Microorganisms

12 pages, 658 KiB

Open AccessArticle

Impact of the Introduction of a Two-Step Laboratory Diagnostic Algorithm in the Incidence and Earlier Diagnosis of Clostridioides difficile Infection

by Nieves Sopena, Jun Hao Wang-Wang, Irma Casas, Lourdes Mateu, Laia Castellà, María José García-Quesada, Sara Gutierrez, Josep M. Llibre, M. Luisa Pedro-Botet and Gema Fernandez-Rivas

Microorganisms 2022, 10(5), 1075; https://doi.org/10.3390/microorganisms10051075 - 23 May 2022

Cited by 4 | Viewed by 2093

Abstract

Our aim was to determine changes in the incidence of CD infection (CDI) following the introduction of a two-step diagnostic algorithm and to analyze CDI cases diagnosed in the study period. We retrospectively studied CDI (January 2009 to July 2018) in adults diagnosed [...] Read more.

Our aim was to determine changes in the incidence of CD infection (CDI) following the introduction of a two-step diagnostic algorithm and to analyze CDI cases diagnosed in the study period. We retrospectively studied CDI (January 2009 to July 2018) in adults diagnosed by toxin enzyme immunoassay (EIA) (2009–2012) or toxin-EIA + polymerase chain reaction (PCR) algorithm (2013 onwards). A total of 443 patients with a first episode of CDI were included, 297 (67.1%) toxin-EIA-positive and 146 (32.9%) toxin-EIA-negative/PCR-positive were only identified through the two-step algorithm including the PCR test. The incidence of CDI increased from 0.9 to 4.7/10,000 patient-days (p < 0.01) and 146 (32.9%) toxin-negative CDI were diagnosed. Testing rate increased from 24.4 to 59.5/10,000 patient-days (p < 0.01) and the percentage of positive stools rose from 3.9% to 12.5% (p < 0.01). CD toxin-positive patients had a higher frequency of severe presentation and a lower rate of immunosuppressive drugs and inflammatory bowel disease. Mortality (16.3%) was significantly higher in patients with hematological neoplasm, intensive care unit admission and complicated disease. Recurrences (14.9%) were significantly higher with proton pump inhibitor exposure. The two-step diagnostic algorithm facilitates earlier diagnosis, potentially impacting patient outcomes and nosocomial spread. CD-toxin-positive patients had a more severe clinical presentation, probably due to increased CD bacterial load with higher toxin concentration. This early and easy marker should alert clinicians of potentially more severe outcomes. Full article

(This article belongs to the Section Medical Microbiology)

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15 pages, 2876 KiB

Open AccessArticle

Easy Express Extraction (TripleE)—A Universal, Electricity-Free Nucleic Acid Extraction System for the Lab and the Pen

by Christian Korthase, Ahmed Elnagar, Martin Beer and Bernd Hoffmann

Microorganisms 2022, 10(5), 1074; https://doi.org/10.3390/microorganisms10051074 - 23 May 2022

Cited by 4 | Viewed by 2846

Abstract

The complexity of the current nucleic acid isolation methods limits their use outside of the modern laboratory environment. Here, we describe a fast and affordable method (easy express extraction, called TripleE) as a centrifugation-free and electricity-free nucleic acid isolation method. The [...] Read more.

The complexity of the current nucleic acid isolation methods limits their use outside of the modern laboratory environment. Here, we describe a fast and affordable method (easy express extraction, called TripleE) as a centrifugation-free and electricity-free nucleic acid isolation method. The procedure is based on the well-established magnetic-bead extraction technology using an in-house self-made magnetic 8-channel and a rod cover. With this extraction system, nucleic acids can be isolated with two simple and universal protocols. One method was designed for the extraction of the nucleic acid in resource-limited “easy labs”, and the other method can be used for RNA/DNA extraction in the field for so-called molecular “pen-side tests”. In both scenarios, users can extract up to 8 samples in 6 to 10 min, without the need for any electricity, centrifuges or robotic systems. In order to evaluate and compare both methods, clinical samples from various viruses (African swine fever virus; lumpy skin disease virus; peste des petits ruminants virus; bluetongue virus), matrices and animals were tested and compared with standard magnetic-bead nucleic acid extraction technology based on the KingFisher platform. Hence, validation data were generated by evaluating two DNA viruses as well as one single-stranded and one double-stranded RNA virus. The results showed that the fast, easy, portable and electricity-free extraction protocols allowed rapid and reliable nucleic acid extraction for a variety of viruses and most likely also for other pathogens, without a substantial loss of sensitivity compared to standard procedures. The speed and simplicity of the methods make them ideally suited for molecular applications, both within and outside the laboratory, including limited-resource settings. Full article

(This article belongs to the Special Issue Diagnosis of Viral Infections)

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19 pages, 24592 KiB

Open AccessArticle

Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics

by Konstantinos Papadimitriou, Rania Anastasiou, Marina Georgalaki, Rimi Bounenni, Argiro Paximadaki, Christina Charmpi, Voula Alexandraki, Maria Kazou and Effie Tsakalidou

Microorganisms 2022, 10(5), 1073; https://doi.org/10.3390/microorganisms10051073 - 23 May 2022

Cited by 17 | Viewed by 3429

Abstract

Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal [...] Read more.

Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing, as well as shotgun metagenomics, to investigate the microbiome of artisanal homemade and industrial Feta cheese samples from different regions of Greece, which has very rarely been investigated. 16S rDNA data suggested the prevalence of the Lactococcus genus in the homemade samples, while Streptococcus and Lactobacillus genera prevailed in the industrial control samples. Species identification deriving from shotgun metagenomics corroborated these findings, as Lactococcus lactis dominated two homemade samples while Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were found to be dominating one industrial sample. ITS data revealed a complex diversity of the yeast population among the samples analyzed. Debaryomyces, Kluyveromyces, Cutaneotrichosporon, Pichia, Candida, and Rhodotorula were the major genera identified, which were distributed in a rather arbitrary manner among the different samples. Furthermore, a number of potential metagenome-assembled genomes (MAGs) could be detected among assembled shotgun bins. The overall analysis of the shotgun metagenomics supported the presence of different foodborne pathogens in homemade samples (e.g., Staphylococcus aureus, Listeria monocytogenes, Enterobacter cloacae, and Streptococcus suis), but with low to very low abundances. Concluding, the combination of both amplicon sequencing and shotgun metagenomics allowed us to obtain an in-depth profile of the artisanal homemade Feta cheese microbiome. Full article

(This article belongs to the Special Issue Food Microbial Diversity 2.0)

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19 pages, 3907 KiB

Open AccessReview

The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management

by Yandong Xia, Junang Liu, Cang Chen, Xiuli Mo, Qian Tan, Yuan He, Zhikai Wang, Jia Yin and Guoying Zhou

Microorganisms 2022, 10(5), 1072; https://doi.org/10.3390/microorganisms10051072 - 23 May 2022

Cited by 47 | Viewed by 5990

Abstract

Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion and from adverse environmental conditions. They produce various metabolites that [...] Read more.

Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion and from adverse environmental conditions. They produce various metabolites that can directly inhibit the growth of pathogens and even promote the growth and development of the host plants. In this review, we focus on the biological control of plant diseases, aiming to elucidate the contribution and key roles of endophytes and their metabolites in this field with the latest research information. Metabolites synthesized by endophytes are part of plant disease management, and the application of endophyte metabolites to induce plant resistance is very promising. Furthermore, multi-omics should be more fully utilized in plant–microbe research, especially in mining novel bioactive metabolites. We believe that the utilization of endophytes and their metabolites for plant disease management is a meaningful and promising research direction that can lead to new breakthroughs in the development of more effective and ecosystem-friendly insecticides and fungicides in modern agriculture. Full article

(This article belongs to the Special Issue Plant Immunity Induced by BioControl Agent (BCAs) in Plant Pathogen Infection)

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13 pages, 2367 KiB

Open AccessArticle

Isolation and Properties of the Bacterial Strain Janthinobacterium sp. SLB01

by Lubov Chernogor, Kseniya Bakhvalova, Alina Belikova and Sergei Belikov

Microorganisms 2022, 10(5), 1071; https://doi.org/10.3390/microorganisms10051071 - 23 May 2022

Cited by 7 | Viewed by 3058

Abstract

Bacteria of the genus Janthinobacterium are widespread in soils and freshwater ecosystems and belong to the phylum Proteobacteria. The Janthinobacterium sp. SLB01 strain was isolated from diseased freshwater Lubomirskia baicalensis (Pallas, 1776) sponge, and the draft genome was published previously. However, the properties [...] Read more.

Bacteria of the genus Janthinobacterium are widespread in soils and freshwater ecosystems and belong to the phylum Proteobacteria. The Janthinobacterium sp. SLB01 strain was isolated from diseased freshwater Lubomirskia baicalensis (Pallas, 1776) sponge, and the draft genome was published previously. However, the properties of the SLB01 strain are not known. The aim of the study is to describe some properties of the Janthinobacterium sp. SLB01 strain, isolated from L. baicalensis sponge. The identification of the SLB01 strain was established as Gram-negative, motile, rod-shaped, and psychrotolerant, with growth at 3 and 22 °C. We found that the SLB01 strain has proteolytic, lipolytic, and saccharolytic activity and can use citrates and reduce nitrates. The bacteria Janthinobacterium sp. SLB01 strain can grow, form biofilms, and produce the violet pigment violacein. We identified the pigments violacein and deoxyviolacein by chromatography and mass spectrometry. These metabolites may be of interest to biotechnology in the future. The studied characteristics of the Janthinobacterium sp. SLB01 strain are an important addition to previous studies of the genome of this strain. This study will help us to understand the relationship between the microbial communities of Lake Baikal and sponges. Full article

(This article belongs to the Special Issue Blue Microbiology—Aquatic Microbial Resources for Sustainable Life on Earth)

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12 pages, 2155 KiB

Open AccessArticle

Whole-Genome Sequencing Reveals Multiple Subpopulations of Dominant and Persistent Lineage I Isolates of Listeria monocytogenes in Two Meat Processing Facilities during 2011–2015

by Elton Burnett, Zuzana Kucerova, Molly Freeman, Sophia Kathariou, Jessica Chen and Monica Smikle

Microorganisms 2022, 10(5), 1070; https://doi.org/10.3390/microorganisms10051070 - 23 May 2022

Cited by 9 | Viewed by 2750

Abstract

Listeria monocytogenes is a foodborne pathogen with a highly clonal population structure comprising multiple phylogenetic sub-groups that can persist within food processing environments and contaminate food. The epidemiology of L. monocytogenes is well-described in some developed countries; however, little is known about the [...] Read more.

Listeria monocytogenes is a foodborne pathogen with a highly clonal population structure comprising multiple phylogenetic sub-groups that can persist within food processing environments and contaminate food. The epidemiology of L. monocytogenes is well-described in some developed countries; however, little is known about the prevalence and population structure of this pathogen in food and food processing environments located in less developed regions. The aim of this study was to determine the genetic characteristics and clonal relatedness of L. monocytogenes that were isolated from two Jamaican meat processing facilities. Of the 37 isolates collected between 2011 and 2015, only a single lineage II isolate was recovered (serotype 1/2c), and the remaining were lineage I isolates representing serotypes 4b, 1/2b, 3b, and two untypeable isolates. Pulsed-field gel electrophoresis (PFGE) delineated isolates into seven pulsotypes, and whole-genome sequencing (WGS) categorized most isolates within one of three clonal complexes (CC): CC2 (N = 12), CC5 (N = 11), and CC288 (N = 11). Isolates representing CC1 (N = 2) and CC9 (N = 1) were also recovered. Virulence-associated genes such as inlA and the LIPI-3 cluster were detected in multiple isolates, along with the stress survival islet cluster-1 (SSI-1), and benzalkonium (bcrABC) and cadmium (cad1, cad2, cad4) resistance cassettes. Multiple isolates that belong to the same CC and matching PFGE patterns were isolated from food and the environment from both facilities across multiple years, suggesting the presence of persistent strains of L. monocytogenes, and/or constant re-entry of the pathogens into the facilities from common sources. These findings highlight the ability of lineage I isolates of L. monocytogenes to colonize, persist, and predominate within two meat-producing environments, and underscores the need for robust surveillance strategies to monitor and mitigate against these important foodborne pathogens. Full article

(This article belongs to the Special Issue An Update on Listeria monocytogenes)

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14 pages, 1001 KiB

Open AccessArticle

Seroprevalence, Direct Detection and Risk Factors for Toxoplasma gondii Infection in Pigs in Serbia, and Influence of Biosecurity Measures

by Nikola Betić, Nedjeljko Karabasil, Olgica Djurković-Djaković, Vladimir Ćirković, Branko Bobić, Ivana Branković Lazić, Vesna Djordjević and Ivana Klun

Microorganisms 2022, 10(5), 1069; https://doi.org/10.3390/microorganisms10051069 - 23 May 2022

Cited by 4 | Viewed by 2308

Abstract

Consumption of Toxoplasma gondii contaminated pork is a major risk factor for human infection. We thus conducted a cross-sectional survey on the seroprevalence of T. gondii infection in a representative sample of slaughter pigs from throughout Serbia and examined the influence of farm [...] Read more.

Consumption of Toxoplasma gondii contaminated pork is a major risk factor for human infection. We thus conducted a cross-sectional survey on the seroprevalence of T. gondii infection in a representative sample of slaughter pigs from throughout Serbia and examined the influence of farm biosecurity-related risk factors on infection. In addition, direct detection of the parasite (by mouse bioassay) or its DNA was performed in the hearts of a subset of seropositive sows. The overall seroprevalence in the sample of 825 pigs as determined by the modified agglutination test (MAT) was 16.5%. Older age and inadequate rodent control were independent infection risk factors for pigs. In a subset of 581 pigs with complete biosecurity-related data, in addition to older age, smallholders’ finishing type farms (as opposed to farrow-to-finish), multispecies farming, and origin from Western and Central and South-Eastern Serbia (vs. the Northern region), all increased the risk of infection, while the absence of disinfection boot-dips in front of each barn and Belgrade district origin (vs. the Northern region) were associated with a 62% and 75% lower risk of infection, respectively. Evidence of viable parasites was obtained in 13 (41.9%) of the 31 bioassayed sow hearts, of which by isolation of brain cysts in seven, by detection of T. gondii DNA in an additional four, and by serology in another two. Recovery of brain cysts mostly (5/7) from sows with a MAT titre of ≥1:100 indicates the risk for consumers. These results highlight the public health risk from pork consumption and point to mandatory use of professional rodent control services, abstaining from multispecies farming, keeping disinfection boot-dips clean and freshly refilled, as well as strict implementation of zoo-hygienic measures on smallholders’ farms as specific farm biosecurity measures needed for its reduction. Full article

(This article belongs to the Special Issue Advances in the Diagnosis, Detection, Epidemiology, and Control of Toxoplasma gondii)

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21 pages, 2312 KiB

Open AccessArticle

Root-Knot Disease Suppression in Eggplant Based on Three Growth Ages of Ganoderma lucidum

by Saba Fatima, Faryad Khan, Mohd Asif, Saqer S. Alotaibi, Khushbu Islam, Mohammad Shariq, Arshad Khan, Mohd Ikram, Faheem Ahmad, Tabreiz Ahmad Khan, Rampratap Meena and Mansoor Ahmad Siddiqui

Microorganisms 2022, 10(5), 1068; https://doi.org/10.3390/microorganisms10051068 - 23 May 2022

Cited by 5 | Viewed by 2536

Abstract

This investigation presents a novel finding showing the effect of culture filtrates (CFs) of macrofungi, Ganoderma lucidum, against Meloidogyne incognita evaluated in vitro and in planta. To determine the nematicidal activity, juveniles of M. incognita were exposed to Ganoderma CFs of three [...] Read more.

This investigation presents a novel finding showing the effect of culture filtrates (CFs) of macrofungi, Ganoderma lucidum, against Meloidogyne incognita evaluated in vitro and in planta. To determine the nematicidal activity, juveniles of M. incognita were exposed to Ganoderma CFs of three different ages (Two, four and eight weeks old) of pileus and stipe at different concentrations, i.e., 100%, 50%, 10% and 1% for different time intervals (12, 24, 48 and 72 h). Ganoderma species were examined morphologically based on external appearance and analytically using SEM. The ethanolic samples of basidiocarp were prepared and analyzed for in vitro nematicidal assay and different bioactive compounds. The in vitro experiment results revealed that among all three ages of pileus and stipe, two-week-old pileus and stipe exhibited great nematotoxic potency and caused 83.8% and 73.8% juveniles’ mortality at 100% concentration after 72 h of exposure time, respectively. Similarly, the two-week-old pileus and stipe showed the highest egg hatching inhibition of 89.2% and 81.0% at the 100% concentration after five days. The eight-week-old pileus and stipe were not more effective than the two- and four-week-old pileus and stipe. The metabolites were characterized using GC-MS, including sugar alcohol, steroids, silanes, glucosides, pyrones, ester, oleic acid, phthalic acid, linoleic acid, palmitates and ketones. The in planta study conducted in the greenhouse demonstrated that the root dip treatment for 30 min with Ganoderma CFs curtailed the infection level of M. incognita and promoted the eggplant plant growth. The maximum percent increase in plant length, plant fresh weight, plant dry weight, total chlorophyll, carotenoids and yield/plant was obtained at 100% conc. of fungus CFs, whereas a reduction was observed in nematode infestation parameters. It was concluded from the study that Ganoderma CFs can be explored as an effective and eco-friendly antinemic biocontrol agent in fields infected with root-knot nematodes. Full article

(This article belongs to the Special Issue Microorganisms as Biocontrol Agents)

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10 pages, 446 KiB

Open AccessArticle

Antibiotic Resistance in Campylobacter spp. Isolated from Broiler Chicken Meat and Human Patients in Estonia

by Triin Tedersoo, Mati Roasto, Mihkel Mäesaar, Liidia Häkkinen, Veljo Kisand, Marina Ivanova, Marikki Heidi Valli and Kadrin Meremäe

Microorganisms 2022, 10(5), 1067; https://doi.org/10.3390/microorganisms10051067 - 22 May 2022

Cited by 7 | Viewed by 2911

Abstract

Poultry meat is considered the most important source of Campylobacter spp. Because of rising antimicrobial resistance in Campylobacter spp., this study investigated the antimicrobial resistance of Campylobacter isolates from fresh broiler chicken meat originating from the Baltic countries sold in Estonian retail settings. [...] Read more.

Poultry meat is considered the most important source of Campylobacter spp. Because of rising antimicrobial resistance in Campylobacter spp., this study investigated the antimicrobial resistance of Campylobacter isolates from fresh broiler chicken meat originating from the Baltic countries sold in Estonian retail settings. Additionally, human clinical isolates obtained from patients with Campylobacter enteritis in Estonia were analysed. The aim of this study was to investigate the susceptibility of Campylobacter spp. to nalidixic acid, ciprofloxacin, tetracycline, streptomycin, erythromycin and gentamicin. The broth microdilution method with the EUCAMP2 panel was used for MIC determination and antimicrobial mechanisms were analysed using WGS data. A total of 46 Campylobacter strains were analysed, of which 26 (42.6%) originated from Lithuanian, 16 (26.2%) from Latvian, and 4 (6.6%) from Estonian fresh broiler chicken meat. In addition, 15 (24.6%) Campylobacter strains of patients with campylobacteriosis were tested. The antimicrobial resistance patterns of Campylobacter spp. isolated from fresh broiler chicken meat samples of Estonian, Latvian and Lithuanian origin collected in Estonian retail, and from patients with Campylobacter enteric infections, were determined. A total of 46 (75%) of the isolates tested were C. jejuni and 15 (25%) were C. coli. Campylobacter resistance was highest to nalidixic acid (90.2% of strains) and ciprofloxacin (90.2%), followed by tetracycline (57.4%), streptomycin (42.6%) and erythromycin (6.6%). All strains were sensitive to gentamicin. Additionally, antimicrobial resistance genes and point mutations were detected in 27 C. jejuni and 8 C. coli isolates previously assigned as resistant with the phenotypic method. A high antibiotic resistance of Campylobacter spp. in Lithuanian- and Latvian-origin broiler chicken meat and Estonian clinical isolates was found. Similar antibiotic resistance patterns were found for broiler chicken meat and human Campylobacter isolates. Full article

(This article belongs to the Special Issue Pathogens and Antimicrobial Drug Resistance in the Food Chain)

11 pages, 4328 KiB

Open AccessArticle

Effects of Humic Substances on the Growth of Pseudomonas plecoglossicida 2,4-D and Wheat Plants Inoculated with This Strain

by Arina Feoktistova, Margarita Bakaeva, Maxim Timergalin, Darya Chetverikova, Aliya Kendjieva, Timur Rameev, Gaisar Hkudaygulov, Aleksey Nazarov, Guzel Kudoyarova and Sergey Chetverikov

Microorganisms 2022, 10(5), 1066; https://doi.org/10.3390/microorganisms10051066 - 22 May 2022

Cited by 11 | Viewed by 2293

Abstract

Both rhizosphere bacteria and humic substances (HSs) can promote plant growth when applied individually and even greater effects of their combination have been demonstrated. We aimed to elucidate the relative importance of the stimulating effects of HSs on bacterial growth and the effects [...] Read more.

Both rhizosphere bacteria and humic substances (HSs) can promote plant growth when applied individually and even greater effects of their combination have been demonstrated. We aimed to elucidate the relative importance of the stimulating effects of HSs on bacterial growth and the effects of the combination of bacteria and HSs on plants themselves. The effects of humic (HA) and fulvic acids (FA) (components of humic substances) on the growth of Pseudomonas plecoglossicida 2,4-D in vitro were studied. We also studied the effects of this bacterial strain and HSs applied individually or in combination on the growth of wheat plants. Although the 2,4-D strain showed low ability to use HSs as the sole source of nutrition, the bacterial growth rate was increased by FA and HA, when other nutrients were available. HSs increased root colonization with bacteria, the effect being greater in the case of HA. The effects on roots and shoots increased when bacteria were associated with HSs. FA+ 2,4-D was more effective in stimulating shoot growth, while HA + 2,4-D was in the case of root growth. The latter effect is likely to be beneficial under edaphic stresses. Full article

(This article belongs to the Special Issue Interactions between Plant Beneficial Pseudomonas spp. and Their Host)

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13 pages, 1054 KiB

Open AccessReview

Functional Foods, Nutraceuticals and Probiotics: A Focus on Human Health

by Morayma Ramírez Damián, Naima G. Cortes-Perez, Erika T. Quintana, Alicia Ortiz-Moreno, Cynthia Garfias Noguez, Carlos Eugenio Cruceño-Casarrubias, María Elena Sánchez Pardo and Luis G. Bermúdez-Humarán

Microorganisms 2022, 10(5), 1065; https://doi.org/10.3390/microorganisms10051065 - 21 May 2022

Cited by 72 | Viewed by 14732

Abstract

Functional foods are classified as traditional or staple foods that provide an essential nutritional level and share potentially positive effects on host health, including the reduction of disease by optimizing the immune system’s ability to prevent and control infections by pathogens, as well [...] Read more.

Functional foods are classified as traditional or staple foods that provide an essential nutritional level and share potentially positive effects on host health, including the reduction of disease by optimizing the immune system’s ability to prevent and control infections by pathogens, as well as pathologies that cause functional alterations in the host. This chapter reviews the most recent research and advances in this area and discusses some perspectives on what the future holds in this area. Full article

(This article belongs to the Special Issue Novel Probiotic Strains and Bacteriotherapy)

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4 pages, 201 KiB

Open AccessEditorial

Editorial for the Special Issue “Microbial Nonribosomal Synthesis of Secondary Metabolites”

by Stéphane Cociancich and Valérie Leclère

Microorganisms 2022, 10(5), 1064; https://doi.org/10.3390/microorganisms10051064 - 21 May 2022

Viewed by 1653

Abstract

Microbial secondary metabolites are natural products that display various therapeutical or agrochemical relevant activities (e [...] Full article

(This article belongs to the Special Issue Microbial Non-Ribosomal Synthesis of Secondary Metabolites)

18 pages, 3675 KiB

Open AccessArticle

Physiological and Metabolic Response of Arthrospira maxima to Organophosphates

by Amalia Piro, Dante Matteo Nisticò, Daniela Oliva, Francesco Antonio Fagà and Silvia Mazzuca

Microorganisms 2022, 10(5), 1063; https://doi.org/10.3390/microorganisms10051063 - 21 May 2022

Cited by 3 | Viewed by 2310

Abstract

The Spirulina spp. exhibited an ability to tolerate the organophosphates. This study aimed to explore the effects of the herbicide glyphosate on a selected strain of the cyanobacteria Arthrospira maxima cultivated in a company. Experimental cultivations acclimated in aquaria were treated with 0.2 [...] Read more.

The Spirulina spp. exhibited an ability to tolerate the organophosphates. This study aimed to explore the effects of the herbicide glyphosate on a selected strain of the cyanobacteria Arthrospira maxima cultivated in a company. Experimental cultivations acclimated in aquaria were treated with 0.2 mM glyphosate [N-(phosphonomethyl) glycine]. The culture biomass, the phycocyanin, and the chlorophyll a concentrations were evaluated every week during 42 days of treatment. The differentially expressed proteins in the treated cyanobacteria versus the control cultivations were evaluated weekly during 21 days of treatment. Even if the glyphosate treatment negatively affected the biomass and the photosynthetic pigments, it induced resistance in the survival A. maxima population. Proteins belonging to the response to osmotic stress and methylation pathways were strongly accumulated in treated cultivation; the response to toxic substances and the negative regulation of transcription seemed to have a role in the resistance. The glyphosate-affected enzyme, chorismate synthase, a key enzyme in the shikimic acid pathway, was accumulated during treatment, suggesting that the surviving strain of A. maxima expressed a glyphosate-resistant target enzyme. Full article

(This article belongs to the Special Issue A Glimpse into Future Research on Microalgae Diversity, Ecology and Biotechnology)

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17 pages, 7673 KiB

Open AccessArticle

Comparative Analysis of Original and Replaced Gut Microbiomes within Same Individuals Identified the Intestinal Microbes Associated with Weight Gaining

by Chongkai Zhai, Ji-Seon Ahn, Md Minarul Islam, Enkhchimeg Lkhagva, Hea-Jong Chung and Seong-Tshool Hong

Microorganisms 2022, 10(5), 1062; https://doi.org/10.3390/microorganisms10051062 - 20 May 2022

Cited by 4 | Viewed by 2287

Abstract

The precise mechanisms of action of the host’s gut microbiome at the level of its constituting bacteria are obscure in most cases despite its definitive role. To study the precise role of the gut microbiome on the phenotypes of a host by excluding [...] Read more.

The precise mechanisms of action of the host’s gut microbiome at the level of its constituting bacteria are obscure in most cases despite its definitive role. To study the precise role of the gut microbiome on the phenotypes of a host by excluding host factors, we analyzed two different gut microbiomes within the same individual mouse after replacing the gut microbiome with a new one to exclude the host factors. The gut microbiome of conventional C57BL/6 mice was randomly reestablished by feeding fecal samples from obese humans to the mice, and depleting their original gut microbiome with an antibiotic and antifungal treatment. Comparison of body weight changes before and 3 months after the replacement of the gut microbiome showed that the gut microbiome replacement affected the body weight gain in three different ways: positive, medium, and negative. The differences in body weight gain were associated with establishment of a different kind of gut microbiome in each of the mice. In addition, body weight gaining was negatively associated with the Firmicutes/Bacteroidetes ratio, which is consistent with previous recent findings. Thorough statistical analysis at low taxonomic levels showed that uncultured bacteria NR_074436.1, NR_144750.1, and NR_0421101.1 were positively associated with body weight gain, while Trichinella pseudospiralis and uncultured bacteria NR_024815.1 and NR_144616.1 were negatively associated. This work shows that replacement of the gut microbiome within the same individual provides an excellent opportunity for the purpose of gut microbiome analysis by excluding the host factors. Full article

(This article belongs to the Special Issue Feature Papers in Gut Microbiota)

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18 pages, 1129 KiB

Open AccessArticle

The Identification and Characterization of Endopolygalacturonases in a South African Isolate of Phytophthora cinnamomi

by Tsakani Magdeline Miyambo, Robert Backer, Juanita Engelbrecht, Fourie Joubert, Nicolaas Albertus van der Merwe and Noëlani van den Berg

Microorganisms 2022, 10(5), 1061; https://doi.org/10.3390/microorganisms10051061 - 20 May 2022

Viewed by 2080

Abstract

Phytophthora cinnamomi is an economically important plant pathogen that has caused devastating losses to the avocado industry worldwide. To facilitate penetration and successful colonization of the host plant, pathogens have been reported to secrete polygalacturonases (PGs). Although a large PG gene family has [...] Read more.

Phytophthora cinnamomi is an economically important plant pathogen that has caused devastating losses to the avocado industry worldwide. To facilitate penetration and successful colonization of the host plant, pathogens have been reported to secrete polygalacturonases (PGs). Although a large PG gene family has been reported in P. cinnamomi, in-depth bioinformatics analyses and characterization of these genes is still lacking. In this study we used bioinformatics tools and molecular biology techniques to identify and characterize endopolygalacturonases in the genome of a South African P. cinnamomi isolate, GKB4. We identified 37 PGs, with 19 characteristics of full-length PGs. Although eight PcPGs were induced in planta during infection, only three showed significant up- and down-regulation when compared with in vitro mycelial growth, suggesting their possible roles in infection. The phylogenetic analysis of PcPGs showed both gain and loss of introns in the evolution of PGs in P. cinnamomi. Furthermore, 17 PGs were related to characterized PGs from oomycete species, providing insight on possible function. This study provides new data on endoPGs in P. cinnamomi and the evolution of introns in PcPG genes. We also provide a baseline for future functional characterization of PGs suspected to contribute to P. cinnamomi pathogenicity/virulence in avocado. Full article

(This article belongs to the Section Plant Microbe Interactions)

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15 pages, 2992 KiB

Open AccessArticle

Effect of Input C/N Ratio on Bacterial Community of Water Biofloc and Shrimp Gut in a Commercial Zero-Exchange System with Intensive Production of Penaeus vannamei

by Wujie Xu, Guoliang Wen, Haochang Su, Yu Xu, Xiaojuan Hu and Yucheng Cao

Microorganisms 2022, 10(5), 1060; https://doi.org/10.3390/microorganisms10051060 - 20 May 2022

Cited by 25 | Viewed by 3541

Abstract

Although increasing attention has been attracted to the study and application of biofloc technology (BFT) in aquaculture, few details have been reported about the bacterial community of biofloc and its manipulation strategy for commercial shrimp production. An 8-week trial was conducted to investigate [...] Read more.

Although increasing attention has been attracted to the study and application of biofloc technology (BFT) in aquaculture, few details have been reported about the bacterial community of biofloc and its manipulation strategy for commercial shrimp production. An 8-week trial was conducted to investigate the effects of three input C/N ratios (8:1, 12:1 and 16:1) on the bacterial community of water biofloc and shrimp gut in a commercial BFT tank system with intensive aquaculture of P. vannamei. Each C/N ratio group had three randomly assigned replicate tanks (culture water volume of 30 m³), and each tank was stocked with juvenile shrimp at a density of 300 shrimp m⁻³. The tank systems were operated with zero-water exchange, pH maintenance and biofloc control. During the trial, the microbial biomass and bacterial density of water biofloc showed similar variation trends, with no significant difference under respective biofloc control measures for the three C/N ratio groups. Significant changes were found in the alpha diversity, composition and relative abundance of bacterial communities across the stages of the trial, and they showed differences in water biofloc and shrimp gut among the three C/N ratio groups. Meanwhile, high similarity could be found in the composition of the bacterial community between water biofloc and shrimp gut. Additionally, nitrogen dynamics in culture water showed some differences while shrimp performance showed no significant difference among the three C/N ratio groups. Together, these results confirm that the manipulation of input C/N ratio could affect the bacterial community of both water biofloc and shrimp gut in the environment of a commercial BFT system with intensive production of P. vannamei. Moreover, there should be different operations for the nitrogen dynamics and biofloc management during shrimp production process under different C/N ratios. Full article

(This article belongs to the Special Issue Marine Bacterial Biofilm)

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18 pages, 2024 KiB

Open AccessArticle

Coculture of Trichoderma harzianum and Bacillus velezensis Based on Metabolic Cross-Feeding Modulates Lipopeptide Production

by Barbara Fifani, Sebastien Steels, Catherine Helmus, Alice Delacuvellerie, Barbara Deracinois, Vincent Phalip, Frank Delvigne and Philippe Jacques

Microorganisms 2022, 10(5), 1059; https://doi.org/10.3390/microorganisms10051059 - 20 May 2022

Cited by 11 | Viewed by 3170

Abstract

Cocultures have been widely explored for their use in deciphering microbial interaction and its impact on the metabolisms of the interacting microorganisms. In this work, we investigate, in different liquid coculture conditions, the compatibility of two microorganisms with the potential for the biocontrol [...] Read more.

Cocultures have been widely explored for their use in deciphering microbial interaction and its impact on the metabolisms of the interacting microorganisms. In this work, we investigate, in different liquid coculture conditions, the compatibility of two microorganisms with the potential for the biocontrol of plant diseases: the fungus Trichoderma harzianum IHEM5437 and the bacterium Bacillus velezensis GA1 (a strong antifungal lipopeptide producing strain). While the Bacillus overgrew the Trichoderma in a rich medium due to its antifungal lipopeptide production, a drastically different trend was observed in a medium in which a nitrogen nutritional dependency was imposed. Indeed, in this minimum medium containing nitrate as the sole nitrogen source, cooperation between the bacterium and the fungus was established. This is reflected by the growth of both species as well as the inhibition of the expression of Bacillus genes encoding lipopeptide synthetases. Interestingly, the growth of the bacterium in the minimum medium was enabled by the amendment of the culture by the fungal supernatant, which, in this case, ensures a high production yield of lipopeptides. These results highlight, for the first time, that Trichoderma harzianum and Bacillus velezensis are able, in specific environmental conditions, to adapt their metabolisms in order to grow together. Full article

(This article belongs to the Special Issue Antimicrobial Lipopeptide Biosurfactant)

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13 pages, 2344 KiB

Open AccessArticle

Comparative Genomics of Acetic Acid Bacteria within the Genus Bombella in Light of Beehive Habitat Adaptation

by Luca Härer, Maik Hilgarth and Matthias A. Ehrmann

Microorganisms 2022, 10(5), 1058; https://doi.org/10.3390/microorganisms10051058 - 20 May 2022

Cited by 6 | Viewed by 2818

Abstract

It is known that the bacterial microbiota in beehives is essential for keeping bees healthy. Acetic acid bacteria of the genus Bombella colonize several niches in beehives and are associated with larvae protection against microbial pathogens. We have analyzed the genomes of 22 [...] Read more.

It is known that the bacterial microbiota in beehives is essential for keeping bees healthy. Acetic acid bacteria of the genus Bombella colonize several niches in beehives and are associated with larvae protection against microbial pathogens. We have analyzed the genomes of 22 Bombella strains of different species isolated in eight different countries for taxonomic affiliation, central metabolism, prophages, bacteriocins and tetracycline resistance to further elucidate the symbiotic lifestyle and to identify typical traits of acetic acid bacteria. The genomes can be assigned to four different species. Three genomes show ANIb values and DDH values below species demarcation values to any validly described species, which identifies them as two potentially new species. All Bombella spp. lack genes in the Embden–Meyerhof–Parnas pathway and the tricarboxylic acid cycle, indicating a focus of intracellular carbohydrate metabolism on the pentose phosphate pathway or the Entner–Doudoroff pathway for which all genes were identified within the genomes. Five membrane-bound dehydrogenases were identified that catalyze oxidative fermentation reactions in the periplasm, yielding oxidative energy. Several complete prophages, but no bacteriocins, were identified. Resistance to tetracycline, used to prevent bacterial infections in beehives, was only found in Bombella apis MRM1^T. Bombella strains exhibit increased osmotolerance in high glucose concentrations compared to Gluconobacter oxydans, indicating adaption to high sugar environments such as beehives. Full article

(This article belongs to the Special Issue Microorganisms in Pollinators: Interactions with Other Factors 2.0)

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13 pages, 696 KiB

Open AccessReview

Azospirillum spp. from Plant Growth-Promoting Bacteria to Their Use in Bioremediation

by María Antonia Cruz-Hernández, Alberto Mendoza-Herrera, Virgilio Bocanegra-García and Gildardo Rivera

Microorganisms 2022, 10(5), 1057; https://doi.org/10.3390/microorganisms10051057 - 20 May 2022

Cited by 22 | Viewed by 5227

Abstract

Xenobiotic contamination, a worldwide environmental concern, poses risks for humans, animals, microbe health, and agriculture. Hydrocarbons and heavy metals top the list of toxins that represent a risk to nature. This review deals with the study of Azospirillum sp., widely reported as plant [...] Read more.

Xenobiotic contamination, a worldwide environmental concern, poses risks for humans, animals, microbe health, and agriculture. Hydrocarbons and heavy metals top the list of toxins that represent a risk to nature. This review deals with the study of Azospirillum sp., widely reported as plant growth-promoting bacteria in various cultures. However, its adaptation properties in adverse environments make it a good candidate for studying remediation processes in environments polluted with hydrocarbons and heavy metals. This review includes studies that address its properties as a plant growth promoter, its genomics, and that evaluate its potential use in the remediation of hydrocarbons and heavy metals. Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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18 pages, 3994 KiB

Open AccessArticle

Tillage Practices and Residue Management Manipulate Soil Bacterial and Fungal Communities and Networks in Maize Agroecosystems

by Yupeng Guan, Bei Xu, Ximei Zhang and Wei Yang

Microorganisms 2022, 10(5), 1056; https://doi.org/10.3390/microorganisms10051056 - 20 May 2022

Cited by 16 | Viewed by 3082

Abstract

Tillage practices and residue management are highly important agricultural practices. However, very few studies have examined the influence of tillage practices and residue management on both bacterial and fungal communities and network patterns in consecutive years. We examined the effects of different tillage [...] Read more.

Tillage practices and residue management are highly important agricultural practices. However, very few studies have examined the influence of tillage practices and residue management on both bacterial and fungal communities and network patterns in consecutive years. We examined the effects of different tillage practices, including no tillage, rotary tillage, and deep tillage, on soil bacterial and fungal communities and co-occurrence networks following residue removal and residue retention in 2017 and 2018. This study showed that both bacterial and fungal communities were unaffected by tillage practices in 2017, but they were significantly impacted in 2018. Soil fungal operational taxonomic unit (OTU) richness was significantly enhanced by deep tillage compared with no tillage in 2018, while bacterial OTU richness was unaffected in either year. Tillage practices had differing effects on soil microbial co-occurrence networks, with rotary and deep tillage increasing the complexity of bacterial networks but simplifying fungal networks. However, residue retention only induced a shift in the fungal community and simplified soil bacterial and fungal networks in 2018. This study highlights the dissimilar responses of bacterial and fungal networks to tillage practices and emphasizes that tillage practice is more important than residue management in shaping soil microbial communities. Full article

(This article belongs to the Special Issue Plant and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems 2.0)

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16 pages, 3623 KiB

Open AccessArticle

Zam Is a Redox-Regulated Member of the RNB-Family Required for Optimal Photosynthesis in Cyanobacteria

by Patrick E. Thomas, Colin Gates, William Campodonico-Burnett and Jeffrey C. Cameron

Microorganisms 2022, 10(5), 1055; https://doi.org/10.3390/microorganisms10051055 - 20 May 2022

Viewed by 2727

Abstract

The zam gene mediating resistance to acetazolamide in cyanobacteria was discovered thirty years ago during a drug tolerance screen. We use phylogenetics to show that Zam proteins are distributed across cyanobacteria and that they form their own unique clade of the ribonuclease II/R [...] Read more.

The zam gene mediating resistance to acetazolamide in cyanobacteria was discovered thirty years ago during a drug tolerance screen. We use phylogenetics to show that Zam proteins are distributed across cyanobacteria and that they form their own unique clade of the ribonuclease II/R (RNB) family. Despite being RNB family members, multiple sequence alignments reveal that Zam proteins lack conservation and exhibit extreme degeneracy in the canonical active site—raising questions about their cellular function(s). Several known phenotypes arise from the deletion of zam, including drug resistance, slower growth, and altered pigmentation. Using room-temperature and low-temperature fluorescence and absorption spectroscopy, we show that deletion of zam results in decreased phycocyanin synthesis rates, altered PSI:PSII ratios, and an increase in coupling between the phycobilisome and PSII. Conserved cysteines within Zam are identified and assayed for function using in vitro and in vivo methods. We show that these cysteines are essential for Zam function, with mutation of either residue to serine causing phenotypes identical to the deletion of Zam. Redox regulation of Zam activity based on the reversible oxidation-reduction of a disulfide bond involving these cysteine residues could provide a mechanism to integrate the ‘central dogma’ with photosynthesis in cyanobacteria. Full article

(This article belongs to the Special Issue Phototrophic Bacteria)

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12 pages, 1713 KiB

Open AccessArticle

The Gut Microbiota May Affect Personality in Mongolian Gerbils

by Lin Gan, Tingbei Bo, Wei Liu and Dehua Wang

Microorganisms 2022, 10(5), 1054; https://doi.org/10.3390/microorganisms10051054 - 20 May 2022

Cited by 4 | Viewed by 2783

Abstract

The “gut–microbiota–brain axis” reveals that gut microbiota plays a critical role in the orchestrating behavior of the host. However, the correlation between the host personalities and the gut microbiota is still rarely known. To investigate whether the gut microbiota of Mongolian gerbils ( [...] Read more.

The “gut–microbiota–brain axis” reveals that gut microbiota plays a critical role in the orchestrating behavior of the host. However, the correlation between the host personalities and the gut microbiota is still rarely known. To investigate whether the gut microbiota of Mongolian gerbils (Meriones unguiculatus) differs between bold and shy personalities, we compared the gut microbiota of bold and shy gerbils, and then we transplanted the gut microbiota of bold and shy gerbils into middle group gerbils (individuals with less bold and shy personalities). We found a significant overall correlation between host boldness and gut microbiota. Even though there were no significant differences in alpha diversity and beta diversity of gut microbiota between bold and shy gerbils, the Firmicutes/Bacteroidetes phyla and Odoribacter and Blautia genus were higher in bold gerbils, and Escherichia_shigella genus was lower. Furthermore, the fecal microbiota transplantation showed that changes in gut microbiota could not evidently cause the increase or decrease in the gerbil’s boldness score, but it increased the part of boldness behaviors by gavaging the “bold fecal microbiota”. Overall, these data demonstrated that gut microbiota were significantly correlated with the personalities of the hosts, and alteration of microbiota could alter host boldness to a certain extent. 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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25 pages, 1029 KiB

Open AccessReview

Root-Associated Bacteria Are Biocontrol Agents for Multiple Plant Pests

by Jang Hoon Lee, Anne J. Anderson and Young Cheol Kim

Microorganisms 2022, 10(5), 1053; https://doi.org/10.3390/microorganisms10051053 - 19 May 2022

Cited by 13 | Viewed by 3688

Abstract

Biological control is an important process for sustainable plant production, and this trait is found in many plant-associated microbes. This study reviews microbes that could be formulated into pesticides active against various microbial plant pathogens as well as damaging insects or nematodes. The [...] Read more.

Biological control is an important process for sustainable plant production, and this trait is found in many plant-associated microbes. This study reviews microbes that could be formulated into pesticides active against various microbial plant pathogens as well as damaging insects or nematodes. The focus is on the beneficial microbes that colonize the rhizosphere where, through various mechanisms, they promote healthy plant growth. Although these microbes have adapted to cohabit root tissues without causing disease, they are pathogenic to plant pathogens, including microbes, insects, and nematodes. The cocktail of metabolites released from the beneficial strains inhibits the growth of certain bacterial and fungal plant pathogens and participates in insect and nematode toxicity. There is a reinforcement of plant health through the systemic induction of defenses against pathogen attack and abiotic stress in the plant; metabolites in the beneficial microbial cocktail function in triggering the plant defenses. The review discusses a wide range of metabolites involved in plant protection through biocontrol in the rhizosphere. The focus is on the beneficial firmicutes and pseudomonads, because of the extensive studies with these isolates. The review evaluates how culture conditions can be optimized to provide formulations containing the preformed active metabolites for rapid control, with or without viable microbial cells as plant inocula, to boost plant productivity in field situations. Full article

(This article belongs to the Special Issue Microorganisms as Biocontrol Agents)

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25 pages, 1665 KiB

Open AccessReview

Biological Control of Acinetobacter baumannii: In Vitro and In Vivo Activity, Limitations, and Combination Therapies

by Benjamin Havenga, Brandon Reyneke, Monique Waso-Reyneke, Thando Ndlovu, Sehaam Khan and Wesaal Khan

Microorganisms 2022, 10(5), 1052; https://doi.org/10.3390/microorganisms10051052 - 19 May 2022

Cited by 7 | Viewed by 3192

Abstract

The survival, proliferation, and epidemic spread of Acinetobacter baumannii (A. baumannii) in hospital settings is associated with several characteristics, including resistance to many commercially available antibiotics as well as the expression of multiple virulence mechanisms. This severely limits therapeutic options, with [...] Read more.

The survival, proliferation, and epidemic spread of Acinetobacter baumannii (A. baumannii) in hospital settings is associated with several characteristics, including resistance to many commercially available antibiotics as well as the expression of multiple virulence mechanisms. This severely limits therapeutic options, with increased mortality and morbidity rates recorded worldwide. The World Health Organisation, thus, recognises A. baumannii as one of the critical pathogens that need to be prioritised for the development of new antibiotics or treatment. The current review will thus provide a brief overview of the antibiotic resistance and virulence mechanisms associated with A. baumannii’s “persist and resist strategy”. Thereafter, the potential of biological control agents including secondary metabolites such as biosurfactants [lipopeptides (surfactin and serrawettin) and glycolipids (rhamnolipid)] as well as predatory bacteria (Bdellovibrio bacteriovorus) and bacteriophages to directly target A. baumannii, will be discussed in terms of their in vitro and in vivo activity. In addition, limitations and corresponding mitigations strategies will be outlined, including curtailing resistance development using combination therapies, product stabilisation, and large-scale (up-scaling) production. Full article

(This article belongs to the Special Issue Microorganisms as Biocontrol Agents)

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11 pages, 1887 KiB

Open AccessArticle

Influence of Metal Concentration and Plumbing Materials on Legionella Contamination

by Anita Rakić, Darija Vukić Lušić and Anamarija Jurčev Savičević

Microorganisms 2022, 10(5), 1051; https://doi.org/10.3390/microorganisms10051051 - 19 May 2022

Cited by 4 | Viewed by 2421

Abstract

Legionella colonization of water supply pipes is a significant public health problem. The objective of this work was to evaluate Legionella colonization in hotel hot water systems and to investigate the relationship between metal concentrations, piping materials (galvanized iron pipes and plastic pipes), [...] Read more.

Legionella colonization of water supply pipes is a significant public health problem. The objective of this work was to evaluate Legionella colonization in hotel hot water systems and to investigate the relationship between metal concentrations, piping materials (galvanized iron pipes and plastic pipes), and Legionella proliferation. Concentrations of calcium and magnesium ions and the presence of Legionella pneumophila were determined in a total of 108 water samples from the hot water systems of four hotels in Split-Dalmatia County over a 12-month period, and additional data on piping materials were collected. L. pneumophila was isolated in 23.1% of all samples—in 28.8% (15/52) of water samples from galvanized iron pipes and in 17.8% (10/56) of samples from plastic pipes. L. pneumophila serogroups 2–14 were isolated from all samples. This study found higher prevalence of L. pneumophila at higher concentrations of Ca and Mg ions (except for Mg and plastic pipes). The metal parts of the water supply may be important factors in Legionella contamination due to the possibility of lime scale or roughness of the pipes. Higher Ca and Mg ion concentrations increased the risk of Legionella colonization. Full article

(This article belongs to the Special Issue Microbial Communities in Changing Aquatic Environments)

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14 pages, 1483 KiB

Open AccessReview

SARS CoV-2-Induced Viral Sepsis: The Role of Gut Barrier Dysfunction

by Stelios F. Assimakopoulos, Gerasimos Eleftheriotis, Maria Lagadinou, Vassilios Karamouzos, Periklis Dousdampanis, Georgios Siakallis and Markos Marangos

Microorganisms 2022, 10(5), 1050; https://doi.org/10.3390/microorganisms10051050 - 19 May 2022

Cited by 20 | Viewed by 6489

Abstract

A considerable proportion of patients with severe COVID-19 meet Sepsis-3 criteria and share common pathophysiological mechanisms of multiorgan injury with bacterial sepsis, in absence of secondary bacterial infections, a process characterized as “viral sepsis”. The intestinal barrier exerts a central role in the [...] Read more.

A considerable proportion of patients with severe COVID-19 meet Sepsis-3 criteria and share common pathophysiological mechanisms of multiorgan injury with bacterial sepsis, in absence of secondary bacterial infections, a process characterized as “viral sepsis”. The intestinal barrier exerts a central role in the pathophysiological sequence of events that lead from SARS-CoV-2 infection to severe systemic complications. Accumulating evidence suggests that SARS-CoV-2 disrupts the integrity of the biological, mechanical and immunological gut barrier. Specifically, microbiota diversity and beneficial bacteria population are reduced, concurrently with overgrowth of pathogenic bacteria (dysbiosis). Enterocytes’ tight junctions (TJs) are disrupted, and the apoptotic death of intestinal epithelial cells is increased leading to increased gut permeability. In addition, mucosal CD4(+) and CD8(+) T cells, Th17 cells, neutrophils, dendritic cells and macrophages are activated, and T-regulatory cells are decreased, thus promoting an overactivated immune response, which further injures the intestinal epithelium. This dysfunctional gut barrier in SARS-CoV-2 infection permits the escape of luminal bacteria, fungi and endotoxin to normally sterile extraintestinal sites and the systemic circulation. Pre-existing gut barrier dysfunction and endotoxemia in patients with comorbidities including cardiovascular disease, obesity, diabetes and immunosuppression predisposes to aggravated endotoxemia. Bacterial and endotoxin translocation promote the systemic inflammation and immune activation, which characterize the SARS-CoV-2 induced “viral sepsis” syndrome associated with multisystemic complications of severe COVID-19. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases and Strategies for Their Prevention and Control)

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14 pages, 2091 KiB

Open AccessArticle

Distinct Elevational Patterns and Their Linkages of Soil Bacteria and Plant Community in An Alpine Meadow of the Qinghai–Tibetan Plateau

by Jing Cong, Wei Cong, Hui Lu and Yuguang Zhang

Microorganisms 2022, 10(5), 1049; https://doi.org/10.3390/microorganisms10051049 - 19 May 2022

Cited by 2 | Viewed by 2083

Abstract

Soil microbes play important roles in determining plant community composition and terrestrial ecosystem functions, as well as the direction and extent of terrestrial ecosystem feedback to environmental changes. Understanding the distribution patterns of plant and soil microbiota along elevation gradients is necessary to [...] Read more.

Soil microbes play important roles in determining plant community composition and terrestrial ecosystem functions, as well as the direction and extent of terrestrial ecosystem feedback to environmental changes. Understanding the distribution patterns of plant and soil microbiota along elevation gradients is necessary to shed light on important ecosystem functions. In this study, soil bacteria along an elevation gradient in an alpine meadow ecosystem of the Qinghai–Tibetan Plateau were investigated using Illumina sequencing and GeoChip technologies. The community structure of the soil bacteria and plants presented a continuous trend along the elevation gradient, and their alpha diversity displayed different distribution patterns; however, there were no linkages between them. Beta diversity of the soil bacteria and plants was significantly influenced by elevational distance changes (p < 0.05). Functional gene categories involved in nitrogen and phosphorus cycling had faster changes than those involved in carbon degradation, and functional genes involved in labile carbon degradation also had faster variations than those involved in recalcitrant carbon degradation with elevational changes. According to Pearson’s correlation, partial Mantel test analysis, and canonical correspondence analysis, soil pH and mean annual precipitation were important environmental variables in influencing soil bacterial diversity. Soil bacterial diversity and plant diversity had different distribution patterns along the elevation gradient. Full article

(This article belongs to the Section Environmental Microbiology)

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7 pages, 244 KiB

Open AccessPerspective

Distinguishing Allies from Enemies—A Way for a New Green Revolution

by Teresa Lino-Neto and Paula Baptista

Microorganisms 2022, 10(5), 1048; https://doi.org/10.3390/microorganisms10051048 - 19 May 2022

Cited by 1 | Viewed by 2148

Abstract

Plants are continually interacting in different ways and levels with microbes, resulting in direct or indirect effects on plant development and fitness. Many plant–microbe interactions are beneficial and promote plant growth and development, while others have harmful effects and cause plant diseases. Given [...] Read more.

Plants are continually interacting in different ways and levels with microbes, resulting in direct or indirect effects on plant development and fitness. Many plant–microbe interactions are beneficial and promote plant growth and development, while others have harmful effects and cause plant diseases. Given the permanent and simultaneous contact with beneficial and harmful microbes, plants should avoid being infected by pathogens while promoting mutualistic relationships. The way plants perceive multiple microbes and trigger plant responses suggests a common origin of both types of interaction. Despite the recent advances in this topic, the exploitation of mutualistic relations has still not been fully achieved. The holistic view of different agroecosystem factors, including biotic and abiotic aspects, as well as agricultural practices, must also be considered. This approach could pave the way for a new green revolution that will allow providing food to a growing human population in the context of threat such as that resulting from climate change. Full article

(This article belongs to the Special Issue Advances in Plant-Microbe Interactions)

22 pages, 6140 KiB

Open AccessReview

Update on the Epidemiological Features and Clinical Implications of Human Papillomavirus Infection (HPV) and Human Immunodeficiency Virus (HIV) Coinfection

by Alexandre Pérez-González, Edward Cachay, Antonio Ocampo and Eva Poveda

Microorganisms 2022, 10(5), 1047; https://doi.org/10.3390/microorganisms10051047 - 18 May 2022

Cited by 34 | Viewed by 5200

Abstract

Human papillomavirus (HPV) infection is the most common sexually transmitted infection (STI) worldwide. Although most HPV infections will spontaneously resolve, a considerable proportion of them will persist, increasing the risk of anogenital dysplasia, especially within certain populations, such as patients infected with human [...] Read more.

Human papillomavirus (HPV) infection is the most common sexually transmitted infection (STI) worldwide. Although most HPV infections will spontaneously resolve, a considerable proportion of them will persist, increasing the risk of anogenital dysplasia, especially within certain populations, such as patients infected with human immunodeficiency virus (HIV). Furthermore, high-risk oncogenic HPV types (HR-HPV) are the main cause of cervix and other anogenital cancers, such as cancer of the vagina, vulva, penis, or anus. HIV and HPV coinfection is common among people living with HIV (PLWH) but disproportionally affects men who have sex with men (MSM) for whom the rate of persistent HPV infection and reinfection is noteworthy. The molecular interactions between HIV and HPV, as well as the interplay between both viruses and the immune system, are increasingly being understood. The immune dysfunction induced by HIV infection impairs the rate of HPV clearance and increases its oncogenic risk. Despite the availability of effective antiretroviral therapy (ART), the incidence of several HPV-related cancers is higher in PLWH, and the burden of persistent HPV-related disease has become a significant concern in an aging HIV population. Several public health strategies have been developed to reduce the transmission of HIV and HPV and mitigate the consequences of this type of coinfection. Universal HPV vaccination is the most effective preventive tool to reduce the incidence of HPV disease. In addition, screening programs for HPV-related cervical and vulvovaginal diseases in women are well-recognized strategies to prevent cervical cancer. Similarly, anal dysplasia screening programs are being implemented worldwide for the prevention of anal cancer among PLWH. Herein, the main epidemiological features and clinical implications of HIV and HPV coinfection are reviewed, focusing mainly on the relationship between HIV immune status and HPV-related diseases and the current strategies used to reduce the burden of HPV-related disease. Full article

(This article belongs to the Special Issue HIV and Other Viral Co-Infections)

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13 pages, 3568 KiB

Open AccessArticle

Sodium Citrate Alleviates Virulence in Pseudomonas aeruginosa

by Maan T. Khayat, Tarek S. Ibrahim, Ahdab N. Khayyat, Majed Alharbi, Moataz A. Shaldam, Khadijah A. Mohammad, El-Sayed Khafagy, Dalia A. El-damasy, Wael A. H. Hegazy and Hisham A. Abbas

Microorganisms 2022, 10(5), 1046; https://doi.org/10.3390/microorganisms10051046 - 18 May 2022

Cited by 31 | Viewed by 3664

Abstract

The development of bacterial resistance is an insistent global health care issue, especially in light of the dwindled supply of new antimicrobial agents. This mandates the development of new innovative approaches to overcome the resistance development obstacle. Mitigation of bacterial virulence is an [...] Read more.

The development of bacterial resistance is an insistent global health care issue, especially in light of the dwindled supply of new antimicrobial agents. This mandates the development of new innovative approaches to overcome the resistance development obstacle. Mitigation of bacterial virulence is an interesting approach that offers multiple advantages. Employing safe chemicals or drugs to mitigate bacterial virulence is an additive advantage. In the current study, the in vitro antivirulence activities of citrate were evaluated. Significantly, sodium citrate inhibited bacterial biofilm formation at sub-MIC concentrations. Furthermore, sodium citrate decreased the production of virulence factors protease and pyocyanin and diminished bacterial motility. Quorum sensing (QS) is the communicative system that bacterial cells utilize to communicate with each other and regulate the virulence of the host cells. In the present study, citrate in silico blocked the Pseudomonas QS receptors and downregulated the expression of QS-encoding genes. In conclusion, sodium citrate showed a significant ability to diminish bacterial virulence in vitro and interfered with QS; it could serve as a safe adjuvant to traditional antibiotic treatment for aggressive resistant bacterial infections such as Pseudomonas aeruginosa infections. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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