Microorganisms

18 pages, 1431 KiB

Open AccessReview

Immunosenescence: How Aging Increases Susceptibility to Bacterial Infections and Virulence Factors

by Nikolaos Theodorakis, Georgios Feretzakis, Christos Hitas, Magdalini Kreouzi, Sofia Kalantzi, Aikaterini Spyridaki, Zoi Kollia, Vassilios S. Verykios and Maria Nikolaou

Microorganisms 2024, 12(10), 2052; https://doi.org/10.3390/microorganisms12102052 (registering DOI) - 11 Oct 2024

Abstract

The process of aging leads to a progressive decline in the immune system function, known as immunosenescence, which compromises both innate and adaptive responses. This includes impairments in phagocytosis and decreased production, activation, and function of T- and B-lymphocytes, among other effects. Bacteria [...] Read more.

The process of aging leads to a progressive decline in the immune system function, known as immunosenescence, which compromises both innate and adaptive responses. This includes impairments in phagocytosis and decreased production, activation, and function of T- and B-lymphocytes, among other effects. Bacteria exploit immunosenescence by using various virulence factors to evade the host’s defenses, leading to severe and often life-threatening infections. This manuscript explores the complex relationship between immunosenescence and bacterial virulence, focusing on the underlying mechanisms that increase vulnerability to bacterial infections in the elderly. Additionally, it discusses how machine learning methods can provide accurate modeling of interactions between the weakened immune system and bacterial virulence mechanisms, guiding the development of personalized interventions. The development of vaccines, novel antibiotics, and antivirulence therapies for multidrug-resistant bacteria, as well as the investigation of potential immune-boosting therapies, are promising strategies in this field. Future research should focus on how machine learning approaches can be integrated with immunological, microbiological, and clinical data to develop personalized interventions that improve outcomes for bacterial infections in the growing elderly population. Full article

(This article belongs to the Special Issue Contemporary Perspectives on Bacterial Virulence Factors)

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10 pages, 6022 KiB

Open AccessArticle

The Challenging Life of Mutators: How Pseudomonas aeruginosa Survives between Persistence and Evolution in Cystic Fibrosis Lung

by Martina Rossitto, Valeria Fox, Gianluca Vrenna, Vanessa Tuccio Guarna Assanti, Nour Essa, Maria Stefania Lepanto, Serena Raimondi, Marilena Agosta, Venere Cortazzo, Vanessa Fini, Annarita Granaglia, Enza Montemitro, Renato Cutrera, Carlo Federico Perno and Paola Bernaschi

Microorganisms 2024, 12(10), 2051; https://doi.org/10.3390/microorganisms12102051 - 11 Oct 2024

Abstract

Cystic fibrosis (CF) is a life-threatening genetic disease characterised by chronic lung infections sustained by opportunistic pathogens such as Pseudomonas aeruginosa. During the chronic long-lasting lung infections, P. aeruginosa adapts to the host environment. Hypermutability, mainly due to defects in the DNA repair [...] Read more.

Cystic fibrosis (CF) is a life-threatening genetic disease characterised by chronic lung infections sustained by opportunistic pathogens such as Pseudomonas aeruginosa. During the chronic long-lasting lung infections, P. aeruginosa adapts to the host environment. Hypermutability, mainly due to defects in the DNA repair system, resulting in an increased spontaneous mutation rate, represents a way to boost the rapid adaptation frequently encountered in CF P. aeruginosa isolates. We selected 609 isolates from 51 patients with CF chronically colonised by P. aeruginosa to study, by full-length genome sequencing, the longitudinal evolution of the bacterium. We recovered at least one hypermutable (mutator) isolate in 57% of patients. By combining genomic information and phenotypic analyses, we followed the evolutionary pathways of the P. aeruginosa mutator strains, identifying their contribution to multi-drug resistance and the emergence of new sub-lineages. By implementing patient clinical data, we observed that mutators preferentially follow a specific evolutionary trajectory in patients with a negative clinical outcome and that maintenance antibiotic polytherapy, based on alternating molecules, apparently reduces the occurrence of hypermutability. Finally, we draw attention to the possibility that modulator-induced changes in the pulmonary environment may be associated with the onset of hypermutability. Full article

(This article belongs to the Special Issue Pseudomonas aeruginosa: Pathogenicity, Drug Resistance Mechanisms and Interaction with the Host)

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12 pages, 651 KiB

Open AccessArticle

Optimizing Hepatitis C Treatment Monitoring: Is Sustained Virologic Response at 4 Weeks Becoming the New Standard?

by Ivana Milošević, Ana Filipović, Branko Beronja, Nikola Mitrović, Maja Ružić, Jelena Simić, Nataša Knežević, Maria Pete, Nevena Todorović and Nataša Nikolić

Microorganisms 2024, 12(10), 2050; https://doi.org/10.3390/microorganisms12102050 - 10 Oct 2024

Abstract

This study, conducted at two university-based infectious disease clinics, included 216 patients with chronic hepatitis C. The primary objective was to assess the positive and negative predictive values, sensitivity, and specificity of achieving a sustained virological response (SVR) at 4 weeks compared to [...] Read more.

This study, conducted at two university-based infectious disease clinics, included 216 patients with chronic hepatitis C. The primary objective was to assess the positive and negative predictive values, sensitivity, and specificity of achieving a sustained virological response (SVR) at 4 weeks compared to 12 weeks post-therapy. The results demonstrated a maximum sensitivity of 100% for achieving SVR at 12 weeks after reaching SVR at 4 weeks for all analyzed genotypes, except for genotype 1b treated with EBR/GZR therapy, where the specificity was 75%. Additionally, younger age and less advanced liver fibrosis were identified as independent predictors of achieving a sustained virological response at both 4 and 12 weeks. The significant normalization of various biochemical parameters was observed after treatment, indicating an overall improvement in liver function. This study suggests that shortening the monitoring period to 4 weeks might be effective for younger patients without significant fibrosis, potentially reducing loss to follow-up, which is a critical issue in HCV treatment. These findings align with the “test and treat” approach. Further research is needed to confirm these findings and incorporate them into official guidelines, which could simplify and enhance the effectiveness of HCV treatment protocols, aiding global efforts to eliminate HCV as a public health issue by 2030. Full article

(This article belongs to the Special Issue Control and Elimination of Viral Hepatitis)

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7 pages, 430 KiB

Open AccessBrief Report

Insights into Porphyromonas somerae in Bladder Cancer Patients: Urinary Detection by ddPCR

by Filippo Russo, Speranza Esposito, Lorella Tripodi, Savio Domenico Pandolfo, Achille Aveta, Felice Amato, Carmela Nardelli, Ciro Imbimbo, Lucio Pastore and Giuseppe Castaldo

Microorganisms 2024, 12(10), 2049; https://doi.org/10.3390/microorganisms12102049 (registering DOI) - 10 Oct 2024

Abstract

To date, the increased awareness of the impact of microbes on human health has promoted scientific interest in microbiome studies for diagnostic and therapeutic purposes, revealing correlations between specific taxa and cancer. In particular, numerous species of Porphyromonas have been associated with several [...] Read more.

To date, the increased awareness of the impact of microbes on human health has promoted scientific interest in microbiome studies for diagnostic and therapeutic purposes, revealing correlations between specific taxa and cancer. In particular, numerous species of Porphyromonas have been associated with several types of tumors. Previously, we studied the urobiome using Next-Generation Sequencing (NGS), and found an increase in Porphyromonas somerae in first morning urine of subjects affected by bladder cancer (BCa). Here, we aimed to confirm the presence of P. somerae in BCa patients by using droplet digital Polymerase Chain Reaction (ddPCR), testing a cohort of 102 male subjects over 50 years. Our findings showed a significant increase in P. somerae in the urine of the BCa group within both ddPCR and NGS, and a correlation between the two methods was observed at a statistical level. Moreover, P. somerae’s identification with ddPCR confirmed a significant association between this bacterium and the presence of BCa, highlighting its potential role as a biomarker. This allows us to propose the ddPCR as a suitable method for first-stage BCa screening and follow-up. Full article

(This article belongs to the Special Issue Microbiome and Genitourinary Diseases)

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13 pages, 2119 KiB

Open AccessArticle

Isolation of Bacillus altitudinis 5-DSW with Protease Activity from Deep-Sea Mineral Water and Preparation of Functional Active Peptide Fractions from Chia Seeds

by Hao Jin, Eun-Gyo Lee, Faiza Khalid, Seung-Wha Jo and Sang-Ho Baik

Microorganisms 2024, 12(10), 2048; https://doi.org/10.3390/microorganisms12102048 - 10 Oct 2024

Abstract

In this study, we successfully isolated Bacillus strains with high protease activity from deep-sea mineral water in Korea and used them to obtain functional peptide fractions from chia seeds. The obtained Bacillus strains showed a high similarity of 99% with B. altitude with [...] Read more.

In this study, we successfully isolated Bacillus strains with high protease activity from deep-sea mineral water in Korea and used them to obtain functional peptide fractions from chia seeds. The obtained Bacillus strains showed a high similarity of 99% with B. altitude with a long rod type (named B. altitudinis 5-DSW) and high protease activity at 40 °C, and 70% of the activity remained even at 70 °C. The defatted chia seed protein (15–50 kDa) was treated with crude protease from B. altitudinis 5-DSW and digested into small peptides below 20 kDa. The obtained chia seed peptides showed 3 times and 1.5 times higher antioxidant activity in DPPH and ABT radical scavenging assays, respectively. Moreover, chia seed peptides showed enhanced AChE inhibitory activity with an IC₅₀ value of 14.48 ± 0.88 μg/mL and BChE inhibition activity with an IC₅₀ value of 10.90 ± 0.80 μg/mL. Our results indicate that the newly isolated B. altitudinis 5-DSW and chia seed protein hydrolysates have potential applications in biotechnology and functional food development, enhancing the nutritional quality and value-added utilization of chia byproducts. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

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12 pages, 2813 KiB

Open AccessArticle

Epidemiological Evidence for Upper Respiratory Infections as a Potential Risk Factor for Meniere’s Disease: A Korean National Health Sample Cohort Study

by Mi Jung Kwon, Ho Suk Kang, Joo-Hee Kim, Ji Hee Kim, Woo Jin Bang, Dae Myoung Yoo, Na-Eun Lee, Kyeong Min Han, Nan Young Kim, Hyo Geun Choi, Min-Jeong Kim and Eun Soo Kim

Microorganisms 2024, 12(10), 2047; https://doi.org/10.3390/microorganisms12102047 - 10 Oct 2024

Abstract

Meniere’s disease (MD) is a chronic inner ear disorder characterized by tinnitus, ear fullness, episodic vertigo, and fluctuating hearing loss, which significantly impacts quality of life and poses management challenges. Recent evidence suggests that upper respiratory infections (URIs) may contribute to MD’s onset. [...] Read more.

Meniere’s disease (MD) is a chronic inner ear disorder characterized by tinnitus, ear fullness, episodic vertigo, and fluctuating hearing loss, which significantly impacts quality of life and poses management challenges. Recent evidence suggests that upper respiratory infections (URIs) may contribute to MD’s onset. This study examines the potential link between URIs and MD using data from the Korean National Health Insurance Service-National Sample Cohort (2002–2019). We analyzed 19,721 individuals with MD and 78,884 matched controls, adjusting for demographic factors and comorbidities using propensity score matching. Our results showed that individuals with a URI within one year prior to the index date exhibited a 2.01-fold greater likelihood of developing MD (95% confidence interval [CI] = 1.91–2.11, p < 0.001), while those with URIs within two years demonstrated a 1.54-fold higher probability (95% CI = 1.50–1.59, p < 0.001). Furthermore, we found that even remote URIs occurring up to two years before the index date significantly increased the risk of developing MD, underscoring the need for long-term patient follow-up. Overall, our study suggests that individuals with a history of URI may have an elevated risk of developing MD over multiple time frames, regardless of demographic or health profiles. Full article

(This article belongs to the Special Issue Advances in Human Infections and Public Health)

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16 pages, 1104 KiB

Open AccessArticle

Gut Microbiota Alterations in Alzheimer’s Disease: Relation with Cognitive Impairment and Mediterranean Lifestyle

by David Mateo, Nerea Carrión, Cristian Cabrera, Luis Heredia, Montse Marquès, Eva Forcadell-Ferreres, Maria Pino, Josep Zaragoza, Alfons Moral, Lluís Cavallé, José M. González-de-Echávarri, Paloma Vicens, José L. Domingo and Margarita Torrente

Microorganisms 2024, 12(10), 2046; https://doi.org/10.3390/microorganisms12102046 - 10 Oct 2024

Abstract

Recently, an association between dysbiosis of the gut microbiota (GMB) and the development of several diseases, such as Alzheimer’s disease (AD), has been proposed. Dysbiosis involves changes in microbial diversity influenced by environmental factors, like diet or lifestyle. In this study, we investigated [...] Read more.

Recently, an association between dysbiosis of the gut microbiota (GMB) and the development of several diseases, such as Alzheimer’s disease (AD), has been proposed. Dysbiosis involves changes in microbial diversity influenced by environmental factors, like diet or lifestyle. In this study, we investigated the role of GMB parameters in Spanish AD patients, assessing the impact of adherence to the Mediterranean lifestyle (ML), as well as to characterize these parameters in relation to neuropsychological, neuropsychiatric, emotional, and functionality parameters. A case–control study was conducted to investigate the association between the composition of the GMB and cognitive, emotional, neuropsychiatric, and functionality status in Spanish AD patients, along with a shotgun metagenomics approach. Richness and alpha-diversity were significantly lower in the AD group compared to the controls. PERMANOVA and ANOSIM tests of Bray–Curtis dissimilarity, Aitchison distance, and Jaccard similarity did not showed significant differences in beta-diversity between the two groups. Moreover, associations between various phyla of the AD group and orientation performance, food consumption, and activities of daily living were identified. Dysbiosis observed in Spanish AD patients is characterized by reductions in richness and alpha-diversity, alongside alterations in GMB composition, which may be linked to adherence to the ML and cognitive and functionality symptoms. Full article

(This article belongs to the Special Issue Diet, Supplements, Lifestyle and Human Microbiota: Impacts on Health and Disease)

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20 pages, 1654 KiB

Open AccessArticle

Carbohydrate Metabolism Differentiates Pectinatus and Megasphaera Species Growing in Beer

by Manuel J. Arnold, Stefan W. Ritter, Matthias A. Ehrmann, Yohanes N. Kurniawan, Koji Suzuki, Thomas M. Becker and Wolfgang Liebl

Microorganisms 2024, 12(10), 2045; https://doi.org/10.3390/microorganisms12102045 - 10 Oct 2024

Abstract

Obligate anaerobic beer spoilage bacteria have been a menace to the brewing industry for several decades. Technological advances in the brewing process aimed at suppressing aerobic spoilers gave rise to problems with obligate anaerobes. In previous studies, the metabolic spectrum of Pectinatus and [...] Read more.

Obligate anaerobic beer spoilage bacteria have been a menace to the brewing industry for several decades. Technological advances in the brewing process aimed at suppressing aerobic spoilers gave rise to problems with obligate anaerobes. In previous studies, the metabolic spectrum of Pectinatus and Megasphaera species has been described, but their metabolism in the beer environment remains largely unknown. We used high-performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) and headspace solid-phase microextraction–gas chromatography–mass spectrometry (HS-SPME-GCMS) to further characterize beer spoiled by 30 different strains from six beer-spoiling species of Pectinatus and Megasphaera (P. cerevisiiphilus, P. frisingensis, P. haikarae, M. cerevisiae, M. paucivorans, and M. sueciensis). We detected differences in carbohydrate utilization and the volatile organic compounds (volatilome) produced during beer spoilage by all six species. We were able to show that glycerol, one of the basic components of beer, is the common carbon source used by all strains. It appears that this carbon source allows for anaerobic beer spoilage by Pectinatus and Megasphaera despite the spoilage-preventing intrinsic barriers of beer (iso-α-acids, ethanol, low pH, scarce nutrients); thus, extrinsic countermeasures are key for prevention. Full article

(This article belongs to the Section Food Microbiology)

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20 pages, 4758 KiB

Open AccessArticle

Soil Microorganism Interactions under Biological Fumigations Compared with Chemical Fumigation

by Hui Li, Huali Man, Jia Han, Xixia Jia, Li Wang, Hongyu Yang and Guiying Shi

Microorganisms 2024, 12(10), 2044; https://doi.org/10.3390/microorganisms12102044 - 10 Oct 2024

Abstract

Background: Biological fumigation, a potential alternative to chemical fumigation, shows a wide range of prospective applications. In this study, we carried out biological fumigation experiments to evaluate its effect on alleviating consecutive cropping problems (CRPs) when compared with chemical fumigation. Methods: We designed [...] Read more.

Background: Biological fumigation, a potential alternative to chemical fumigation, shows a wide range of prospective applications. In this study, we carried out biological fumigation experiments to evaluate its effect on alleviating consecutive cropping problems (CRPs) when compared with chemical fumigation. Methods: We designed five treatments, namely, CR (no treatment), LN (chemical fumigation with lime nitrogen), Ta (fumigation with marigold), Ra (fumigation with radish), and Br (fumigation with mustard), for soils for replanting eggplant and measured the crop’s growth status, soil bacterial and fungal communities, and soil physicochemical properties. Results: The results showed that the Br and Ra treatments formed similar microbial communities, while the Ta treatment formed unique microbial communities. The genera Olpidiomycota and Rozellomycota could be used as indicator species for the transformation process of soil microbial communities after the Br and Ta treatments, respectively. When compared with the CR and LN treatments, the soil’s physicochemical properties were optimized under the Br treatment, and the soil organic matter content increased by 64.26% and 79.22%, respectively. Moreover, under the Br treatment, the soil’s biological properties enhanced the bacterial and fungal alpha diversity, and the saprotrophic fungi increased with the depletion of pathotrophic fungi, while some specific probiotic microorganisms (such as Olpidiomycota, Microascales, Bacillus, etc.) were significantly enriched. In contrast, under the Ta treatment, soil nutrient levels decreased and the soil’s biological indices deteriorated, whereas the bacterial diversity decreased and the pathogenic fungi increased. Conclusions: Among these three biological fumigation methods, the Br pre-treatment was the best way to alleviate the crop’s CRPs and may be a good substitute for chemical fumigation in some situations. However, the Ta treatment also had some risks, such as the loss of land quality and reduced productivity. Full article

(This article belongs to the Special Issue Insights into Plant–Soil–Microbe Interactions)

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11 pages, 560 KiB

Open AccessArticle

Performance Evaluation of Novaplex^TM Multiplex Real-Time PCR Assay for Detection of Streptococcus agalactiae Serotypes

by Mallikarjun Handigund and Jaehyeon Lee

Microorganisms 2024, 12(10), 2043; https://doi.org/10.3390/microorganisms12102043 - 10 Oct 2024

Abstract

Streptococcus agalactiae, or group B streptococcus (GBS), is a Gram-positive pathogen with an extended track record of colonization in the gastrointestinal and genitourinary tracts. GBS can induce disease in individuals across all age demographics, yet it predominantly triggers infections in neonates and [...] Read more.

Streptococcus agalactiae, or group B streptococcus (GBS), is a Gram-positive pathogen with an extended track record of colonization in the gastrointestinal and genitourinary tracts. GBS can induce disease in individuals across all age demographics, yet it predominantly triggers infections in neonates and the elderly. Identification of the serotype is vital for effective management of the disease as it provides critical information for clinicians on the cause of the disease. In this study, we evaluated the rapid, simple, and easy-to-adopt multiplex real-time PCR technique, Novaplex^TM (NovaPCR). A total of 131 clinical isolates of different serotypes were tested using NovaPCR. Observations revealed that 129 isolates showed the same observations as LA and conventional mPCR. NovaPCR accurately identified serotypes IV and V, which were first classified as serotype Ia in the LA test and mPCR, and the difference between the traditional (LA test and mPCR) and NovaPCR methods is only 1.52%. Accurate serotype identification is helpful for monitoring the epidemics and achieving optimal clinical outcomes, and NovaPCR showed a reliable, fast, easy-to-interpret, and cost-efficient performance in GBS serotyping. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)

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34 pages, 3979 KiB

Open AccessArticle

Cross-Over Application of Algerian Dairy Lactic Acid Bacteria for the Design of Plant-Based Products: Characterization of Weissella cibaria and Lactiplantibacillus plantarum for the Formulation of Quinoa-Based Beverage

by Radjaa Cirat, Zineb Benmechernene, Hülya Cunedioğlu, Mariacinzia Rutigliano, Angela Scauro, Khaled Abderrahmani, Kihal Mebrouk, Vittorio Capozzi, Giuseppe Spano, Barbara la Gatta, Maria Teresa Rocchetti, Daniela Fiocco and Mariagiovanna Fragasso

Microorganisms 2024, 12(10), 2042; https://doi.org/10.3390/microorganisms12102042 - 9 Oct 2024

Abstract

The food industry constantly seeks new starter cultures with superior characteristics to enhance the sensory and overall quality of final products. Starting from a collection of Algerian dairy (goat and camel) lactic acid bacteria, this work focused on the exploration of the technological [...] Read more.

The food industry constantly seeks new starter cultures with superior characteristics to enhance the sensory and overall quality of final products. Starting from a collection of Algerian dairy (goat and camel) lactic acid bacteria, this work focused on the exploration of the technological and probiotic potential of Weissella cibaria (VR81 and LVT1) and Lactiplantibacillus plantarum R12 strains isolated from raw camel milk and fermented milk, respectively. These bioactive strains were selected for their high performance among ten other LAB strains and were used as starter cultures to develop a novel and nutritionally enhanced dairy-like plant-based yogurt using quinoa (Chenopodium quinoa Willd) as a raw matrix. The strains were evaluated for their antagonistic effects against Listeria innocua, Listeria ivanovii, Staphylococcus aureus, Escherichia coli, Salmonella enterica, and Pseudomonas aeruginosa, resilience to acidic and osmotic challenges, and tolerance to gastrointestinal mimicking conditions (i.e., pepsin and bile salt). Their aggregation and adhesion profiles were also analyzed. Furthermore, L. plantarum and W. cibaria were tested in single and co-culture for the fermentation and biocontrol of quinoa. The strains exhibited probiotic properties, including a high potential for biocontrol applications, specifically against L. innocua and P. aeruginosa (20 mm diameter zone with the neutralized cell-free supernatant), which disappeared after protease treatment, suggesting that bioactive peptides might be responsible for the observed antimicrobial effect. Additionally, they demonstrated resilience to acidic (pH 2) and osmotic challenges (1M sucrose), tolerance to gastro-intestinal conditions, as well as good aggregation and adhesion profile. Furthermore, the strains were able to produce metabolites of interest, such as exopolysaccharide (yielding up to 4.7 mg/mL) and riboflavin, reaching considerable production levels of 2.5 mg/L upon roseoflavin selection. The application of W. cibaria and L. plantarum as primary starters (both in single and co-culture) for fermenting quinoa resulted in effective acidification of the matrix (ΔpH of 2.03 units) and high-quality beverage production. in vivo challenge tests against L. innocua showed the complete inhibition of this pathogen when L. plantarum was included in the starter, either alone or in combination with W. cibaria. Both species also inhibited Staphylococcus and filamentous fungi. Moreover, the co-culture of mutant strains of L. plantarum R12d and W. cibaria VR81d produced riboflavin levels of 175.41 µg/100 g in fermented quinoa, underscoring their potential as starters for the fermentation, biopreservation, and biofortification of quinoa while also displaying promising probiotic characteristics. Full article

(This article belongs to the Special Issue Microbial Fermentation, Food and Food Sustainability)

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19 pages, 2595 KiB

Open AccessArticle

Stratification of Gut Microbiota Profiling Based on Autism Neuropsychological Assessments

by Chiara Marangelo, Pamela Vernocchi, Federica Del Chierico, Matteo Scanu, Riccardo Marsiglia, Emanuela Petrolo, Elisa Fucà, Silvia Guerrera, Giovanni Valeri, Stefano Vicari and Lorenza Putignani

Microorganisms 2024, 12(10), 2041; https://doi.org/10.3390/microorganisms12102041 - 9 Oct 2024

Abstract

Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Investigations of gut microbiota (GM) play an important role in deciphering disease severity and symptoms. Overall, we stratified 70 ASD patients by neuropsychological assessment, based on Calibrated Severity Scores (CSSs) of the Autism Diagnostic Observation [...] Read more.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Investigations of gut microbiota (GM) play an important role in deciphering disease severity and symptoms. Overall, we stratified 70 ASD patients by neuropsychological assessment, based on Calibrated Severity Scores (CSSs) of the Autism Diagnostic Observation Schedule-Second edition (ADOS-2), Child Behavior Checklist (CBCL) and intelligent quotient/developmental quotient (IQ/DQ) parameters. Hence, metataxonomy and PICRUSt-based KEGG predictions of fecal GM were assessed for each clinical subset. Here, 60% of ASD patients showed mild to moderate autism, while the remaining 40% showed severe symptoms; 23% showed no clinical symptoms, 21% had a risk of behavior problems and 56% had clinical symptoms based on the CBCL, which assesses internalizing problems; further, 52% had no clinical symptoms, 21% showed risk, and 26% had clinical symptoms classified by CBCL externalizing problems. Considering the total CBCL index, 34% showed no clinical symptoms, 13% showed risk, and 52% had clinical symptoms. Here, 70% of ASD patients showed cognitive impairment/developmental delay (CI/DD). The GM of ASDs with severe autism was characterized by an increase in Veillonella, a decrease in Monoglobus pectinilyticus and a higher microbial dysbiosis index (MDI) when compared to mild-moderate ASDs. Patients at risk for behavior problems and showing clinical symptoms were characterized by a GM with an increase of Clostridium, Eggerthella, Blautia, Intestinibacter, Coprococcus, Ruminococcus, Onthenecus and Bariatricus, respectively. Peptidoglycan biosynthesis and biofilm formation KEGGs characterized patients with clinical symptoms, while potential microbiota-activated PPAR-γ-signaling was seen in CI/DD patients. This evidence derived from GM profiling may be used to further improve ASD understanding, leasing to a better comprehension of the neurological phenotype. Full article

(This article belongs to the Special Issue State of the Art of Gut Microbiota in Italy (2023, 2024))

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21 pages, 301 KiB

Open AccessArticle

Deciphering Hyperammonia-Producing Bacteria (HAB) in the Rumen of Water Buffaloes (Bubalus bubalis) and Their Inhibition through Plant Extracts and Essential Oils

by Yendrembam Mery Chanu, Shyam Sundar Paul, Avijit Dey and Jerome Andonissamy

Microorganisms 2024, 12(10), 2040; https://doi.org/10.3390/microorganisms12102040 - 9 Oct 2024

Abstract

Hyperammonia-producing bacteria (HAB) are a class of microbes present in the stomach of ruminants, responsible for the rapid rate of ammonia production from protein degradation beyond the capacity of these animals for their utilization. Thus, ruminant nutritionists are interested in decreasing ruminal protein [...] Read more.

Hyperammonia-producing bacteria (HAB) are a class of microbes present in the stomach of ruminants, responsible for the rapid rate of ammonia production from protein degradation beyond the capacity of these animals for their utilization. Thus, ruminant nutritionists are interested in decreasing ruminal protein degradation and ammonia genesis by focusing on controlling the activity of HAB. The investigations of the present study were carried out to determine predominant hyperammonia-producing bacteria in the rumen of buffaloes, their isolation and characterization, as well as the inhibition of these isolates with various sources of plant secondary compounds (tannins, saponins, and essential oils). Studies employing high-throughput sequencing of amplicons of the 16S rRNA gene from genomic DNA recovered from enrichment culture of HAB of buffalo rumina indicated that, at the phylum level, Proteobacteria (61.1 to 68.2%) was the most predominant HAB. Acidaminococcus was most predominant among the identified genera. In vitro experiments were conducted with enrichment culture of buffalo rumen contents incubated with different types of feed additives such as essential oils (eucalyptus oil, lemon grass oil, and clove oil) and extracts of plants (Sapindus mukorossi fruits and Ficus bengalensis leaves), each at graded dose levels. The reduction in ammonia production by clove and lemon grass oils was evident due to the presence of major bioactive compounds, especially eugenol and limonene, which have strong antimicrobial activity. However, clove oil and Indian soapberry/reetha (Sapindus mukorossi) fruit were found to be promising and effective in reducing the growth, protease production, and ammonia production of HAB culture. Full article

(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)

13 pages, 883 KiB

Open AccessArticle

An Analytical View on the Use of Flucloxacillin for Outpatient Parenteral Antimicrobial Therapy

by Tam Nguyen, Isabel Spriet, Charlotte Quintens, Lotte Vander Elst, Pham Thi Thanh Ha, Ann Van Schepdael and Erwin Adams

Microorganisms 2024, 12(10), 2039; https://doi.org/10.3390/microorganisms12102039 - 9 Oct 2024

Abstract

Although the addition of buffers provides improved stability to flucloxacillin (FLU) solutions, unbuffered solutions are often preferred in clinical practice. The first purpose of this study was to investigate whether a 50 mg/mL solution of FLU in normal saline is stable for 24 [...] Read more.

Although the addition of buffers provides improved stability to flucloxacillin (FLU) solutions, unbuffered solutions are often preferred in clinical practice. The first purpose of this study was to investigate whether a 50 mg/mL solution of FLU in normal saline is stable for 24 h at 33 °C so that it can be applied for outpatient parenteral antimicrobial therapy (OPAT) using portable elastomeric infusion pumps (PEIPs). When the PEIPs were stored in an oven at 33 °C and deflated over 24 h, the volume of the collected solution, pH, and FLU concentration were checked every 4 h. Obtaining better results than expected based on the literature data, other storage conditions, such as refrigeration, room temperature (RT), 37 °C, refrigeration followed by 24 h at 33 °C and 37 °C, and different batches/brands, were also tested. This study confirmed the pronounced effect of temperature on the stability of FLU and also showed the relationship between the stability of FLU and the initial pH of the solution. FLU was quite stable at refrigeration and RT conditions, with more than 99% and 95% remaining. After 24 h at 33 °C, more than 92% of FLU was still present in the solution, while this number decreased to less than 85% when the storage temperature reached 37 °C. The remaining percentage was found to be even lower when the solution was stored at 2–8 °C for 6 days, followed by 24 h storage at 33 °C or 37 °C, with losses of 17% and 30%, respectively. The stability of FLU became worse when the initial pH of the solution was lower than 5.9 since the concentration of FLU dropped to less than 90% after 24 h at 33 °C, and a precipitate started to form when the initial pH of the solution was around 5.3. Therefore, FLU in PEIPs could be employed for 24 h if the temperature was ideally not more than 33 °C, while the pH should be not less than 5.9 upon reconstituting the FLU solution. Full article

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

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10 pages, 510 KiB

Open AccessArticle

Vector Competence of Aedes aegypti from São Tomé and Príncipe for West Nile Virus Transmission

by Rafael Marmé, Filipe Tomaz, Carla A. Sousa, João Pinto, Gregory C. Lanzaro, Ricardo Parreira and Gonçalo Seixas

Microorganisms 2024, 12(10), 2038; https://doi.org/10.3390/microorganisms12102038 - 9 Oct 2024

Abstract

The global distribution of Aedes aegypti mosquitoes, particularly in tropical regions, poses a significant public health risk due to their apparent ability to transmit arboviruses such as West Nile virus (WNV). This study aimed to evaluate the vector competence of Ae. aegypti from [...] Read more.

The global distribution of Aedes aegypti mosquitoes, particularly in tropical regions, poses a significant public health risk due to their apparent ability to transmit arboviruses such as West Nile virus (WNV). This study aimed to evaluate the vector competence of Ae. aegypti from São Tomé and Príncipe (STP) for the transmission of the WNV PT6.39 strain, considering its potential role as a bridge vector in a region where Culex quinquefasciatus would be the main vector. Aedes aegypti mosquitoes were collected, reared, and experimentally infected with WNV, with viral dissemination and transmission potential assessed 7, 14, and 21 days post infection (dpi). The results showed an increasing trend in infection rates, from 5% at 7 dpi to 35% at 21 dpi, with corresponding dissemination rates of 0%, 100%, and 43%. The transmission rates also increased from 0% at 7 dpi to 67% at 21 dpi, with a maximum transmission efficiency of 10% observed at the final time point. Although Ae. aegypti from STP demonstrated the potential to transmit WNV, the overall transmission efficiency remained relatively low. These findings provide necessary insights into the vector competence of Ae. aegypti in this region, highlighting the importance of continued monitoring and targeted vector control measures to mitigate the risk of potential WNV outbreaks. Full article

(This article belongs to the Special Issue Vector-Borne Zoonoses: Surveillance, Transmission and Interventions)

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13 pages, 9704 KiB

Open AccessArticle

Regulation Effect of Toxocara canis and Anthelmintics on Intestinal Microbiota Diversity and Composition in Dog

by Na Wang, Soben Sieng, Ping Chen, Tian Liang, Jingyun Xu and Qian Han

Microorganisms 2024, 12(10), 2037; https://doi.org/10.3390/microorganisms12102037 - 9 Oct 2024

Abstract

Toxocara canis is an intestinal roundworm that can cause serious zoonotic parasitic diseases. Drontal Plus^® Tasty (Dog) is a kind of commercial drug used to treat T. canis infection. Febantel, Praziquantel, and Pyrantel pamoate (PP) are its main component. However, there are [...] Read more.

Toxocara canis is an intestinal roundworm that can cause serious zoonotic parasitic diseases. Drontal Plus^® Tasty (Dog) is a kind of commercial drug used to treat T. canis infection. Febantel, Praziquantel, and Pyrantel pamoate (PP) are its main component. However, there are few studies investigating the impact of Drontal Plus^® Tasty (Dog) and its primary ingredients on the intestinal microbiota of dogs. In this study, we first collected the intestinal content samples of the dogs which administrated with anthelmintics or saline by sterile catheters, then used 16S rRNA high-throughput sequencing technology combined with a variety of bioinformatic analysis methods to analyze the effect of anthelmintics on intestinal microbiota. First, the results of the

α

and

β

diversity analysis showed that the abundance and diversity of intestinal microbiota decreased with T. canis infection, and increased after anthelmintic treatment. Then, we found the dominant species (the value of relative abundance > 0.05) was both 28 on phylum and genus levels, besides the most dominant species was Bacillota on phylum level and Segatella and Clostridium_sensu_stricto were most dominant on genus level. Futher analyzing the differences in microbiotal composition on phylum level, we found that Drontal Plus^® Tasty treatment could significantly increase the proportion of Bacillota, while Febantel, Praziquantel, or PP could induce the significantly changes of Bacillota and Bacteroidota. In addition, by analyzing the differences in microbiotal composition on genus level, we found that anthelmintic could significantly decreased the relative abundance of Clostridium_sensu_stricto and significantly increased the abundance of Segatella. However, Drontal Plus^® Tasty had no regulatory effect on the abundance of Segatella. In short, these finding showed that various anthelmintics all have significant effects for changing the abundance and diversity of host intestinal microbiota. Full article

(This article belongs to the Special Issue Antimicrobial Resistance Bacteria in Pets, Livestock and Wild Animals)

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14 pages, 1767 KiB

Open AccessReview

Impact of Enteric Nervous Cells on Irritable Bowel Syndrome: Potential Treatment Options

by Ploutarchos Pastras, Ioanna Aggeletopoulou and Christos Triantos

Microorganisms 2024, 12(10), 2036; https://doi.org/10.3390/microorganisms12102036 - 9 Oct 2024

Abstract

Irritable bowel syndrome (IBS) is a condition that significantly impacts the lifestyle, health, and habits of numerous individuals worldwide. Its diagnosis and classification are based on the Rome criteria, updated periodically to reflect new research findings in this field. IBS can be classified [...] Read more.

Irritable bowel syndrome (IBS) is a condition that significantly impacts the lifestyle, health, and habits of numerous individuals worldwide. Its diagnosis and classification are based on the Rome criteria, updated periodically to reflect new research findings in this field. IBS can be classified into different types based on symptoms, each with distinct treatment approaches and some differences in their pathophysiology. The exact pathological background of IBS remains unclear, with many aspects still unknown. Recent research developments suggest that disorders in the brain-gut–microbiota axis are key contributors to the symptoms and severity of IBS. The central nervous system (CNS) interacts bidirectionally with intestinal processes within the lumen and the intestinal wall, with the autonomic nervous system, particularly the vagus nerve, playing an important role. However, the enteric nervous system (ENS) is also crucial in the pathophysiological pathway of IBS. The apeline–corticotropin-releasing factor (CRF)–toll-like receptor 4 (TLR4) signaling route via enteric glia and serotonin production in enteroendocrine cells at the enteric barrier are among the most well-understood new findings that affect IBS through the ENS. Additionally, the microbiota regulates neuronal signals, modifying enteric function by altering the number of enteric bacteria and other mechanisms. Given the limited therapeutic options currently available, it is essential to identify new treatment targets, with the brain-gut axis, particularly the enteric nervous system, being a promising focus. This study aims to delineate the molecular mechanisms that induce IBS and to suggest potential targets for future research and treatment of this potentially debilitating disease. Full article

(This article belongs to the Special Issue Gut Microbiota, Diet, and Gastrointestinal Cancer)

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17 pages, 13371 KiB

Open AccessArticle

Laboratory-Simulated Inhibitory Effects of the Floating-Bed Plants on Microcystis aeruginosa and Their Microbial Communities’ Responses to Microcystins

by Shuwen Zhang, Yuanpu Sha, Yuanyuan Tang, Longjie Li, Feihu Wang, Jing Dong, Xuejun Li, Yunni Gao, Xiaofei Gao, Huatao Yuan and Jingxiao Zhang

Microorganisms 2024, 12(10), 2035; https://doi.org/10.3390/microorganisms12102035 - 9 Oct 2024

Abstract

Three common floating bed plants, Eichhornia crassipes, Pistia stratiotes, and Ipomoea aquatica, were selected in the present study to investigate their inhibitory effects on toxic Microcystis aeruginosa. The results showed that all three types of floating-bed plants could considerably [...] Read more.

Three common floating bed plants, Eichhornia crassipes, Pistia stratiotes, and Ipomoea aquatica, were selected in the present study to investigate their inhibitory effects on toxic Microcystis aeruginosa. The results showed that all three types of floating-bed plants could considerably inhibit the growth of M. aeruginosa and effectively remove the microcystins (MCs) from water systems, among which, E. crassipes and P. stratiotes were more effective in resisting M. aeruginosa, and the removal rate of the intracellular MCs could be up to 100%. In addition, the roots and leaves of the three plants were enriched with a large number of MCs and demonstrated significant antioxidant responses, as evidenced by the increase in the content of catalase (CAT), glutathione peroxidase (GSH-PX), superoxide dismutase (SOD), and malondialdehyde (MDA) in the roots, stems, and leaves of the plants. Furthermore, this study also showed that Proteobacteria, Bacteroidota, Myxococcota, Verrucomicrobiota, and Actinobacteriota dominated the root microorganisms of the three plants. Moreover, a variety of MC-degrading bacteria, including Sphingomonas, Acinetobacter, Novosphingobium, and Pseudomonas, were found at the genus level, which further provides important basic data for the regulation of eutrophic water bodies and the removal of MCs. Full article

(This article belongs to the Section Environmental Microbiology)

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11 pages, 1995 KiB

Open AccessArticle

Are Changes Occurring in Bacterial Taxa Community and Diversity with the Utilization of Different Substrates within SIR Measurements?

by Yosef Steinberger, Tirza Doniger, Itaii Applebaum and Chen Sherman

Microorganisms 2024, 12(10), 2034; https://doi.org/10.3390/microorganisms12102034 - 9 Oct 2024

Abstract

This research explores how the availability of substrates affects the regulation of soil microbial communities and the taxonomical composition of bacteria. The goal is to understand the impact of organic matter and substrate availability and quality on the diversity of soil bacteria. The [...] Read more.

This research explores how the availability of substrates affects the regulation of soil microbial communities and the taxonomical composition of bacteria. The goal is to understand the impact of organic matter and substrate availability and quality on the diversity of soil bacteria. The study observed gradual changes in bacterial diversity in response to the addition of different substrate-induced respiration (SIR) substrates. Understanding the structure, dynamics, and functions of soil microbial communities is essential for assessing soil quality in sustainable agriculture. The preference for carbon sources among bacterial phyla is largely influenced by their life history and trophic strategies. Bacterial phyla like Proteobacteria, Bacteroidetes, and Actinobacteria, which thrive in nutrient-rich environments, preferentially utilize glucose. On the other hand, oligotrophic bacterial phyla such as Acidobacteria or Chloroflexi, which are found in lower numbers, have a lower ability to utilize labile C. The main difference between the two lies in their substrate utilization strategies. Understanding these distinct strategies is crucial for uncovering the bacterial functional traits involved in soil organic carbon turnover. Additionally, adding organic matter can promote the growth of copiotrophic bacteria, thus enhancing soil fertility. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)

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