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)
- 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
Identification of Causal Relationships between Gut Microbiota and Influenza A Virus Infection in Chinese by Mendelian Randomization
Microorganisms 2024, 12(6), 1170; https://doi.org/10.3390/microorganisms12061170 (registering DOI) - 8 Jun 2024
Abstract
Numerous studies have reported a correlation between gut microbiota and influenza A virus (IAV) infection and disease severity. However, the causal relationship between these factors remains inadequately explored. This investigation aimed to assess the influence of gut microbiota on susceptibility to human infection
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Numerous studies have reported a correlation between gut microbiota and influenza A virus (IAV) infection and disease severity. However, the causal relationship between these factors remains inadequately explored. This investigation aimed to assess the influence of gut microbiota on susceptibility to human infection with H7N9 avian IAV and the severity of influenza A (H1N1)pdm09 infection. A two-sample Mendelian randomization analysis was conducted, integrating our in-house genome-wide association study (GWAS) on H7N9 susceptibility and H1N1pdm09 severity with a metagenomics GWAS dataset from a Chinese population. Twelve and fifteen gut microbiotas were causally associated with H7N9 susceptibility or H1N1pdm09 severity, separately. Notably, Clostridium hylemonae and Faecalibacterium prausnitzii were negative associated with H7N9 susceptibility and H1N1pdm09 severity, respectively. Moreover, Streptococcus peroris and Streptococcus sanguinis were associated with H7N9 susceptibility, while Streptococcus parasanguini and Streptococcus suis were correlated with H1N1pdm09 severity. These results provide novel insights into the interplay between gut microbiota and IAV pathogenesis as well as new clues for mechanism research regarding therapeutic interventions or IAV infections. Future studies should concentrate on clarifying the regulatory mechanisms of gut microbiota and developing efficacious approaches to reduce the incidence of IAV infections, which could improve strategy for preventing and treating IAV infection worldwide.
Full article
(This article belongs to the Special Issue Influenza Prevention: Exploring the Progress and Persevering through Challenges)
Open AccessArticle
Detection of Salmonella Reservoirs in Birds of Prey Hosted in an Italian Wildlife Centre: Molecular and Antimicrobial Resistance Characterisation
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Carlo Corradini, Andrea Francesco De Bene, Valeria Russini, Virginia Carfora, Patricia Alba, Gessica Cordaro, Matteo Senese, Giuliana Terracciano, Ilaria Fabbri, Alessandro Di Sirio, Fabiola Di Giamberardino, Pierpaolo Boria, Maria Laura De Marchis and Teresa Bossù
Microorganisms 2024, 12(6), 1169; https://doi.org/10.3390/microorganisms12061169 (registering DOI) - 8 Jun 2024
Abstract
In the European Union, salmonellosis is one of the most important zoonoses reported. Poultry meat and egg products are the most common food matrices associated with Salmonella presence. Moreover, wild and domestic animals could represent an important reservoir that could favour the direct
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In the European Union, salmonellosis is one of the most important zoonoses reported. Poultry meat and egg products are the most common food matrices associated with Salmonella presence. Moreover, wild and domestic animals could represent an important reservoir that could favour the direct and indirect transmission of pathogens to humans. Salmonella spp. can infect carnivorous or omnivorous wild birds that regularly ingest food and water exposed to faecal contamination. Birds kept in captivity can act as reservoirs of Salmonella spp. following ingestion of infected prey or feed. In this paper, we describe the isolation of different Salmonella serovars in several species of raptors hosted in aviaries in an Italian wildlife centre and in the raw chicken necks used as their feed but intended for human consumption. Characterisations of strains were carried out by integrating classical methods and whole genome sequencing analysis. The strains of S. bredeney isolated in poultry meat and birds belonged to the same cluster, with some of them being multidrug-resistant (MDR) and carrying the Col(pHAD28) plasmid-borne qnrB19 (fluoro)quinolone resistance gene, thus confirming the source of infection. Differently, the S. infantis found in feed and raptors were all MDR, carried a plasmid of emerging S. infantis (pESI)-like plasmid and belonged to different clusters, possibly suggesting a long-lasting infection or the presence of additional undetected sources. Due to the high risk of fuelling a reservoir of human pathogens, the control and treatment of feed for captive species are crucial.
Full article
(This article belongs to the Special Issue Domestic Animals and Wildlife Zoonotic Microorganisms)
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Open AccessArticle
Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing
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Yanzhen Mao, Ye Yang, Fu Lin, Hanyu Chu, Lijie Zhou, Jiaojiao Han, Jun Zhou and Xiurong Su
Microorganisms 2024, 12(6), 1168; https://doi.org/10.3390/microorganisms12061168 (registering DOI) - 8 Jun 2024
Abstract
A Gram-positive, rod-shaped, aerobic, motile, and spore-forming bacterium, designated SCL10, was isolated from Acaudina molpadioides exposure to Co-60 radiation. In this study, whole-genome sequencing was performed to identify the strain as Bacillus cereus and functional characterization, with a focus on stress resistance. The
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A Gram-positive, rod-shaped, aerobic, motile, and spore-forming bacterium, designated SCL10, was isolated from Acaudina molpadioides exposure to Co-60 radiation. In this study, whole-genome sequencing was performed to identify the strain as Bacillus cereus and functional characterization, with a focus on stress resistance. The genome of the B. cereus SCL10 strain was sequenced and assembled, revealing a size of 4,979,182 bp and 5167 coding genes. The genes involved in biological functions were annotated by using the GO, COG, KEGG, NR, and Swiss-Prot databases. The results showed that genes related to alkyl hydroperoxide reductase (ahpC, ahpF), DNA-binding proteins from starved cells (dps), spore and biofilm formation (spoVG, spo0A, gerP), cold shock-like protein (cspC, cspE), ATP-dependent chaperone (clpB), and photolyase, small, acid-soluble spore protein (SASP) and DNA repair protein (recA, radD) could explain the stress resistance. These findings suggest that antioxidant activity, sporulation, biofilm formation, and DNA protection may be considered as the main resistance mechanisms under exposure to radiation in the B. cereus SCL10 strain.
Full article
(This article belongs to the Special Issue Food Microorganisms and Genomics)
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Open AccessArticle
Adaptive Evolution for the Efficient Production of High-Quality d-Lactic Acid Using Engineered Klebsiella pneumoniae
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Bo Jiang, Jiezheng Liu, Jingnan Wang, Guang Zhao and Zhe Zhao
Microorganisms 2024, 12(6), 1167; https://doi.org/10.3390/microorganisms12061167 (registering DOI) - 8 Jun 2024
Abstract
d-Lactic acid serves as a pivotal platform chemical in the production of poly d-lactic acid (PDLA) and other value-added products. This compound can be synthesized by certain bacteria, including Klebsiella pneumoniae. However, industrial-scale lactic acid production in Klebsiella pneumoniae faces challenges due
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d-Lactic acid serves as a pivotal platform chemical in the production of poly d-lactic acid (PDLA) and other value-added products. This compound can be synthesized by certain bacteria, including Klebsiella pneumoniae. However, industrial-scale lactic acid production in Klebsiella pneumoniae faces challenges due to growth inhibition caused by lactic acid stress, which acts as a bottleneck in commercial microbial fermentation processes. To address this, we employed a combination of evolutionary and genetic engineering approaches to create an improved Klebsiella pneumoniae strain with enhanced lactic acid tolerance and production. In flask fermentation experiments, the engineered strain achieved an impressive accumulation of 19.56 g/L d-lactic acid, representing the highest production yield observed in Klebsiella pneumoniae to date. Consequently, this strain holds significant promise for applications in industrial bioprocessing. Notably, our genome sequencing and experimental analyses revealed a novel correlation between UTP-glucose-1-phosphate uridylyltransferase GalU and lactic acid resistance in Klebsiella pneumoniae. Further research is warranted to explore the potential of targeting GalU for enhancing d-lactic acid production.
Full article
(This article belongs to the Special Issue Bacterial Engineering and Metabolism Regulation)
Open AccessArticle
Virulence Potential and Antimicrobial Resistance of Listeria monocytogenes Isolates Obtained from Beef and Beef-Based Products Deciphered Using Whole-Genome Sequencing
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Ayanda Manqele, Abiodun Adesiyun, Thendo Mafuna, Rian Pierneef, Rebone Moerane and Nomakorinte Gcebe
Microorganisms 2024, 12(6), 1166; https://doi.org/10.3390/microorganisms12061166 (registering DOI) - 8 Jun 2024
Abstract
Listeria monocytogenes is a ubiquitous bacterial pathogen that threatens the food chain and human health. In this study, whole-genome sequencing (WGS) was used for the genomic characterization of L. monocytogenes (n = 24) from beef and beef-based products. Multilocus Sequence Type (MLST) analysis
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Listeria monocytogenes is a ubiquitous bacterial pathogen that threatens the food chain and human health. In this study, whole-genome sequencing (WGS) was used for the genomic characterization of L. monocytogenes (n = 24) from beef and beef-based products. Multilocus Sequence Type (MLST) analysis revealed that ST204 of CC204 was the most common sequence type (ST). Other sequence types detected included ST1 and ST876 of CC1, ST5 of CC5, ST9 of CC9, ST88 of CC88, ST2 and ST1430 of CC2, and ST321 of CC321. Genes encoding for virulence factors included complete LIPI-1 (pfrA-hly-plcA-plcB-mpl-actA) from 54% (13/24) of the isolates of ST204, ST321, ST1430, and ST9 and internalin genes inlABC that were present in all the STs. All the L. monocytogenes STs carried four intrinsic/natural resistance genes, fosX, lin, norB, and mprF, conferring resistance to fosfomycin, lincosamide, quinolones, and cationic peptides, respectively. Plasmids pLGUG1 and J1776 were the most detected (54% each), followed by pLI100 (13%) and pLM5578 (7%). The prophage profile, vB_LmoS_188, was overrepresented amongst the isolates, followed by LP_101, LmoS_293_028989, LP_030_2_021539, A006, and LP_HM00113468. Listeria genomic island 2 (LGI-2) was found to be present in all the isolates, while Listeria genomic island 3 (LGI-3) was present in a subset of isolates (25%). The type VII secretion system was found in 42% of the isolates, and sortase A was present in all L. monocytogenes genomes. Mobile genetic elements and genomic islands did not harbor any virulence, resistance, or environmental adaptation genes that may benefit L. monocytogenes. All the STs did not carry genes that confer resistance to first-line antibiotics used for the treatment of listeriosis. The characterization of L. monocytogenes in our study highlighted the environmental resistance and virulence potential of L. monocytogenes and the risk posed to the public, as this bacterium is frequently found in food and food processing environments.
Full article
(This article belongs to the Section Food Microbiology)
Open AccessArticle
Pfaffia paniculata Extract, a Potential Antimicrobial Agent against Candida spp., Pseudomonas aeruginosa, and Streptococcus mutans Biofilms
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Diego Garcia Miranda, Lucas de Paula Ramos, Nina Attik, Thaís Cristine Pereira, Luciane Dias de Oliveira, Maria Cristina Marcucci, Flavia Pires Rodrigues, Graziella Nuernberg Back Brito and Florence Carrouel
Microorganisms 2024, 12(6), 1165; https://doi.org/10.3390/microorganisms12061165 (registering DOI) - 8 Jun 2024
Abstract
The World Health Organization (WHO) has prioritized developing new drugs against specific bacteria and fungi, such as Enterobacteriaceae and Candida spp. While Pfaffia paniculata is commonly called the “cure-everything”, its scientifically proven benefits are limited to anti-inflammatory and antioxidant actions. Therefore, this study
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The World Health Organization (WHO) has prioritized developing new drugs against specific bacteria and fungi, such as Enterobacteriaceae and Candida spp. While Pfaffia paniculata is commonly called the “cure-everything”, its scientifically proven benefits are limited to anti-inflammatory and antioxidant actions. Therefore, this study aims to determine the spectrum of antimicrobial activity of Pfaffia paniculata and assess its cytotoxicity. Thus, broth microdilution test was conducted according to the CLSI M7-A9 and M27-A3 reference methods. After screening, microbial species with minimum inhibitory concentration (MIC) values were selected for biofilm tests. These tests evaluated biomass using the crystal violet (CV) test, metabolic activity using the MTT assay, and structural analysis via Scanning Electron Microscopy (SEM). Cytotoxicity was evaluated in human gingival fibroblasts (FMM-1). There were reductions of 29.4 and 42.7% in CV and MTT assays for Candida spp. biofilm. S. mutans and P. aeruginosa biofilms showed a decrease of 15.7 and 28.6%, respectively. Cell viability tests indicated 55.1, 56.9, and 65.5% of viability after contact with 1.93, 0.96, and 0.48 mg/mL of the extract, respectively. The P. paniculata extract showed antimicrobial action, displayed MIC values, and antibiofilm action on P. aeruginosa, S. mutans, and C. albicans. The cytotoxicity on the FMM-1 cell line was dose-dependent. Therefore, P. paniculata extract holds significant potential for developing new drugs.
Full article
(This article belongs to the Special Issue Antimicrobial and Anti-biofilm Potentials of Plant Extracts, Natural Products and Their Formulations)
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Open AccessArticle
Molecular Characterization and Functional Analysis of a Schistosoma mansoni Serine Protease Inhibitor, Smserpin-p46
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Christine N. Lee, Brooke Ashlyn Hall, Leah Sanford and Adebayo J. Molehin
Microorganisms 2024, 12(6), 1164; https://doi.org/10.3390/microorganisms12061164 - 7 Jun 2024
Abstract
Serine protease inhibitors are a superfamily of proteins that regulate various physiological processes including fibrinolysis, inflammation and immune responses. In parasite systems, serpins are believed to play important roles in parasite colonization, inhibition of host immune serine proteases and penetration of defensive barriers.
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Serine protease inhibitors are a superfamily of proteins that regulate various physiological processes including fibrinolysis, inflammation and immune responses. In parasite systems, serpins are believed to play important roles in parasite colonization, inhibition of host immune serine proteases and penetration of defensive barriers. However, serpins are less well characterized in schistosomes. In this study, a Schistosoma mansoni serpin (Smserpin-p46) containing a 1360 base pair open reading frame, was cloned, expressed and functionally characterized. Bioinformatics analysis revealed that Smserpin-p46 contains the key residues, structural domains and motifs characteristic of inhibitory serpins. Gene expression profiling demonstrated stage-specific expression of Smserpin-p46 with the highest expression in adult male worms. Recombinant Smserpin-p46 (rSmserpin-p46) inhibited both human neutrophil cathepsin G and elastase, key serine proteases involved in NETosis, a program for the formation of neutrophil extracellular traps. Using specific rabbit antiserum, Smserpin-p46 was detected in soluble worm antigen preparation and was localized to the adult worm tegument. Cumulatively, the expression of Smserpin-p46 on the parasite tegument and its ability to inhibit proteases involved in NETosis highlights the importance of this serpin in parasite-host interactions and encourages its further investigation as a candidate vaccine antigen for the control of schistosomiasis.
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(This article belongs to the Section Parasitology)
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Benefits and Challenges of Applying Bacteriophage Biocontrol in the Consumer Water Cycle
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Brandon Reyneke, Benjamin Havenga, Monique Waso-Reyneke, Sehaam Khan and Wesaal Khan
Microorganisms 2024, 12(6), 1163; https://doi.org/10.3390/microorganisms12061163 - 7 Jun 2024
Abstract
Bacteria (including disinfection- and antibiotic-resistant bacteria) are abundant in the consumer water cycle, where they may cause disease, and lead to biofouling and infrastructure damage in distributions systems, subsequently resulting in significant economic losses. Bacteriophages and their associated enzymes may then offer a
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Bacteria (including disinfection- and antibiotic-resistant bacteria) are abundant in the consumer water cycle, where they may cause disease, and lead to biofouling and infrastructure damage in distributions systems, subsequently resulting in significant economic losses. Bacteriophages and their associated enzymes may then offer a biological control solution for application within the water sector. Lytic bacteriophages are of particular interest as biocontrol agents as their narrow host range can be exploited for the targeted removal of specific bacteria in a designated environment. Bacteriophages can also be used to improve processes such as wastewater treatment, while bacteriophage-derived enzymes can be applied to combat biofouling based on their effectiveness against preformed biofilms. However, the host range, environmental stability, bacteriophage resistance and biosafety risks are some of the factors that need to be considered prior to the large-scale application of these bacterial viruses. Characteristics of bacteriophages that highlight their potential as biocontrol agents are thus outlined in this review, as well as the potential application of bacteriophage biocontrol throughout the consumer water cycle. Additionally, the limitations of bacteriophage biocontrol and corresponding mitigation strategies are outlined, including the use of engineered bacteriophages for improved host ranges, environmental stability and the antimicrobial re-sensitisation of bacteria. Finally, the potential public and environmental risks associated with large-scale bacteriophage biocontrol application are considered, and alternative applications of bacteriophages to enhance the functioning of the consumer water cycle, including their use as water quality or treatment indicators and microbial source tracking markers, are discussed.
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(This article belongs to the Special Issue New Insights into the Antibiotic Resistance of Aquatic Microorganisms)
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Open AccessArticle
Soil Parameters and Forest Structure Commonly Form the Microbiome Composition and Activity of Topsoil Layers in Planted Forests
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Katalin Bereczki, Endre György Tóth, Tibor Szili-Kovács, Melinda Megyes, Kristóf Korponai, Botond Boldizsár Lados, Gábor Illés, Attila Benke and Károly Márialigeti
Microorganisms 2024, 12(6), 1162; https://doi.org/10.3390/microorganisms12061162 - 6 Jun 2024
Abstract
Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and
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Soil bacterial communities play a remarkable role in nutrient cycling, significantly affecting soil organic material content, soil fertility, and, in an indirect way, plant succession processes. Conversely, vegetation type influences microbial soil life. The present study compared the bacterial microbiome composition, diversity and catabolic activity profile of topsoil samples collected under three different forest types (a twice-coppiced black locust stand, a young, naturally reforested, and a middle-aged mixed pedunculate oak stand) planted on former arable land in the early 20th century. Diversity indices determined during 16S ribosomal RNA sequencing-based metagenome analysis indicated that the black locust stand had the highest soil bacterial community diversity. At the phylum level, Acidobacteriota, Actinobacteriota, Proteobacteria, Verrucomicrobiota, Bacteroidota, and Gemmatimonadota were the most abundant taxa in the forest soils. Concerning soil parameters, redundancy analysis revealed that pH had the highest impact on bacterial community structure and pH, and soil organic carbon content on the samples’ respiration patterns. As for catabolic activity, the recently clearcut oak forest showed the lowest substrate-induced respiration, and citrate was the main driver for the inter-stand variability of microbial activity. Our results confirm that soil parameters and forest type influence the composition and functioning of the soil bacterial microbiome.
Full article
(This article belongs to the Section Environmental Microbiology)
Open AccessArticle
Development of an Ex Vivo Porcine Eye Model for Exploring the Pathogenicity of Acanthamoeba
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Ming-Der Shi, Ko-Chiang Sung, Jian-Ming Huang, Chun-Hsien Chen and Yu-Jen Wang
Microorganisms 2024, 12(6), 1161; https://doi.org/10.3390/microorganisms12061161 - 6 Jun 2024
Abstract
Acanthamoeba, a widely distributed free-living amoeba found in various environments, is an opportunistic pathogen responsible for causing Acanthamoeba keratitis, a condition that may lead to blindness. However, identifying the pathogenicity of Acanthamoeba is challenging due to its complex life cycle, ability to
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Acanthamoeba, a widely distributed free-living amoeba found in various environments, is an opportunistic pathogen responsible for causing Acanthamoeba keratitis, a condition that may lead to blindness. However, identifying the pathogenicity of Acanthamoeba is challenging due to its complex life cycle, ability to adapt to different environments, variable virulence factors, and intricate interactions with the host immune system. Additionally, the development of an effective model for studying Acanthamoeba pathogenicity is limited, hindering a comprehensive understanding of the mechanisms underlying its virulence and host interactions. The aim of this study was to develop an ex vivo model for Acanthamoeba infection using porcine eyeballs and to evaluate the pathogenicity of the Acanthamoeba isolates. Based on slit lamp and biopsy analysis, the developed ex vivo model is capable of successfully infecting Acanthamoeba within 3 days. Histopathological staining revealed that clinical isolates of Acanthamoeba exhibited greater corneal stroma destruction and invasion in this model than environmental isolates. Our results highlight the importance of an ex vivo porcine eye model in elucidating the pathogenesis of Acanthamoeba infection and its potential implications for understanding and managing Acanthamoeba-related ocular diseases.
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(This article belongs to the Section Medical Microbiology)
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The Importance of Maintaining and Improving a Healthy Gut Microbiota in Athletes as a Preventive Strategy to Improve Heat Tolerance and Acclimatization
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Sergi Cinca-Morros and Jesús Álvarez-Herms
Microorganisms 2024, 12(6), 1160; https://doi.org/10.3390/microorganisms12061160 - 6 Jun 2024
Abstract
Exposure to passive heat (acclimation) and exercise under hot conditions (acclimatization), known as heat acclimation (HA), are methods that athletes include in their routines to promote faster recovery and enhance physiological adaptations and performance under hot conditions. Despite the potential positive effects of
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Exposure to passive heat (acclimation) and exercise under hot conditions (acclimatization), known as heat acclimation (HA), are methods that athletes include in their routines to promote faster recovery and enhance physiological adaptations and performance under hot conditions. Despite the potential positive effects of HA on health and physical performance in the heat, these stimuli can negatively affect gut health, impairing its functionality and contributing to gut dysbiosis. Blood redistribution to active muscles and peripheral vascularization exist during exercise and HA stimulus, promoting intestinal ischemia. Gastrointestinal ischemia can impair intestinal permeability and aggravate systemic endotoxemia in athletes during exercise. Systemic endotoxemia elevates the immune system as an inflammatory responses in athletes, impairing their adaptive capacity to exercise and their HA tolerance. Better gut microbiota health could benefit exercise performance and heat tolerance in athletes. This article suggests that: (1) the intestinal modifications induced by heat stress (HS), leading to dysbiosis and altered intestinal permeability in athletes, can decrease health, and (2) a previously acquired microbial dysbiosis and/or leaky gut condition in the athlete can negatively exacerbate the systemic effects of HA. Maintaining or improving the healthy gut microbiota in athletes can positively regulate the intestinal permeability, reduce endotoxemic levels, and control the systemic inflammatory response. In conclusion, strategies based on positive daily habits (nutrition, probiotics, hydration, chronoregulation, etc.) and preventing microbial dysbiosis can minimize the potentially undesired effects of applying HA, favoring thermotolerance and performance enhancement in athletes.
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(This article belongs to the Special Issue Intestinal Dysbiosis)
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Open AccessArticle
EPS Production by Lacticaseibacillus casei Using Glycerol, Glucose, and Molasses as Carbon Sources
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Guilherme Deomedesse Minari, Rodolfo Debone Piazza, Daiane Cristina Sass and Jonas Contiero
Microorganisms 2024, 12(6), 1159; https://doi.org/10.3390/microorganisms12061159 - 6 Jun 2024
Abstract
This study demonstrates that Lactobacillus can produce exopolysaccharides (EPSs) using alternative carbon sources, such as sugarcane molasses and glycerol. After screening 22 strains of Lactobacillus to determine which achieved the highest production of EPS based on dry weight at 37 °C, the strain
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This study demonstrates that Lactobacillus can produce exopolysaccharides (EPSs) using alternative carbon sources, such as sugarcane molasses and glycerol. After screening 22 strains of Lactobacillus to determine which achieved the highest production of EPS based on dry weight at 37 °C, the strain Ke8 (L. casei) was selected for new experiments. The EPS obtained using glycerol and glucose as carbon sources was classified as a heteropolysaccharide composed of glucose and mannose, containing 1730 g.mol−1, consisting of 39.4% carbohydrates and 18% proteins. The EPS obtained using molasses as the carbon source was characterized as a heteropolysaccharide composed of glucose, galactose, and arabinose, containing 1182 g.mol−1, consisting of 52.9% carbohydrates and 11.69% proteins. This molecule was characterized using Size Exclusion Chromatography (HPLC), Gas chromatography–mass spectrometry (GC-MS), Fourier-transform infrared spectroscopy (FTIR), and proton nuclear magnetic resonance spectroscopy (1H-NMR). The existence of polysaccharides was confirmed via FT-IR and NMR analyses. The results obtained suggest that Lacticaseibacillus casei can grow in media that use alternative carbon sources such as glycerol and molasses. These agro-industry residues are inexpensive, and their use contributes to sustainability. The lack of studies regarding the use of Lacticaseibacillus casei for the production of EPS using renewable carbon sources from agroindustry should be noted.
Full article
(This article belongs to the Special Issue Advances in Bioprocessing during Lactic Fermentation Technology)
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Open AccessReview
Contribution of Toxin–Antitoxin Systems to Adherent-Invasive E. coli Pathogenesis
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Paula Bustamante, María Núria Ramos-Corominas and Margarita Martinez-Medina
Microorganisms 2024, 12(6), 1158; https://doi.org/10.3390/microorganisms12061158 - 6 Jun 2024
Abstract
Pathobionts have been implicated in various chronic diseases, including Crohn’s disease (CD), a multifactorial chronic inflammatory condition that primarily affects the gastrointestinal tract, causing inflammation and damage to the digestive system. While the exact cause of CD remains unclear, adherent-invasive Escherichia coli (AIEC)
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Pathobionts have been implicated in various chronic diseases, including Crohn’s disease (CD), a multifactorial chronic inflammatory condition that primarily affects the gastrointestinal tract, causing inflammation and damage to the digestive system. While the exact cause of CD remains unclear, adherent-invasive Escherichia coli (AIEC) strains have emerged as key contributors to its pathogenesis. AIEC are characterized by their ability to adhere to and invade intestinal epithelial cells and survive and replicate inside macrophages. However, the mechanisms underlying the virulence and persistence of AIEC within their host remain the subject of intensive research. Toxin–antitoxin systems (TAs) play a potential role in AIEC pathogenesis and may be therapeutic targets. These systems generally consist of two components: a toxin harmful to the cell and an antitoxin that neutralizes the toxin’s effects. They contribute to bacterial survival in adverse conditions and regulate bacterial growth and behavior, affecting various cellular processes in bacterial pathogens. This review focuses on the current information available to determine the roles of TAs in the pathogenicity of AIEC. Their contribution to the AIEC stress response, biofilm formation, phage inhibition, the maintenance of mobile genetic elements, and host lifestyles is discussed.
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(This article belongs to the Special Issue Pathogenic Mechanisms of Bacterial Infections)
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Open AccessArticle
Disease Occurrence and Climatic Factors Jointly Structure Pomelo Leaf Fungal Succession in Disturbed Agricultural Ecosystem
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Feng Huang, Jinfeng Ling, Guohua Li, Xiaobing Song and Rui Liu
Microorganisms 2024, 12(6), 1157; https://doi.org/10.3390/microorganisms12061157 - 6 Jun 2024
Abstract
For perennial plants, newly emerged organs are fresh hot spots for environmental microbes to occupy and assemble to form mature microbial communities. In the microbial community, some commensal fungi can play important roles in microbial succession, thus significantly improving host plant growth and
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For perennial plants, newly emerged organs are fresh hot spots for environmental microbes to occupy and assemble to form mature microbial communities. In the microbial community, some commensal fungi can play important roles in microbial succession, thus significantly improving host plant growth and disease resistance. However, their participating patterns in microbial assembly and succession remain largely unknown. In this study, we profiled the fungal community and found a similar fungal succession pattern of spring-emerged leaves from March to October in two pomelo orchards. Specifically, the fungal species, tracked on the old leaves, dominated the spring leaves after emergence and then decreased in relative abundance. This reduction in priority effects on the spring leaves was then followed by an increase in the number of observed species, Shannon and phylogenetic diversity indices, and the pathogen-associated fungal groups. In addition, we found that the temporal fungal succession on the spring leaves highly correlated with the disease occurrence in the orchards and with the temperature and precipitation variation from spring to summer. Of the pathogen-associated fungal groups, an increase in the relative abundance of Mycosphaerellaceae, hosting the causal agent of citrus greasy spot, correlated with the occurrence of the disease, while the relative abundance of Diaporthaceae, hosting the causal agent of melanose, was extremely low during the fungal succession. These results confirm that the two kinds of pathogen-associated fungal groups share different lifestyles on citrus, and also suggest that the study of temporal fungal succession in microbial communities can add to our understanding of the epidemiology of potential plant pathogens.
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(This article belongs to the Section Plant Microbe Interactions)
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Nocardiosis in Solid Organ Transplant Recipients: 10-Year Single Center Experience and Review of Literature
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Julia Bini Viotti, Jacques Simkins, John M. Reynolds, Gaetano Ciancio, Giselle Guerra, Lilian Abbo and Shweta Anjan
Microorganisms 2024, 12(6), 1156; https://doi.org/10.3390/microorganisms12061156 - 6 Jun 2024
Abstract
Solid organ transplant recipients (SOTRs) are at an increased risk of nocardiosis, a rare but life-threatening opportunistic infection. Universal PCP prophylaxis with trimethoprim–sulfamethoxazole (TMP-SMX) is used at our center, which is active in vitro against most species of the Nocardia genus and may
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Solid organ transplant recipients (SOTRs) are at an increased risk of nocardiosis, a rare but life-threatening opportunistic infection. Universal PCP prophylaxis with trimethoprim–sulfamethoxazole (TMP-SMX) is used at our center, which is active in vitro against most species of the Nocardia genus and may have a role in preventing early infections. This is a single-center retrospective cohort study of nocardiosis in adult SOTRs at a large transplant center between January 2012 and June 2022, with comprehensive review of literature. Out of 6179 consecutive cases, 13 (0.2%) were diagnosed with nocardiosis. The patients were predominantly male (76.9%) and kidney transplant recipients (62%). Infection was diagnosed at median of 8.8 months (range, 3.7–98) after transplant. Patients were followed for a median of 457 days (range 8–3367). Overall mortality within one year after diagnosis was 46% (6/13), of which 17% (1/6) of deaths was attributable to Nocardia infection. No recurrence was reported. Nocardia infections were noted in a small proportion of our SOTRs and carried significant morbidity and mortality. TMP-SMX prophylaxis may be protective in some cases given low incidence of cases.
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(This article belongs to the Special Issue Advances in Medical Microbiology)
Open AccessReview
The State-of-the-Art Antibacterial Activities of Glycyrrhizin: A Comprehensive Review
by
Ru-Yi Chen, Jin-Jin Shi, Yan-Jun Liu, Jing Yu, Chang-Yun Li, Fan Tao, Jia-Feng Cao, Guan-Jun Yang and Jiong Chen
Microorganisms 2024, 12(6), 1155; https://doi.org/10.3390/microorganisms12061155 - 6 Jun 2024
Abstract
Licorice (Glycyrrhiza glabra) is a plant of the genus Glycyrrhiza in the family Fabaceae/Leguminosae and is a renowned natural herb with a long history of medicinal use dating back to ancient times. Glycyrrhizin (GLY), the main active component of
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Licorice (Glycyrrhiza glabra) is a plant of the genus Glycyrrhiza in the family Fabaceae/Leguminosae and is a renowned natural herb with a long history of medicinal use dating back to ancient times. Glycyrrhizin (GLY), the main active component of licorice, serves as a widely utilized therapeutic agent in clinical practice. GLY exhibits diverse medicinal properties, including anti-inflammatory, antibacterial, antiviral, antitumor, immunomodulatory, intestinal environment maintenance, and liver protection effects. However, current research primarily emphasizes GLY’s antiviral activity, while providing limited insight into its antibacterial properties. GLY demonstrates a broad spectrum of antibacterial activity via inhibiting the growth of bacteria by targeting bacterial enzymes, impacting cell membrane formation, and altering membrane permeability. Moreover, GLY can also bolster host immunity by activating pertinent immune pathways, thereby enhancing pathogen clearance. This paper reviews GLY’s inhibitory mechanisms against various pathogenic bacteria-induced pathological changes, its role as a high-mobility group box 1 inhibitor in immune regulation, and its efficacy in combating diseases caused by pathogenic bacteria. Furthermore, combining GLY with other antibiotics reduces the minimum inhibitory concentration, potentially aiding in the clinical development of combination therapies against drug-resistant bacteria. Sources of information were searched using PubMed, Web of Science, Science Direct, and GreenMedical for the keywords “licorice”, “Glycyrrhizin”, “antibacterial”, “anti-inflammatory”, “HMGB1”, and combinations thereof, mainly from articles published from 1979 to 2024, with no language restrictions. Screening was carried out by one author and supplemented by others. Papers with experimental flaws in their experimental design and papers that did not meet expectations (antifungal papers, etc.) were excluded.
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(This article belongs to the Special Issue Research on Natural Products against Pathogens)
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Open AccessArticle
Managing Microbiota Activity of Apis mellifera with Probiotic (Bactocell®) and Antimicrobial (Fumidil B®) Treatments: Effects on Spring Colony Strength
by
Joy Gaubert, Pierre-Luc Mercier, Georges Martin, Pierre Giovenazzo and Nicolas Derome
Microorganisms 2024, 12(6), 1154; https://doi.org/10.3390/microorganisms12061154 - 6 Jun 2024
Abstract
Against a backdrop of declining bee colony health, this study aims to gain a better understanding of the impact of an antimicrobial (Fumidil B®, Can-Vet Animal Health Supplies Ltd., Guelph, ON, Canada) and a probiotic (Bactocell®, Lallemand Inc., Montreal,
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Against a backdrop of declining bee colony health, this study aims to gain a better understanding of the impact of an antimicrobial (Fumidil B®, Can-Vet Animal Health Supplies Ltd., Guelph, ON, Canada) and a probiotic (Bactocell®, Lallemand Inc., Montreal, QC, Canada) on bees’ microbiota and the health of their colonies after wintering. Therefore, colonies were orally exposed to these products and their combination before wintering in an environmental room. The results show that the probiotic significantly improved the strength of the colonies in spring by increasing the total number of bees and the number of capped brood cells. This improvement translated into a more resilient structure of the gut microbiota, highlighted by a more connected network of interactions between bacteria. Contrastingly, the antimicrobial treatment led to a breakdown in this network and a significant increase in negative interactions, both being hallmarks of microbiota dysbiosis. Although this treatment did not translate into a measurable colony strength reduction, it may impact the health of individual bees. The combination of these products restored the microbiota close to control, but with mixed results for colony performance. More tests will be needed to validate these results, but the probiotic Bactocell® could be administrated as a food supplement before wintering to improve colony recovery in spring.
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(This article belongs to the Section Veterinary Microbiology)
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Open AccessPerspective
Chagas Disease across the Ages: A Historical View and Commentary on Navigating Future Challenges
by
Denis Sereno, Bruno Oury and Mario J. Grijalva
Microorganisms 2024, 12(6), 1153; https://doi.org/10.3390/microorganisms12061153 - 6 Jun 2024
Abstract
Chagas disease, discovered over a century ago, continues to pose a global health challenge, affecting millions mainly in Latin America. This historical review with commentary outlines the disease’s discovery, its evolution into a global concern due to migration, and highlights significant advances in
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Chagas disease, discovered over a century ago, continues to pose a global health challenge, affecting millions mainly in Latin America. This historical review with commentary outlines the disease’s discovery, its evolution into a global concern due to migration, and highlights significant advances in diagnostics and treatment strategies. Despite these advancements, the paper discusses ongoing challenges in eradication, including vector control, congenital transmission, the disease’s asymptomatic nature, and socioeconomic barriers to effective management. It calls for a multidisciplinary approach, enhanced diagnostics, improved treatment accessibility, and sustained vector control efforts. The review emphasizes the importance of global collaboration and increased funding to reduce Chagas disease’s impact.
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(This article belongs to the Special Issue Epidemiology of Vector Born Diseases 3.0)
Open AccessArticle
Genetic Variation among the Partial Gene Sequences of the Ribosomal Protein Large-Two, the Internal Transcribed Spacer, and the Small Ribosomal Subunit of Blastocystis sp. from Human Fecal Samples
by
Guiehdani Villalobos, Eduardo Lopez-Escamilla, Angelica Olivo-Diaz, Mirza Romero-Valdovinos, Arony Martinez, Pablo Maravilla and Fernando Martinez-Hernandez
Microorganisms 2024, 12(6), 1152; https://doi.org/10.3390/microorganisms12061152 - 5 Jun 2024
Abstract
In the present study, we compared the genetic variability of fragments from the internal transcribed spacer region (ITS) and the small subunit ribosomal DNA (SSUrDNA) as nuclear markers, in contrast with the ribosomal protein large two (rpl2) loci, placed in
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In the present study, we compared the genetic variability of fragments from the internal transcribed spacer region (ITS) and the small subunit ribosomal DNA (SSUrDNA) as nuclear markers, in contrast with the ribosomal protein large two (rpl2) loci, placed in the mitochondrion-related organelles (MROs) within and among human fecal samples with Blastocystis. Samples were analyzed using polymerase chain reaction (PCR)-sequencing, phylogenies, and genetics of population structure analyses were performed. In total, 96 sequences were analyzed, i.e., 33 of SSUrDNA, 35 of rpl2, and 28 of ITS. Only three subtypes (STs) were identified, i.e., ST1 (11.4%), ST2 (28.6%), and ST3 (60%); in all cases, kappa indexes were 1, meaning a perfect agreement among ST assignations. The topologies of phylogenetic inferences were similar among them, clustering to each ST in its specific cluster; discrepancies between phylogeny and assignment of STs were not observed. The STRUCTURE v2.3.4 software assigned three subpopulations corresponding to the STs 1–3, respectively. The population indices were consistent with those previously reported by other groups. Our results suggest the potential use of the ITS and rpl2 genes as molecular markers for Blastocystis subtyping as an alternative approach for the study of the genetic diversity observed within and between human isolates of this microorganism.
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(This article belongs to the Section Parasitology)
Open AccessArticle
The Presence of esat-6 and cfp10 and Other Gene Orthologs of the RD 1 Region in Non-Tuberculous Mycobacteria, Mycolicibacteria, Mycobacteroides and Mycolicibacter as Possible Impediments for the Diagnosis of (Animal) Tuberculosis
by
Nomakorinte Gcebe, Tiny Motlatso Hlokwe, Agnes Bouw, Anita Michel and Victor P. M. G. Rutten
Microorganisms 2024, 12(6), 1151; https://doi.org/10.3390/microorganisms12061151 - 5 Jun 2024
Abstract
The Esx-1 family proteins of the Type VII secretion systems of Mycobacterium bovis and Mycobacterium tuberculosis have been assessed and are frequently used as candidates for tuberculosis (TB) diagnosis in both humans and animals. The presence of ESAT-6 and CFP 10 proteins, which
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The Esx-1 family proteins of the Type VII secretion systems of Mycobacterium bovis and Mycobacterium tuberculosis have been assessed and are frequently used as candidates for tuberculosis (TB) diagnosis in both humans and animals. The presence of ESAT-6 and CFP 10 proteins, which are the most immunogenic proteins of the Esx-1 system and have been widely investigated for the immunodiagnosis of tuberculosis, in some Mycobacteriaceae and in Mycobacterium leprae, poses limitations for their use in specific diagnoses of TB. As such, to improve the specificity of the ESAT-6/CFP 10-based cell-mediated immunity (CMI) assays, other proteins encoded by genes within and outside the RD 1 region of the esx-1 locus have been evaluated as candidate antigens for CMI, as well as to investigate humoral responses in combination with ESAT-6 and or CFP 10, with varying specificity and sensitivity results. Hence, in this study, we evaluated various non-tuberculous mycobacteria (NTM), Mycolicibacterium, Mycolicibacter and Mycobacteroides species genomes available on the NCBI database for the presence and composition of the RD1 region of the esx-1 locus. In addition, we also assayed by polymerase chain reaction (PCR) and sequencing of Mycobacteriaceae available in our culture collection for the presence and sequence diversity of esxA and esxB genes encoding ESAT-6 and CFP 10, respectively. Whole genome sequence (WGS) data analysis revealed the presence of RD 1 gene orthologs in 70 of the over 100 published genomes of pathogenic and non- pathogenic Mycobcteriaceae other than tuberculosis. Among species evaluated from our culture collection, in addition to earlier reports of the presence of esxA and esxB in certain Mycolicibacterium, Mycolicibacterium septicum/peregrinum, Mycolicibacterium porcinum and Mycobacterium sp. N845T were also found to harbour orthologs of both genes. Orthologs of esxA only were detected in Mycobacterium brasiliensis, Mycolicibacterium elephantis and Mycolicibacterium flouroantheinivorans, whereas in Mycolicibacter engbackii, Mycolicibacterium mageritense and Mycobacterium paraffinicum, only esxB orthologs were detected. A phylogenetic analysis based on esxA and esxB sequences separated slow-growing from rapidly growing bacteria. These findings strengthen previous suggestions that esxA and esxB may be encoded in the majority of Mycobacteriaceae. The role of the Esx-1 system in both pathogenic and non-pathogenic Mycobacteriaceae needs further investigation, as these species may pose limitations to immunological assays for TB.
Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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