcriptomic responses of P. aeruginosa Gxun-7 to feather degradation and offers insights into potential degradation mechanisms, thereby aiding in the formulation of effective feather waste management strategies in poultry farming.
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(This article belongs to the Special Issue Transcriptional Regulation in Bacteria)
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Open AccessArticle
Investigation of Effects of Novel Bifidobacterium longum ssp. longum on Gastrointestinal Microbiota and Blood Serum Parameters in a Conventional Mouse Model
by
Merle Rätsep, Kalle Kilk, Mihkel Zilmer, Sirje Kuusik, Liina Kuus, Mirjam Vallas, Oksana Gerulis, Jelena Štšepetova, Aivar Orav and Epp Songisepp
Microorganisms 2024, 12(4), 840; https://doi.org/10.3390/microorganisms12040840 - 22 Apr 2024
Abstract
Representatives of the genus Bifidobacterium are widely used as probiotics to modulate the gut microbiome and alleviate various health conditions. The action mechanisms of probiotics rely on their direct effect on the gut microbiota and the local and systemic effect of its metabolites.
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Representatives of the genus Bifidobacterium are widely used as probiotics to modulate the gut microbiome and alleviate various health conditions. The action mechanisms of probiotics rely on their direct effect on the gut microbiota and the local and systemic effect of its metabolites. The main purpose of this animal experiment was to assess the biosafety of the Bifidobacterium longum strain BIOCC1719. Additional aims were to characterise the influence of the strain on the intestinal microbiota and the effect on several health parameters of the host during 15- and 30-day oral administration of the strain to mice. The strain altered the gut microbial community, thereby altering luminal short-chain fatty acid metabolism, resulting in a shift in the proportions of acetic, butyric, and propionic acids in the faeces and serum of the test group mice. Targeted metabolic profiling of serum revealed the possible ability of the strain to positively affect the hosts’ amino acids and bile acids metabolism, as the cholic acid, deoxycholic acid, aspartate, and glutamate concentration were significantly higher in the test group. The tendency to increase anti-inflammatory polyamines (spermidine, putrescine) and neuroprotective 3-indolepropionic acid metabolism and to lower uremic toxins (P-cresol-SO4, indoxyl-SO4) was registered. Thus, B. longum BIOCC1719 may exert health-promoting effects on the host through modulation of the gut microbiome and the host metabolome via inducing the production of health-promoting bioactive compounds. The health effects of the strain need to be confirmed in clinical trials with human volunteers.
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(This article belongs to the Special Issue Probiotics, Prebiotics, and Gut Microbes)
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Open AccessArticle
Cell-Free Culture Supernatant of Lactobacillus acidophilus AG01 and Bifidobacterium animalis subsp. lactis AG02 Reduces the Pathogenicity of NetB-Positive Clostridium perfringens in a Chicken Intestinal Epithelial Cell Line
by
Darshana Kadekar, Andreea Cornelia Udrea, Steffen Yde Bak, Niels Christensen, Kirsty Gibbs, Chong Shen and Marion Bernardeau
Microorganisms 2024, 12(4), 839; https://doi.org/10.3390/microorganisms12040839 - 22 Apr 2024
Abstract
The worldwide reduction in the use of antibiotics in animal feed is fueling the need for alternatives for the prevention and control of poultry intestinal diseases such as necrotic enteritis (NE), which is caused by Clostridium perfringens. This is the first report
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The worldwide reduction in the use of antibiotics in animal feed is fueling the need for alternatives for the prevention and control of poultry intestinal diseases such as necrotic enteritis (NE), which is caused by Clostridium perfringens. This is the first report on the use of an intestinal epithelial chicken cell line (CHIC-8E11) to study the pathogenic traits of C. perfringens and to investigate the mode of action of cell-free supernatants (CFS) from probiotic Lactobacillus acidophilus AG01 and Bifidobacterium animalis subsp. lactis AG02 in reducing the pathogenicity of C. perfringens. The cell adhesion, permeability and cytotoxicity were assessed under challenge with four C. perfringens strains isolated from broiler NE episodes of differing geographical origin (CP1–UK; CP10–Sweden; 25037–CP01 and CP22–USA). All the C. perfringens strains could adhere to the CHIC-8E11 cells, with varying affinity (0.05–0.48% adhesion across the strains). The CFS from one out of two strains (CP22) increased the cell permeability (+4.5-fold vs. the control, p < 0.01), as measured by the fluorescein isothiocyanate-dextran (FD4) content, with NetB toxin implicated in this effect. The CFS from all the strains was cytotoxic against the CHIC-8E11 cells in a dose- and strain-dependent manner (cytotoxicity 23–62% across the strains when dosed at 50 µL/mL, as assessed by the MTT cell viability assay). Pre-treatment of the cells with CFS from B. animalis subsp. lactis AG02 but not L. acidophilus AG01 reduced the cell adhesion of three out of four C. perfringens strains (by 77–85% vs. the control, p < 0.001) and reduced the negative effect of two NetB-positive strains on the cell permeability. The CFS of both probiotics alleviated the cytotoxicity of all the C. perfringens strains, which was dependent on the dose. The results confirm the suitability of the CHIC-8E11 cell line for the study of host–pathogen cell interactions in the context of NE caused by C. perfringens and reveal a beneficial mode of action of B. animalis subsp. lactis AG02 in reducing C. perfringens cell adhesion and, together with L. acidophilus AG01, in reducing C. perfringens cytotoxicity.
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(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond 2.0)
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Open AccessCommunication
Serological Evidence of Crimean–Congo Haemorrhagic Fever in Livestock in the Omaheke Region of Namibia
by
Alaster Samkange, Pricilla Mbiri, Ophelia Chuma Matomola, Georgina Zaire, Anna Homateni, Elifas Junias, Israel Kaatura, Siegfried Khaiseb, Simson Ekandjo, Johannes Shoopala, Magrecia Hausiku, Albertina Shilongo, Mushabati Linus Mujiwa, Klaas Dietze, Frank Busch, Christian Winter, Carolina Matos, Sabrina Weiss and Simbarashe Chitanga
Microorganisms 2024, 12(4), 838; https://doi.org/10.3390/microorganisms12040838 - 22 Apr 2024
Abstract
This research examined the positivity ratio of Crimean–Congo haemorrhagic fever (CCHF) antibodies in cattle and sheep within Namibia’s Omaheke region after a human disease outbreak in the same geographical area. A total of 200 samples (100 cattle and 100 sheep) were randomly collected
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This research examined the positivity ratio of Crimean–Congo haemorrhagic fever (CCHF) antibodies in cattle and sheep within Namibia’s Omaheke region after a human disease outbreak in the same geographical area. A total of 200 samples (100 cattle and 100 sheep) were randomly collected from animals brought to two regional auction sites, and then tested using the ID Screen® CCHF Double Antigen Multi-Species Enzyme-Linked Immunosorbent Assay kit. Of the cattle samples, 36% tested positive, while 22% of the sheep samples were seropositive. The cattle had a significantly higher positivity ratio than sheep at the individual animal level (p = 0.0291). At the herd level, 62.5% of cattle herds and 45.5% of sheep flocks had at least one positive animal, but this difference was statistically insignificant (p = 0.2475). The fourteen cattle farms with at least one seropositive animal were dispersed across the Omaheke region. In contrast, the ten sheep farms with seropositive cases were predominantly situated in the southern half of the region. The study concluded that the CCHF is endemic in the Omaheke region and likely in most of Namibia, underscoring the importance of continued surveillance and preventive measures to mitigate the impact of CCHFV on animal health and potential spillover into human populations.
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(This article belongs to the Special Issue Emerging Pathogens in the Context of One Health)
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