Microbiology Research

11 pages, 9223 KiB

Open AccessCommunication

Scanning Electron Microscopy Analysis of Biofilm-Encased Bacteria Exposed to Cuprous Oxide-Impregnated Wound Dressings

by Tohar Roth, Einat Zelinger, Tally Kossovsky and Gadi Borkow

Microbiol. Res. 2024, 15(4), 2358-2368; https://doi.org/10.3390/microbiolres15040158 - 22 Nov 2024

Microbial infections in wounds can significantly delay the healing process, with bacteria often forming protective biofilms that shield them from external threats. In this study, we evaluated the impact of copper oxide-impregnated wound dressings (referred to as COD) on a bacterial mixture comprising [...] Read more.

Microbial infections in wounds can significantly delay the healing process, with bacteria often forming protective biofilms that shield them from external threats. In this study, we evaluated the impact of copper oxide-impregnated wound dressings (referred to as COD) on a bacterial mixture comprising common Gram-positive and Gram-negative wound pathogens encased in biofilm. The bacterial mix was exposed to COD or control dressings for 0, 1, 2, and 3 h, and the effects were analyzed using scanning electron microscopy. After just 1 h of exposure to COD, notable leakage of bacterial cytoplasmic contents was observed. By the 3 h mark, the Gram-negative bacteria exhibited a formation of holes in their cell walls, while Gram-positive bacteria showed a reduction in cell width. These findings demonstrate the ability of COD to effectively kill bacteria even when protected by biofilm, supporting clinical observations of its efficacy in managing infected wounds. Full article

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17 pages, 2864 KiB

Open AccessArticle

A Metabarcoding Approach for Investigating the Stomach Microbiota of the Corallivorous Snail Coralliophila meyendorffii (Muricidae, Coralliophilinae) and Its Venomous Host, the Sea-Anemone Parazoanthus axinellae (Zoanthidea, Parazoanthidae)

by Chiara Benvenuti, Giulia Fassio, Valeria Russini, Maria Vittoria Modica, Marco Oliverio, Domenico Davolos and Elisa Nocella

Microbiol. Res. 2024, 15(4), 2341-2357; https://doi.org/10.3390/microbiolres15040157 - 21 Nov 2024

Abstract

The corallivorous snails Coralliophila meyendorffii and its coral host Parazoanthus axinellae are appealing candidates for studying symbiotic interactions at the microbiome level. In this study, we investigated for the first time the microbial community in the stomach of C. meyendorffii and in the [...] Read more.

The corallivorous snails Coralliophila meyendorffii and its coral host Parazoanthus axinellae are appealing candidates for studying symbiotic interactions at the microbiome level. In this study, we investigated for the first time the microbial community in the stomach of C. meyendorffii and in the polyps of its coral host P. axinellae using as markers multiple regions of the 16S rRNA gene. The bacterial community in the stomach of another corallivorous snail, Babelomurex cariniferus, that feeds on Cladocora hexacorals, was also investigated for comparison. The obtained results indicated the phylum Proteobacteria as the most abundant among the analysed samples, with Alphaproteobacteria and Gammaproteobacteria as the main classes. Among the investigated communities, some bacterial taxa were recognised in line with previous findings in the microbiota of marine invertebrates. As both organisms are exposed to the same bacteria in their habitats, this might suggest shared environmental influences for their microbiota composition. Most of the detected taxa found exclusively or predominantly in P. axinellae samples suggest the presence of holobiont components within the microbial community of this coral, mirroring those identified in other corals, while the stomach microbiome of C. meyendorffii did not indicate a primary role in parasitism. Finally, we provide evidence that many of these bacterial taxa are horizontally transferred between Parazohantus and Corallliophila. Full article

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11 pages, 386 KiB

Open AccessArticle

Effect of an Add-On Multi-Strain Probiotic Formulation in the Prevention of Recurrent Urinary Tract Infections: A Double-Blind Randomized Placebo-Controlled Trial

by Archana Mishra, Saubhagya Kumar Jena, Anand Srinivasan, Amruta Tripathy, Rituparna Maiti and Debasish Hota

Microbiol. Res. 2024, 15(4), 2330-2340; https://doi.org/10.3390/microbiolres15040156 - 16 Nov 2024

Abstract

Urinary tract infections (UTIs) present a significant health challenge for women globally, particularly due to high recurrence rates. This randomized, double-blinded, placebo-controlled study conducted at AIIMS Bhubaneswar, India, evaluated the effectiveness of a multi-strain lactobacilli probiotic formulation as an adjunct to standard antibiotic [...] Read more.

Urinary tract infections (UTIs) present a significant health challenge for women globally, particularly due to high recurrence rates. This randomized, double-blinded, placebo-controlled study conducted at AIIMS Bhubaneswar, India, evaluated the effectiveness of a multi-strain lactobacilli probiotic formulation as an adjunct to standard antibiotic therapy in preventing recurrent UTIs. Fifty-one adult women (18–50 years) with recurrent UTIs received either the probiotic or a placebo for 24 weeks. The primary outcome was UTI recurrence, while secondary outcomes included the number of UTI episodes and changes in urinary nerve growth factor (NGF) and serum macrophage colony-stimulating factor (M-CSF) levels. The results showed a significant reduction in UTI recurrence in the probiotic group, with 75% remaining recurrence-free, compared to 33% in the placebo group (p = 0.007). The relative risk for recurrence absence was 2.67 (95% CI: 1.19–5.99). Although the mean number of UTI episodes decreased in the probiotic group, the difference was not statistically significant (p = 0.379). The urinary NGF and serum M-CSF levels significantly decreased from baseline in both groups, but there were no significant differences between them. This study suggests probiotics may be a valuable adjunct therapy for preventing recurrent UTIs. Full article

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14 pages, 3495 KiB

Open AccessArticle

A Target to Combat Antibiotic Resistance: Biochemical and Biophysical Characterization of 3-Dehydroquinate Dehydratase from Methicillin-Resistant Staphylococcus aureus

by Alfredo Téllez-Valencia, Jesús Oria-Hernández, Adriana Castillo-Villanueva, Erick Sierra-Campos, Mónica Valdez-Solana, Jorge Cisneros-Martínez and Claudia Avitia-Domínguez

Microbiol. Res. 2024, 15(4), 2316-2329; https://doi.org/10.3390/microbiolres15040155 - 13 Nov 2024

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is associated with the acquisition of nosocomial infections, community-acquired infections, and infections related to livestock animals. In the pursuit of molecular targets in the development process of antibacterial drugs, enzymes within the shikimate pathway, such as 3-dehydroquinate dehydratase (DHQD), [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) is associated with the acquisition of nosocomial infections, community-acquired infections, and infections related to livestock animals. In the pursuit of molecular targets in the development process of antibacterial drugs, enzymes within the shikimate pathway, such as 3-dehydroquinate dehydratase (DHQD), are regarded as promising targets. Therefore, through biochemical and biophysical techniques, in the present work, the characterization of DHQD from MRSA (SaDHQD) was performed. The kinetic results showed that the enzyme had a V_max of 107 μmol/min/mg, a K_m of 54 μM, a k_cat of 48 s⁻¹, and a catalytic efficiency of 0.9 μM⁻¹ s⁻¹. Within the biochemical parameters, the enzyme presented an optimal temperature of 55 °C and was thermostable at temperatures from 10 to 20 °C, being completely inactivated at 60 °C in 10 min. Furthermore, SaDHQD showed an optimal pH of 8.0 and was inactivated at pH 4.0 and 12.0. Moreover, the activity of the enzyme was affected by the presence of ions, surfactants, and chelating agents. The thermodynamic data showed that the rate of inactivation of the enzyme was a temperature-dependent process. Furthermore, the enthalpy change, entropy change, and Gibbs free energy change of inactivation were positive and practically constant, which suggested that the inactivation of SaDHQD by temperature was driven principally by enthalpic contributions. These results provide, for the first time, valuable information that contributes to the knowledge of this enzyme and will be useful in the search of SaDHQD inhibitors that can serve as leads to design a new drug against MRSA to combat antibiotic resistance. Full article

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18 pages, 5626 KiB

Open AccessArticle

Bacterial Degradation of Ibuprofen: Insights into Metabolites, Enzymes, and Environmental Fate Biodegradation of Ibuprofen by Achromobacter Species

by Nashwa A. H. Fetyan, Ayan A. Asair, Ismail M. Ismail, Tamer A. Elsakhawy, Sherif M. Elnagdy and Mahmoud S. M. Mohamed

Microbiol. Res. 2024, 15(4), 2298-2315; https://doi.org/10.3390/microbiolres15040154 - 11 Nov 2024

Abstract

In recent years, pharmaceuticals have emerged as pollutants due to their incomplete degradation in sewage treatment plants and their ability to cause physiological problems in humans even at low doses. Understanding the environmental fate of pharmaceutical pollutants and the mechanisms involved in their [...] Read more.

In recent years, pharmaceuticals have emerged as pollutants due to their incomplete degradation in sewage treatment plants and their ability to cause physiological problems in humans even at low doses. Understanding the environmental fate of pharmaceutical pollutants and the mechanisms involved in their degradation is crucial for developing strategies to mitigate their impact on ecosystems and human health. In this study, the degradation of pharmaceutical compound ibuprofen was achieved by employing two bacterial strains, Achromobacter spanius strain S11 and Achromobacter piechaudii S18, previously isolated from contaminated water. These strains were capable of degrading ibuprofen as their sole carbon source. The study aimed to identify intermediate metabolites, determine the enzymes involved, and detect specific genes related to ibuprofen degradation. Different concentrations of ibuprofen, temperatures, and pH levels were tested. Both A. spanius S11 and A. piechaudii S18 successfully degraded ibuprofen. A. spanius S11 showed a degradation efficiency of 91.18% after only 72 h and reached 95.7% after 144 h, while A. piechaudii S18 exhibited degradation efficiencies of 72.39% and 73.01% after three and seven days, respectively. The LC-MS technique was used to identify biodegradation metabolites produced by A. spanius S11. The results indicated that the first step was hydroxylation followed by oxidation via the combination of monooxygenases that catalyze the C-H hydroxylation and dehydrogenases. Furthermore, the detection of intermediate metabolites of trihydroxyibuprofen suggested that the biodegradation of ibuprofen by A. spanius S11 can occur through multiple mechanisms. The highest enzyme activities were recorded for catechol 1,2-dioxygenase, 4.230 ± 0.026 U/mg, followed by laccase, 2.001 ± 0.215 U/mg. This study demonstrates the potential of Achromobacter strains, particularly A. spanius (S11), in degrading ibuprofen. These findings provide insights into the ibuprofen degradation process, intermediate metabolites, and relevant genes. Full article

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12 pages, 1392 KiB

Open AccessArticle

Extended-Spectrum Beta-Lactamase-Producing and Multidrug-Resistant Escherichia coli and Klebsiella spp. from the Human–Animal–Environment Interface on Cattle Farms in Burkina Faso

by Djifahamaï Soma, Isidore Juste Ouindgueta Bonkoungou, Zakaria Garba, Fatimata Bintou Josiane Diarra, Namwin Siourimè Somda, Marguerite Edith Malatala Nikiema, Evariste Bako, Souleymane Sore, Natéwindé Sawadogo, Nicolas Barro and Kaisa Haukka

Microbiol. Res. 2024, 15(4), 2286-2297; https://doi.org/10.3390/microbiolres15040153 - 11 Nov 2024

Abstract

Extended-spectrum beta-lactamase (ESBL)-producing and multidrug-resistant Enterobacterales pose a major threat to both human and animal health. This study assessed the prevalence of ESBL-producing Escherichia coli (ESBL-Ec) and Klebsiella spp. (ESBL-K) on cattle farms in Ouagadougou, Burkina Faso, using a [...] Read more.

Extended-spectrum beta-lactamase (ESBL)-producing and multidrug-resistant Enterobacterales pose a major threat to both human and animal health. This study assessed the prevalence of ESBL-producing Escherichia coli (ESBL-Ec) and Klebsiella spp. (ESBL-K) on cattle farms in Ouagadougou, Burkina Faso, using a One Health approach. From May 2021 to September 2022, cattle faeces, farmers’ stools, their drinking water and farm soil samples were collected from semi-intensive and traditional farms. An ESBL-selective medium was used to obtain resistant isolates, which were further characterised using biochemical tests. Antimicrobial susceptibility testing was performed using the Kirby–Bauer disc diffusion method. ESBL-Ec and/or ESBL-K were detected in 188 of 322 samples (58.0%). The prevalence of ESBL-Ec isolates was 42.2% (136/322) and that of ESBL-K isolates was 24.5% (79/322). Notably, 156 of the 188 ESBL isolates (83.0%) exhibited multidrug resistance. The highest resistance rates were observed against tetracycline and cotrimoxazole. Importantly, no isolates showed resistance to meropenem, which was used to test for carbapenem resistance. This study highlights the presence of ESBL-Ec and ESBL-K among the humans, animals and environment of the cattle farms. Good hygiene and biosafety practices are essential to limit the potential spread of multidrug-resistant bacteria between different interfaces on farms. Full article

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12 pages, 2937 KiB

Open AccessArticle

Isolation and Molecular Characterization of Corynebacterium pseudotuberculosis from Goats in Andaman and Nicobar Islands, India

by Jai Sunder, Arun Kumar De, Tamilvanan Sujatha, Gayatri Chakraborty, Srikoti Chandershekhar Mayuri, Debasis Bhattacharya, Rafeeque Rahman Alyethodi and Eaknath Bhanudasrao Chakurkar

Microbiol. Res. 2024, 15(4), 2274-2285; https://doi.org/10.3390/microbiolres15040152 - 8 Nov 2024

Abstract

Caseous lymphadenitis (CLA), caused by the bacteria Corynebacterium pseudotuberculosis, is a highly contagious disease of small ruminants, especially of goats and sheep. Here, we report an outbreak of the disease in goats for the first time from the Andaman and Nicobar Islands [...] Read more.

Caseous lymphadenitis (CLA), caused by the bacteria Corynebacterium pseudotuberculosis, is a highly contagious disease of small ruminants, especially of goats and sheep. Here, we report an outbreak of the disease in goats for the first time from the Andaman and Nicobar Islands along with isolation and molecular characterization of the pathogen. A total of 22 goats were affected, with an attack rate of 12.02%, and six isolates were identified from the clinical samples. Molecular characterization of the pathogen was carried out based on the sequence information of 16S rRNA and RNA polymerase β subunit (rpoB) gene fragments. rpoB-based phylogenetic analysis indicated that the isolates belonged to Corynebacterium pseudotuberculosis biovar ovis. The antimicrobial resistance study revealed that the isolates were 100% resistant against erythromycin and rifampicin. Fifty percent resistance was found against amoxicillin/clavulanic acid, ciprofloxacin, penicillin, and vancomycin. All the isolates were sensitive to tetracycline, chloramphenicol, cotrimoxazole, sulphafurazole, ampicillin/cloxacillin, and oxytetracycline. In conclusion, the present study reports the occurrence of CLA in goats for the first time from an isolated archipelago of India and unveils the molecular signature and antibiotic resistance patten of the pathogen. The findings of this study will be helpful to control or eradicate the disease from the Andaman and Nicobar Islands. Full article

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13 pages, 13195 KiB

Open AccessArticle

Biological Strategies to Minimize Fertilizer Use in Maize: Efficacy of Trichoderma harzianum and Bacillus subtilis

by Dalilla Berlanda de Lima Gonilha, Carlos Henrique Barbosa Santos, Edvan Teciano Frezarin, Josiane Soares Siqueira and Everlon Cid Rigobelo

Microbiol. Res. 2024, 15(4), 2261-2273; https://doi.org/10.3390/microbiolres15040151 - 4 Nov 2024

Abstract

The present study investigated the efficacy of Trichoderma harzianum and Bacillus subtilis in minimizing phosphorus fertilizer use in maize cultivation. Maize plants, cultivar Bm207, were subjected to 10 treatments with varying levels of phosphorus fertilization (0, 50, and 100%) and inoculation with B. [...] Read more.

The present study investigated the efficacy of Trichoderma harzianum and Bacillus subtilis in minimizing phosphorus fertilizer use in maize cultivation. Maize plants, cultivar Bm207, were subjected to 10 treatments with varying levels of phosphorus fertilization (0, 50, and 100%) and inoculation with B. subtilis, T. harzianum, or both. The plant growth parameters, including the height, stem diameter, shoot, and root dry weight, root volume, phosphorus content in the soil and plant tissues, and chlorophyll and carotenoid content, were evaluated. Treatments without mineral fertilization showed the lowest values for most parameters, despite the microbial inoculation. The combination of 100% mineral fertilizers with microbes did not improve the plant growth compared with the controls. However, the treatments with 50% mineral fertilization along with microbial inoculation generally maintained parameter values similar to those of the 100% fertilized control, suggesting the potential for reducing fertilizer doses by 50% without compromising plant development. Inoculation with B. subtilis and T. harzianum coupled with the use of mineral fertilizers improved the soil phosphorus availability compared to fertilizer application alone. This study highlights the potential of these microorganisms to enhance soil fertility and plant growth while reducing chemical fertilizer use in maize cultivation, although further field research is necessary to verify the long-term sustainability of this approach. Full article

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14 pages, 1421 KiB

Open AccessArticle

Enteroviruses, Respiratory Syncytial Virus and Seasonal Coronaviruses in Influenza-like Illness Cases in Nepal

by Sanjaya K. Shrestha, Jasmin Shrestha, Binob Shrestha, Tor A. Strand, Susanne Dudman, Ashild K. Andreassen, Shree Krishna Shrestha, Anup Bastola, Prativa Pandey and Stefan Fernandez

Microbiol. Res. 2024, 15(4), 2247-2260; https://doi.org/10.3390/microbiolres15040150 - 31 Oct 2024

Abstract

Acute respiratory infection is one of the leading causes of morbidity and mortality among children in low- and middle-income countries. Due to limited diagnostic capability, many respiratory pathogens causing influenza-like illness go undetected. This study aims to detect enterovirus, respiratory syncytial virus, seasonal [...] Read more.

Acute respiratory infection is one of the leading causes of morbidity and mortality among children in low- and middle-income countries. Due to limited diagnostic capability, many respiratory pathogens causing influenza-like illness go undetected. This study aims to detect enterovirus, respiratory syncytial virus, seasonal coronavirus and respiratory pathogens other than influenza in patients with influenza-like illness. A total of 997 (54.3%) respiratory samples (collected in the years 2016–2018) were randomly selected from 1835 influenza-negative samples. The xTAG Respiratory Viral Panel (RVP) FAST v2 panel was used to detect respiratory pathogens including enterovirus/rhinovirus (EV/RV), respiratory syncytial virus (RSV) and seasonal coronavirus (HKU1, OC43, NL63 and 229E). A total of 78.7% (785/997) were positive for respiratory viruses. Of these viruses, EV/RV was detected in 36.3% (362/997), which is the highest number, followed by RSV in 13.7% (137/997). The seasonal coronaviruses HKU1 and OC43 (1.5%, 15/997), NL63 (1.2%, 12/997) and 229E (1%, 10/997) were also detected. The EV/RV-positive samples were sequenced, of which 16.7% (5/30) were confirmed as EVs and were identified as coxsackievirus (CV) types CVB5, CVB3, CV21 and CVB2. The findings of this study highlight the importance of strengthening influenza-like illness surveillance programs in the region by including other respiratory viruses in their scope besides seasonal human influenza viruses. Full article

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15 pages, 4006 KiB

Open AccessArticle

Dietary Mycotoxins Effects on Nile Tilapia (Oreochromis niloticus) Microbiomes Can Be Mitigated with Addition of Organically Modified Clinoptilolites

by Wanvisa Hussein, Paulina Cholewińska, Konrad Wojnarowski, Natalia Szeligowska, Fangyuan Hu, Monika Greguła-Kania, Jiraporn Rojtinnakorn and Dušan Palić

Microbiol. Res. 2024, 15(4), 2232-2246; https://doi.org/10.3390/microbiolres15040149 - 31 Oct 2024

Abstract

Mechanisms of action attributed to feed additives are of continuous research interest, increasing our knowledge about the side effects (direct or indirect) of their application. The primary role of organically modified clinoptilolite is to bind multiple polar and non-polar mycotoxins contaminating the feed [...] Read more.

Mechanisms of action attributed to feed additives are of continuous research interest, increasing our knowledge about the side effects (direct or indirect) of their application. The primary role of organically modified clinoptilolite is to bind multiple polar and non-polar mycotoxins contaminating the feed and remove them during the digestion process and through feces, therefore preventing adsorption and consequences of mycotoxicosis on fish health. However, it is not fully understood if this binding action can influence bacterial communities in the fish digestive tract and possibly other organs, as well as the aquatic environment. Therefore, in this study, Nile tilapias (Oreochromis niloticus) (average weight: 30 ± 2 g; n = 48) were simultaneously exposed to low-level mycotoxins (AFB1 40 µg/kg, FB 600 µg/kg, ZEN 50 µg/kg, and DON 150 µg/kg) added to diet, with and without supplementation of commercially available organically modified clinoptilolite feed additive (MinazelPlus^®, 2 g/kg). After 42 days of continuous exposure, gill tissue, feces, and water were collected, and DNA was extracted from the samples. Results of RT-PCR analysis have revealed significant changes in microbiomes in fish from different groups, most prominently in mycotoxin-exposed fish. No significant changes were detected in water samples between the control and MinazelPlus^® groups, confirming the safety of MinazelPlus^® for aquatic microbial communities. MinazelPlus^® addition to the mycotoxin spiked diet, stabilized fish natural microbiota, and prevented the disbalance of microbial homeostasis observed in fish exposed to dietary mycotoxins. Full article

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22 pages, 2385 KiB

Open AccessArticle

Dietary Administration Effects of Microbial Exopolysaccharide from Bacillus subtilis P1 on Growth Performance and Immunity in Nile Tilapia (Oreochromis niloticus)

by Kannika Bunkaew, Auraiwan Yenraksa, Akkanee Pewhom, Suphada Kiriratnikom, Mariya Sewaka, Monthon Lertworapreecha and Wankuson Chanasit

Microbiol. Res. 2024, 15(4), 2210-2231; https://doi.org/10.3390/microbiolres15040148 - 28 Oct 2024

Abstract

Exopolysaccharide (EPS)-producing bacteria were isolated from the intestines of freshwater fish as prebiotics. Among the isolates, Bacillus sp. P1 was the potent EPS producer, with a high EPS production, and was then identified as Bacillus subtilis P1 based on 16S rRNA and biochemical [...] Read more.

Exopolysaccharide (EPS)-producing bacteria were isolated from the intestines of freshwater fish as prebiotics. Among the isolates, Bacillus sp. P1 was the potent EPS producer, with a high EPS production, and was then identified as Bacillus subtilis P1 based on 16S rRNA and biochemical characteristics. The produced microbial EPS was characterized by its functional groups by FTIR, showing a 90.20% correlation to inulin, while the EPS molecular weight was approximately 10⁵ Da with a high PDI (>1.5). Moreover, the EPS from B. subtilis P1 was assessed for prebiotic properties by growing probiotic bacteria, and significant cell growth occurred in sugar-free TSB with 0.5% EPS (p < 0.05). EPS exhibited approximately 55.37% DPPH radical scavenging at 20 mg/mL and inhibited certain fish pathogens at 400 μg/mL (10–13 mm inhibition zone). Low EPS cytotoxicity was confirmed (<1% hemolysis) prior to use as immunobiotics in Nile Tilapia (Oreochromis niloticus) diet supplementation. Nile tilapia growth and immune response were monitored after feeding with control (C), basal diet (BD), and treatment (T): BD + EPS 5 g/kg. In the T-group, the weight gain (WG), % specific growth rate (SGR), and average daily gain (ADG) significantly increased compared to the control (p < 0.05) by week 4, with no negative effects on blood chemistry parameters. Lysozyme activity and respiratory burst activity in T-groups were significantly higher than the control (p < 0.05), with a 50% RLP survival rate of Nile Tilapia infected by Aeromonas veronii in the T-group after a two-week challenge. On the other hand, the proximate analysis revealed higher protein content in the T-group. These findings suggest that EPS from B. subtilis P1 in fish diets efficiently supports fish growth and stimulates innate immune response in Nile Tilapia, thus showing potential as the immunobiotics for aquaculture. Full article

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11 pages, 538 KiB

Open AccessReview

Alteration of the Intestinal Bacterial Community in Rainbow Trout (Oncorhynchus mykiss): The Role of Animal, Plant, and Microbial Diets

by Aleksandra S. Chervochkina, Nadezhda O. Pastukhova and Andrey S. Aksenov

Microbiol. Res. 2024, 15(4), 2199-2209; https://doi.org/10.3390/microbiolres15040147 - 26 Oct 2024

Abstract

Intestinal bacterial community in rainbow trout (Oncorhynchus mykiss) is increasingly recognized as important for aquaculture and fish health. This review summarizes the current knowledge on how various feed components, including animal- and plant-derived ingredients, as well as other feed additives, influence [...] Read more.

Intestinal bacterial community in rainbow trout (Oncorhynchus mykiss) is increasingly recognized as important for aquaculture and fish health. This review summarizes the current knowledge on how various feed components, including animal- and plant-derived ingredients, as well as other feed additives, influence the gut microbiota of rainbow trout. Studies using 16S rRNA gene profiling and metagenomics demonstrate how dietary changes affect the composition, diversity, and functionality of bacterial communities. The findings suggest that there is no single optimal alternative ingredient for fish feeds, but emphasize that the ratio of natural components plays a more significant role in shaping the intestinal bacterial community of trout. This balance is crucial for maintaining diversity, functionality, and overall fish health, thereby promoting growth and disease resistance, while enhancing aquaculture efficiency. The use of popular animal protein derived from the larva of Hermetia illucens increases the amount of Pseudomonadota, but the chitin they contain can prevent the absorption of nutrients. Thus, the development of optimal feed formulas requires careful selection and balancing of various natural ingredients to sustain a healthy microbiota and overall fish well-being. Full article

(This article belongs to the Special Issue Veterinary Microbiology and Diagnostics)

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15 pages, 1369 KiB

Open AccessArticle

Blood Parasites (Haemosporida, Trypanosomatida) in Culex pipiens: A Study and Review of Hibernating and Active Mosquitoes

by Kristina Valavičiūtė-Pocienė, Margarita Kazak, Tatjana Iezhova, Gabrielė Kalinauskaitė and Rasa Bernotienė

Microbiol. Res. 2024, 15(4), 2184-2198; https://doi.org/10.3390/microbiolres15040146 - 25 Oct 2024

Abstract

Culex pipiens mosquitoes (Diptera: Culicidae) are widespread during warm periods and actively feed on blood while serving as vectors for various human and animal pathogens. Culex mosquitoes overwinter as adults in temperate zones, raising the question of whether hibernating Cx. pipiens can act [...] Read more.

Culex pipiens mosquitoes (Diptera: Culicidae) are widespread during warm periods and actively feed on blood while serving as vectors for various human and animal pathogens. Culex mosquitoes overwinter as adults in temperate zones, raising the question of whether hibernating Cx. pipiens can act as pathogen reservoirs. In this study, hibernating mosquitoes and mosquitoes collected during the warm season were tested for the presence of trypanosomatids and avian haemosporidian parasites using PCR. Midgut preparations were made from Cx. pipiens females in order to search for trypanosomatids morphologically. In total, 1037 Cx. pipiens mosquitoes (556 collected during the warm season and 481 overwintering mosquitos) were investigated. The parasite prevalence differed for mosquitoes collected during the warm season and hibernating ones for both Haemosporida (2.9% in warm-season and no infections in overwintering mosquitoes) and Trypanosomatida (1.6% and 0.4%, respectively) parasites. A phylogenetic analysis confirmed that the trypanosomatids found in hibernating mosquitoes were monoxenous and were not parasites of vertebrates. The peak prevalence of Haemosporida parasites was detected in July (4.9%) and August (2.8%), and for Trypanosomatida, it was detected in May (3.5%). The results of the present study show that overwintering Cx. pipiens mosquitoes are questionable reservoirs for avian haemosporidian parasites, but some monoxenous trypanosomatids can be found in overwintering females. Full article

(This article belongs to the Special Issue Veterinary Microbiology and Diagnostics)

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22 pages, 2073 KiB

Open AccessReview

Algorithms for Effector Prediction in Plant Pathogens and Pests: Achievements and Current Challenges

by César De los Santos-Briones, Karla Gisel Carreón-Anguiano, Sara E. Vila-Luna, Jewel Nicole Anna Todd, Ignacio Islas-Flores, Luis Sáenz-Carbonell, Pablo Alejandro Gamas-Trujillo and Blondy Canto-Canché

Microbiol. Res. 2024, 15(4), 2162-2183; https://doi.org/10.3390/microbiolres15040145 - 24 Oct 2024

Abstract

Effectors are key organism-associated molecules that aid in the establishment of interactions with other organisms. Effectoromics has become an important area of research in phytopathology. The lack of sequence conservation among effectors, even in closely related organisms, has led us to believe that [...] Read more.

Effectors are key organism-associated molecules that aid in the establishment of interactions with other organisms. Effectoromics has become an important area of research in phytopathology. The lack of sequence conservation among effectors, even in closely related organisms, has led us to believe that effectors from organisms of different kingdoms are completely unrelated, which has fostered the independent development of effector identification strategies in bacteria, fungi, phytoplasmas, etc. This review focuses on the different algorithms available for effector identification in different plant pathogens and pests, using the following classification: (1) translocated effectors (bacteria, oomycete) and (2) secreted effectors (phytoplasmas, fungi, insects, nematodes). The objective of this type of classification is to identify, for the first time, the common features that exist among these organisms to streamline future effectoromics identification strategies. Among the organisms’ commonalities, certain bacteria, fungi, phytoplasmas, and nematodes may cause similar symptoms, and some of their effectors may target the same proteins or biological processes in the plant hosts. The integration of effector analyses of organisms of different living kingdoms, through the identification of common short linear motifs, domains, and three-dimensional structures, may aid in the development of novel algorithms for effectoromics. Future algorithms may contemplate these highlighted features and will be better equipped to identify not only canonical effectors but highly elusive non-canonical effectors as well. Full article

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16 pages, 1606 KiB

Open AccessReview

Fungal Extracellular Vesicles: Isolation, Characterization, and the Immune System Response

by Marcelo Augusto Kazuo Ikeda, Renato Massis Souza Campos, Jennifer Lacerda Da Silva and Karen Spadari Ferreira

Microbiol. Res. 2024, 15(4), 2146-2161; https://doi.org/10.3390/microbiolres15040144 - 22 Oct 2024

Abstract

Like other organisms, fungi produce extracellular vesicles (EVs) that are involved in various biological processes, including intercellular communication and the transport of molecules between cells. These EVs can be applied in fungal pathogenesis, virulence, and interactions with other organisms, including host cells, in [...] Read more.

Like other organisms, fungi produce extracellular vesicles (EVs) that are involved in various biological processes, including intercellular communication and the transport of molecules between cells. These EVs can be applied in fungal pathogenesis, virulence, and interactions with other organisms, including host cells, in the case of fungal infections. While some types of mycoses are relatively common and easily treatable, certain neglected mycoses pose significant public health challenges, such as sporotrichosis, chromoblastomycosis, and paracoccidioidomycosis. These infectious diseases can cause significant morbidity and disability, leading to a reduced quality of life for the patients. So, research about the virulence factor is essential to understand how fungi escape the immune system. In this context, this manuscript reviews the study of fungal EVs, their cargo, how they are obtained, and their role during the infectious process, which is extremely important for understanding this neglected mycosis. Full article

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17 pages, 4777 KiB

Open AccessArticle

Development of a Quadruplex RT-qPCR for the Detection of Feline Kobuvirus, Feline Astrovirus, Feline Bufavirus, and Feline Rotavirus

by Kaichuang Shi, Mengyi He, Feng Long, Junxian He, Yanwen Yin, Shuping Feng and Zongqiang Li

Microbiol. Res. 2024, 15(4), 2129-2145; https://doi.org/10.3390/microbiolres15040143 - 21 Oct 2024

Abstract

Feline kobuvirus (FeKoV), feline astrovirus (FeAstV), feline bufavirus (FeBuV), and feline rotavirus (FRV) are important pathogens for gastroenteritis, which is characterized by vomiting, diarrhea, and dehydration. Four pairs of primers and probes were designed to target the FeKoV VP1, FeAstV ORF2, FeBuV VP2, [...] Read more.

Feline kobuvirus (FeKoV), feline astrovirus (FeAstV), feline bufavirus (FeBuV), and feline rotavirus (FRV) are important pathogens for gastroenteritis, which is characterized by vomiting, diarrhea, and dehydration. Four pairs of primers and probes were designed to target the FeKoV VP1, FeAstV ORF2, FeBuV VP2, and FRV NSP4 genes, and a quadruplex real-time quantitative RT-PCR (RT-qPCR) assay capable of the simultaneous detection of four feline enteroviruses was developed after optimization of reaction conditions. The established quadruplex RT-qPCR assay showed high specificity, sensitivity, and reproducibility. The assay could detect and discriminate FeKoV, FeAstV, FeBuV, and FRV, but not other feline-related pathogens. The limits of detection (LODs) of FeKoV, FeAstV, FeBuV, and FRV were 109.761, 115.834, 125.481, and 113.875 copies/reaction, respectively. The intra- and inter-assay coefficients of variation (CV) were 0.15–1.61% and 0.15–1.59%, respectively. In all, 1869 clinical samples from Guangxi province in Southern China were tested using the developed assay, and the positivity rates of FeKoV, FeAstV, FeBuV, and FRV were 1.93%, 9.36%, 0.32%, and 0.75%, respectively. These samples were also tested using reference assays, and the coincidence rates of the results between the developed and reference methods were 99.63% (FeKoV), 98.72% (FeAstV), 100% (FeBuV), and 100% (FRV), respectively. The results indicated that the developed assay could provide a new detection method for these four viruses associated with feline gastroenteritis. Full article

(This article belongs to the Special Issue Veterinary Microbiology and Diagnostics)

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16 pages, 3838 KiB

Open AccessArticle

Identification of Listeria Isolates by Using a Pragmatic Multilocus Phylogenetic Analysis

by Antonio Martínez-Murcia, Aaron Navarro and Caridad Miró-Pina

Microbiol. Res. 2024, 15(4), 2114-2128; https://doi.org/10.3390/microbiolres15040142 - 14 Oct 2024

Abstract

Species identification of Listeria isolates remained a tedious process still based on culturing methods that, in recent years, have led to the description of many species that are not even part of the genus Listeria. It is advisable to provide new precise [...] Read more.

Species identification of Listeria isolates remained a tedious process still based on culturing methods that, in recent years, have led to the description of many species that are not even part of the genus Listeria. It is advisable to provide new precise techniques since this taxon includes two pathogens that are usually transmitted through the food chain, Listeria monocytogenes and L. ivanovii. The approach, so-called multilocus phylogenetic analysis (MLPA) that uses several concatenated housekeeping gene sequences, provides accurate and affordable classification frameworks to easily identify Listeria species by simple Sanger sequencing. Fragments of seven housekeeping genes (gyrA, cpn60, parE, recA, rpoB, atpA, and gyrB) from 218 strains of all Listeria species currently described were used to build an MLPA of the concatenated sequence, a total of 4375 bp. All isolates subjected to identification were clustered within the species of Listeria sensu stricto, L. monocytogenes, L. innocua, and L. welshimeri, and some reference strains were reclassified as L. ivanovii and L. seeligeri. Housekeeping-gene sequencing has been demonstrated to represent a pragmatic tool that can be firmly considered in food control. Full article

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12 pages, 1357 KiB

Open AccessArticle

Probiotic Enterococcus faecium CRL 183 Inhibits Candida albicans Biofilm In Vitro

by Virgínia Barreto Lordello, Sarah Raquel de Annunzio, Eliane Vale da Silva, Maria Pía Taranto, Carla Raquel Fontana and Daniela Cardoso Umbelino Cavallini

Microbiol. Res. 2024, 15(4), 2102-2113; https://doi.org/10.3390/microbiolres15040141 - 13 Oct 2024

Abstract

Candida albicans is the most prevalent fungal microorganism of human microbiota and one of the few fungi capable of causing diseases in humans, depending on the host’s immune defense capacity. The similarity between fungal and host cells promotes several adverse effects during antifungal [...] Read more.

Candida albicans is the most prevalent fungal microorganism of human microbiota and one of the few fungi capable of causing diseases in humans, depending on the host’s immune defense capacity. The similarity between fungal and host cells promotes several adverse effects during antifungal pharmacotherapy, and antimicrobial resistance increase is a major concern. Therefore, the search for alternative treatments and prevention strategies is urgent. In this context, probiotic bacteria, such as the strain Enterococcus faecium CRL 183, seem to be a viable alternative with its benefits to the immune system, activity against pathogens, and safety use well-documented through in vitro, in vivo, and clinical studies. Thus, this study aimed to evaluate if this probiotic strain prevents C. albicans ATCC 90028 biofilm colonization in vitro. To test the anti-Candida activity of the probiotic strain E. faecium CRL 183, we combined polymicrobial biofilms (C. albicans + E. faecium) with different proportions of fungi: a probiotic was formed (1:1, 1:10, 1:100) during the formation (24 h) and maturation (48 h) periods of the biofilm. The results show that E. faecium established itself with C. albicans in polymicrobial biofilms without losing its cellular viability. The probiotic strain significantly antagonized (p < 0.0001) C. albicans biofilm formation (up to 99.9% reduction in 24 h) and maturation (up to 99.43% reduction in 48 h). According to these results, E. faecium CRL183 may be a promising resource to prevent the formation of fungal biofilms. Full article

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17 pages, 2241 KiB

Open AccessArticle

Antibacterial and Antioxidant Activities of Flavonoids, Phenolic and Flavonoid Glycosides from Gouania longispicata Leaves

by Hannington Gumisiriza, Eunice Apio Olet, Lydia Mwikali, Racheal Akatuhebwa, Timothy Omara, Julius Bunny Lejju and Duncan Crispin Sesaazi

Microbiol. Res. 2024, 15(4), 2085-2101; https://doi.org/10.3390/microbiolres15040140 - 11 Oct 2024

Abstract

The leaves of Gouania longispicata Engl. (GLE) have been traditionally used to treat more than forty ailments in Uganda, including stomachache, lung and skin cancers, syphilis, toothache, and allergies. In this study, pure compounds were isolated from the methanolic extract of GLE leaves [...] Read more.

The leaves of Gouania longispicata Engl. (GLE) have been traditionally used to treat more than forty ailments in Uganda, including stomachache, lung and skin cancers, syphilis, toothache, and allergies. In this study, pure compounds were isolated from the methanolic extract of GLE leaves and their structures elucidated using ultraviolet visible spectroscopy, liquid chromatography–tandem mass spectrometry, high performance liquid chromatography, and 1D and 2D NMR techniques. The antibacterial and antioxidant activities of the compounds were assessed using the broth dilution and DPPH assays, respectively. Two known flavonoid glycosides (kaempferol-3-O-α-rhamnopyranoside and rutin), a phenolic glycoside (4,6-dihydroxy-3-methylacetophenone-2-O-β-D-glucopyranoside), and flavonoids (kaempferol and quercetin) were characterized. This is the first time that the kaempferol derivative, the acetophenone as well as free forms of quercetin, kaempferol, and rutin, are being reported in GLE and the Gouania genus. The compounds exhibited antibacterial activity against Streptococcus pneumoniae and Escherichia coli with minimum inhibitory concentrations between 16 µg/mL and 125 µg/mL. The radical scavenging activities recorded half-minimum inhibitory concentrations (IC₅₀) ranging from 18.6 ± 1.30 µg/mL to 28.1 ± 0.09 µg/mL. The IC₅₀ of kaempferol and quercetin were not significantly different from that of ascorbic acid (p > 0.05), highlighting their potential as natural antioxidant agents. These results lend credence to the use of GLE leaves in herbal treatment of microbial infections and oxidative stress-mediated ailments. Full article

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