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
Purpureocillium jiangxiense sp. nov.: Entomopathogenic Effects on Ostrinia furnacalis and Galleria mellonella
Microorganisms 2024, 12(6), 1041; https://doi.org/10.3390/microorganisms12061041 (registering DOI) - 21 May 2024
Abstract
The genus Purpureocillium is renowned for its role in biocontrol and biotechnological applications. The identification of new species within this genus is crucial for broadening our understanding of its ecological roles and potential utility in sustainable agriculture. This study aimed to characterize a
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The genus Purpureocillium is renowned for its role in biocontrol and biotechnological applications. The identification of new species within this genus is crucial for broadening our understanding of its ecological roles and potential utility in sustainable agriculture. This study aimed to characterize a new species of Purpureocillium, isolated from soil in eastern China, and to evaluate its bioactivity against Ostrinia furnacalis (corn moth) and Galleria mellonella (greater wax moth). We utilized morphological characterization; molecular phylogenetic analysis employing ITS, nrLSU, and tef1 genes; and bioactivity assays to identify and characterize the new species. The newly identified species, Purpureocillium jiangxiense sp. nov., displays unique morphological and genetic profiles compared to known species. Bioactivity tests showed that this species exhibits inhibitory effects against O. furnacalis and G. mellonella, highlighting its potential in biocontrol applications. By the ninth day at a spore concentration of 1 × 108 spores/mL, the mortality rate of the corn moth and greater wax moth reached 30% to 50% respectively. The discovery of P. jiangxiense sp. nov. adds to the genetic diversity known within this genus and offers a promising candidate for the development of natural biocontrol agents. It underscores the importance of continued biodiversity exploration and the potential for natural solutions in pest and disease management.
Full article
(This article belongs to the Section Systems Microbiology)
Open AccessArticle
A Study on the Effect of Various Media and the Supplementation of Organic Compounds on the Enhanced Production of Astaxanthin from Haematococcus lacustris (Girod—Chantrans) Rostafinski (Chlorophyta)
by
Vijay Rayamajhi, Yunji An, Huijeong Byeon, Jihyun Lee, Taesoo Kim, AhJung Choi, JongDae Lee, KwangSoo Lee, ChulHyun Kim, HyunWoung Shin and SangMok Jung
Microorganisms 2024, 12(6), 1040; https://doi.org/10.3390/microorganisms12061040 (registering DOI) - 21 May 2024
Abstract
Natural astaxanthin is in high demand due to its multiple health benefits. The microalga Haematococcus lacustris has been used for the commercial production of astaxanthin. In this study, we investigated the effects of six different media with and without a nitrogen source and
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Natural astaxanthin is in high demand due to its multiple health benefits. The microalga Haematococcus lacustris has been used for the commercial production of astaxanthin. In this study, we investigated the effects of six different media with and without a nitrogen source and supplementation with nine organic compounds on the growth and astaxanthin accumulation of H. lacustris. The highest astaxanthin contents were observed in cultures of H. lacustris in Jaworski’s medium (JM), with a level of 9.099 mg/L in JM with a nitrogen source supplemented with leucine (0.65 g/L) and of 20.484 mg/L in JM without a nitrogen source supplemented with sodium glutamate (0.325 g/L). Six of the nine organic compounds examined (leucine, lysine, alanine, sodium glutamate, glutamine, and cellulose) enhanced the production of astaxanthin in H. lacustris, while malic acid, benzoic acid, and maltose showed no beneficial effects.
Full article
(This article belongs to the Special Issue Biosynthesis of Plant-Derived Bioactive Components by Photosynthetic Microorganisms)
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Open AccessCommunication
Association between Exposure to Leptospira spp. and Abortion in Mares in Croatia
by
Iva Zečević, Mathieu Picardeau, Silvijo Vince, Suzana Hađina, Matko Perharić, Zrinka Štritof, Vladimir Stevanović, Iva Benvin, Nenad Turk, Ivana Lohman Janković and Josipa Habuš
Microorganisms 2024, 12(6), 1039; https://doi.org/10.3390/microorganisms12061039 (registering DOI) - 21 May 2024
Abstract
Leptospirosis is one of the most common zoonotic infections and a major problem in terms of both veterinary medicine and public health. However, the disease is under-recognised and under-diagnosed worldwide, particularly in horses. Clinical leptospirosis in horses is mainly associated with recurrent uveitis
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Leptospirosis is one of the most common zoonotic infections and a major problem in terms of both veterinary medicine and public health. However, the disease is under-recognised and under-diagnosed worldwide, particularly in horses. Clinical leptospirosis in horses is mainly associated with recurrent uveitis (ERU), which has recently been studied more intensively, and reproductive disorders, the epidemiology of which is still relatively poorly understood. To enhance our comprehension of abortions caused by leptospirosis in horses and to identify the causative strains, a serological study was carried out with subsequent molecular characterisation of the isolate obtained. Using the microscopic agglutination test (MAT), serum samples from mares that aborted and foetal fluids (when available) were tested for antibodies against Leptospira spp. Furthermore, bacteria isolation from kidney cultures was conducted. Of 97 mare serum samples, 21 (21.64%) tested positive, with Grippotyphosa and Pomona being the most frequently detected serogroups. A significantly higher seroprevalence was found in aborting mares compared to the healthy horse population from the same geographical area, as well as a pronounced seasonal variation. Leptospiral antibodies were not detected in any of the foetal fluids, but isolation was successful in 1 case out of 39 (2.56%). Genotyping by multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) identified the obtained isolate as Leptospira kirschneri, serogroup Pomona, serovar Mozdok. Further surveillance and molecular typing of Leptospira strains causing abortion in horses would be invaluable in understanding the prevalence and impact of leptospirosis on equine reproductive health in Europe.
Full article
(This article belongs to the Special Issue Epidemiology of Leptospira sp. Infection: Current Status, Insights and Future Prospects 2.0)
Open AccessReview
Bioplastic Production from Agri-Food Waste through the Use of Haloferax mediterranei: A Comprehensive Initial Overview
by
Angela Longo, Francesca Fanelli, Marianna Villano, Marco Montemurro and Carlo Giuseppe Rizzello
Microorganisms 2024, 12(6), 1038; https://doi.org/10.3390/microorganisms12061038 (registering DOI) - 21 May 2024
Abstract
The research on bioplastics (both biobased and biodegradable) is steadily growing and discovering environmentally friendly substitutes for conventional plastic. This review highlights the significance of bioplastics, analyzing, for the first time, the state of the art concerning the use of agri-food waste as
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The research on bioplastics (both biobased and biodegradable) is steadily growing and discovering environmentally friendly substitutes for conventional plastic. This review highlights the significance of bioplastics, analyzing, for the first time, the state of the art concerning the use of agri-food waste as an alternative substrate for biopolymer generation using Haloferax mediterranei.. H. mediterranei is a highly researched strain able to produce polyhydroxybutyrate (PHB) since it can grow and produce bioplastic in high-salinity environments without requiring sterilization. Extensive research has been conducted on the genes and pathways responsible for PHB production using H. mediterranei to find out how fermentation parameters can be regulated to enhance cell growth and increase PHB accumulation. This review focuses on the current advancements in utilizing food waste as a substitute for costly substrates to reduce feedstock expenses. Specifically, it examines the production of biomass and the recovery of PHB from agri-food waste. Furthermore, it emphasizes the characterization of PHB and the significance of hydroxyvalerate (HV) abundance in the formation of Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) copolymer. The downstream processing options are described, and the crucial factors associated with industrial scale-up are assessed, including substrates, bioreactors, process parameters, and bioplastic extraction and purification. Additionally, the economic implications of various options are discussed.
Full article
(This article belongs to the Special Issue Microbial Fermentation, Food and Food Sustainability)
Open AccessArticle
Lactobacillus rhamnosus PL1 and Lactobacillus plantarum PM1 Versus Placebo as Prophylaxis for Recurrence of Urinary Tract Infections in Children
by
Maria Daniel, Hanna Szymanik-Grzelak, Janusz Sierdziński and Małgorzata Pańczyk-Tomaszewska
Microorganisms 2024, 12(6), 1037; https://doi.org/10.3390/microorganisms12061037 (registering DOI) - 21 May 2024
Abstract
Urinary tract infections (UTIs) rank among the most prevalent bacterial infections in children. Probiotics appear to reduce the risk of recurrence of UTIs. This study aimed to evaluate whether probiotics containing Lactobacillus rhamnosus PL1 and Lactobacillus plantarum PM1 therapy prevent UTIs in the
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Urinary tract infections (UTIs) rank among the most prevalent bacterial infections in children. Probiotics appear to reduce the risk of recurrence of UTIs. This study aimed to evaluate whether probiotics containing Lactobacillus rhamnosus PL1 and Lactobacillus plantarum PM1 therapy prevent UTIs in the pediatric population compared to a placebo. A superiority, double-blind, randomized, controlled trial was conducted. In total, 54 children aged 3–18 years with recurrent UTIs or ≥one acute pyelonephritis and ≥one risk factor of recurrence of UTIs were randomly assigned (27 patients in each arm) to a 90-day probiotic or placebo arm. The age, sex, diagnosis, renal function, risk factors, and etiology of UTIs did not vary between the groups. During the intervention, 26% of children taking the probiotic had episodes of UTI, and it was not significantly less than in the placebo group. The number of UTI episodes during the intervention and the follow-up period decreased significantly in both groups, but the difference between them was insignificant. We observed a decrease in UTIs during the study of almost 50% in the probiotic group compared to the placebo group. Probiotics can be used as natural, safe prophylaxis for children with risk factors for UTIs in whom antibiotic prevention is not indicated.
Full article
(This article belongs to the Special Issue Effects of Probiotics on Health, 2nd Edition)
Open AccessArticle
The Probiotic Strain Lactobacillus acidophilus CL1285 Reduces Fat Deposition and Oxidative Stress and Increases Lifespan in Caenorhabditis elegans
by
Samir Bouasker, Sonja Nodland and Mathieu Millette
Microorganisms 2024, 12(6), 1036; https://doi.org/10.3390/microorganisms12061036 - 21 May 2024
Abstract
Caenorhabditis elegans was recently shown to be a powerful model for studying and identifying probiotics with specific functions. Lactobacillus acidophilus CL1285, Lacticaseibacillus casei LBC80R, and Lacticaseibacillus rhamnosus CLR2, which are three bacteria that were marketed by Bio-K+, were evaluated using the nematode C. elegans
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Caenorhabditis elegans was recently shown to be a powerful model for studying and identifying probiotics with specific functions. Lactobacillus acidophilus CL1285, Lacticaseibacillus casei LBC80R, and Lacticaseibacillus rhamnosus CLR2, which are three bacteria that were marketed by Bio-K+, were evaluated using the nematode C. elegans to study fat accumulation, lifespan, and resistance to oxidative stress. Although the general effects of probiotics in terms of protection against oxidative stress were highlighted, the CL1285 strain had an interesting and specific feature, namely its ability to prevent fat accumulation in nematodes; this effect was verified by both the Oil Red and Nile Red methods. This observed phenotype requires daf-16 and is affected by glucose levels. In addition, in a daf-16- and glucose-dependent manner, CL1285 extended the lifespan of C. elegans; this effect was unique to CL1285 and not found in the other L. acidophilus subtypes in this study. Our findings indicate that L. acidophilus CL1285 impacts fat/glucose metabolism in C. elegans and provides a basis to further study this probiotic, which could have potential health benefits in humans and/or in mammals.
Full article
(This article belongs to the Special Issue Probiotic and Postbiotic Properties of Lactobacillus)
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Open AccessReview
Contemporary Insights into Hepatitis C Virus: A Comprehensive Review
by
Malik Sallam and Roaa Khalil
Microorganisms 2024, 12(6), 1035; https://doi.org/10.3390/microorganisms12061035 - 21 May 2024
Abstract
Hepatitis C virus (HCV) remains a significant global health challenge. Approximately 50 million people were living with chronic hepatitis C based on the World Health Organization as of 2024, contributing extensively to global morbidity and mortality. The advent and approval of several direct-acting
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Hepatitis C virus (HCV) remains a significant global health challenge. Approximately 50 million people were living with chronic hepatitis C based on the World Health Organization as of 2024, contributing extensively to global morbidity and mortality. The advent and approval of several direct-acting antiviral (DAA) regimens significantly improved HCV treatment, offering potentially high rates of cure for chronic hepatitis C. However, the promising aim of eventual HCV eradication remains challenging. Key challenges include the variability in DAA access across different regions, slightly variable response rates to DAAs across diverse patient populations and HCV genotypes/subtypes, and the emergence of resistance-associated substitutions (RASs), potentially conferring resistance to DAAs. Therefore, periodic reassessment of current HCV knowledge is needed. An up-to-date review on HCV is also necessitated based on the observed shifts in HCV epidemiological trends, continuous development and approval of therapeutic strategies, and changes in public health policies. Thus, the current comprehensive review aimed to integrate the latest knowledge on the epidemiology, pathophysiology, diagnostic approaches, treatment options and preventive strategies for HCV, with a particular focus on the current challenges associated with RASs and ongoing efforts in vaccine development. This review sought to provide healthcare professionals, researchers, and policymakers with the necessary insights to address the HCV burden more effectively. We aimed to highlight the progress made in managing and preventing HCV infection and to highlight the persistent barriers challenging the prevention of HCV infection. The overarching goal was to align with global health objectives towards reducing the burden of chronic hepatitis, aiming for its eventual elimination as a public health threat by 2030.
Full article
(This article belongs to the Collection Advances in Public Health Microbiology)
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Open AccessArticle
Effect of Altitude Gradients on the Spatial Distribution Mechanism of Soil Bacteria in Temperate Deciduous Broad-Leaved Forests
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Wenxin Liu, Shengqian Guo, Huiping Zhang, Yun Chen, Yizhen Shao and Zhiliang Yuan
Microorganisms 2024, 12(6), 1034; https://doi.org/10.3390/microorganisms12061034 - 21 May 2024
Abstract
Soil bacteria are an important part of the forest ecosystem, and they play a crucial role in driving energy flow and material circulation. Currently, many uncertainties remain about how the composition and distribution patterns of bacterial communities change along altitude gradients, especially in
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Soil bacteria are an important part of the forest ecosystem, and they play a crucial role in driving energy flow and material circulation. Currently, many uncertainties remain about how the composition and distribution patterns of bacterial communities change along altitude gradients, especially in forest ecosystems with strong altitude gradients in climate, vegetation, and soil properties. Based on dynamic site monitoring of the Baiyun Mountain Forest National Park (33°38′–33°42′ N, 111°47′–111°51′ E), this study used Illumina technology to sequence 120 soil samples at the site and explored the spatial distribution mechanisms and ecological processes of soil bacteria under different altitude gradients. Our results showed that the composition of soil bacterial communities varied significantly between different altitude gradients, affecting soil bacterial community building by influencing the balance between deterministic and stochastic processes; in addition, bacterial communities exhibited broader ecological niche widths and a greater degree of stochasticity under low-altitude conditions, implying that, at lower altitudes, community assembly is predominantly influenced by stochastic processes. Light was the dominant environmental factor that influenced variation in the entire bacterial community as well as other taxa across different altitude gradients. Moreover, changes in the altitude gradient could cause significant differences in the diversity and community composition of bacterial taxa. Our study revealed significant differences in bacterial community composition in the soil under different altitude gradients. The bacterial communities at low elevation gradients were mainly controlled by stochasticity processes, and bacterial community assembly was strongly influenced by deterministic processes at middle altitudes. Furthermore, light was an important environmental factor that affects differences. This study revealed that the change of altitude gradient had an important effect on the development of the soil bacterial community and provided a theoretical basis for the sustainable development and management of soil bacteria.
Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology)
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Open AccessArticle
Colonic Microbiota Improves Fiber Digestion Ability and Enhances Absorption of Short-Chain Fatty Acids in Local Pigs of Hainan
by
Pengxiang Xue, Mingming Xue, Yabiao Luo, Qiguo Tang, Feng Wang, Ruiping Sun, Yanxia Song, Zhe Chao and Meiying Fang
Microorganisms 2024, 12(6), 1033; https://doi.org/10.3390/microorganisms12061033 - 21 May 2024
Abstract
Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. In this study, we fed Ding’an and DLY pigs high and low levels of dietary fiber, respectively, to
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Compared to commercial breeds, Chinese local pig breeds have a greater ability to digest dietary fiber, which may be due to differences in intestinal microbiota. In this study, we fed Ding’an and DLY pigs high and low levels of dietary fiber, respectively, to investigate factors contributing to high dietary fiber adaption in Ding’an pigs. Twelve Ding’an pigs and DLY pigs were randomly divided into a 2 (diet) × 2 (breed) factorial experiment (n = 3). Compared with commercial pigs, Ding’an pigs have a stronger ability to digest dietary fiber. Prevotella was more prevalent in Ding’an pigs than in DLY pigs, which may be an important reason for the stronger ability of fiber degradation in Ding’an pigs. When the effects of feed and breed factors are considered, differences in abundance of 31 species and 14 species, respectively, may result in a greater ability of fiber degradation in Ding’an pigs. Among them, Prevotella. sp. CAG:520 may be a newly discovered bacterium related to fiber degradation, which positively correlated with many fiber-degrading bacteria (r > 0.7). We also found that the concentration of plant metabolites with anti-inflammatory and antioxidant effects was higher in the colonic chyme of Ding’an pigs after increasing the fiber content, which resulted in the downregulated expression of inflammatory factors in colonic mucosa. Spearman’s correlation coefficient revealed a strong correlation between microbiota and the apparent digestibility of dietary fiber (r > 0.7). The mRNA expressions of SLC16A1, PYY, and GCG were significantly increased in the colonic mucosa of Ding’an pigs fed on high-fiber diets, which indicates that Ding’an pigs have an enhanced absorption of SCFAs. Our results suggested that an appropriate increase in dietary fiber content can reduce the inflammatory response and improve feed efficiency in Ding’an pigs, and differences in the intestinal microbial composition may be an important reason for the difference in the fiber degradation capacity between the two breeds of pigs.
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(This article belongs to the Section Microbiomes)
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Open AccessArticle
Identifying Mortality Predictors in Hospitalized COVID-19 Patients: Insights from a Single-Center Retrospective Study at a University Hospital
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Ondrej Zahornacky, Alena Rovnakova, Maria Surimova, Stefan Porubcin and Pavol Jarcuska
Microorganisms 2024, 12(5), 1032; https://doi.org/10.3390/microorganisms12051032 - 20 May 2024
Abstract
Introduction: The pandemic instigated by the SARS-CoV-2 virus has led to over 7 million deaths globally, primarily attributable to viral pneumonia. Identifying fundamental markers associated with an elevated risk of mortality can aid in the early identification of patients prone to disease progression
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Introduction: The pandemic instigated by the SARS-CoV-2 virus has led to over 7 million deaths globally, primarily attributable to viral pneumonia. Identifying fundamental markers associated with an elevated risk of mortality can aid in the early identification of patients prone to disease progression to a severe state, enabling prompt intervention. Methods: This was a single-center, retrospective study. Results: In this study, we examined 299 patients admitted to the Department of Infectology and Travel Medicine in Košice, Slovakia, with PCR-confirmed COVID-19 pneumonia. Patients were monitored from 1 January 2021 to 31 March 2021, with the endpoint being discharge from the hospital or death. All patient-related data were retrospectively collected from medical records. This study identified several risk factors significantly associated with an increased risk of mortality, including the requirement of HFNO (p < 0.001), age over 60 years (p < 0.001), Ne/Ly values of >6 (p < 0.001), as well as certain lymphocyte subtypes—CD4+ < 0.2 × 109/L (p = 0.035), CD8+ < 0.2 × 109/L (p < 0.001), and CD19+ < 0.1 × 109/L (p < 0.001)—alongside selected biochemical inflammatory markers—IL-6 > 50 ng/L (p < 0.001) and lactate > 3 mmol/L (p < 0.001). Conclusions: We confirmed that the mentioned risk factors were significantly associated with the death of patients from viral pneumonia in the hospital.
Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection—Third Edition)
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Open AccessReview
Expanding the Spectrum of Diseases and Disease Associations Caused by Edwardsiella tarda and Related Species
by
J. Michael Janda and Muhammed Duman
Microorganisms 2024, 12(5), 1031; https://doi.org/10.3390/microorganisms12051031 - 20 May 2024
Abstract
The genus Edwardsiella, previously residing in the family Enterobacteriaceae and now a member of the family Hafniaceae, is currently composed of five species, although the taxonomy of this genus is still unsettled. The genus can primarily be divided into two pathogenic
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The genus Edwardsiella, previously residing in the family Enterobacteriaceae and now a member of the family Hafniaceae, is currently composed of five species, although the taxonomy of this genus is still unsettled. The genus can primarily be divided into two pathogenic groups: E. tarda strains are responsible for almost all human infections, and two other species (E. ictaluri, E. piscicida) cause diseases in fish. Human infections predominate in subtropical habitats of the world and in specific geospatial regions with gastrointestinal disease, bloodborne infections, and wound infections, the most common clinical presentations in decreasing order. Gastroenteritis can present in many different forms and mimic other intestinal disturbances. Chronic gastroenteritis is not uncommon. Septicemia is primarily found in persons with comorbid conditions including malignancies and liver disease. Mortality rates range from 9% to 28%. Most human infections are linked to one of several risk factors associated with freshwater or marine environments such as seafood consumption. In contrast, edwardsiellosis in fish is caused by two other species, in particular E. ictaluri. Both E. ictaluri and E. piscicida can cause massive outbreaks of disease in aquaculture systems worldwide, including enteric septicemia in channel catfish and tilapia. Collectively, these species are increasingly being recognized as important pathogens in clinical and veterinary medicine. This article highlights and provides a current perspective on the taxonomy, microbiology, epidemiology, and pathogenicity of this increasingly important group.
Full article
(This article belongs to the Special Issue Microorganisms and Diseases Associated with Aquatic Animals 2.0)
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Open AccessArticle
Characteristics of Vaginal Microbiota of Women of Reproductive Age with Infections
by
Wanting Dong, Siyi Wang, Xi Wang, Guojin Xu, Qiuying Liu, Zheng Li, Na Lv, Yuanlong Pan, Qian Xiong, Donglai Liu and Baoli Zhu
Microorganisms 2024, 12(5), 1030; https://doi.org/10.3390/microorganisms12051030 - 20 May 2024
Abstract
The vaginal microbiota can be classified into five major community state types (CSTs) based on the bacterial content. However, the link between different CST subtypes and vaginal infection remains unclear. Here, we analyzed 2017 vaginal microbiota samples from women of a reproductive age
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The vaginal microbiota can be classified into five major community state types (CSTs) based on the bacterial content. However, the link between different CST subtypes and vaginal infection remains unclear. Here, we analyzed 2017 vaginal microbiota samples from women of a reproductive age with vaginal infections that were published in the last decade. We found that L. iners was the most dominant in 34.8% of the vaginal samples, followed by L. crispatus (21.2%). CST I was common in healthy individuals, whereas CST III and IV were associated with dysbiosis and infection. CST III-B, IV-A, IV-B, and IV-C0 were prevalent in patients with bacterial vaginosis (BV). Based on the relative abundance of bacteria at the (sub)genus level, a random forest classifier was developed to predict vaginal infections with an area under the curve of 0.83. We further identified four modules of co-occurring bacterial taxa: L. crispatus, Gardnerella, Prevotella, and Bacteroides. The functional prediction revealed that nucleotide biosynthesis pathways were upregulated in patients with human papilloma virus, and carbohydrate degradation pathways were downregulated in patients with BV. Overall, our study identified the bacterial signatures of healthy and infected vaginal microbiota, providing unique insights into the clinical diagnosis and health status prediction of women of a reproductive age.
Full article
(This article belongs to the Special Issue Vaginal Microbiome in Women's Health)
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Open AccessArticle
Selective Isolation and Identification of Microorganisms with Dual Capabilities: Leather Biodegradation and Heavy Metal Resistance for Industrial Applications
by
Manuela Bonilla-Espadas, Basilio Zafrilla, Irene Lifante-Martínez, Mónica Camacho, Elena Orgilés-Calpena, Francisca Arán-Aís, Marcelo Bertazzo and María-José Bonete
Microorganisms 2024, 12(5), 1029; https://doi.org/10.3390/microorganisms12051029 - 20 May 2024
Abstract
Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium’s oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological
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Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium’s oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products’ end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications.
Full article
(This article belongs to the Special Issue New Insights into the Diversity and Characterization of Extremophiles)
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Open AccessArticle
Exploring the Frozen Armory: Antiphage Defense Systems in Cold-Adapted Bacteria with a Focus on CRISPR-Cas Systems
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Greta Daae Sandsdalen, Animesh Kumar and Erik Hjerde
Microorganisms 2024, 12(5), 1028; https://doi.org/10.3390/microorganisms12051028 - 20 May 2024
Abstract
Our understanding of the antiphage defense system arsenal in bacteria is rapidly expanding, but little is known about its occurrence in cold-adapted bacteria. In this study, we aim to shed light on the prevalence and distribution of antiphage defense systems in cold-adapted bacteria,
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Our understanding of the antiphage defense system arsenal in bacteria is rapidly expanding, but little is known about its occurrence in cold-adapted bacteria. In this study, we aim to shed light on the prevalence and distribution of antiphage defense systems in cold-adapted bacteria, with a focus on CRISPR-Cas systems. Using bioinformatics tools, Prokaryotic Antiviral Defense LOCator (PADLOC) and CRISPRCasTyper, we mapped the presence and diversity of antiphage defense systems in 938 available genomes of cold-adapted bacteria from diverse habitats. We confirmed that CRISPR-Cas systems are less frequent in cold-adapted bacteria, compared to mesophilic and thermophilic species. In contrast, several antiphage defense systems, such as dXTPases and DRTs, appear to be more frequently compared to temperate bacteria. Additionally, our study provides Cas endonuclease candidates with a potential for further development into cold-active CRISPR-Cas genome editing tools. These candidates could have broad applications in research on cold-adapted organisms. Our study provides a first-time map of antiphage defense systems in cold-adapted bacteria and a detailed overview of CRISPR-Cas diversity.
Full article
(This article belongs to the Special Issue Cold-Adapted Bacteria and Marine Bacteria)
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Open AccessArticle
Transcriptome Analysis Reveals Candidate Genes for Light Regulation of Elsinochrome Biosynthesis in Elsinoë arachidis
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Dan Liu, Jingzi Piao, Yang Li, Haiwen Guan, Jingwen Hao and Rujun Zhou
Microorganisms 2024, 12(5), 1027; https://doi.org/10.3390/microorganisms12051027 - 19 May 2024
Abstract
Light regulation is critical in fungal growth, development, morphogenesis, secondary metabolism, and the biological clock. The fungus Elsinoë arachidis is known to produce the mycotoxin Elsinochrome (ESC), a key factor contributing to its pathogenicity, under light conditions. Although previous studies have predominantly focused
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Light regulation is critical in fungal growth, development, morphogenesis, secondary metabolism, and the biological clock. The fungus Elsinoë arachidis is known to produce the mycotoxin Elsinochrome (ESC), a key factor contributing to its pathogenicity, under light conditions. Although previous studies have predominantly focused on the light-induced production of ESC and its biosynthetic pathways, the detailed mechanisms underlying this process remain largely unexplored. This study explores the influence of light on ESC production and gene expression in E. arachidis. Under white light exposure for 28 days, the ESC yield was observed to reach 33.22 nmol/plug. Through transcriptome analysis, 5925 genes were identified as differentially expressed between dark and white light conditions, highlighting the significant impact of light on gene expression. Bioinformatics identified specific light-regulated genes, including eight photoreceptor genes, five global regulatory factors, and a cluster of 12 genes directly involved in the ESC biosynthesis, with expression trends confirmed by RT-qPCR. In conclusion, the study reveals the substantial alteration in gene expression associated with ESC biosynthesis under white light and identifies potential candidates for in-depth functional analysis. These findings advance understanding of ESC biosynthesis regulation and suggest new strategies for fungal pathogenicity control.
Full article
(This article belongs to the Section Microbiomes)
Open AccessReview
A Review of the Mechanisms of Bacterial Colonization of the Mammal Gut
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Qingjie Lin, Shiying Lin, Zitao Fan, Jing Liu, Dingcheng Ye and Pingting Guo
Microorganisms 2024, 12(5), 1026; https://doi.org/10.3390/microorganisms12051026 - 19 May 2024
Abstract
A healthy animal intestine hosts a diverse population of bacteria in a symbiotic relationship. These bacteria utilize nutrients in the host’s intestinal environment for growth and reproduction. In return, they assist the host in digesting and metabolizing nutrients, fortifying the intestinal barrier, defending
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A healthy animal intestine hosts a diverse population of bacteria in a symbiotic relationship. These bacteria utilize nutrients in the host’s intestinal environment for growth and reproduction. In return, they assist the host in digesting and metabolizing nutrients, fortifying the intestinal barrier, defending against potential pathogens, and maintaining gut health. Bacterial colonization is a crucial aspect of this interaction between bacteria and the intestine and involves the attachment of bacteria to intestinal mucus or epithelial cells through nonspecific or specific interactions. This process primarily relies on adhesins. The binding of bacterial adhesins to host receptors is a prerequisite for the long-term colonization of bacteria and serves as the foundation for the pathogenicity of pathogenic bacteria. Intervening in the adhesion and colonization of bacteria in animal intestines may offer an effective approach to treating gastrointestinal diseases and preventing pathogenic infections. Therefore, this paper reviews the situation and mechanisms of bacterial colonization, the colonization characteristics of various bacteria, and the factors influencing bacterial colonization. The aim of this study was to serve as a reference for further research on bacteria–gut interactions and improving animal gut health.
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(This article belongs to the Section Veterinary Microbiology)
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Open AccessReview
Insights into the Impact of Physicochemical and Microbiological Parameters on the Safety Performance of Deep Geological Repositories
by
Mar Morales-Hidalgo, Cristina Povedano-Priego, Marcos F. Martinez-Moreno, Miguel A. Ruiz-Fresneda, Margarita Lopez-Fernandez, Fadwa Jroundi and Mohamed L. Merroun
Microorganisms 2024, 12(5), 1025; https://doi.org/10.3390/microorganisms12051025 - 19 May 2024
Abstract
Currently, the production of radioactive waste from nuclear industries is increasing, leading to the development of reliable containment strategies. The deep geological repository (DGR) concept has emerged as a suitable storage solution, involving the underground emplacement of nuclear waste within stable geological formations.
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Currently, the production of radioactive waste from nuclear industries is increasing, leading to the development of reliable containment strategies. The deep geological repository (DGR) concept has emerged as a suitable storage solution, involving the underground emplacement of nuclear waste within stable geological formations. Bentonite clay, known for its exceptional properties, serves as a critical artificial barrier in the DGR system. Recent studies have suggested the stability of bentonite within DGR relevant conditions, indicating its potential to enhance the long-term safety performance of the repository. On the other hand, due to its high resistance to corrosion, copper is one of the most studied reference materials for canisters. This review provides a comprehensive perspective on the influence of nuclear waste conditions on the characteristics and properties of DGR engineered barriers. This paper outlines how evolving physico-chemical parameters (e.g., temperature, radiation) in a nuclear repository may impact these barriers over the lifespan of a repository and emphasizes the significance of understanding the impact of microbial processes, especially in the event of radionuclide leakage (e.g., U, Se) or canister corrosion. Therefore, this review aims to address the long-term safety of future DGRs, which is critical given the complexity of such future systems.
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(This article belongs to the Special Issue Microorganisms and Hazardous Waste: Insights into Bioremediation and Safe Disposal)
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Open AccessArticle
Reference Genes for Expression Analyses by qRT-PCR in Enterobacter cancerogenus
by
Yang Pan, Yue Zhao, Hua-Rui Zeng, Jia-Qi Wu, Ying-Ying Song, Ya-Hao Rao, Guo-Qing Li and Lin Jin
Microorganisms 2024, 12(5), 1024; https://doi.org/10.3390/microorganisms12051024 - 19 May 2024
Abstract
The Enterobacter cancerogenus strain EcHa1 was isolated from the dead larvae of Helicoverpa armigera, and has the potential for biocontrol of some Lepidoptera insects. In order to screen insecticidal-related genes by qRT-PCR, stable endogenous reference genes used for normalizing qRT-PCR data were
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The Enterobacter cancerogenus strain EcHa1 was isolated from the dead larvae of Helicoverpa armigera, and has the potential for biocontrol of some Lepidoptera insects. In order to screen insecticidal-related genes by qRT-PCR, stable endogenous reference genes used for normalizing qRT-PCR data were selected and evaluated from 13 housekeeping genes (HKGs). The expression levels of the HKGs were determined using qRT-PCR under different experimental conditions, including two culture temperatures and three bacterial OD values. Five stability analysis methods (Ct, BestKeeper, NormFinder, geNorm, and RefFinder) were used to comprehensively rank the candidate genes. The results showed that the optimal reference genes varied under different experimental conditions. The combination of gyrA and gyrB was recommended as the best reference gene combination at 28 °C, while gyrA and rpoB was the best combination at 37 °C. When the OD values were 0.5, 1.0 and 2.0, the recommended reference gene combinations were ftsZ and gyrA, rpoB and gyrB, and gyrA and pyk, respectively. The most suitable reference genes were gyrA and gyrB under all experimental conditions. Using gyrA and gyrB as the reference genes for qRT-PCR, EcHa1 was found to invade all tissues of the H. armigera larvae, and expressed a candidate pathogenic factor Hcp at high levels in gut, Malpighian tubules, and epidermis tissues. This study not only establishes an accurate and reliable normalization for qRT-PCR in entomopathogenic bacteria but also lays a solid foundation for further study of functional genes in E. cancerogenus.
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(This article belongs to the Section Microbiomes)
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Open AccessCommunication
Customized 16S-23S rDNA ITS Amplicon Metagenomics for Acetic Acid Bacteria Species Identification in Vinegars and Kombuchas
by
Alja Ribič and Janja Trček
Microorganisms 2024, 12(5), 1023; https://doi.org/10.3390/microorganisms12051023 - 18 May 2024
Abstract
Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products’ pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology
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Acetic acid bacteria (AAB) are involved in food and beverage production bioprocesses, like those in vinegar and kombucha. They oxidize sugars and alcohols into various metabolites, resulting in the final products’ pleasant taste and aroma. The 16S rDNA amplicon metagenomics using Illumina technology is usually used to follow the microbiological development of these processes. However, the 16S rRNA gene sequences among different species of AAB are very similar, thus not enabling a reliable identification down to the species level but only to the genus. In this study, we have constructed primers for amplifying half of the 16S-23S rRNA gene internal transcribed spacer (ITS) for library construction and further sequencing using Illumina technology. This approach was successfully used to estimate the relative abundance of AAB species in defined consortia. Further application of this method for the analysis of different vinegar and kombucha samples proves it suitable for assessing the relative abundance of AAB species when these bacteria represent a predominant part of a microbial community.
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(This article belongs to the Section Microbiomes)
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Open AccessArticle
Interplay of Demographic Influences, Clinical Manifestations, and Longitudinal Profile of Laboratory Parameters in the Progression of SARS-CoV-2 Infection: Insights from the Saudi Population
by
Sarah Al-Hassinah, Sooad Al-Daihan, Mashael Alahmadi, Sara Alghamdi, Rawabi Almulhim, Dalia Obeid, Yaseen Arabi, Abdulrahman Alswaji, Marwh Aldriwesh and Majed Alghoribi
Microorganisms 2024, 12(5), 1022; https://doi.org/10.3390/microorganisms12051022 - 18 May 2024
Abstract
Understanding the factors driving SARS-CoV-2 infection progression and severity is complex due to the dynamic nature of human physiology. Therefore, we aimed to explore the severity risk indicators of SARS-CoV-2 through demographic data, clinical manifestations, and the profile of laboratory parameters. The study
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Understanding the factors driving SARS-CoV-2 infection progression and severity is complex due to the dynamic nature of human physiology. Therefore, we aimed to explore the severity risk indicators of SARS-CoV-2 through demographic data, clinical manifestations, and the profile of laboratory parameters. The study included 175 patients either hospitalized at King Abdulaziz Medical City–Riyadh or placed in quarantine at designated hotels in Riyadh, Saudi Arabia, from June 2020 to April 2021. Hospitalized patients were followed up through the first week of admission. Demographic data, clinical presentations, and laboratory results were retrieved from electronic patient records. Our results revealed that older age (OR: 1.1, CI: [1.1–1.12]; p < 0.0001), male gender (OR: 2.26, CI: [1.0–5.1]; p = 0.047), and blood urea nitrogen level (OR: 2.56, CI: [1.07–6.12]; p = 0.034) were potential predictors of severity level. In conclusion, the study showed that apart from laboratory parameters, age and gender could potentially predict the severity of SARS-CoV-2 infection in the early stages. To our knowledge, this study is the first in Saudi Arabia to explore the longitudinal profile of laboratory parameters among risk factors, shedding light on SARS-CoV-2 infection progression parameters.
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(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection—Third Edition)
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