Microorganisms

16 pages, 2262 KiB

Open AccessArticle

Dual Action of Beauveria bassiana (Hypocreales; Cordycipitaceae) Endophytic Stains as Biocontrol Agents against Sucking Pests and Plant Growth Biostimulants on Melon and Strawberry Field Plants

by Spiridon Mantzoukas, Eufrosini Daskalaki, Foteini Kitsiou, Vasileios Papantzikos, Dimitrios Servis, Stergios Bitivanos, George Patakioutas and Panagiotis A. Eliopoulos

Microorganisms 2022, 10(11), 2306; https://doi.org/10.3390/microorganisms10112306 - 21 Nov 2022

Cited by 6 | Viewed by 2241

Abstract

Entomopathogenic fungi (EPF) can colonize plant tissues and serve crops not only as biopesticides but also as biostimulants that promote plant growth and trigger defense mechanisms. In this context, field trials were conducted evaluating two commercial strains of the entomopathogen Beauveria bassiana (Hypocreales: [...] Read more.

Entomopathogenic fungi (EPF) can colonize plant tissues and serve crops not only as biopesticides but also as biostimulants that promote plant growth and trigger defense mechanisms. In this context, field trials were conducted evaluating two commercial strains of the entomopathogen Beauveria bassiana (Hypocreales: Cordycipitaceae), GHA (Botanigard) and PPRI 5339 (Velifer^® ES) and a wild strain (AP0101) isolated from Achaia, Greece. The three strains were investigated in the field for their endophytic effects on melon Cucumis melo (Cucurbitales: Cucurbitaceae) and strawberry Fragaria sp. (Rosales: Rosaceae) plants and in particular for their ability to colonize plant tissues, control infestations of sucking insects Aphis gossypii (Hemiptera: Aphididae), Chaetosiphon fragaefolii (Hemiptera: Aphididae) and Frankliniella occidentalis (Thysanoptera: Thripidae), and improve plant growth parameters (plant height, number of flowers and fruits). All experimental fungal strains successfully colonized both plants. A significant decrease in the aphid and thrip populations was observed in the treated plants compared to the untreated control. As for plant growth, the number of flowers and fruits was significantly increased in plants treated with B. bassiana strains AP0101 and PPRI 5339. Our results clearly indicate that fungal endophytes can efficiently act as dual action agents demonstrating both insecticidal and growth-promoting effects. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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18 pages, 16359 KiB

Open AccessArticle

Functional Microbial Communities in Hybrid Linear Flow Channel Reactors for Desulfurization of Tannery Effluent

by Emma J. Horn, Rob P. van Hille, Oluwaseun O. Oyekola and Pamela J. Welz

Microorganisms 2022, 10(11), 2305; https://doi.org/10.3390/microorganisms10112305 - 21 Nov 2022

Cited by 2 | Viewed by 1509

Abstract

Recent research has demonstrated that hybrid linear flow channel reactors (HLFCRs) can desulfurize tannery effluent via sulfate reduction and concurrent oxidation of sulfide to elemental sulfur. The reactors can be used to pre-treat tannery effluent to improve the efficiency of downstream anaerobic digestion [...] Read more.

Recent research has demonstrated that hybrid linear flow channel reactors (HLFCRs) can desulfurize tannery effluent via sulfate reduction and concurrent oxidation of sulfide to elemental sulfur. The reactors can be used to pre-treat tannery effluent to improve the efficiency of downstream anaerobic digestion and recover sulfur. This study was conducted to gain insight into the bacterial communities in HLFCRs operated in series and identify structure-function relationships. This was accomplished by interpreting the results obtained from amplicon sequencing of the 16S rRNA gene and quantification of the dissimilatory sulfite reducing (dsrB) gene. In an effort to provide a suitable inoculum, microbial consortia were harvested from saline estuaries and enriched. However, it was found that bioaugmentation was not necessary because native communities from tannery wastewater were selected over exogenous communities from the enriched consortia. Overall, Dethiosulfovibrio sp. and Petrimonas sp. were strongly selected (maximum relative abundances of 29% and 26%, respectively), while Desulfobacterium autotrophicum (57%), and Desulfobacter halotolerans (27%) dominated the sulfate reducing bacteria. The presence of elemental sulfur reducing genera such as Dethiosulfovibrio and Petrimonas is not desirable in HLFCRs, and strategies to counter their selection need to be considered to ensure efficiency of these systems for pre-treatment of tannery effluent. Full article

(This article belongs to the Section Microbial Biotechnology)

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17 pages, 2310 KiB

Open AccessArticle

Consumption of N₂O by Flavobacterium azooxidireducens sp. nov. Isolated from Decomposing Leaf Litter of Phragmites australis (Cav.)

by Undine Behrendt, Tobias Spanner, Jürgen Augustin, Dominik H. Zak, Marcus A. Horn, Steffen Kolb and Andreas Ulrich

Microorganisms 2022, 10(11), 2304; https://doi.org/10.3390/microorganisms10112304 - 21 Nov 2022

Cited by 3 | Viewed by 1691

Abstract

Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N₂O) are gaining increasing attention in the development of strategies to control N₂O emissions. Non-denitrifying N₂O reducers are of particular interest because they can provide a real [...] Read more.

Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N₂O) are gaining increasing attention in the development of strategies to control N₂O emissions. Non-denitrifying N₂O reducers are of particular interest because they can provide a real sink without contributing to N₂O release. The bacterial strain under investigation (IGB 4-14^T), isolated in a mesocosm experiment to study the litter decomposition of Phragmites australis (Cav.), is such an organism. It carries only a nos gene cluster with the sec-dependent Clade II nosZ and is able to consume significant amounts of N₂O under anoxic conditions. However, consumption activity is considerably affected by the O₂ level. The reduction of N₂O was not associated with cell growth, suggesting that no energy is conserved by anaerobic respiration. Therefore, the N₂O consumption of strain IGB 4-14^T rather serves as an electron sink for metabolism to sustain viability during transient anoxia and/or to detoxify high N₂O concentrations. Phylogenetic analysis of 16S rRNA gene similarity revealed that the strain belongs to the genus Flavobacterium. It shares a high similarity in the nos gene cluster composition and the amino acid similarity of the nosZ gene with various type strains of the genus. However, phylogenomic analysis and comparison of overall genome relatedness indices clearly demonstrated a novel species status of strain IGB 4-14^T, with Flavobacterium lacus being the most closely related species. Various phenotypic differences supported a demarcation from this species. Based on these results, we proposed a novel species Flavobacterium azooxidireducens sp. nov. (type strain IGB 4-14^T = LMG 29709^T = DSM 103580^T). Full article

(This article belongs to the Special Issue Bacterial Functions in Carbon, Nitrogen, and Sulfur Cycles)

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31 pages, 4058 KiB

Open AccessReview

Developing New Tools to Fight Human Pathogens: A Journey through the Advances in RNA Technologies

by Vanessa G. Costa, Susana M. Costa, Margarida Saramago, Marta V. Cunha, Cecília M. Arraiano, Sandra C. Viegas and Rute G. Matos

Microorganisms 2022, 10(11), 2303; https://doi.org/10.3390/microorganisms10112303 - 21 Nov 2022

Cited by 1 | Viewed by 2641

Abstract

A long scientific journey has led to prominent technological advances in the RNA field, and several new types of molecules have been discovered, from non-coding RNAs (ncRNAs) to riboswitches, small interfering RNAs (siRNAs) and CRISPR systems. Such findings, together with the recognition of [...] Read more.

A long scientific journey has led to prominent technological advances in the RNA field, and several new types of molecules have been discovered, from non-coding RNAs (ncRNAs) to riboswitches, small interfering RNAs (siRNAs) and CRISPR systems. Such findings, together with the recognition of the advantages of RNA in terms of its functional performance, have attracted the attention of synthetic biologists to create potent RNA-based tools for biotechnological and medical applications. In this review, we have gathered the knowledge on the connection between RNA metabolism and pathogenesis in Gram-positive and Gram-negative bacteria. We further discuss how RNA techniques have contributed to the building of this knowledge and the development of new tools in synthetic biology for the diagnosis and treatment of diseases caused by pathogenic microorganisms. Infectious diseases are still a world-leading cause of death and morbidity, and RNA-based therapeutics have arisen as an alternative way to achieve success. There are still obstacles to overcome in its application, but much progress has been made in a fast and effective manner, paving the way for the solid establishment of RNA-based therapies in the future. Full article

(This article belongs to the Special Issue Advances in RNA Biology in Pathogenic Microorganisms)

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19 pages, 2421 KiB

Open AccessArticle

A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source

by Pauline Chaignaud, Christelle Gruffaz, Adrien Borreca, Stéphanie Fouteau, Lauriane Kuhn, Jérémy Masbou, Zoé Rouy, Philippe Hammann, Gwenaël Imfeld, David Roche and Stéphane Vuilleumier

Microorganisms 2022, 10(11), 2302; https://doi.org/10.3390/microorganisms10112302 - 21 Nov 2022

Cited by 4 | Viewed by 2493

Abstract

Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects [...] Read more.

Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects on aquatic life and potentially also on humans. We report on the isolation and characterisation of strain MD1, an aerobic methylotrophic bacterium growing with metformin as its sole carbon, nitrogen and energy source. Strain MD1 degrades metformin into dimethylamine used for growth, and guanylurea as a side-product. Sequence analysis of its fully assembled genome showed its affiliation to Aminobacter niigataensis. Differential proteomics and transcriptomics, as well as mini-transposon mutagenesis of the strain, point to genes and proteins essential for growth with metformin and potentially associated with hydrolytic C-N cleavage of metformin or with cellular transport of metformin and guanylurea. The obtained results suggest the recent evolution of the growth-supporting capacity of strain MD1 to degrade metformin. Our results identify candidate proteins of the enzymatic system for metformin transformation in strain MD1 and will inform future research on the fate of metformin and its degradation products in the environment and in humans. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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13 pages, 950 KiB

Open AccessArticle

Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility

by Shahjahon Begmatov, Alexey V. Beletsky, Eugeny V. Gruzdev, Andrey V. Mardanov, Lubov B. Glukhova, Olga V. Karnachuk and Nikolai V. Ravin

Microorganisms 2022, 10(11), 2301; https://doi.org/10.3390/microorganisms10112301 - 20 Nov 2022

Cited by 5 | Viewed by 2046

Abstract

The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition [...] Read more.

The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide–lincosamide–streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide–lincosamide–streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants. Full article

(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)

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19 pages, 363 KiB

Open AccessReview

Applications of MALDI-TOF Mass Spectrometry to the Identification of Parasites and Arthropod Vectors of Human Diseases

by Fernando Sánchez-Juanes, Noelia Calvo Sánchez, Moncef Belhassen García, Carmen Vieira Lista, Raul Manzano Román, Rufino Álamo Sanz, Antonio Muro Álvarez and Juan Luis Muñoz Bellido

Microorganisms 2022, 10(11), 2300; https://doi.org/10.3390/microorganisms10112300 - 20 Nov 2022

Cited by 4 | Viewed by 2060

Abstract

Arthropod vectors and parasites are identified morphologically or, more recently, by molecular methods. Both methods are time consuming and require expertise and, in the case of molecular methods, specific devices. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification of bacteria has [...] Read more.

Arthropod vectors and parasites are identified morphologically or, more recently, by molecular methods. Both methods are time consuming and require expertise and, in the case of molecular methods, specific devices. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification of bacteria has meant a major change in clinical microbiology laboratories because of its simplicity, speed and specificity, and its capacity to identify microorganisms, in some cases, directly from the sample (urine cultures, blood cultures). Recently, MALDI-TOF MS has been shown as useful for the identification of some parasites. On the other hand, the identification of vector arthropods and the control of their populations is essential for the control of diseases transmitted by arthropods, and in this aspect, it is crucial to have fast, simple and reliable methods for their identification. Ticks are blood-sucking arthropods with a worldwide distribution, that behave as efficient vectors of a wide group of human and animal pathogens, including bacteria, protozoa, viruses, and even helminths. They are capable of parasitizing numerous species of mammals, birds and reptiles. They constitute the second group of vectors of human diseases, after mosquitoes. MALDI-TOF MS has been shown as useful for the identification of different tick species, such as Ixodes, Rhipicephalus and Amblyomma. Some studies even suggest the possibility of being able to determine, through MALDI-TOF MS, if the arthropod is a carrier of certain microorganisms. Regarding mosquitoes, the main group of vector arthropods, the possibility of using MALDI-TOF MS for the identification of different species of Aedes and Anopheles has also been demonstrated. In this review, we address the possibilities of this technology for the identification of parasites and arthropod vectors, its characteristics, advantages and possible limitations. Full article

(This article belongs to the Special Issue Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogenic Microorganisms 2.0)

16 pages, 374 KiB

Open AccessReview

Salmonella enterica Outbreaks Linked to the Consumption of Tahini and Tahini-Based Products

by Geneviève Coulombe and Sandeep Tamber

Microorganisms 2022, 10(11), 2299; https://doi.org/10.3390/microorganisms10112299 - 19 Nov 2022

Cited by 2 | Viewed by 3412

Abstract

Salmonella is a leading cause of bacterial foodborne illness in the world. Although typically associated with foods of animal origin, low-moisture foods, such as tahini, are quickly gaining recognition as an important vehicle of Salmonella exposure. This review offers the Canadian perspective on [...] Read more.

Salmonella is a leading cause of bacterial foodborne illness in the world. Although typically associated with foods of animal origin, low-moisture foods, such as tahini, are quickly gaining recognition as an important vehicle of Salmonella exposure. This review offers the Canadian perspective on the issue of Salmonella in tahini and tahini-based products. A summary of several recent food product recalls and foodborne outbreaks related to the presence of Salmonella in tahini and tahini-based products such as halva are presented. The properties of the food vehicles, their production practices, and potential routes of contamination are discussed. Particular focus is placed on the ecology of Salmonella in the tahini production continuum, including its survival characteristics and response to intervention technologies. Full article

(This article belongs to the Special Issue Foodborne Pathogens: Detection Methods, Food Safety, and Public Health)

19 pages, 3318 KiB

Open AccessArticle

First Report and Comparative Genomic Analysis of Mycoplasma capricolum subsp. capricolum HN-B in Hainan Island, China

by Zhenxing Zhang, Meirong He, Junming Jiang, Xubo Li, Haoyang Li, Wencan Zhang, Si Chen, Li Du, Churiga Man, Qiaoling Chen, Hongyan Gao and Fengyang Wang

Microorganisms 2022, 10(11), 2298; https://doi.org/10.3390/microorganisms10112298 - 19 Nov 2022

Viewed by 1542

Abstract

Mycoplasma capricolum subsp. Capricolum (Mcc) is an important member of the Mycoplasma mycoides cluster (Mm cluster) and causes caprine contagious agalactia. Mcc can infect goats of all age groups, especially pregnant ewes and kids. It can cause the abortion in pregnant ewes and [...] Read more.

Mycoplasma capricolum subsp. Capricolum (Mcc) is an important member of the Mycoplasma mycoides cluster (Mm cluster) and causes caprine contagious agalactia. Mcc can infect goats of all age groups, especially pregnant ewes and kids. It can cause the abortion in pregnant ewes and the death of goat kids, leading to enormous losses in the goat breeding industry. To date, the prevalence of epidemic Mcc strains on Hainan Island, China, remains unclear. This study aimed to isolate and identify Mcc strains endemic to Hainan Island, China. Genome sequencing and comparative genomic analysis were performed to reveal the molecular characteristics and evolutionary relationships of the isolated strain. Mcc HN-B was isolated and identified in Hainan Island, China. The Mcc HN-B genome consists of a 1,117,925 bp circular chromosome with a 23.79% G + C content. It contains 912 encoding genes, 3 gene islands, and 14 potential virulence genes. The core genome with the features of the Mm cluster and the specific genes of Mcc HN-B were identified by comparative genomic analysis. These results revealed the evolutionary relationship between Mcc HN-B and other members of the Mm cluster. Our findings provide a reference for further studies on the pathogenic mechanism and local vaccine development of Mcc. Full article

(This article belongs to the Special Issue Mycoplasma Pathogenicity, Persistence and Virulence)

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17 pages, 808 KiB

Open AccessArticle

Avian Oropharyngeal Trichomonosis: Treatment, Failures and Alternatives, a Systematic Review

by María Teresa Gómez-Muñoz, Miguel Ángel Gómez-Molinero, Fernando González, Iris Azami-Conesa, María Bailén, Marina García Piqueras and Jose Sansano-Maestre

Microorganisms 2022, 10(11), 2297; https://doi.org/10.3390/microorganisms10112297 - 19 Nov 2022

Viewed by 3903

Abstract

Oropharyngeal avian trichomonosis is a potentially lethal parasitic disease that affects several avian orders. This review is focused on the disease treatments since prophylactic treatment is prohibited in most countries and resistant strains are circulating. A systematic review following the PRISMA procedure was [...] Read more.

Oropharyngeal avian trichomonosis is a potentially lethal parasitic disease that affects several avian orders. This review is focused on the disease treatments since prophylactic treatment is prohibited in most countries and resistant strains are circulating. A systematic review following the PRISMA procedure was conducted and included 60 articles. Successful and non-toxic treatments of avian oropharyngeal trichomonosis started with enheptin, a drug replaced by dimetridazole, metronidazole, ornidazole, carnidazole and ronidazole. Administration in drinking water was the most employed and recommended method, although hierarchy of the avian flocks and palatability of the medicated water can interfere with the treatments. Besides pigeons, treatments with nitroimidazoles were reported in budgerigars, canaries, finches, bald eagles, a cinereous vulture and several falcon species, but resistant strains were reported mainly in domestic pigeons and budgerigars. Novel treatments include new delivery systems proved with traditional drugs and some plant extracts and its main components. Ethanolic extracts from ginger, curry leaf tree and Dennettia tripetala, alkaloid extracts of Peganum harmala and essential oils of Pelargonium roseum and some Lamiaceae were highly active. Pure active compounds from the above extracts displayed good anti-trichomonal activity, although most studies lack a cytotoxicity or in vivo test. Full article

(This article belongs to the Special Issue Biologic and Molecular Characterisation of Parasites and Antiparasitic Activity of Natural Products: A Themed Issue Dedicated to Dr. Rafael A. Martínez-Díaz)

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13 pages, 1075 KiB

Open AccessArticle

Protective Effect of [Cu(NN₁)₂](ClO₄) Complex in Rainbow Trout Challenged against Flavobacterium psychrophilum

by Maialen Aldabaldetrecu, Mick Parra, Sarita Soto-Aguilera, Pablo Arce, Amaya Paz de la Vega Quiroz, Rodrigo Segura, Mario Tello, Juan Guerrero and Brenda Modak

Microorganisms 2022, 10(11), 2296; https://doi.org/10.3390/microorganisms10112296 - 19 Nov 2022

Cited by 1 | Viewed by 1253

Abstract

Previously, we reported an in vitro evaluation regarding antibacterial effects against F. psychrophilum by a new Cu (I) complex, [Cu(NN₁)₂](ClO₄). This study presents the results of an in vivo evaluation of [Cu(NN₁)₂](ClO₄ [...] Read more.

Previously, we reported an in vitro evaluation regarding antibacterial effects against F. psychrophilum by a new Cu (I) complex, [Cu(NN₁)₂](ClO₄). This study presents the results of an in vivo evaluation of [Cu(NN₁)₂](ClO₄) added as a dietary supplement against F. psychrophilum in rainbow trout. The results showed that the administration of [Cu(NN₁)₂](ClO₄) at 29 and 58 µg/g of fish for 15 days does not affect the growth of rainbow trout. On the other hand, the amount of copper present in the liver, intestine, and muscle of rainbow trout was determined. The results showed that the amount of copper in the liver, when compared between treated fish and control fish, does not change. While, in the intestine, an increase in the fish fed at 58 µg/g of fish was observed. In muscle, a slight decrease at 29 µg/g was obtained. Additionally, copper concentrations in the pond water after 15 days of feeding with the [Cu(NN₁)₂](ClO₄) complex showed the highest levels of copper. Finally, the effect of the administration of [Cu(NN₁)₂](ClO₄) for 15 days at 58 µg/g of fish was evaluated against F. psychrophilum, where a 75% survival was obtained during 20 days of challenge. Full article

(This article belongs to the Section Microbial Biotechnology)

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16 pages, 2805 KiB

Open AccessArticle

Improvement of the Nutraceutical Profile of Brewer’s Spent Grain after Treatment with Trametes versicolor

by Anđela Zeko-Pivač, Anja Bošnjaković, Mirela Planinić, Jelena Parlov Vuković, Predrag Novak, Tomislav Jednačak and Marina Tišma

Microorganisms 2022, 10(11), 2295; https://doi.org/10.3390/microorganisms10112295 - 19 Nov 2022

Cited by 6 | Viewed by 2303

Abstract

Brewer’s spent grain (BSG) is an important secondary raw material that provides a readily available natural source of nutraceuticals. It finds its largest application as animal feed and part of the human diet, while the future perspective predicts an application in the production [...] Read more.

Brewer’s spent grain (BSG) is an important secondary raw material that provides a readily available natural source of nutraceuticals. It finds its largest application as animal feed and part of the human diet, while the future perspective predicts an application in the production of value-added products. In order to investigate a sustainable BSG treatment method, two BSG samples (BSG1 and BSG2) were evaluated as substrates for the production of hydrolytic (xylanase, β-glucosidase and cellulase) and lignolytic enzymes (laccase, manganese peroxidase and lignin peroxidase) by solid-state fermentation (SSF) with Trametes versicolor while improving BSG nutritional value. The biological treatment was successful for the production of all hydrolytic enzymes and laccase and manganese peroxidase, while it was unsuccessful for the production of lignin peroxidase. Because the two BSGs were chemically different, the Trametes versicolor enzymes were synthesized at different fermentation times and had different activities. Consequently, the chemical composition of the two BSG samples at the end of fermentation was also different. The biological treatment had a positive effect on the increase in protein content, ash content, polyphenolic compounds, and sugars in BSG1. In BSG2, there was a decrease in the content of reducing sugars. Cellulose, hemicellulose, and lignin were degraded in BSG1, whereas only cellulose was degraded in BSG2, and the content of hemicellulose and lignin increased. The fat content decreased in both samples. The safety-related correctness analysis showed that the biologically treated sample did not contain any harmful components and was therefore safe for use in nutritionally enriched animal feed. Full article

(This article belongs to the Special Issue Special Abilities of Microbes and Their Application in Agro-Biology)

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14 pages, 2558 KiB

Open AccessArticle

Pheromone Activity after Stimulation with Ampicillin in a Plasmid-Free Enterococcus faecalis Strain

by José Arellano-Galindo, Sergio Zavala-Vega, Rosario Vázquez-Larios, Sara A. Ochoa, Ariadnna Cruz-Córdova, Adolfo Sierra-Santoyo, Lourdes López-González, Rigoberto Hernández-Castro, Silvia Giono-Cerezo and Juan Xicohtencatl-Cortes

Microorganisms 2022, 10(11), 2294; https://doi.org/10.3390/microorganisms10112294 - 19 Nov 2022

Viewed by 1353

Abstract

Enterococci exhibit clumping under the selective pressure of antibiotics. The aim of this study was to analyze the effect of supernatants from a plasmid-free clone (C29) of Enterococcus faecalis subjected to 0.25×, 0.5×, and 0.75× of the minimal inhibitory concentration (MIC) of ampicillin [...] Read more.

Enterococci exhibit clumping under the selective pressure of antibiotics. The aim of this study was to analyze the effect of supernatants from a plasmid-free clone (C29) of Enterococcus faecalis subjected to 0.25×, 0.5×, and 0.75× of the minimal inhibitory concentration (MIC) of ampicillin on the expression of an aggregation substance (AS) by a donor plasmid clone (1390R). A clumping assay was performed. The relative expression of prgB (gene that encodes AS) was determined and semiquantified in 1390R, and iad1 expression was determined and semiquantified in C29. AS expression was analyzed in the stimulated 1390R cells by confocal microscopy, flow cytometry, and ELISA. Adherence was also measured. Maximal clumping was observed with the pheromone medium 0.25×. Only the 1390R strain stimulated with the C29 supernatant without ampicillin and with 0.25× was able to express prgB. No expression of prgB was observed at 0.5× and 0.75×. The difference in relative expression (RE) of 1390R without ampicillin and with 0.25× was 0.5-fold. AS expression in 1390R showed the greatest increase upon stimulation with 0.25×. When 1390R was stimulated with 0.5× and 0.75×, AS expression was also observed but was significantly lower. Ampicillin stimulated C29 switch-off pheromone expression in recipient cells, which in turn switched off AS expression in donor cells. We observed that although prgB was switched off after 0.5× stimulation in C29, the supernatants induced expression in certain 1390R strains. In conclusion, ampicillin was able to modulate pheromone expression in free plasmid clones which, in turn, modulated AS expression in plasmid donor cells. The fact that PrgB gene expression was switched off after the ampicillin stimulus at 0.5× MIC, whereas AS proteins were present on the surface of the bacteria, suggested that a mechanism of rescue associated with mechanism pheromone sensing may be involved. Full article

(This article belongs to the Special Issue Virulence Factors and Antibiotic Resistance of Enterobacterales)

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16 pages, 1657 KiB

Open AccessArticle

Probiotic Therapy with Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis Results in Infarct Size Limitation in Rats with Obesity and Chemically Induced Colitis

by Yury Y. Borshchev, Inessa Y. Burovenko, Alena B. Karaseva, Sarkis M. Minasian, Egor S. Protsak, Victor Y. Borshchev, Natalia Y. Semenova, Olga V. Borshcheva, Alexander N. Suvorov and Michael M. Galagudza

Microorganisms 2022, 10(11), 2293; https://doi.org/10.3390/microorganisms10112293 - 18 Nov 2022

Cited by 5 | Viewed by 2105

Abstract

In this study, we investigated the effect of three different probiotics, namely, a combination of Lactobacillus acidophilus (LA–5) and Bifidobacterium animalis subsp. lactis (BB–12), Saccharomyces boulardii, and Enterococcus faecium L3 on myocardial infarct size in rats with diet-induced obesity (DIO) and [...] Read more.

In this study, we investigated the effect of three different probiotics, namely, a combination of Lactobacillus acidophilus (LA–5) and Bifidobacterium animalis subsp. lactis (BB–12), Saccharomyces boulardii, and Enterococcus faecium L3 on myocardial infarct size in rats with diet-induced obesity (DIO) and chemically-induced colitis (CIC). Potential associations between the effects of probiotics on myocardial ischemia-reperfusion injury and gut microbiome patterns as well as the serum levels of pro- and anti-inflammatory cytokines, lipopolysaccharide, and short chain fatty acids were also studied. Intragastric administration of lyophilized Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis at a dose of 1.2 × 10⁸ CFU/mL for 15 days resulted in myocardial infarct size reduction in rats with DIO, CIC, and antibiotic-induced dysbiosis. This cardioprotective effect was associated with specific changes in cytokine concentrations, namely reduced levels of IL–1β, TNF–α, IL–2, and IL–8. At the same time, the use of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis was accompanied by a significant reduction in lipopolysaccharide level, suggesting normalization of intestinal epithelial barrier permeability. However, the cardioprotective effect of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis is not secondary to improved healing of the intestinal mucosa in CIC, as evidenced by the lack of difference in histopathological scores. Full article

(This article belongs to the Special Issue The Role of the Gut Microbiota in Human Health and Disease)

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19 pages, 3110 KiB

Open AccessEditor’s ChoiceArticle

Modulation of Virulence-Associated Traits in Aspergillus fumigatus by BET Inhibitor JQ1

by Anastasia Orekhova, Marta De Angelis, Andrea Cacciotti, Massimo Reverberi, Dante Rotili, Alessandra Giorgi, Virginia Protto, Graziana Bonincontro, Francesco Fiorentino, Victor Zgoda, Antonello Mai, Anna Teresa Palamara and Giovanna Simonetti

Microorganisms 2022, 10(11), 2292; https://doi.org/10.3390/microorganisms10112292 - 18 Nov 2022

Cited by 2 | Viewed by 1442

Abstract

Aspergillus fumigatus is a disease-causing, opportunistic fungus that can establish infection due to its capacity to respond to a wide range of environmental conditions. Secreted proteins and metabolites, which play a critical role in fungal–host interactions and pathogenesis, are modulated by epigenetic players, [...] Read more.

Aspergillus fumigatus is a disease-causing, opportunistic fungus that can establish infection due to its capacity to respond to a wide range of environmental conditions. Secreted proteins and metabolites, which play a critical role in fungal–host interactions and pathogenesis, are modulated by epigenetic players, such as bromodomain and extraterminal domain (BET) proteins. In this study, we evaluated the in vitro and in vivo capability of the BET inhibitor JQ1 to modulate the extracellular proteins and virulence of A. fumigatus. The abundance of 25 of the 76 extracellular proteins identified through LC-MS/MS proteomic analysis changed following JQ1 treatment. Among them, a ribonuclease, a chitinase, and a superoxide dismutase were dramatically downregulated. Moreover, the proteomic analysis of A. fumigatus intracellular proteins indicated that Abr2, an intracellular laccase involved in the last step of melanin synthesis, was absent in the JQ1-treated group. To investigate at which level this downregulation occurred and considering the ability of JQ1 to modulate gene expression we checked the level of ABR2, Chitinase, and Superoxide dismutase mRNA expression by qRT-PCR. Finally, the capacity of JQ1 to reduce the virulence of A. fumigatus has been proved using Galleria mellonella larvae, which are an in vivo model to evaluate fungal virulence. Overall, the promising activity exhibited by JQ1 suggests that A. fumigatus is sensitive to BET inhibition and BET proteins may be a viable target for developing antifungal agents. Full article

(This article belongs to the Special Issue Virulence Regulation and Drug-Resistance Mechanism of Fungal Infection)

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16 pages, 615 KiB

Open AccessReview

From Mouth to Muscle: Exploring the Potential Relationship between the Oral Microbiome and Cancer-Related Cachexia

by Shreya R. Raman, Christopher Liu, Kelly M. Herremans, Andrea N. Riner, Vignesh Vudatha, Devon C. Freudenberger, Kelley L. McKinley, Eric W. Triplett and Jose G. Trevino

Microorganisms 2022, 10(11), 2291; https://doi.org/10.3390/microorganisms10112291 - 18 Nov 2022

Viewed by 2705

Abstract

Cancer cachexia is a multifactorial wasting syndrome associated with skeletal muscle and adipose tissue loss, as well as decreased appetite. It affects approximately half of all cancer patients and leads to a decrease in treatment efficacy, quality of life, and survival. The human [...] Read more.

Cancer cachexia is a multifactorial wasting syndrome associated with skeletal muscle and adipose tissue loss, as well as decreased appetite. It affects approximately half of all cancer patients and leads to a decrease in treatment efficacy, quality of life, and survival. The human microbiota has been implicated in the onset and propagation of cancer cachexia. Dysbiosis, or the imbalance of the microbial communities, may lead to chronic systemic inflammation and contribute to the clinical phenotype of cachexia. Though the relationship between the gut microbiome, inflammation, and cachexia has been previously studied, the oral microbiome remains largely unexplored. As the initial point of digestion, the oral microbiome plays an important role in regulating systemic health. Oral dysbiosis leads to the upregulation of pro-inflammatory cytokines and an imbalance in natural flora, which in turn may contribute to muscle wasting associated with cachexia. Reinstating this equilibrium with the use of prebiotics and probiotics has the potential to improve the quality of life for patients suffering from cancer-related cachexia. Full article

(This article belongs to the Special Issue Tumor-Related Host-Microbiota Interactions)

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19 pages, 1598 KiB

Open AccessReview

Bioactive Compounds from Red Microalgae with Therapeutic and Nutritional Value

by Flora Tsvetanova and Dragomir Yankov

Microorganisms 2022, 10(11), 2290; https://doi.org/10.3390/microorganisms10112290 - 18 Nov 2022

Cited by 6 | Viewed by 2292

Abstract

Red microalgae represent a natural reservoir of beneficial substances with applications in different industrial sectors. They are rich in natural biomolecules known for their antihypertensive, antioxidant, antimicrobial, antiviral, anti-inflammatory, antitumor, and anticoagulant activities. Many red microalgae are a source of vitamins, minerals, photochemicals, [...] Read more.

Red microalgae represent a natural reservoir of beneficial substances with applications in different industrial sectors. They are rich in natural biomolecules known for their antihypertensive, antioxidant, antimicrobial, antiviral, anti-inflammatory, antitumor, and anticoagulant activities. Many red microalgae are a source of vitamins, minerals, photochemicals, polyunsaturated fatty acids, and a wide spectrum of polysaccharides. The content of their valuable compounds and their activities have turned red microalgae into cellular factories of special interest in food, nutraceutical, and pharmaceutical industries. Like all microalgae, the red ones are superior to traditional crops for the aims of biotechnology as they are renewable sources widely available in great quantities and are easy to culture. Moreover, some of the most studied red microalgae are generally recognized as safe. This review summarizes the valuable biochemicals from red microalgae and highlights their health and nutritional benefits. Full article

(This article belongs to the Special Issue Anti-inflammatory Property of Probiotics)

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20 pages, 1164 KiB

Open AccessReview

Probiotics in Periodontal and Peri-Implant Health Management: Biofilm Control, Dysbiosis Reversal, and Host Modulation

by Massimo Amato, Federica Di Spirito, Francesco D’Ambrosio, Giovanni Boccia, Giuseppina Moccia and Francesco De Caro

Microorganisms 2022, 10(11), 2289; https://doi.org/10.3390/microorganisms10112289 - 18 Nov 2022

Cited by 25 | Viewed by 3197

Abstract

Periodontitis and peri-implantitis are microbially associated diseases of the tissues supporting the teeth and dental implants that are mediated by host inflammation and eventually lead to tooth and dental implant loss. Given the probiotics’ role in biofilm control, dysbiosis reversal, and host modulation, [...] Read more.

Periodontitis and peri-implantitis are microbially associated diseases of the tissues supporting the teeth and dental implants that are mediated by host inflammation and eventually lead to tooth and dental implant loss. Given the probiotics’ role in biofilm control, dysbiosis reversal, and host modulation, their potential beneficial effects on the improvement of periodontitis and peri-implantitis have been recently investigated. Moreover, probiotics use has also been proposed in periodontal health management in patients undergoing fixed orthodontic therapy. Therefore, the present study aimed to review, considering the periodontal microbiome composition around teeth and dental implants in healthy and pathological conditions, the putative favorable effects of probiotics on gingivitis, periodontitis, and peri-implantitis. The secondary aim of the present narrative review was to synthesize the supporting evidence and proposed protocols for probiotics use as adjuncts in periodontitis and peri-implantitis treatment and the periodontal health management of orthodontic patients with fixed appliances. Contrasting findings from the literature may be due to the different methods, posology, and duration of probiotics prescriptions and due to the heterogeneous biological and clinical measurement methods employed. Thus, no definitive conclusions could be drawn about the effectiveness of probiotics in periodontal management, both in healthy and pathological conditions. Further studies are needed to validate probiotics for periodontal management and provide recommended protocols. Full article

(This article belongs to the Special Issue Probiotics and the Immune System: The Potential for Postimmunobiotics)

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14 pages, 3861 KiB

Open AccessArticle

The Spouses of Stroke Patients Have a Similar Oral Microbiome to Their Partners with an Elevated Risk of Stroke

by Huidi Wang, Mengjia Yang, Sanping Cheng, Yueran Ren, Yiting Deng, Jingru Liang, Xiaofei Lin, Jie Li, Jia Yin and Qiheng Wu

Microorganisms 2022, 10(11), 2288; https://doi.org/10.3390/microorganisms10112288 - 18 Nov 2022

Cited by 1 | Viewed by 2060

Abstract

Spousal members who share no genetic relatedness show similar oral microbiomes. Whether a shared microbiome increases the risk of cerebrovascular disease is challenging to investigate. The aim of this study was to compare the oral microbiota composition of poststroke patients, their partners, and [...] Read more.

Spousal members who share no genetic relatedness show similar oral microbiomes. Whether a shared microbiome increases the risk of cerebrovascular disease is challenging to investigate. The aim of this study was to compare the oral microbiota composition of poststroke patients, their partners, and controls and to compare the risk of stroke between partners of poststroke patients and controls. Forty-seven pairs of spouses and 34 control subjects were recruited for the study. Alcohol use, smoking, metabolic disease history, clinical test results, and oral health were documented. Oral microbiome samples were measured by 16S rRNA gene sequencing. The risk of stroke was measured by risk factor assessment (RFA) and the Framingham Stroke Profile (FSP). Poststroke patients and their partners exhibited higher alpha diversity than controls. Principal-coordinate analysis (PCoA) showed that poststroke patients share a more similar microbiota composition with their partners than controls. The differentially abundant microbial taxa among the 3 groups were identified by linear discriminant analysis effect size (LEfSe) analysis. The risk factor assessment indicated that partners of poststroke patients had a higher risk of stroke than controls. Spearman correlation analysis showed that Prevotellaceae was negatively associated with RFA. Lactobacillales was negatively associated with FSP, while Campilobacterota and [Eubacterium]_nodatum_group were positively associated with FSP. These results suggest that stroke risk may be transmissible between spouses through the oral microbiome, in which several bacteria might be involved in the pathogenesis of stroke. Full article

(This article belongs to the Section Medical Microbiology)

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21 pages, 1444 KiB

Open AccessArticle

Coriander (Coriandrum sativum L.) in Combination with Organic Amendments and Arbuscular Mycorrhizal Inoculation: An Efficient Option for the Phytomanagement of Trace Elements-Polluted Soils

by Joël Fontaine, Jérome Duclercq, Natacha Facon, Dorothée Dewaele, Frédéric Laruelle, Benoit Tisserant and Anissa Lounès-Hadj Sahraoui

Microorganisms 2022, 10(11), 2287; https://doi.org/10.3390/microorganisms10112287 - 17 Nov 2022

Cited by 2 | Viewed by 1592

Abstract

The cultivation of coriander (Coriandrum sativum L.) destined for essential oils production was recently presented as an innovative and economically viable alternative for the phytomanagement of trace elements (TE)-polluted soils. However, Cd accumulation in shoots has proven to be an obstacle in [...] Read more.

The cultivation of coriander (Coriandrum sativum L.) destined for essential oils production was recently presented as an innovative and economically viable alternative for the phytomanagement of trace elements (TE)-polluted soils. However, Cd accumulation in shoots has proven to be an obstacle in the valorization of the distillation residues and the development of these phytotechnologies. The present study aimed to evaluate the effect of arbuscular mycorrhizal fungus (Funneliformis mosseae) inoculation and organic amendment application on the soil TE bioavailability and plant uptake, as well as on the soil quality and health improvement. The application of compost and sewage sludge improved the growth of coriander and Cd and Zn immobilization in soil, resulting in reduced Cd plant uptake. A synergistic effect of arbuscular mycorrhizal fungi (AMF) inoculation and organic amendments was observed in the decrease in the extractable soil Cd and Zn concentrations, but not in the Cd plant uptake. Despite a significant decrease in Cd accumulation in shoots, coriander retained its accumulative phenotype, with a metal bioconcentration factor close to 1. Furthermore, both the vegetation and the organic amendments improved the soil quality and health by increasing its microbial biomass, as estimated by phospholipid fatty acids, soil enzyme activities (dehydrogenase, phosphatase, β-glucosidase, and cellubiosidase), and the bacterial metabolic function and diversity. The findings demonstrate the potential of C. sativum, particularly in combination with organic amendments and AMF inoculation, for the phytomanagement of TE-polluted soils and soil quality and health improvement. Full article

(This article belongs to the Special Issue Beneficial Microbiomes in Agriculture and Human Health: The Food Connection)

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15 pages, 1334 KiB

Open AccessArticle

Seroepidemiology of Borrelia burgdorferi s.l. among German National Cohort (NAKO) Participants, Hanover

by Max J. Hassenstein, Irina Janzen, Gérard Krause, Manuela Harries, Vanessa Melhorn, Tobias Kerrinnes, Yvonne Kemmling and Stefanie Castell

Microorganisms 2022, 10(11), 2286; https://doi.org/10.3390/microorganisms10112286 - 17 Nov 2022

Cited by 2 | Viewed by 1967

Abstract

Lyme borreliosis is the leading tick-related illness in Europe, caused by Borrelia Burgdorferi s.l. Lower Saxony, Germany, including its capital, Hanover, has a higher proportion of infected ticks than central European countries, justifying a research focus on the potential human consequences. The current [...] Read more.

Lyme borreliosis is the leading tick-related illness in Europe, caused by Borrelia Burgdorferi s.l. Lower Saxony, Germany, including its capital, Hanover, has a higher proportion of infected ticks than central European countries, justifying a research focus on the potential human consequences. The current knowledge gap on human incident infections, particularly in Western Germany, demands serological insights, especially regarding a potentially changing climate-related tick abundance and activity. We determined the immunoglobulin G (IgG) and immunoglobulin M (IgM) serostatuses for 8009 German National Cohort (NAKO) participants from Hanover, examined in 2014–2018. We used an enzyme-linked immunosorbent assay (ELISA) as the screening and a line immunoblot as confirmation for the Borrelia Burgdorferi s.l. antibodies. We weighted the seropositivity proportions to estimate general population seropositivity and estimated the force of infection (FOI). Using logistic regression, we investigated risk factors for seropositivity. Seropositivity was 3.0% (IgG) and 0.9% (IgM). The FOI varied with age, sharply increasing in participants aged ≥40 years. We confirmed advancing age and male sex as risk factors. We reported reduced odds for seropositivity with increasing body mass index and depressive symptomatology, respectively, pointing to an impact of lifestyle-related behaviors. The local proportion of seropositive individuals is comparable to previous estimates for northern Germany, indicating a steady seroprevalence. Full article

(This article belongs to the Section Public Health Microbiology)

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11 pages, 2648 KiB

Open AccessCase Report

Detection of Helicobacter pylori from Extracted Teeth of a Patient with Idiopathic Thrombocytopenic Purpura

by Masakazu Hamada, Ryota Nomura, Saaya Matayoshi, Yuko Ogaya, Hiroyasu Kameyama, Narikazu Uzawa and Kazuhiko Nakano

Microorganisms 2022, 10(11), 2285; https://doi.org/10.3390/microorganisms10112285 - 17 Nov 2022

Viewed by 2935

Abstract

Immune thrombocytopenic purpura (ITP) is an autoimmune disease characterized by isolated cryptogenic thrombocytopenia due to a transient or persistent reduction in platelet count. Many patients with ITP have shown improved platelet count after Helicobacter pylori eradication therapy. However, there have been no studies [...] Read more.

Immune thrombocytopenic purpura (ITP) is an autoimmune disease characterized by isolated cryptogenic thrombocytopenia due to a transient or persistent reduction in platelet count. Many patients with ITP have shown improved platelet count after Helicobacter pylori eradication therapy. However, there have been no studies regarding H. pylori in the oral cavity of patients with ITP. Here, we describe a patient with ITP whose oral samples exhibited H. pylori. A 64-year-old woman with ITP came to our hospital with chief complaints that required oral surgery, including tooth extraction and cystectomy. Bacterial DNA from H. pylori was confirmed on the extracted tooth, but was not detected in the saliva taken at the time. Bacterial DNA from H. pylori was detected on the suture around the extraction socket, which was removed at 10 days post-operation. However, H. pylori DNA was not detected in other oral samples at 10 or 30 days post-operation. A urea breath test was carried out in the gastrointestinal clinic at 60 days post-operation, which revealed no presence of H. pylori in the gastrointestinal tract. These results suggest that teeth with severe bacterial infections may be a potential reservoir of H. pylori for patients with ITP. Full article

(This article belongs to the Special Issue Advances in the Diagnosis and Treatment of Helicobacter pylori)

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15 pages, 306 KiB

Open AccessArticle

Clostridioides Difficile Infection before and during Coronavirus Disease 2019 Pandemic—Similarities and Differences

by Nadica Kovačević, Vedrana Petrić, Maria Pete, Milica Popović, Aleksandra Plećaš-Đurić, Slađana Pejaković, Slavica Tomić, Dimitrije Damjanov, Dijana Kosijer and Milica Lekin

Microorganisms 2022, 10(11), 2284; https://doi.org/10.3390/microorganisms10112284 - 17 Nov 2022

Cited by 3 | Viewed by 1092

Abstract

The aim of this study was to investigate the differences of Clostridioides difficile infection (CDI) during the COVID-19 pandemic compared to the pre-COVID-19 era. CDI patients treated at the Clinic for Infectious Diseases, Clinical Center of Vojvodina, Serbia during 2017–2019 (n = [...] Read more.

The aim of this study was to investigate the differences of Clostridioides difficile infection (CDI) during the COVID-19 pandemic compared to the pre-COVID-19 era. CDI patients treated at the Clinic for Infectious Diseases, Clinical Center of Vojvodina, Serbia during 2017–2019 (n = 304) were compared with COVID-19/CDI patients treated in period September 2021–September 2022 (n = 387). Groups were compared by age, gender, comorbidities, previous medications, laboratory findings, and outcome within 30 days. In the CDI/COVID-19 group, we found: greater percentage of males 59.8% vs. 42.6% (p ≤ 0.001), older age 72.8 ± 9.4 vs. 65.6 ± 11.7 (p ≤ 0.001), higher Charlson comorbidity score (CCS) (3.06 ± 1.54 vs. 2.33 ± 1.34 (p ≤ 0.001), greater percentage of chronic renal failure (33.9% vs. 23.4% (p = 0.003), malignances (24.3% vs. 13.5% (p ≤ 0.001), chronic obstructive pulmonary disease (22.7% vs. 15.5% (p = 0.017), higher usage of macrolide (38.5% vs. 8.6% (p ≤ 0.001), greater percentage of patients with hypoalbuminemia ≤25 g/L (19.6% vs. 12.2% (p ≤ 0.001), lower percentage of patients with elevated creatinine (≥200 mmol/L) (31.5% vs. 43.8%) (p = 0.002), and greater percentage of lethal outcome 29.5% vs. 6.6% (p ≤ 0.001). In the prediction of lethal outcome multivariate regression analysis extracted as an independent predictor, only higher CRP values in the non-COVID-19 group and in the COVID-19 group: older age (p ≤ 0.001), CCS (p = 0.019) and CRP (p = 0.015). COVID-19 changes the disease course of CDI and should be taken into consideration when managing those patients. Full article

(This article belongs to the Special Issue Clostridium difficile Infection in Clinical Practice: From Bench to Bedside)

12 pages, 297 KiB

Open AccessArticle

Characterization of Genomic Diversity among Carbapenem-Resistant Escherichia coli Clinical Isolates and Antibacterial Efficacy of Silver Nanoparticles from Pakistan

by Aamir Jamal Gondal, Nakhshab Choudhry, Hina Bukhari, Zainab Rizvi and Nighat Yasmin

Microorganisms 2022, 10(11), 2283; https://doi.org/10.3390/microorganisms10112283 - 17 Nov 2022

Cited by 6 | Viewed by 1775

Abstract

The emergence of carbapenem-resistant Escherichia coli (E. coli) is considered an important threat to public health resulting in resistance accumulation due to antibiotics misuse and selection pressure. This warrants periodic efforts to investigate and develop strategies for infection control. A total [...] Read more.

The emergence of carbapenem-resistant Escherichia coli (E. coli) is considered an important threat to public health resulting in resistance accumulation due to antibiotics misuse and selection pressure. This warrants periodic efforts to investigate and develop strategies for infection control. A total of 184 carbapenem-resistant clinical strains of E. coli were characterized for resistance pattern, resistance genes, plasmids, sequence types and in vitro efficacy of silver nanoparticles (AgNPs). Carbapenem resistance was prevalent in E. coli isolated from female patients (64.7%), urine samples (40.8%) and surgical wards (32.1%). Polymyxin-B showed higher susceptibility. ESBLs and carbapenemases were produced in 179 and 119 isolates, respectively. Carbapenemase-encoding genes were observed among 104 strains with bla_NDM-1 (45.1%), bla_OXA-48 (27%), bla_NDM-7 (3.8%), bla_NDM-1/bla_OXA-48 (15.4%), bla_NDM-7/bla_OXA-48 (2.9%), bla_OXA-48/bla_VIM (3.8%) and bla_NDM-1/bla_VIM (2%). ESBL resistance genes were detected in 147 isolates, namely bla_SHV (24.9%), bla_CTX-M (17.7%), bla_TEM (4.8%), bla_SHV/bla_CTX-M (29.2%), bla_SHV/bla_TEM (15%) and bla_CTX-M/bla_TEM (8.8%). ST405 (44.4%) and ST131 (29.2%) were more frequent sequence types with ST101 (9.7%), ST10 (9.7%) and ST648 (7%). The replicon types IncFII, IncFIIK, IncA/C, IncN and IncL/M were detected. The combination of MEM/AgNPs remained effective against carbapenemase-positive E. coli. We reported genetically diverse E. coli strains coharboring carbapenemases/ESBLs from Pakistan. Moreover, this study highlights the enhanced antibacterial activity of MEM/AgNPs and may be used to manage bacterial infections. Full article

(This article belongs to the Special Issue Antimicrobial Stewardship Strategies to Improve Antimicrobial Use)

21 pages, 2399 KiB

Open AccessArticle

Genetic and Physiological Characterization of Soybean-Nodule-Derived Isolates from Bangladeshi Soils Revealed Diverse Array of Bacteria with Potential Bradyrhizobia for Biofertilizers

by Md Firoz Mortuza, Salem Djedidi, Takehiro Ito, Shin-ichiro Agake, Hitoshi Sekimoto, Tadashi Yokoyama, Shin Okazaki and Naoko Ohkama-Ohtsu

Microorganisms 2022, 10(11), 2282; https://doi.org/10.3390/microorganisms10112282 - 17 Nov 2022

Cited by 2 | Viewed by 1941

Abstract

Genetic and physiological characterization of bacteria derived from nodules of leguminous plants in the exploration of biofertilizer is of paramount importance from agricultural and environmental perspectives. Phylogenetic analysis of the 16S rRNA gene of 84 isolates derived from Bangladeshi soils revealed an unpredictably [...] Read more.

Genetic and physiological characterization of bacteria derived from nodules of leguminous plants in the exploration of biofertilizer is of paramount importance from agricultural and environmental perspectives. Phylogenetic analysis of the 16S rRNA gene of 84 isolates derived from Bangladeshi soils revealed an unpredictably diverse array of nodule-forming and endosymbiotic bacteria—mostly belonging to the genus Bradyrhizobium. A sequence analysis of the symbiotic genes (nifH and nodD1) revealed similarities with the 16S rRNA gene tree, with few discrepancies. A phylogenetic analysis of the partial rrn operon (16S-ITS-23S) and multi-locus sequence analysis of atpD, glnII, and gyrB identified that the Bradyrhizobium isolates belonged to Bradyrhizobium diazoefficiens, Bradyrhizobium elkanii, Bradyrhizobium liaoningense and Bradyrhizobium yuanmingense species. In the pot experiment, several isolates showed better activity than B. diazoefficiens USDA110, and the Bho-P2-B2-S1-51 isolate of B. liaoningense showed significantly higher acetylene reduction activity in both Glycine max cv. Enrei and Binasoybean-3 varieties and biomass production increased by 9% in the Binasoybean-3 variety. Tha-P2-B1-S1-68 isolate of B. diazoefficiens significantly enhanced shoot length and induced 10% biomass production in Binasoybean-3. These isolates grew at 1–4% NaCl concentration and pH 4.5–10 and survived at 45 °C, making the isolates potential candidates for eco-friendly soybean biofertilizers in salty and tropical regions. Full article

(This article belongs to the Section Plant Microbe Interactions)

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15 pages, 1752 KiB

Open AccessArticle

Genomics of Klebsiella pneumoniae Species Complex Reveals the Circulation of High-Risk Multidrug-Resistant Pandemic Clones in Human, Animal, and Environmental Sources

by Sergio Morgado, Erica Fonseca and Ana Carolina Vicente

Microorganisms 2022, 10(11), 2281; https://doi.org/10.3390/microorganisms10112281 - 17 Nov 2022

Cited by 8 | Viewed by 3199

Abstract

The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by [...] Read more.

The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by strains recovered from animals and the environment to humans. We therefore performed a genomic surveillance analysis of the KpSC using every public genome in Brazil, aiming to show their local and global relationships, and the connectivity of antibiotic resistance and virulence considering human, animal, and environmental sources. The 390 genomes from distinct sources encompassed the K. pneumoniae, Klebsiella quasipneumoniae subsp. quasipneumoniae, Klebsiella quasipneumoniae subsp. similipneumoniae, Klebsiella variicola subsp. variicola, Klebsiella variicola subsp. tropica, and Klebsiella grimontii species and subspecies. K. pneumoniae harbored dozens of antibiotic resistance genes, while most of the genomes belong to the high-risk pandemic CC258 occurring in humans, animals, and the environment. In K. pneumoniae ST11, a high prevalence of the virulence determinants yersiniabactin, colibactin, and T6SS was revealed in association with multi-drug resistance (MDR), including carbapenem resistance. A diversity of resistance genes is carried by plasmids, some shared between strains from different STs, regions, and sources. Therefore, here were revealed some factors driving the success of KpSC as a pathogen. Full article

(This article belongs to the Special Issue 10th Anniversary of Microorganisms: Past, Present and Future)

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10 pages, 1587 KiB

Open AccessArticle

Establishment of the Bacterial Microbiota in a Lab-Reared Model Teleost Fish, the Medaka Oryzias latipes

by Charlotte Duval, Benjamin Marie, Pierre Foucault and Sébastien Duperron

Microorganisms 2022, 10(11), 2280; https://doi.org/10.3390/microorganisms10112280 - 17 Nov 2022

Cited by 4 | Viewed by 1573

Abstract

Oryzias latipes is an important model organism for physiology, genetics, and developmental studies, and has also emerged as a relevant vertebrate model for aquatic ecotoxicology. Knowledge regarding its associated microbiota on the other hand is still scarce and limited to adults, despite the [...] Read more.

Oryzias latipes is an important model organism for physiology, genetics, and developmental studies, and has also emerged as a relevant vertebrate model for aquatic ecotoxicology. Knowledge regarding its associated microbiota on the other hand is still scarce and limited to adults, despite the relevance of the associated microbiome to the host’s biology. This study provides the first insights into the establishment of bacterial microbiota during early developmental stages of laboratory-reared medaka using a 16S-rRNA-sequencing-based approach. Major shifts in community compositions are observed, from a Proteobacteria-dominated community in larvae and juveniles to a more phylum-diverse community towards adulthood, with no obvious difference between female and male specimens. Major bacterial taxa found in adults, including genera Cetobacterium and ZOR0006, establish progressively and are rare during early stages. Dominance shifts are comparable to those documented in another major model teleost, the zebrafish. Results from this study provide a basis for future work investigating the influence of medaka-associated bacteria during host development. Full article

(This article belongs to the Special Issue The Microbial Population of the Gastrointestinal Tract of Animals: Impacts on Host Physiology)

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16 pages, 3421 KiB

Open AccessArticle

TA-AgNPs/Alginate Hydrogel and Its Potential Application as a Promising Antibiofilm Material against Polymicrobial Wound Biofilms Using a Unique Biofilm Flow Model

by Oranee Srichaiyapol, Sarah E. Maddocks, Saengrawee Thammawithan, Sakda Daduang, Sompong Klaynongsruang and Rina Patramanon

Microorganisms 2022, 10(11), 2279; https://doi.org/10.3390/microorganisms10112279 - 16 Nov 2022

Cited by 3 | Viewed by 1748

Abstract

The presence of biofilm within a chronic wound may delay the healing process. Thus, control of biofilm formation and providing bactericidal effect are crucial factors for wound healing management. Alginate-based nanocomposite hydrogels have been suggested as dressing materials for wound treatment, which are [...] Read more.

The presence of biofilm within a chronic wound may delay the healing process. Thus, control of biofilm formation and providing bactericidal effect are crucial factors for wound healing management. Alginate-based nanocomposite hydrogels have been suggested as dressing materials for wound treatment, which are employed as a biocompatible matrix. Therefore, in this study, we aimed to develop a biocompatible antimicrobial wound dressing containing AgNPs and demonstrate its efficacy against polymicrobial wound biofilms by using a biofilm flow device to simulate a chronic infected, exuding wound and specific wound environment. The results from agar well diffusion, the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) assays showed that TA-AgNPs exhibited antibacterial activity against wound pathogens. Additionally, the Minimum Biofilm Eradication Concentration assay (MBEC) demonstrated it could impair biofilm formation. Importantly, our TA-AgNPs/Alginate hydrogel clearly showed antibacterial activities against Streptococcus pyogenes, Staphylococcus aureus and Pseudomonas aeruginosa. Furthermore, we used the biofilm flow device to test the topical antimicrobial hydrogel against a three-species biofilm. We found that TA-AgNPs/Alginate hydrogel significantly showed a 3–4 log reduction in bacterial numbers when applied with multiple doses at 24 h intervals, and was especially effective against the chronic wound pathogen P. aeruginosa. This work highlighted that the TA-AgNPs/Alginate hydrogel is a promising material for treating complex wound biofilms. Full article

(This article belongs to the Special Issue Nanoparticles and Their Biological Applications: Recent Advances in 2022–2023)

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14 pages, 18829 KiB

Open AccessArticle

Exploring Structural Diversity among Adhesion Devices Encoded by Lactococcal P335 Phages with AlphaFold2

by Adeline Goulet, Jennifer Mahony, Christian Cambillau and Douwe van Sinderen

Microorganisms 2022, 10(11), 2278; https://doi.org/10.3390/microorganisms10112278 - 16 Nov 2022

Cited by 2 | Viewed by 1702

Abstract

Bacteriophages, or phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, as well as to introduce it into the cytoplasm of their bacterial prey. Successful phage infection commences with specific recognition of, and [...] Read more.

Bacteriophages, or phages, are the most abundant biological entities on Earth. They possess molecular nanodevices to package and store their genome, as well as to introduce it into the cytoplasm of their bacterial prey. Successful phage infection commences with specific recognition of, and adhesion to, a suitable host cell surface. Adhesion devices of siphophages infecting Gram-positive bacteria are very diverse and remain, for the majority, poorly understood. These assemblies often comprise long, flexible, and multi-domain proteins, which limit their structural analyses by experimental approaches. The protein structure prediction program AlphaFold2 is exquisitely adapted to unveil structural and functional details of such molecular machineries. Here, we present structure predictions of adhesion devices from siphophages belonging to the P335 group infecting Lactococcus spp., one of the most extensively applied lactic acid bacteria in dairy fermentations. The predictions of representative adhesion devices from types I-IV P335 phages illustrate their very diverse topology. Adhesion devices from types III and IV phages share a common topology with that of Skunavirus p2, with a receptor binding protein anchored to the virion by a distal tail protein loop. This suggests that they exhibit an activation mechanism similar to that of phage p2 prior to host binding. Full article

(This article belongs to the Special Issue Phages from the Fermented Products)

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12 pages, 299 KiB

Open AccessArticle

Efficacy of Artemisia annua against Coccidiosis in Broiler Chickens: A Field Trial

by Mircea Coroian, Loredana Maria Pop, Virgilia Popa, Zsuzsa Friss, Ovidiu Oprea, Zsuzsa Kalmár, Adela Pintea, Silvia-Diana Borșan, Viorica Mircean, Iustina Lobonțiu, Dumitru Militaru, Rodica Vârban and Adriana Györke

Microorganisms 2022, 10(11), 2277; https://doi.org/10.3390/microorganisms10112277 - 16 Nov 2022

Cited by 3 | Viewed by 1791

Abstract

(1) Background: Various studies on artemisinin and its derivatives have shown that Artemisia annua may be of therapeutic interest for different diseases, including chicken coccidiosis. This study aimed to evaluate the effects of Artemisia annua on farm-reared broiler chickens by analyzing both the [...] Read more.

(1) Background: Various studies on artemisinin and its derivatives have shown that Artemisia annua may be of therapeutic interest for different diseases, including chicken coccidiosis. This study aimed to evaluate the effects of Artemisia annua on farm-reared broiler chickens by analyzing both the anticoccidial efficacy and its effect on the intestinal microbiota of poultry. (2) Methods: The experiment was performed within three houses on a broiler chicken farm located in Romania. House 1 was the experimental group and received a diet with an addition of A. annua. Houses 2 and 4 were the control groups and received anticoccidials. The prophylactic efficacy of A. annua against coccidiosis was evaluated by recording the weight gain, feed conversion rate, number of oocysts per gram of feces, lesion score, and mortality rate. (3) Results: The chickens fed with A. annua showed a decreasing trend in the number of oocysts per gram of faeces, and their lesion score was 80% lower than in the control group. The weight gains of the chickens treated with A. annua was lower, whilst the feed conversion rate was better than in controls. (4) Conclusions: Artemisia annua showed promising results in the prophylaxis of coccidiosis. Overall, the broiler chickens that received A. annua presented promising zootechnical performances and medical data related to coccidiosis and gut microbiota. Full article

(This article belongs to the Special Issue Protozoan Parasites in Animals: Updates in Epidemiology, Diagnosis and Control)

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Microorganisms, Volume 10, Issue 11 (November 2022) – 215 articles

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