Impact of Probiotics on Gut Microbiota Diversity the Faecal Metabolome in Seniors
Insights on Cystic Fibrosis Pseudomonas aeruginosa Carbohydrate Binding Profiles using Fluorescent Glycopolymers
Categorization of Microbial Genomes by Encoded Denitrification Traits
Novelty Production of Assyrtiko Wines from the Volcanic Terroir of Santorini Island Using Lachancea thermotolerans

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 13.4 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2024).
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: 4.1 (2023); 5-Year Impact Factor: 4.5 (2023)

Imprint Information Journal Flyer Open Access ISSN: 2076-2607

Latest Articles

17 pages, 8680 KiB

Open AccessArticle

Effects of Rehydration on Bacterial Diversity in the Rhizosphere of Broomcorn Millet (Panicum miliaceum L.) after Drought Stress at the Flowering Stage

by Yuhan Liu, Jiao Mao, Yuanmeng Xu, Jiangling Ren, Mengyao Wang, Shu Wang, Sichen Liu, Ruiyun Wang, Lun Wang, Liwei Wang, Zhijun Qiao and Xiaoning Cao

Microorganisms 2024, 12(8), 1534; https://doi.org/10.3390/microorganisms12081534 - 26 Jul 2024

Abstract

This study aimed to elucidate responses of the bacterial structure and diversity of the rhizosphere in flowering broomcorn millet after rehydration following drought stress. In this study, the broomcorn millet varieties ‘Hequ red millet’ (A1) and ‘Yanshu No.10′ (A2), known for their different drought tolerance levels, were selected as experimental materials. The plants were subjected to rehydration after drought stress at the flowering stage, while normal watering (A1CK and A2CK) served as the control. Soil samples were collected at 10 days (A11, A21, A1CK1, and A2CK1) and 20 days (A12, A22, A1CK2, and A2CK2) after rehydration. High-throughput sequencing technology was employed to investigate the variations in bacterial community structure, diversity, and metabolic functions in the rhizosphere of the broomcorn millet at different time points following rehydration. The findings indicated that the operational taxonomic units (OTUs) of bacteria in the rhizosphere of broomcorn millet were notably influenced by the duration of treatment, with a significant decrease in OTUs observed after 20 days of rehydration. However, bacterial Alpha diversity was not significantly impacted by rehydration following drought stress. The bacterial community in the rhizosphere of broomcorn millet was mainly composed of Actinobacteria and Proteobacteria. After rewatering for 10 to 20 days after drought stress, the abundance of Sphingomonas and Aeromicrobium in the rhizosphere soil of the two varieties of broomcorn millet decreased gradually. Compared with Yanshu No.10, the abundance of Pseudarthrobacter in the rhizosphere of Hequ red millet gradually increased. A Beta diversity analysis revealed variations in the dissimilarities of the bacterial community which corresponded to different rehydration durations. The relative abundance of bacterial metabolic functions in the rhizosphere of broomcorn millet was lower after 20 days of rehydration, compared to measurements after 10 days of rehydration. This observation might be attributed to the exchange of materials between broomcorn millet and microorganisms during the initial rehydration stage to repair the effects of drought, as well as to the enrichment of numerous microorganisms to sustain the stability of the community structure. This study helps to comprehend the alterations to the bacterial structure and diversity in the rhizosphere of broomcorn millet following drought stress and rehydration. It sheds light on the growth status of broomcorn millet and its rhizosphere microorganisms under real environmental influences, thereby enhancing research on the drought tolerance mechanisms of broomcorn millet. Full article

(This article belongs to the Special Issue Microbial Interactions in Plant Adaptation to Abiotic and Biotic Stress)

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20 pages, 3974 KiB

Open AccessArticle

Whole Genome Sequencing of Bacillus velezensis AMR25, an Effective Antagonist Strain against Plant Pathogens

by Alexey A. Ananev, Zlata V. Ogneva, Nikolay N. Nityagovsky, Andrey R. Suprun, Konstantin V. Kiselev and Olga A. Aleynova

Microorganisms 2024, 12(8), 1533; https://doi.org/10.3390/microorganisms12081533 - 26 Jul 2024

Abstract

The most serious problems for cultivated grapes are pathogenic microorganisms, which reduce the yield and quality of fruit. One of the most widespread disease of grapes is “gray mold”, caused by the fungus Botrytis cinerea. Some strains of Bacillus, such as Bacillus halotolerans, Bacillus amyloliquefaciens, and Bacillus velezensis, are known to be active against major post-harvest plant rots. In this study, we showed that the endophytic bacteria B. velezensis strain AMR25 isolated from the leaves of wild grapes Vitis amurensis Rupr. exhibited antimicrobial activity against grape pathogens, including B. cinerea. The genome of B. velezensis AMR25 has one circular chromosome with a length of 3,909,646 bp. with 3689 open reading frames. Genomic analysis identified ten gene clusters involved in the nonribosomal synthesis of polyketides (macrolactin, bacillene, and difficidin), lipopeptides (surfactin, fengycin, and bacillizin), and bacteriocins (difficidin). Also, the genome under study contains a number of genes involved in root colonization, biofilm formation, and biosynthesis of phytohormones. Thus, the endophytic bacteria B. velezensis strain AMR25 shows great promise in developing innovative biological products for enhancing plant resistance against various pathogens. Full article

(This article belongs to the Section Plant Microbe Interactions)

17 pages, 11192 KiB

Open AccessArticle

Functional Characterization of Ao4g24: An Uncharacterized Gene Involved in Conidiation, Trap Formation, Stress Response, and Secondary Metabolism in Arthrobotrys oligospora

by Lirong Zhu, Meichen Zhu, Xuemei Li, Yanmei Shen, Shipeng Duan and Jinkui Yang

Microorganisms 2024, 12(8), 1532; https://doi.org/10.3390/microorganisms12081532 - 26 Jul 2024

Abstract

Arthrobotrys oligospora is a typical nematode-trapping (NT) fungus, which can secrete food cues to lure, capture, and digest nematodes by triggering the production of adhesive networks (traps). Based on genomic and proteomic analyses, multiple pathogenic genes and proteins involved in trap formation have been characterized; however, there are numerous uncharacterized genes that play important roles in trap formation. The functional studies of these unknown genes are helpful in systematically elucidating the complex interactions between A. oligospora and nematode hosts. In this study, we screened the gene AOL_s00004g24 (Ao4g24). This gene is similar to the SWI/SNF chromatin remodeling complex, which was found to play a potential role in trap formation in our previous transcriptome analysis. Here, we characterized the function of Ao4g24 by gene disruption, phenotypic analysis, and metabolomics. The deletion of Ao4g24 led to a remarkable decrease in conidia yield, trap formation, and secondary metabolites. Meanwhile, the absence of Ao4g24 influenced the mitochondrial membrane potential, ATP content, autophagy, ROS level, and stress response. These results indicate that Ao4g24 has crucial functions in sporulation, trap formation, and pathogenicity in NT fungi. Our study provides a reference for understanding the role of unidentified genes in mycelium growth and trap formation in NT fungi. Full article

(This article belongs to the Section Environmental Microbiology)

17 pages, 5153 KiB

Open AccessArticle

Development of Broad-Range Microbial Minimal Culture Medium for Lanthanide Studies

by Gianmaria Oliva, Giovanni Vigliotta, Luca Di Stasio, Ermanno Vasca and Stefano Castiglione

Microorganisms 2024, 12(8), 1531; https://doi.org/10.3390/microorganisms12081531 - 26 Jul 2024

Abstract

Rare Earth Elements (REE), also known as Lanthanides (Ln³⁺), are a group of 17 elements showing peculiar physical and chemical properties. Unlike technological applications, very little is known about the physiological role and toxicity of Ln³⁺ on biological systems, in particular on microorganisms (e.g., bacteria), which represent the most abundant domains on our planet. Up to now, very limited studies have been conducted due to Ln³⁺ precipitation with some anions commonly present in the culture media. Therefore, the development of a minimal medium is essential to allow the study of Ln³⁺-microbial interactions, limiting considerably the precipitation of insoluble salts. In this regard, a new minimal culture medium capable of solubilizing large amounts of Ln³⁺ and allowing the growth of different microbial taxa was successfully developed. Assays have shown that the medium is capable of solubilizing Ln³⁺ up to 100 times more than other common culture media and allowing the growth of 63 bacteria and 5 fungi. The kinetic growth of one yeast and one Gram-positive bacterium has been defined, proving to support superior growth and biomass compared to other commonly used minimal media. Moreover, the sensitivity and uptake/absorption of a Bacillus stratosphericus strain were tested, highlighting its capability to tolerate concentrations up to 10 mM of either Cerium, Gadolinium or Lanthanum and accumulate different quantities of the three. Full article

(This article belongs to the Section Environmental Microbiology)

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22 pages, 9313 KiB

Open AccessArticle

IAA Synthesis Pathway of Fitibacillus barbaricus WL35 and Its Regulatory Gene Expression Levels in Potato (Solanum tuberosum L.)

by Xiaoyu Li, Huan Tao, Shisong Wang, Di Zhang, Xingyao Xiong and Yanfei Cai

Microorganisms 2024, 12(8), 1530; https://doi.org/10.3390/microorganisms12081530 - 26 Jul 2024

Abstract

Indole-3-acetic acid (IAA), as an important regulator of potato growth, seriously affects the growth and yield of potato. Although many studies have reported that IAA-producing Bacillus can promote plant growth, little research has been conducted on its synthesis pathway and molecular mechanisms. In this study, an IAA-producing strain WL35 was identified as Fitibacillus barbaricus, and its yield was 48.79 mg·L⁻¹. The results of the pot experiments showed that WL35 significantly increased plant height, stem thickness, chlorophyll content, and number of leaves of potato plants by 31.68%, 30.03%, 32.93%, and 36.59%, respectively. In addition, in the field experiments, WL35-treated plants increased commercial potato yield by 16.45%, vitamin C content by 16.35%, protein content by 75%, starch content by 6.60%, and the nitrogen, phosphorus, and potassium accumulation by 9.98%, 12.70%, and 26.76%, respectively. Meanwhile, the synthetic pathway of WL35 was found to be dominated by the tryptophan-dependent pathway, the IAM, TAM, and IPA pathways worked together, and the pathways that played a role at different times were different. Furthermore, RNA-seq analysis showed that there were a total of 2875 DEGs regulated in the samples treated with WL35 seed dressing compared with the CK, of which 1458 genes were up-regulated and 1417 genes were down-regulated. Potato roots express differential genes enriched in processes such as carbohydrate metabolism processes and cellular polysaccharide metabolism, which regulate potato plant growth and development. The above results provide a theoretical basis for the further exploration of the synthesis pathway of IAA and its growth-promoting mechanism in potato. Full article

(This article belongs to the Special Issue Research on Plant—Bacteria Interactions)

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17 pages, 1864 KiB

Open AccessArticle

Antimicrobial Resistance and Phylogenetic Relatedness of Salmonella Serovars in Indigenous Poultry and Their Drinking Water Sources in North Central Nigeria

by Nancy M. Sati, Roderick M. Card, Lisa Barco, Maryam Muhammad, Pam D. Luka, Thomas Chisnall, Idowu O. Fagbamila, Giulia Cento, Nnaemeka E. Nnadi, Clovice Kankya, Innocent B. Rwego, Kokas Ikwap, Lawrence Mugisha, Joseph Erume and Frank N. Mwiine

Microorganisms 2024, 12(8), 1529; https://doi.org/10.3390/microorganisms12081529 - 26 Jul 2024

Abstract

There is scant information on Salmonella in indigenous poultry in Nigeria. We investigated the occurrence and characterized Salmonella serovars in indigenous poultry and their drinking water sources to enhance the monitoring of the infection in poultry and to promote public health. We collected 1208 samples, poultry droppings (n = 1108), and water (n = 100) across 15 markets in North Central Nigeria. Salmonella spp. were isolated following World Organisation for Animal Health guidelines. Salmonella spp., confirmed through invA gene detection by a polymerase chain reaction assay, were 6.8% (75/1108) droppings and 3% (3/100) water. Susceptibility testing against 13 antimicrobials showed 60.3% (47/78) susceptibility to all the antimicrobials tested while 14.1% (11/78) were multidrug resistant. Serotyping and whole-genome sequencing were carried out on 44 of the isolates, and 23 different serovars were identified. Genomes of serovars Luedinghausen, Laredo, Widemarsh, and Lansing are being documented in Africa for the first time. Twenty (20) antimicrobial resistance (AMR) gene markers encoding for resistance to aminoglycosides, tetracyclines, sulphonamides, quinolones, trimethoprim, penicillins and phenicols were found. Phylogenetic cluster analysis showed close relatedness among isolates from different sources. This study shows both low Salmonella prevalence and AMR, but since uncommon serovars are circulating, continuous monitoring is recommended so as to ensure food safety and poultry health. Full article

(This article belongs to the Section Veterinary Microbiology)

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14 pages, 8249 KiB

Open AccessReview

Resuscitation Promotion Factor: A Pronounced Bacterial Cytokine in Propelling Bacterial Resuscitation

by Xinxin Li, Qing Ren, Zhanbin Sun, Yanan Wu and Hanxu Pan

Microorganisms 2024, 12(8), 1528; https://doi.org/10.3390/microorganisms12081528 - 25 Jul 2024

Abstract

While confronted with unfavorable growth conditions, bacteria may transform into the dormant state, such as viable but nonculturable (VBNC) state, which is a reversible state characterized by low metabolic activity and lack of division. These dormant cells can be reactivated through the influence of the resuscitation promoting factor (Rpf) family, which are classified as autocrine growth factors and possess peptidoglycan hydrolase activities. To date, with the significant resuscitation or growth promotion ability of Rpf, it has been extensively applied to increasing bacterial diversity and isolating functional microbial species. This review provides a comprehensive analysis of the distribution, mode of action, and functional mechanisms of Rpf proteins in various bacterial species. The aim is to create opportunities for decoding microbial communities and extracting microbial resources from real samples across different research fields. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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20 pages, 8316 KiB

Open AccessSystematic Review

Fungi-Derived Bioactive Compounds as Potential Therapeutic Agents for Pancreatic Cancer: A Systematic Review

by Francisco Quiñonero, Alba Ortigosa-Palomo, Raul Ortiz, Consolacion Melguizo and Jose Prados

Microorganisms 2024, 12(8), 1527; https://doi.org/10.3390/microorganisms12081527 - 25 Jul 2024

Abstract

Pancreatic cancer (PC) is one of the tumors with the lowest 5-year survival rate worldwide due to late diagnosis and lack of effective therapy. Because of this, it is necessary to discover new ways of treatment to increase the quality of life of patients. In this context, the secondary metabolites of several fungi have been shown as a possible therapeutic strategy in several types of cancer, such as colorectal cancer, being able to trigger their action through the induction of apoptosis. The objective was to perform a systematic review process to analyze the studies carried out during the last ten years using secondary metabolites derived from fungi as antitumor treatment against PC. After the search process in three databases (PubMed, SCOPUS, and Web of Science) a total of 199 articles were found, with 27 articles finally being included after screening. The results extracted from this systematic review process made it possible to determine the existence of bioactive compounds extracted from fungi that have been effective in in vitro and in vivo conditions and that may be applicable as a possible therapy to avoid drug resistance in PC, one of the major problems of this disease. Full article

(This article belongs to the Section Medical Microbiology)

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28 pages, 4507 KiB

Open AccessArticle

Development of a Robust Saccharomyces cerevisiae Strain for Efficient Co-Fermentation of Mixed Sugars and Enhanced Inhibitor Tolerance through Protoplast Fusion

by Jianzhi Zhao, Yuping Zhao, Longhao Wu, Ning Yan, Shuo Yang, Lili Xu, Deyun He, Hongxing Li and Xiaoming Bao

Microorganisms 2024, 12(8), 1526; https://doi.org/10.3390/microorganisms12081526 - 25 Jul 2024

Abstract

The economical and efficient commercial production of second-generation bioethanol requires fermentation microorganisms capable of entirely and rapidly utilizing all sugars in lignocellulosic hydrolysates. In this study, we developed a recombinant Saccharomyces cerevisiae strain, BLH510, through protoplast fusion and metabolic engineering to enhance its ability to co-ferment glucose, xylose, cellobiose, and xylooligosaccharides while tolerating various inhibitors commonly found in lignocellulosic hydrolysates. The parental strains, LF1 and BLN26, were selected for their superior glucose/xylose co-fermentation capabilities and inhibitor tolerance, respectively. The fusion strain BLH510 demonstrated efficient utilization of mixed sugars and high ethanol yield under oxygen-limited conditions. Under low inoculum conditions, strain BLH510 could completely consume all four kinds of sugars in the medium within 84 h. The fermentation produced 33.96 g/L ethanol, achieving 84.3% of the theoretical ethanol yield. Despite the challenging presence of mixed inhibitors, BLH510 successfully metabolized all four sugars above after 120 h of fermentation, producing approximately 30 g/L ethanol and reaching 83% of the theoretical yield. Also, strain BLH510 exhibited increased intracellular trehalose content, particularly under conditions with mixed inhibitors, where the intracellular trehalose reached 239.3 mg/g yeast biomass. This elevated trehalose content contributes to the enhanced stress tolerance of BLH510. The study also optimized conditions for protoplast preparation and fusion, balancing high preparation efficiency and satisfactory regeneration efficiency. The results indicate that BLH510 is a promising candidate for industrial second-generation bioethanol production from lignocellulosic biomass, offering improved performance under challenging fermentation conditions. Our work demonstrates the potential of combining protoplast fusion and metabolic engineering to develop superior S. cerevisiae strains for lignocellulosic bioethanol production. This approach can also be extended to develop robust microbial platforms for producing a wide array of lignocellulosic biomass-based biochemicals. Full article

(This article belongs to the Section Microbial Biotechnology)

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17 pages, 3909 KiB

Open AccessArticle

Harnessing Machine Learning to Uncover Hidden Patterns in Azole-Resistant CYP51/ERG11 Proteins

by Otávio Guilherme Gonçalves de Almeida and Marcia Regina von Zeska Kress

Microorganisms 2024, 12(8), 1525; https://doi.org/10.3390/microorganisms12081525 - 25 Jul 2024

Abstract

Fungal resistance is a public health concern due to the limited availability of antifungal resources and the complexities associated with treating persistent fungal infections. Azoles are thus far the primary line of defense against fungi. Specifically, azoles inhibit the conversion of lanosterol to ergosterol, producing defective sterols and impairing fluidity in fungal plasmatic membranes. Studies on azole resistance have emphasized specific point mutations in CYP51/ERG11 proteins linked to resistance. Although very insightful, the traditional approach to studying azole resistance is time-consuming and prone to errors during meticulous alignment evaluation. It relies on a reference-based method using a specific protein sequence obtained from a wild-type (WT) phenotype. Therefore, this study introduces a machine learning (ML)-based approach utilizing molecular descriptors representing the physiochemical attributes of CYP51/ERG11 protein isoforms. This approach aims to unravel hidden patterns associated with azole resistance. The results highlight that descriptors related to amino acid composition and their combination of hydrophobicity and hydrophilicity effectively explain the slight differences between the resistant non-wild-type (NWT) and WT (nonresistant) protein sequences. This study underscores the potential of ML to unravel nuanced patterns in CYP51/ERG11 sequences, providing valuable molecular signatures that could inform future endeavors in drug development and computational screening of resistant and nonresistant fungal lineages. Full article

(This article belongs to the Special Issue Healthcare-Associated Infections and Antimicrobial Therapy)

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2 pages, 153 KiB

Open AccessCorrection

Correction: Rimoldi et al. The Replacement of Fish Meal with Poultry By-Product Meal and Insect Exuviae: Effects on Growth Performance, Gut Health and Microbiota of the European Seabass, Dicentrarchus labrax. Microorganisms 2024, 12, 744

by Simona Rimoldi, Ambra Rita Di Rosa, Rosangela Armone, Biagina Chiofalo, Imam Hasan, Marco Saroglia, Violeta Kalemi and Genciana Terova

Microorganisms 2024, 12(8), 1524; https://doi.org/10.3390/microorganisms12081524 - 25 Jul 2024

Abstract

In the original publication [...] Full article

(This article belongs to the Section Veterinary Microbiology)

14 pages, 1608 KiB

Open AccessArticle

Comparing the Microbiome of the Adenoids in Children with Secretory Otitis Media and Children without Middle Ear Effusion

by Oļegs Sokolovs-Karijs, Monta Brīvība, Rihards Saksis, Maija Rozenberga, Laura Bunka, Francesca Girotto, Jana Osīte, Aigars Reinis, Gunta Sumeraga and Angelika Krūmiņa

Microorganisms 2024, 12(8), 1523; https://doi.org/10.3390/microorganisms12081523 - 25 Jul 2024

Abstract

Background: The adenoids, primary sites of microbial colonization in the upper airways, can influence the development of various conditions, including otitis media with effusion (OME). Alterations in the adenoid microbiota have been implicated in the pathogenesis of such conditions. Aim: This study aims to utilize 16S rRNA genetic sequencing to identify and compare the bacterial communities on the adenoid surfaces of children with OME and children with healthy middle ears. Additionally, we seek to assess the differences in bacterial diversity between these two groups. Materials and Methods: We collected adenoid surface swabs from forty children, divided into two groups: twenty samples from children with healthy middle ears and twenty samples from children with OME. The V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Alpha and beta diversity indices were calculated, and statistical analyses were performed to identify significant differences in bacterial composition. Results: Alpha diversity analysis, using Pielou’s index, revealed significantly greater evenness in the bacterial communities on the adenoid surfaces of the healthy ear group compared with the OME group. Beta diversity analysis indicated greater variability in the microbial composition of the OME group. The most common bacterial genera in both groups were Haemophilus, Fusobacterium, Streptococcus, Moraxella, and Peptostreptococcus. The healthy ear group was primarily dominated by Haemophilus and Streptococcus, whereas the OME group showed higher abundance of Fusobacterium and Peptostreptococcus. Additionally, the OME group exhibited statistically significant higher levels of Alloprevotella, Peptostreptococcus, Porphyromonas, Johnsonella, Parvimonas, and Bordetella compared with the healthy ear group. Conclusion: Our study identified significant differences in the bacterial composition and diversity on the adenoid surfaces of children with healthy middle ears and those with OME. The OME group exhibited greater microbial variability and higher abundances of specific bacterial genera. These findings suggest that the adenoid surface microbiota may play a role in the pathogenesis of OME. Further research with larger sample sizes and control groups is needed to validate these results and explore potential clinical applications. Full article

(This article belongs to the Section Microbiomes)

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14 pages, 283 KiB

Open AccessReview

Biofilm Production and Its Implications in Pediatrics

by Nicola Principi and Susanna Esposito

Microorganisms 2024, 12(8), 1522; https://doi.org/10.3390/microorganisms12081522 - 25 Jul 2024

Abstract

Biofilms, aggregates of bacteria enclosed in a self-produced matrix, have been implicated in various pediatric respiratory infections, including acute otitis media (AOM), otitis media with effusion (OME), adenoiditis, protracted bacterial bronchitis, and pulmonary exacerbations in cystic fibrosis. These infections are prevalent in children and often associated with biofilm-producing pathogens, leading to recurrent and chronic conditions. Biofilms reduce antibiotic efficacy, contributing to treatment failure and disease persistence. This narrative review discusses biofilm production by respiratory pathogens such as Streptococcus pneumoniae, non-typeable Haemophilus influenzae, Pseudomonas aeruginosa, and Staphylococcus aureus. It examines their mechanisms of biofilm formation, antibiotic resistance, and the challenges they present in clinical treatment. Various antibiofilm strategies have shown promise in vitro and in animal studies, including the use of N-acetylcysteine, enzymes like dispersin B, and agents disrupting quorum sensing and biofilm matrix components. However, their clinical application, particularly in children, remains limited. Traditional treatments for biofilm-associated diseases have not significantly evolved, even with biofilm detection. The transition from experimental findings to clinical practice is complex and requires robust clinical trials and standardized biofilm detection protocols. Addressing biofilms in pediatric respiratory infections is crucial for improving treatment outcomes and managing recurrent and chronic diseases effectively. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilm)

32 pages, 4780 KiB

Open AccessArticle

Spent Mushroom Substrate Improves Microbial Quantities and Enzymatic Activity in Soils of Different Farming Systems

by Maša Pintarič, Ana Štuhec, Eva Tratnik and Tomaž Langerholc

Microorganisms 2024, 12(8), 1521; https://doi.org/10.3390/microorganisms12081521 - 24 Jul 2024

Abstract

Organic fertilizers, such as spent mushroom substrate (SMS), improve soil fertility, but studies comparing their effects on different agricultural soils are limited. In this study, the effects of standard, SMS and composed fertilizers on soils from conventional–integrated, organic and biodynamic farming were investigated. Soil samples were analyzed for microorganisms and the activity of β-glucosidase (β-GLU), β-1,4-N-acetylglucosaminidase (NAG), urease (URE), arylamidase (ARN), phosphatase (PHOS), acid phosphatase (PAC), alkaline phosphatase (PAH) and arylsulphatase (ARS). Biodynamic soil showed the highest microbial counts and enzyme activities, followed by organic and conventional soils. SMS significantly increased the number of microorganisms and enzyme activities, especially in biodynamic and organic soils. Seasonal variations affected all microorganisms and most enzymes in all soils, except NAG in conventional and organic soils. Biodynamic soil showed stable activity of enzymes and microorganisms throughout the year, indicating greater stability. This study concludes that soil microorganisms and enzyme activities respond differently to fertilization depending on the soil type, with SMS demonstrating beneficial effects in all tested soils. Full article

(This article belongs to the Special Issue Microbial Advances in a Sustainable Environment: Biological Waste Treatment and Bioconversion Technology 2.0)

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19 pages, 5489 KiB

Open AccessArticle

The Hypogeous Roman Archeological Museum of Positano: Study of the Evolution of Biological Threaten and Development of Adequate Control Protocols

by Federica Antonelli, Sara Iafrate, Marco Tescari, Manuel Giandomenico, Alma Kumbaric and Marco Bartolini

Microorganisms 2024, 12(8), 1520; https://doi.org/10.3390/microorganisms12081520 - 24 Jul 2024

Abstract

Hypogea are natural or artificial spaces located underground often of great interest from an anthropological, archeological, religious, artistic, or historic point of view. Due to their features, these environments usually present conservative problems and biological colonization could be considered as one of the main threats. The present three-year study was carried out by specialists of the Central Institute for Restoration of Rome (ICR) in the hypogeous site preserved in the Roman Archeological Museum of Positano (Positano MAR) and focused on characterizing biological alterations present on the mural paintings; setting up efficient strategies and protocols for biodeterioration control; and monitoring the efficacy of direct and indirect interventions. Patinas with different morphologies were analyzed through microscopic observations, cultural analyses and next-generation sequencing. The results proved that the alterations comprised a great variety of microorganisms forming very distinct communities, differently distributed over space and time. The main taxa represented were bacteria of phyla Pseudomonadota and Actinomycetota, fungi belonging to the genus Fusarium and Gliocladium, and algae of the genus Chlorococcum. Preservation protocols were set up considering the alterations’ composition and included the application of biocides, limiting daily temperature changes, decreasing illuminance values on painted surfaces, and the screening of natural light sources. Full article

(This article belongs to the Special Issue Microorganisms and Cultural Heritage: From Deterioration to Preservation Protocols)

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11 pages, 2727 KiB

Open AccessArticle

Parasitism with Protozoa and Monogeneans in Fish from the Natural Waters of Romania

by Gheorghe Dărăbuș, Kristian Robert Ujvari and Mirela Imre

Microorganisms 2024, 12(8), 1519; https://doi.org/10.3390/microorganisms12081519 - 24 Jul 2024

Abstract

Parasitism by protozoa and monogenean flatworms in freshwater fish from Romania was studied by collecting and examining samples from two major river systems there: 183 fish from 17 species from the Olt River and its tributaries; and 155 fish from 16 species from the Mureș River and its tributary, Târnava Mare. The average rates of parasitism in the samples from the two rivers and their tributaries were as follows: Ichthyiophthirius multifiliis (2%), Trichodina spp. (21%), Apiosoma spp. (18%), Mixobolus spp. (8%), Dactylogyrus spp. (9%), and Gyrodactylus spp. (10%). The number of parasite species varied from one river to another. I. multifiliis was found in only 3 fish species, Trichodina spp. in 13 species, Glosatella spp. in 6 species, and Mixobollus spp., Dactylogyrus spp., and Gyrodactylus spp. in 7 different species each. The highest number of parasite species (six) were identified in the European chub (Squalius cephalus) and schneider (Alburnoides bipunctatus), which seem more susceptible to parasitic infections. The aquatic environment of these rivers may represent a source of parasites for fish from neighboring countries through which these rivers pass. Full article

(This article belongs to the Special Issue Pathogens and Aquaculture)

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12 pages, 1417 KiB

Open AccessArticle

Coronal and Root Canal Microbiota in Apical Periodontitis with Different PAI

by Adelaide Teofani, Antonio Libonati, Valeria Unida, Silvia Biocca, Alessandro Desideri and Vincenzo Campanella

Microorganisms 2024, 12(8), 1518; https://doi.org/10.3390/microorganisms12081518 - 24 Jul 2024

Abstract

Apical periodontitis is an inflammatory disease triggered by oral pathogens invading necrotic root canals. The aim of this study was to evaluate the coronal and root canal bacterial community profiles in primary endodontic infections with different periapical (PAI) indices in comparison to oral mucosa controls. A total of 31 patients with primary apical periodontitis, 14 with PAI-1 and 17 with PAI-3 were recruited. Microbial specimens from mucosa (control samples) and endodontic necrotic tissues were collected in each patient. Microbiota composition was studied through 16S ribosomal RNA gene amplicon sequencing analysis. Overall, 2953 taxa from 168 different genera of 451 various microbial species were retrieved in the controls and PAI-1 and PAI-3 groups. Firmicutes is the predominant phylum in the oral controls (34.5%) and PAI-1 (44.4%) groups, while Bacteroidetes is predominant in PAI-3 (38.6%). The Proteobacteria (21.5%) and Fusobacteria (12.5%) relative abundance is higher in oral controls while that of Synergistetes is higher in the PAI-1 (3.5%) and PAI-3 (2.5%) groups, being almost absent in controls (less than 0.1%). Most of the increased bacterial species found in the PAI groups were strict anaerobes. A diminished microbial diversity was found in apical periodontitis with higher PAI. These samples were also characterized by an increase in bacteria belonging to phyla and genera with an increased anaerobic character. Full article

(This article belongs to the Special Issue Microbiota in Human Health and Disease)

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11 pages, 629 KiB

Open AccessArticle

Bacterial Resistances and Sensibilities in a Tertiary Care Hospital in Romania—A Retrospective Analysis

by Lazar Chisavu, Flavia Chisavu, Luciana Marc, Adelina Mihaescu, Flaviu Bob, Monica Licker, Viviana Ivan and Adalbert Schiller

Microorganisms 2024, 12(8), 1517; https://doi.org/10.3390/microorganisms12081517 - 24 Jul 2024

Abstract

The increase in bacterial resistance is currently a global burden for the health care system. In order to evaluate the resistance rates of several bacteria from the most encountered cultures in clinical practice, we performed a retrospective analysis of all of the positive cultures from the year 2021 in a tertiary care hospital in Romania. Our analysis captured 3299 positive cultures. The median age of the patients was 62 years (IQR: 41–71 years old) with a slight predominance among females (53.1%). Overall, the most common cultures were urocultures, wound secretion cultures and blood cultures, and the most common identified bacteria were Escherichia coli, Staphylococcus aureus and Klebsiella spp. Positive cultures with the highest resistance rates were found in the bronchial aspirate cultures, catheter tip cultures, urocultures and blood cultures. Escherichia coli (n = 996) had the highest resistance to ampicillin (19.8%) and trimetoprim-sulfametoxazole (16.4%), while Staphylococcus aureus (n = 698) presented the highest resistance rates to clindamycin (27.4%) and oxaciline (19.7%). Klebsiella (n = 481) presented the highest resistance rates to piperaciline-tazobactam (25.2%) and ampicillin (20.4%), whereas Acinetobacter baumanii (n = 123) presented a resistance rate of more than 50% to carbapenems, gentamicin, ciprofloxacin and ceftazidime. The aim of our study was to identify bacterial resistance rates in order to provide updated clinical data to guide physicians in choosing the best empirical antibiotic treatment, especially in the west part of Romania. Full article

(This article belongs to the Special Issue State-of-the-Art Parasitic and Bacterial Infections in Romania 2.0)

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14 pages, 9863 KiB

Open AccessArticle

Relationships between Wheat Development, Soil Properties, and Rhizosphere Mycobiota

by Hang Jiang, Liguo Ma, Peixin Gao, Yueli Zhang, Bo Zhang, Guoping Ma, Kai Qi and Junshan Qi

Microorganisms 2024, 12(8), 1516; https://doi.org/10.3390/microorganisms12081516 - 24 Jul 2024

Abstract

Wheat is a vital global food crop, yet it faces challenges in saline–alkali soils where Fusarium crown rot significantly impacts growth. Variations in wheat growth across regions are often attributed to uneven terrain. To explore these disparities, we examined well-growing and poorly growing wheat samples and their rhizosphere soils. Measurements included wheat height, root length, fresh weight, and Fusarium crown rot severity. Well-growing wheat exhibited greater height, root length, and fresh weight, with a lower Fusarium crown rot disease index compared to poorly growing wheat. Analysis of rhizosphere soil revealed higher alkalinity; lower nutrient levels; and elevated Na, K, and Ca levels in poorly growing wheat compared to well-growing wheat. High-throughput sequencing identified a higher proportion of unique operational taxonomic units (OTUs) in poorly growing wheat, suggesting selection for distinct fungal species under stress. FUNGuild analysis indicated a higher prevalence of pathogenic microbial communities in poorly growing wheat rhizosphere soil. This study underscores how uneven terrains in saline–alkali soils affect pH, nutrient dynamics, mineral content, wheat health, and rhizosphere fungal community structure. Full article

(This article belongs to the Special Issue Rhizosphere Microbial Community 3.0)

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14 pages, 2666 KiB

Open AccessArticle

Counteracting Grey Mould (Botrytis cinerea) in Grapevine ‘Glera’ Using Three Putative Biological Control Agent Strains (Paraburkholderia sp., Pseudomonas sp., and Acinetobacter sp.): Impact on Symptoms, Yield, and Gene Expression

by Giovanni Mian, Nicola Belfiore, Patrick Marcuzzo, Francesco Spinelli, Diego Tomasi and Andrea Colautti

Microorganisms 2024, 12(8), 1515; https://doi.org/10.3390/microorganisms12081515 - 24 Jul 2024

Abstract

This study examined the potential use of three bacterial strains—Paraburkholderia sp. strain CRV74, Pseudomonas sp. strain CRV21, and Acinetobacter sp. strain CRV19—as biocontrol agents of Botrytis cinerea in grapevine. These strains were selected for their ability to inhibit B. cinerea growth in vitro and used in field conditions for the control of grey mould symptoms in ‘Glera’ grapes. To this end, after inoculating these microorganisms onto plants sprayed with B. cinerea spores, the final yield, the physicochemical characteristics of the must, disease incidence, and the possible influence on the expression of plant-defence proteins were evaluated. Strain CRV21 resulted as being the most effective in combating grey mould (−20% of disease incidence). Although yield was not affected, significantly different values of total soluble solids content was observed. Additionally, a significant up-regulation of the genes PR-1, PR-5, β-1,3-glucanase, and class III chitinase was observed. These findings highlight the potential application of strains with anti-botrytis activity as sustainable alternatives to chemical defence for the control of this pathogen. Full article

(This article belongs to the Section Plant Microbe Interactions)

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