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
Bacterial Lipopeptides Are Effective against Pear Fire Blight
Microorganisms 2024, 12(5), 896; https://doi.org/10.3390/microorganisms12050896 (registering DOI) - 29 Apr 2024
Abstract
Fire blight, a devastating disease caused by Erwinia amylovora, poses a significant threat to pear and apple trees in Xinjiang province, China. In an effort to combat this pathogen, we isolated 10 bacteria from various components of apple and crabapple trees and
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Fire blight, a devastating disease caused by Erwinia amylovora, poses a significant threat to pear and apple trees in Xinjiang province, China. In an effort to combat this pathogen, we isolated 10 bacteria from various components of apple and crabapple trees and conducted screenings to assess their ability to inhibit E. amylovora in vitro. Through biochemical tests and partial 16S rRNA gene sequencing, we identified two promising strains, Priestia megaterium strain H1 and Bacillus subtilis strain I2. These strains were then evaluated for their efficacy in biocontrol under controlled laboratory conditions, focusing on immature fruits and leaves. Remarkably, all selected antagonists exhibited the capability to reduce the severity of the disease on both fruit and leaves. P. megaterium strain H1 and B. subtilis strain I2 exhibited significant reductions in disease incidence on both immature fruits and leaves compared to the control. Specifically, on immature fruits, they achieved reductions of 53.39% and 44.76%, respectively, while on leaves, they demonstrated reductions of 59.55% and 55.53%, respectively. Furthermore, during the study, we detected the presence of lipopeptides, including surfactin, iturins, bacillomycin D, and fengycins, in the methanol extract obtained from these two antagonistic bacteria using thin-layer chromatography (TLC). Based on the results obtained, B. subtilis strain I2 and P. megaterium strain H1 exhibit considerable potential for controlling fire blight. However, further evaluation of their efficacy under natural field conditions is essential to validate their practicality as a biocontrol method.
Full article
(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)
Open AccessArticle
Partial Characterization of Three Bacteriophages Isolated from Aquaculture Hatchery Water and Their Potential in the Biocontrol of Vibrio spp.
by
İhsan Yaşa, Serap Evran, Asiye Esra Eren Eroğlu, Cengiz Önder, Maryam Allahyari, Gülçin Menderes and Müberra Kullay
Microorganisms 2024, 12(5), 895; https://doi.org/10.3390/microorganisms12050895 (registering DOI) - 29 Apr 2024
Abstract
Bacteriophages are currently considered one of the most promising alternatives to antibiotics under the ‘One Health’ approach due to their ability to effectively combat bacterial infections. This study aimed to characterize Vibrio species in hatchery water samples collected from an aquaculture farm and
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Bacteriophages are currently considered one of the most promising alternatives to antibiotics under the ‘One Health’ approach due to their ability to effectively combat bacterial infections. This study aimed to characterize Vibrio species in hatchery water samples collected from an aquaculture farm and investigate the biocontrol potential of their bacteriophages. Vibrio spp. (n = 32) isolates confirmed by LNA probe-based qPCR were used as hosts. Three Vibrio phages were isolated. IKEM_vK exhibited a broad host range, infecting V. harveyi (n = 8), V. alginolyticus (n = 2), V. azureus (n = 1), and V. ordalii (n = 1). IKEM_v5 showed lytic activity against V. anguillarum (n = 4) and V. ordalii (n = 1), while IKEM_v14 was specific to V. scophtalmi (n = 4). The morphological appearance of phages and their lytic effects on the host were visualized using scanning electron microscopy (SEM). All three phages remained relatively stable within the pH range of 6–11 and up to 60 °C. The lytic activities and biofilm inhibition capabilities of these phages against planktonic Vibrio cells support their potential applications in controlling vibriosis in aquaculture systems.
Full article
(This article belongs to the Special Issue Bacteria Control by Phages)
Open AccessCase Report
Community-Acquired Solitary Brain Abscesses Caused by Hypervirulent Klebsiella pneumoniae in a Healthy Adult
by
Joo-Hee Hwang, Jung Soo Park, Tae Won Bae, Jeong-Hwan Hwang and Jaehyeon Lee
Microorganisms 2024, 12(5), 894; https://doi.org/10.3390/microorganisms12050894 (registering DOI) - 29 Apr 2024
Abstract
A 42-year-old man was admitted to the emergency room complaining of fever and headache. His cerebrospinal fluid showed a cloudy appearance, and his white blood cell count was elevated at 2460/mm3, with a predominance of neutrophils (81%), and abnormal protein and
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A 42-year-old man was admitted to the emergency room complaining of fever and headache. His cerebrospinal fluid showed a cloudy appearance, and his white blood cell count was elevated at 2460/mm3, with a predominance of neutrophils (81%), and abnormal protein and glucose levels (510.7 mg/dL and 5 mg/dL, respectively). A lobulated lesion with rim enhancement, suggestive of abscess, was detected through magnetic resonance imaging. Klebsiella pneumoniae was detected in nasopharyngeal swab and blood cultures. The capsular serotype of K. pneumoniae was K2 and the sequence type determined by multilocus sequence typing was 23. The hypervirulent phenotype was associated with multiple virulent genes, including rmpA, rmpA2, entB, ybtS, kfu, iucA, iutA, iroB mrkD, allS, peg-344, peg-589, and peg-1631. After six weeks of receiving appropriate antibiotics and exhibiting clinical resolution of the brain abscesses, the patient was discharged. We present the first reported case of a healthy community-dwelling adult with solitary brain abscesses, and no other invasive abscesses, related to hypervirulent K. pneumoniae.
Full article
(This article belongs to the Special Issue Advances in Medical Microbiology)
Open AccessReview
Imaging of Spondylodiscitis: A Comprehensive Updated Review—Multimodality Imaging Findings, Differential Diagnosis, and Specific Microorganisms Detection
by
Amandine Crombé, David Fadli, Roberta Clinca, Giorgio Reverchon, Luca Cevolani, Marco Girolami, Olivier Hauger, George R. Matcuk and Paolo Spinnato
Microorganisms 2024, 12(5), 893; https://doi.org/10.3390/microorganisms12050893 (registering DOI) - 29 Apr 2024
Abstract
Spondylodiscitis is defined by infectious conditions involving the vertebral column. The incidence of the disease has constantly increased over the last decades. Imaging plays a key role in each phase of the disease. Indeed, radiological tools are fundamental in (i) the initial diagnostic
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Spondylodiscitis is defined by infectious conditions involving the vertebral column. The incidence of the disease has constantly increased over the last decades. Imaging plays a key role in each phase of the disease. Indeed, radiological tools are fundamental in (i) the initial diagnostic recognition of spondylodiscitis, (ii) the differentiation against inflammatory, degenerative, or calcific etiologies, (iii) the disease staging, as well as (iv) to provide clues to orient towards the microorganisms involved. This latter aim can be achieved with a mini-invasive procedure (e.g., CT-guided biopsy) or can be non-invasively supposed by the analysis of the CT, positron emission tomography (PET) CT, or MRI features displayed. Hence, this comprehensive review aims to summarize all the multimodality imaging features of spondylodiscitis. This, with the goal of serving as a reference for Physicians (infectious disease specialists, spine surgeons, radiologists) involved in the care of these patients. Nonetheless, this review article may offer starting points for future research articles.
Full article
(This article belongs to the Section Medical Microbiology)
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Open AccessReview
The Role of Metallurgical Features in the Microbially Influenced Corrosion of Carbon Steel: A Critical Review
by
Muhammad Awais Javed, Nicolò Ivanovich, Elena Messinese, Ruiliang Liu, Solange E. Astorga, Yee Phan Yeo, Sridhar Idapalapati, Federico M. Lauro and Scott A. Wade
Microorganisms 2024, 12(5), 892; https://doi.org/10.3390/microorganisms12050892 (registering DOI) - 29 Apr 2024
Abstract
Microbially influenced corrosion (MIC) is a potentially critical degradation mechanism for a wide range of materials exposed to environments that contain relevant microorganisms. The likelihood and rate of MIC are affected by microbiological, chemical, and metallurgical factors; hence, the understanding of the mechanisms
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Microbially influenced corrosion (MIC) is a potentially critical degradation mechanism for a wide range of materials exposed to environments that contain relevant microorganisms. The likelihood and rate of MIC are affected by microbiological, chemical, and metallurgical factors; hence, the understanding of the mechanisms involved, verification of the presence of MIC, and the development of mitigation methods require a multidisciplinary approach. Much of the recent focus in MIC research has been on the microbiological and chemical aspects, with less attention given to metallurgical attributes. Here, we address this knowledge gap by providing a critical synthesis of the literature on the metallurgical aspects of MIC of carbon steel, a material frequently associated with MIC failures and widely used in construction and infrastructure globally. The article begins by introducing the process of MIC, then progresses to explore the complexities of various metallurgical factors relevant to MIC in carbon steel. These factors include chemical composition, grain size, grain boundaries, microstructural phases, inclusions, and welds, highlighting their potential influence on MIC processes. This review systematically presents key discoveries, trends, and the limitations of prior research, offering some novel insights into the impact of metallurgical factors on MIC, particularly for the benefit of those already familiar with other aspects of MIC. The article concludes with recommendations for documenting metallurgical data in MIC research. An appreciation of relevant metallurgical attributes is essential for a critical assessment of a material’s vulnerability to MIC to advance research practices and to broaden the collective knowledge in this rapidly evolving area of study.
Full article
(This article belongs to the Special Issue Microorganisms and Marine Biodeterioration)
Open AccessArticle
Fermented Rapeseed and Soybean Alone and in Combination with Macro Algae Inhibit Human and Pig Pathogenic Bacteria In Vitro
by
Frederik Beck, Ninfa Rangel Pedersen and Dennis Sandris Nielsen
Microorganisms 2024, 12(5), 891; https://doi.org/10.3390/microorganisms12050891 (registering DOI) - 29 Apr 2024
Abstract
Higher plants produce secondary metabolites expressing antimicrobial effects as a defense mechanism against opportunistic microorganisms living in close proximity with the plant. Fermentation leads to bioconversion of plant substrates to these bioactive compounds and their subsequent release via breakdown of plant cell walls.
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Higher plants produce secondary metabolites expressing antimicrobial effects as a defense mechanism against opportunistic microorganisms living in close proximity with the plant. Fermentation leads to bioconversion of plant substrates to these bioactive compounds and their subsequent release via breakdown of plant cell walls. Fermented feed products have recently started to become implemented in the pig industry to reduce overall disease pressure and have been found to reduce events such as post-weaning diarrhea. In this study, we investigate the antimicrobial potential of fermented soybean- and rapeseed-based pig feed supplements with and without added seaweed. The antimicrobial effect was tested in a plate well diffusion assay against a range of known human and livestock pathogenic bacteria. Further, we investigate the metabolite profiles based on liquid-chromatography mass-spectrometry (LC-MS) analysis of the fermented products in comparison to their unfermented constituents. We observed a pronounced release of potential antimicrobial secondary metabolites such as benzoic acids when the plant material was fermented, and a significantly increased antimicrobial effect compared to the unfermented controls against several pathogenic bacteria, especially Salmonella enterica Typhimurium, Listeria monocytogenes, Yersinia enterocolitica, and a strain of atopic dermatitis causing Staphylococcus aureus CC1. In conclusion, fermentation significantly enhances the antimicrobial properties of rapeseed, soybean, and seaweed, offering a promising alternative to zinc oxide for controlling pathogens in piglet feed. This effect is attributed to the release of bioactive metabolites effective against pig production-relevant bacteria.
Full article
(This article belongs to the Section Food Microbiology)
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Open AccessArticle
An In-Depth Study on the Inhibition of Quorum Sensing by Bacillus velezensis D-18: Its Significant Impact on Vibrio Biofilm Formation in Aquaculture
by
Luis Monzón-Atienza, Jimena Bravo, Silvia Torrecillas, Antonio Gómez-Mercader, Daniel Montero, José Ramos-Vivas, Jorge Galindo-Villegas and Félix Acosta
Microorganisms 2024, 12(5), 890; https://doi.org/10.3390/microorganisms12050890 (registering DOI) - 29 Apr 2024
Abstract
Amid growing concerns about antibiotic resistance, innovative strategies are imperative in addressing bacterial infections in aquaculture. Quorum quenching (QQ), the enzymatic inhibition of quorum sensing (QS), has emerged as a promising solution. This study delves into the QQ capabilities of the probiotic strain
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Amid growing concerns about antibiotic resistance, innovative strategies are imperative in addressing bacterial infections in aquaculture. Quorum quenching (QQ), the enzymatic inhibition of quorum sensing (QS), has emerged as a promising solution. This study delves into the QQ capabilities of the probiotic strain Bacillus velezensis D-18 and its products, particularly in Vibrio anguillarum 507 communication and biofilm formation. Chromobacterium violaceum MK was used as a biomarker in this study, and the results confirmed that B. velezensis D-18 effectively inhibits QS. Further exploration into the QQ mechanism revealed the presence of lactonase activity by B. velezensis D-18 that degraded both long- and short-chain acyl homoserine lactones (AHLs). PCR analysis demonstrated the presence of a homologous lactonase-producing gene, ytnP, in the genome of B. velezensis D-18. The study evaluated the impact of B. velezensis D-18 on V. anguillarum 507 growth and biofilm formation. The probiotic not only controls the biofilm formation of V. anguillarum but also significantly restrains pathogen growth. Therefore, B. velezensis D-18 demonstrates substantial potential for preventing V. anguillarum diseases in aquaculture through its QQ capacity. The ability to disrupt bacterial communication and control biofilm formation positions B. velezensis D-18 as a promising eco-friendly alternative to conventional antibiotics in managing bacterial diseases in aquaculture.
Full article
(This article belongs to the Section Veterinary Microbiology)
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Open AccessArticle
Effects of Dried Tea Residues of Different Processing Techniques on the Nutritional Parameters, Fermentation Quality, and Bacterial Structure of Silaged Alfalfa
by
Xingcheng Lei, Binbin Na, Tong Zhou, Yuangan Qian, Yixiao Xie, Yulong Zheng, Qiming Cheng, Ping Li, Chao Chen and Hong Sun
Microorganisms 2024, 12(5), 889; https://doi.org/10.3390/microorganisms12050889 (registering DOI) - 29 Apr 2024
Abstract
The effects of dried tea residues on the nutritional parameters and fermentation quality, microbial community, and in vitro digestibility of alfalfa silage were investigated. In this study, dried tea residues generated from five different processing techniques (green tea, G; black tea, B; white
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The effects of dried tea residues on the nutritional parameters and fermentation quality, microbial community, and in vitro digestibility of alfalfa silage were investigated. In this study, dried tea residues generated from five different processing techniques (green tea, G; black tea, B; white tea, W; Pu’er raw tea, Z; Pu’er ripe tea, D) were added at two addition levels (5% and 10% fresh weight (FW)) to alfalfa and fermented for 90 days. The results showed that the tea residues increased the crude protein (CP) content (Z10: 23.85%), true protein nitrogen (TPN) content, DPPH, and ABST radical scavenging capacity, total antioxidant capacity (TAOC), and in vitro dry matter digestibility (IVDMD) of the alfalfa silage. Moreover, the pH, ammonia-N (NH3-N) content, and acetic acid (AA) content decreased (p < 0.05). The effects of tea residues were promoted on these indicators with increasing tea residue addition. In addition, this study revealed that the influence of dried tea residues on the nutritional quality of alfalfa silage was greater than that on fermentation quality. Based on the nutrient composition, the addition of B or G to alfalfa silage can improve its silage quality, and these tea byproducts have the potential to be used as silage additives.
Full article
(This article belongs to the Section Microbial Biotechnology)
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Open AccessArticle
Transcriptome Analysis of mfs2-Defective Penicillium digitatum Mutant to Reveal Importance of Pdmfs2 in Developing Fungal Prochloraz Resistance
by
Rongrong Cuan, Shaoting Liu, Chuanyou Zhou, Shengqiang Wang, Yongliang Zheng and Yongze Yuan
Microorganisms 2024, 12(5), 888; https://doi.org/10.3390/microorganisms12050888 (registering DOI) - 28 Apr 2024
Abstract
Demethylation inhibitors (DMIs), including prochloraz, are popular fungicides to control citrus postharvest pathogens such as Penicillium digitatum (green mold). However, many P. digitatum strains have developed prochloraz resistance, which decreases drug efficacy. Specific major facilitator superfamily (MFS) transporter gene mfs2, encoding drug-efflux
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Demethylation inhibitors (DMIs), including prochloraz, are popular fungicides to control citrus postharvest pathogens such as Penicillium digitatum (green mold). However, many P. digitatum strains have developed prochloraz resistance, which decreases drug efficacy. Specific major facilitator superfamily (MFS) transporter gene mfs2, encoding drug-efflux pump protein MFS2, has been identified in P. digitatum strain F6 (PdF6) to confer fungal strain prochloraz resistance. However, except for the drug-efflux pump function of MFS2, other mechanisms relating to the Pdmfs2 are not fully clear. The present study reported a transcriptome investigation on the mfs2-defective P. digitatum strain. Comparing to the wild-type strain, the mfs2-defective strain showed 717 differentially expressed genes (DEGs) without prochloraz induction, and 1221 DEGs with prochloraz induction. The obtained DEGs included multiple isoforms of MFS transporter-encoding genes, ATP-binding cassette (ABC) transporter-encoding genes, and multidrug and toxic compound extrusion (MATE) family protein-encoding genes. Many of these putative drug-efflux pump protein-encoding genes had significantly lower transcript abundances in the mfs2-defective P. digitatum strain at prochloraz induction, as compared to the wild-type strain, including twenty-two MFS transporter-encoding genes (MFS1 to MFS22), two ABC transporter-encoding genes (ABC1 and ABC2), and three MATE protein-encoding genes (MATE1 to MATE3). The prochloraz induction on special drug-efflux pump protein genes in the wild-type strain was not observed in the mfs2-defective strain, including MFS21, MFS22, ABC2, MATE1, MATE2, and MATE3. On the other hand, the up-regulation of other drug-efflux pump protein genes in the mfs2-defective strain cannot recover the fungal prochloraz resistance, including MFS23, MFS26, MFS27, MFS31, MFS33, and ABC3 to ABC8. The functional enrichment of DEGs based on Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and euKaryotic Orthologous Groups (KOG) database resources suggested some essential contributors to the mfs2-relating prochloraz resistance, including ribosome biosynthesis-related genes, oxidative phosphorylation genes, steroid biosynthesis-related genes, fatty acid and lipid metabolism-related genes, and carbon- and nitrogen-metabolism-related genes. The results indicated that the MFS2 transporter might be involved in the regulation of multiple drug-efflux pump protein gene expressions and multiple metabolism-related gene expressions, thus playing an important role in developing P. digitatum prochloraz resistance.
Full article
(This article belongs to the Special Issue Fungicide Resistance in Plant Pathogen)
Open AccessArticle
Managing Super Pests: Interplay between Pathogens and Symbionts Informs Biocontrol of Whiteflies
by
Weili Yan, Saixian Wang, Jialei Liu, Dan Zhai, Hang Lu, Jingjing Li, Rune Bai, Caiyan Lei, Luyang Song, Chenchen Zhao and Fengming Yan
Microorganisms 2024, 12(5), 887; https://doi.org/10.3390/microorganisms12050887 (registering DOI) - 28 Apr 2024
Abstract
Bemisia tabaci is distributed globally and incurs considerable economic and ecological costs as an agricultural pest and viral vector. The entomopathogenic fungus Metarhizium anisopliae has been known for its insecticidal activity, but its impacts on whiteflies are understudied. We investigated how infection with
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Bemisia tabaci is distributed globally and incurs considerable economic and ecological costs as an agricultural pest and viral vector. The entomopathogenic fungus Metarhizium anisopliae has been known for its insecticidal activity, but its impacts on whiteflies are understudied. We investigated how infection with the semi-persistently transmitted Cucurbit chlorotic yellows virus (CCYV) affects whitefly susceptibility to M. anisopliae exposure. We discovered that viruliferous whiteflies exhibited increased mortality when fungus infection was present compared to non-viruliferous insects. High throughput 16S rRNA sequencing also revealed significant alterations of the whitefly bacterial microbiome diversity and structure due to both CCYV and fungal presence. Specifically, the obligate symbiont Portiera decreased in relative abundance in viruliferous whiteflies exposed to M. anisopliae. Facultative Hamiltonella and Rickettsia symbionts exhibited variability across groups but dominated in fungus-treated non-viruliferous whiteflies. Our results illuminate triangular interplay between pest insects, their pathogens, and symbionts—dynamics which can inform integrated management strategies leveraging biopesticides This work underscores the promise of M. anisopliae for sustainable whitefly control while laying the groundwork for elucidating mechanisms behind microbe-mediated shifts in vector competence.
Full article
(This article belongs to the Special Issue Plant Pathogens: Monitoring, Identification and Biological Control)
Open AccessReview
What do We Know about Cryptic Aspergillosis?
by
Nicholas Geremia, Federico Giovagnorio, Agnese Colpani, Andrea De Vito, Giorgia Caruana, Maria Chiara Meloni, Giordano Madeddu, Sandro Panese and Saverio Giuseppe Parisi
Microorganisms 2024, 12(5), 886; https://doi.org/10.3390/microorganisms12050886 (registering DOI) - 28 Apr 2024
Abstract
Cryptic Aspergillus species are increasingly recognized as pathogens involved in human disease. They are ubiquitarian fungi with high tenacity in their environment and can express various resistance mechanisms, often due to exposure to antifungal agents employed in agriculture and farming. The identification of
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Cryptic Aspergillus species are increasingly recognized as pathogens involved in human disease. They are ubiquitarian fungi with high tenacity in their environment and can express various resistance mechanisms, often due to exposure to antifungal agents employed in agriculture and farming. The identification of such species is increasing thanks to molecular techniques, and a better description of this type of pathogen is granted. Nevertheless, the number of species and their importance in the clinical setting still need to be well studied. Furthermore, their cross-sectional involvement in animal disease, plants, and human activities requires a multidisciplinary approach involving experts from various fields. This comprehensive review aims to provide a sharp vision of the cryptic Aspergillus species, from the importance of correct identification to the better management of the infections caused by these pathogens. The review also accentuates the importance of the One Health approach for this kind of microorganism, given the interconnection between environmental exposure and aspergillosis, embracing transversely the multidisciplinary process for managing the cryptic Aspergillus species. The paper advocates the need for improving knowledge in this little-known species, given the burden of economic and health implications related to the diffusion of these bugs.
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(This article belongs to the Special Issue Emerging Pathogens in the Context of One Health)
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Paulownia Witches’ Broom Disease: A Comprehensive Review
by
Yajie Zhang, Zesen Qiao, Jidong Li and Assunta Bertaccini
Microorganisms 2024, 12(5), 885; https://doi.org/10.3390/microorganisms12050885 (registering DOI) - 28 Apr 2024
Abstract
Phytoplasmas are insect-transmitted bacterial pathogens associated with diseases in a wide range of host plants, resulting in significant economic and ecological losses. Perennial deciduous trees in the genus Paulownia are widely planted for wood harvesting and ornamental purposes. Paulownia witches’ broom (PaWB) disease,
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Phytoplasmas are insect-transmitted bacterial pathogens associated with diseases in a wide range of host plants, resulting in significant economic and ecological losses. Perennial deciduous trees in the genus Paulownia are widely planted for wood harvesting and ornamental purposes. Paulownia witches’ broom (PaWB) disease, associated with a 16SrI-D subgroup phytoplasma, is a destructive disease of paulownia in East Asia. The PaWB phytoplasmas are mainly transmitted by insect vectors in the Pentatomidae (stink bugs), Miridae (mirid bugs) and Cicadellidae (leafhoppers) families. Diseased trees show typical symptoms, such as branch and shoot proliferation, which together are referred to as witches’ broom. The phytoplasma presence affects the physiological and anatomical structures of paulownia. Gene expression in paulownia responding to phytoplasma presence have been studied at the transcriptional, post-transcriptional, translational and post-translational levels by high throughput sequencing techniques. A PaWB pathogenic mechanism frame diagram on molecular level is summarized. Studies on the interactions among the phytoplasma, the insect vectors and the plant host, including the mechanisms underlying how paulownia effectors modify processes of gene expression, will lead to a deeper understanding of the pathogenic mechanisms and to the development of efficient control measures.
Full article
(This article belongs to the Special Issue Phloem Localized Insect Transmitted Bacteria Associated with Plant Diseases)
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Open AccessReview
Addressing Sexually Transmitted Infections Due to Neisseria gonorrhoeae in the Present and Future
by
Julia Colón Pérez, Rosa-Antía Villarino Fernández, Adrián Domínguez Lago, María Mercedes Treviño Castellano, María Luisa Pérez del Molino Bernal, Sandra Sánchez Poza and Eva Torres-Sangiao
Microorganisms 2024, 12(5), 884; https://doi.org/10.3390/microorganisms12050884 (registering DOI) - 28 Apr 2024
Abstract
It was in the 1800s when the first public publications about the infection and treatment of gonorrhoea were released. However, the first prevention programmes were only published a hundred years later. In the 1940s, the concept of vaccination was introduced into clinical prevention
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It was in the 1800s when the first public publications about the infection and treatment of gonorrhoea were released. However, the first prevention programmes were only published a hundred years later. In the 1940s, the concept of vaccination was introduced into clinical prevention programmes to address early sulphonamide resistance. Since then, tons of publications on Neisseria gonorrhoeae are undisputed, around 30,000 publications today. Currently, the situation seems to be just as it was in the last century, nothing has changed or improved. So, what are we doing wrong? And more importantly, what might we do? The review presented here aims to review the current situation regarding the resistance mechanisms, prevention programmes, treatments, and vaccines, with the challenge of better understanding this special pathogen. The authors have reviewed the last five years of advancements, knowledge, and perspectives for addressing the Neisseria gonorrhoeae issue, focusing on new therapeutic alternatives.
Full article
(This article belongs to the Special Issue Infectious Diseases: New Approaches to Old Problems 3.0)
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Open AccessArticle
Genetic Analyses of Rare ESBL ST628 Klebsiella pneumoniae Detected during a Protracted Nosocomial Outbreak in the United Kingdom
by
Stephen Mark Edward Fordham, Francis Drobniewski, Magdalena Barrow, Melissa Hutchings, Kate Crowther, Denise Richards, Paul Bolton, Anna Mantzouratou and Elizabeth Sheridan
Microorganisms 2024, 12(5), 883; https://doi.org/10.3390/microorganisms12050883 (registering DOI) - 28 Apr 2024
Abstract
Klebsiella pneumoniae (K. pneumoniae) cultures from a hospital-wide outbreak in the UK, which lasted for over 12 months, were sequenced. We sought to sequence and genetically characterise the outbreak strain. Antibiotic Susceptibility Testing (AST) was performed on 65 K. pneumoniae isolates
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Klebsiella pneumoniae (K. pneumoniae) cultures from a hospital-wide outbreak in the UK, which lasted for over 12 months, were sequenced. We sought to sequence and genetically characterise the outbreak strain. Antibiotic Susceptibility Testing (AST) was performed on 65 K. pneumoniae isolates saved from the outbreak. All isolates were sequenced using the Oxford Nanopore Technologies (ONT) MinION flowcell: 10 isolates, including the isolate with the earliest collection date in 2017, were additionally sequenced on the NovaSeq 6000 platform to build high-accuracy nanopore-illumina assemblies. Among the sequenced strains, 60 were typed as ST628. 96.6% (n = 58/60) ST628 strains harboured a large ~247-kb FIB(K) plasmid carrying up to 11 antimicrobial resistance genes, including the extended-spectrum beta-lactamase (ESBL) gene, blaCTX-M-15. Clonality between the outbreak isolates was confirmed using single nucleotide polymorphism (SNP) typing. The outbreak strains were phylogenetically related to clinical ST628 strains identified in 2012, 6 years prior to the outbreak. A rare ESBL K. pneumoniae K2 ST628 strain harbouring a multi-drug resistant (MDR) plasmid encoding the ESBL gene blaCTX-M-15 was detected across multiple independent wards during the protracted nosocomial outbreak. Surveillance of this strain is recommended to prevent future nosocomial outbreaks.
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(This article belongs to the Section Systems Microbiology)
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Open AccessArticle
Advancements in Fermented Beverage Safety: Isolation and Application of Clavispora lusitaniae Cl-p for Ethyl Carbamate Degradation and Enhanced Flavor Profile
by
Yingchun Zhao, Jun Liu, Han Wang, Fayuan Gou, Yiwei He and Lijuan Yang
Microorganisms 2024, 12(5), 882; https://doi.org/10.3390/microorganisms12050882 (registering DOI) - 28 Apr 2024
Abstract
Ethyl carbamate (EC) is a natural by-product in the production of fermented food and alcoholic beverages and is carcinogenic and genotoxic, posing a significant food safety concern. In this study, Clavispora lusitaniae Cl-p with a strong EC degradation ability was isolated from Daqu
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Ethyl carbamate (EC) is a natural by-product in the production of fermented food and alcoholic beverages and is carcinogenic and genotoxic, posing a significant food safety concern. In this study, Clavispora lusitaniae Cl-p with a strong EC degradation ability was isolated from Daqu rich in microorganisms by using EC as the sole nitrogen source. When 2.5 g/L of EC was added to the fermentation medium, the strain decomposed 47.69% of ethyl carbamate after five days of fermentation. It was unexpectedly found that the strain had the ability to produce aroma and ester, and the esterification power reached 30.78 mg/(g·100 h). When the strain was added to rice wine fermentation, compared with the control group, the EC content decreased by 41.82%, and flavor substances such as ethyl acetate and β-phenylethanol were added. The EC degradation rate of the immobilized crude enzyme in the finished yellow rice wine reached 31.01%, and the flavor substances of yellow rice wine were not affected. The strain is expected to be used in the fermented food industry to reduce EC residue and improve the safety of fermented food.
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(This article belongs to the Section Food Microbiology)
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Open AccessArticle
Optimizing Akkermansia muciniphila Isolation and Cultivation: Insights into Gut Microbiota Composition and Potential Growth Promoters in a Chinese Cohort
by
Xiangyu Meng, Chen Xv, Jiaping Lv, Shuwen Zhang, Changlu Ma and Xiaoyang Pang
Microorganisms 2024, 12(5), 881; https://doi.org/10.3390/microorganisms12050881 (registering DOI) - 28 Apr 2024
Abstract
The study aims to analyze the composition of the gut microbiota in Chinese individuals using metagenomic sequencing technology, with a particular focus on the abundance of Akkermansia muciniphila (Akk). To improve the efficiency of Akk isolation and identification accuracy, modifications were made to
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The study aims to analyze the composition of the gut microbiota in Chinese individuals using metagenomic sequencing technology, with a particular focus on the abundance of Akkermansia muciniphila (Akk). To improve the efficiency of Akk isolation and identification accuracy, modifications were made to the enrichment culture medium and 16S rRNA universal primers. Additionally, potential growth-promoting factors that stimulate Akk growth were explored through in vitro screening. The research results revealed that the abundance of Akk in Chinese fecal samples ranged from 0.004% to 0.4%. During optimization, a type of animal protein peptide significantly enhanced the enrichment efficiency of Akk, resulting in the isolation of three Akk strains from 14 fecal samples. Furthermore, 17 different growth-promoting factors were compared, and four factors, including galactose, sialic acid, lactose, and chitosan, were identified as significantly promoting Akk growth. Through orthogonal experiments, the optimal ratio of these four growth-promoting factors was determined to be 1:1:2:1. After adding 1.25% of this growth-promoting factor combination to the standard culture medium, Akk was cultivated at 37° for 36 h, achieving an OD600nm value of 1.169, thus realizing efficient proliferation and optimized cultivation of Akk. This study provides important clues for a deeper understanding of the gut microbiota composition in Chinese individuals, while also offering effective methods for the isolation and cultivation of Akk, laying the groundwork for its functional and application research in the human body.
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(This article belongs to the Special Issue Effects of Gut Microbiota on Human Health and Disease)
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Open AccessArticle
Wine Barrel Biofilm as a Source of Yeasts with Non-Conventional Properties
by
Giorgia Perpetuini, Alessio Pio Rossetti, Arianna Rapagnetta, Giuseppe Arfelli, Roberta Prete and Rosanna Tofalo
Microorganisms 2024, 12(5), 880; https://doi.org/10.3390/microorganisms12050880 (registering DOI) - 27 Apr 2024
Abstract
This study investigated the main microbial groups characterizing the interior surface of oak barrels from different years (1890, 1895, 1920, 1975, 2008) used in the production of vino cotto. The yeasts were characterized for the following properties: γ-aminobutyric acid (GABA) production, antioxidant activity,
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This study investigated the main microbial groups characterizing the interior surface of oak barrels from different years (1890, 1895, 1920, 1975, 2008) used in the production of vino cotto. The yeasts were characterized for the following properties: γ-aminobutyric acid (GABA) production, antioxidant activity, air–liquid interfacial biofilm formation, and anthocyanin adsorption capacity. Community-level physiological profile analysis revealed that the microbial communities inside the barrels used the tested carbon sources in different manners. The following yeast species were identified: Millerozyma farinosa, Zygosaccharomyces bisporus, Wickerhamiella versatilis, Zygosaccharomyces bailii, Starmerella lactis-condensi, and Zygosaccharomyces rouxii. All the strains were able to produce GABA, and S. lactis-condensi, Z. bisporus and Z. rouxii were the highest producers (more than 600 mg/L). The Z. rouxii and Z. bailii strains showed the highest antioxidant activity. Only seven strains out of ten M. farinosa formed air–liquid interfacial biofilm. None of the M. farinosa strains adsorbed anthocyanins on their cell wall. The other strains adsorbed anthocyanins in a strain-dependent way, and the highest adsorption was observed for the W. versatilis strains. The yeasts isolated in this study could be used to increase the functional properties and the quality of fermented foods and beverages.
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(This article belongs to the Section Biofilm)
Open AccessReview
Transmission and Persistence of Infant Gut-Associated Bifidobacteria
by
Margaret A. Hilliard and David A. Sela
Microorganisms 2024, 12(5), 879; https://doi.org/10.3390/microorganisms12050879 (registering DOI) - 27 Apr 2024
Abstract
Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from
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Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from mother to infant via the fecal-oral route is likely contingent on the bifidobacterial strain and phenotype, whereas transmission via the vaginal microbiota may be restricted to Bifidobacterium breve. Additional reservoirs include breastmilk, horizontal transfer from the environment, and potentially in utero transfer. Given that diet is a strong predictor of Bifidobacterium colonization in early life and the absence of Bifidobacterium is observed regardless of breastfeeding, it is likely that additional factors are responsible for bifidobacterial colonization early in life.
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(This article belongs to the Special Issue Beneficial Microbes and Gastrointestinal Microbiota 2.0)
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Open AccessArticle
New Species-Specific Real-Time PCR Assays for Colletotrichum Species Causing Bitter Rot of Apple
by
Diana J. McHenry and Srđan G. Aćimović
Microorganisms 2024, 12(5), 878; https://doi.org/10.3390/microorganisms12050878 (registering DOI) - 27 Apr 2024
Abstract
Bitter rot of apple is an economically important worldwide disease caused by different Colletotrichum species, depending on many factors such as climate, geography, other hosts, and crop management practices. Culture, morphology, and single-locus sequencing-based methods for identifying the Colletotrichum species are severely limited
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Bitter rot of apple is an economically important worldwide disease caused by different Colletotrichum species, depending on many factors such as climate, geography, other hosts, and crop management practices. Culture, morphology, and single-locus sequencing-based methods for identifying the Colletotrichum species are severely limited in effectiveness, while the multilocus sequence typing methods available for delineating species are costly, time-intensive, and require high expertise. We developed species-specific hydrolysis probe real-time PCR assays for the following nine Colletotrichum species causing bitter rot in the Mid-Atlantic U.S.A.: C. fructicola, C. chrysophilum, C. noveboracense, C. gloeosporioides s.s., C. henanense, C. siamense and C. theobromicola from the C. gloeosporioides species complex, and C. fioriniae and C. nymphaeae from the C. acutatum species complex. After searching 14 gene regions, we designed primers and probes in 5 of them for the nine target species. Four primer–probe set pairs were able to be duplexed. Sensitivity tests showed as little as 0.5 pg DNA were detectable. These real-time PCR assays will provide rapid and reliable identification of these key Colletotrichum species and will be critically important for studies aiming to elucidate their biology, epidemiology, and management on apples as the number one produced and consumed tree fruit in the U.S.A.
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(This article belongs to the Special Issue Colletotrichum Pathogens in Plants)
Open AccessArticle
Isolation of Vibrio cholerae and Vibrio vulnificus from Estuarine Waters, and Genotyping of V. vulnificus Isolates Using Loop-Mediated Isothermal Amplification
by
Shin-ichi Miyoshi, Megumi Kurata, Riho Hirose, Masaya Yoshikawa, Yong Liang, Yosuke Yamagishi and Tamaki Mizuno
Microorganisms 2024, 12(5), 877; https://doi.org/10.3390/microorganisms12050877 (registering DOI) - 27 Apr 2024
Abstract
Bacteria in the genus Vibrio are ubiquitous in estuarine and coastal waters. Some species (including Vibrio cholerae and Vibrio vulnificus) are known human pathogens causing ailments like cholera, diarrhea, or septicemia. Notably, V. vulnificus can also cause a severe systemic infection (known as
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Bacteria in the genus Vibrio are ubiquitous in estuarine and coastal waters. Some species (including Vibrio cholerae and Vibrio vulnificus) are known human pathogens causing ailments like cholera, diarrhea, or septicemia. Notably, V. vulnificus can also cause a severe systemic infection (known as vibriosis) in eels raised in aquaculture facilities. Water samples were periodically collected from the estuary of the Asahi River, located in the southern part of Okayama City, Japan. These samples were directly plated onto CHROMagar Vibrio plates, and colonies displaying turquoise-blue coloration were selected. Thereafter, polymerase chain reaction was used to identify V. cholerae and V. vulnificus. A total of 30 V. cholerae strains and 194 V. vulnificus strains were isolated during the warm season when the water temperature (WT) was higher than 20 °C. Concurrently, an increase in coliforms was observed during this period. Notably, V. vulnificus has two genotypes, designated as genotype 1 and genotype 2. Genotype 1 is pathogenic to humans, while genotype 2 is pathogenic to both humans and eels. The loop-mediated isothermal amplification method was developed to rapidly determine genotypes at a low cost. Of the 194 strains isolated, 80 (41.2%) were identified as genotype 1 strains. Among the 41 strains isolated when the WTs were higher than 28 °C, 25 strains (61.0%) belonged to genotype 1. In contrast, of the 32 strains isolated when the WTs were lower than 24 °C, 27 strains (84.4%) belonged to genotype 2. These results suggest that the distribution of the two genotypes was influenced by WT.
Full article
(This article belongs to the Special Issue Water Microorganisms Associated with Human Health)
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