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Microorganisms, Volume 10, Issue 3 (March 2022) – 185 articles

Cover Story (view full-size image): Aquaculture is the fastest-growing food-producing sector; however, due to its intensification, infectious diseases pose a major threat. Regarding this, probiotics are a viable alternative to traditional chemotherapy agents. Lactococcus lactis subsp. cremoris WA2-67 has previously demonstrated several probiotic features, including a strong antimicrobial activity against ichthyopathogens. Its whole-genome sequence (WGS) reveals the bacteriocinogenic genetic clusters encoding the lantibiotic nisin Z and two new bacteriocins, in addition to several probiotic traits, as well as the absence of transferable antibiotic resistances and genes encoding detrimental enzymatic activities and virulence factors. All these results support the use of L. cremoris WA2-67 as a probiotic for aquaculture. View this paper
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12 pages, 2057 KiB  
Article
Molecular Characterization of Staphylococcus aureus Strains Isolated from Mobile Phones
by Aída Hamdan-Partida, Samuel González-García, Francisco Javier Martínez-Ruíz, Miguel Ángel Zavala-Sánchez, Anaíd Bustos-Hamdan and Jaime Bustos-Martínez
Microorganisms 2022, 10(3), 669; https://doi.org/10.3390/microorganisms10030669 - 21 Mar 2022
Cited by 4 | Viewed by 2896
Abstract
The widespread use of mobile phones (MP) among healthcare personnel might be considered as an important source of contamination. One of the most pathogenic bacteria to humans is Staphylococcus aureus, which can be transmitted through the constant use of MP. Nevertheless, which [...] Read more.
The widespread use of mobile phones (MP) among healthcare personnel might be considered as an important source of contamination. One of the most pathogenic bacteria to humans is Staphylococcus aureus, which can be transmitted through the constant use of MP. Nevertheless, which specific type of strains are transmitted and which are their sources have not been sufficiently studied. The aim of this study is to determine the source of contamination of MP and characterize the corresponding genotypic and phenotypic properties of the strains found. Nose, pharynx, and MP samples were taken from a group of health science students. We were able to determinate the clonality of the isolated strains by pulsed-field gel electrophoresis (PFGE) and spa gene typing (spa-type). Adhesin and toxin genes were detected, and the capacity of biofilm formation was determined. Several of the MP exhibited strains of S. aureus present in the nose and/or pharynx of their owners. methicillin-susceptible Staphylococcus aureus (MSSA), hospital-acquired methicillin-resistant S. aureus (HA-MRSA), and community-acquired methicillin-resistant S. aureus (CA-MRSA) strains were found, which indicated a variety of genotypes. This study concludes that MP can be contaminated with the strains of S. aureus present in the nose and/or pharynx of the owners; these strains can be of different types and there is no dominant genotype. Full article
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17 pages, 909 KiB  
Review
Utilization of Host and Microbiome Features in Determination of Biological Aging
by Karina Ratiner, Suhaib K. Abdeen, Kim Goldenberg and Eran Elinav
Microorganisms 2022, 10(3), 668; https://doi.org/10.3390/microorganisms10030668 - 21 Mar 2022
Cited by 8 | Viewed by 8734
Abstract
The term ‘old age’ generally refers to a period characterized by profound changes in human physiological functions and susceptibility to disease that accompanies the final years of a person’s life. Despite the conventional definition of old age as exceeding the age of 65 [...] Read more.
The term ‘old age’ generally refers to a period characterized by profound changes in human physiological functions and susceptibility to disease that accompanies the final years of a person’s life. Despite the conventional definition of old age as exceeding the age of 65 years old, quantifying aging as a function of life years does not necessarily reflect how the human body ages. In contrast, characterizing biological (or physiological) aging based on functional parameters may better reflect a person’s temporal physiological status and associated disease susceptibility state. As such, differentiating ‘chronological aging’ from ‘biological aging’ holds the key to identifying individuals featuring accelerated aging processes despite having a young chronological age and stratifying them to tailored surveillance, diagnosis, prevention, and treatment. Emerging evidence suggests that the gut microbiome changes along with physiological aging and may play a pivotal role in a variety of age-related diseases, in a manner that does not necessarily correlate with chronological age. Harnessing of individualized gut microbiome data and integration of host and microbiome parameters using artificial intelligence and machine learning pipelines may enable us to more accurately define aging clocks. Such holobiont-based estimates of a person’s physiological age may facilitate prediction of age-related physiological status and risk of development of age-associated diseases. Full article
(This article belongs to the Special Issue Microorganisms and Aging)
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15 pages, 5074 KiB  
Article
Wheat Straw Return Influences Soybean Root-Associated Bacterial and Fungal Microbiota in a Wheat–Soybean Rotation System
by Hongjun Yang, Yao Zhao, Jiaxin Ma, Zhenyang Rong, Jiajia Chen, Yuanchao Wang, Xiaobo Zheng and Wenwu Ye
Microorganisms 2022, 10(3), 667; https://doi.org/10.3390/microorganisms10030667 - 21 Mar 2022
Cited by 6 | Viewed by 2652
Abstract
Roots hold complex microbial communities at the soil–root interface, which can affect plant nutrition, growth, and health. Although the composition of plant microbiomes has been extensively described for various plant species and environments, little is known about the effect of wheat straw return [...] Read more.
Roots hold complex microbial communities at the soil–root interface, which can affect plant nutrition, growth, and health. Although the composition of plant microbiomes has been extensively described for various plant species and environments, little is known about the effect of wheat straw return (WSR) on the soybean root microbiota. We used Illumina-based 16S rRNA and ITS amplicon sequencing to track changes in bacterial and fungal microbiota in bulk soil and soybean rhizosphere, rhizoplane, s1and endosphere during the third and fourth years after implementing WSR in a wheat–soybean rotation system. The results revealed that WSR had a greater impact on fungal communities than bacterial communities, particularly in bulk soil, rhizosphere, and rhizoplane. WSR enriched the relative abundance of cellulose-degrading fungi (e.g., Acremonium, Trichoderma, and Myrmecridium, among which Trichoderma also had antimicrobial activity), saprotroph (e.g., Exophiala), and nitrogen cycling bacteria (e.g., Chryseolinea). Furthermore, WSR depleted the relative abundance of pathogenic fungi (e.g., Fusarium and Alternaria). These data revealed for the first time that WSR had diverse effects on soybean root-associated microbial community composition, not only in soil but also in the rhizosphere, rhizoplane, and endosphere. Full article
(This article belongs to the Section Plant Microbe Interactions)
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14 pages, 2318 KiB  
Article
Dihydrolipoamide Acetyltransferase AceF Influences the Type III Secretion System and Resistance to Oxidative Stresses through RsmY/Z in Pseudomonas aeruginosa
by Haozhou Li, Yushan Xia, Zhenyang Tian, Yongxin Jin, Fang Bai, Zhihui Cheng, Wieslaw Swietnicki, Weihui Wu and Xiaolei Pan
Microorganisms 2022, 10(3), 666; https://doi.org/10.3390/microorganisms10030666 - 21 Mar 2022
Cited by 2 | Viewed by 2337
Abstract
Carbon metabolism plays an important role in bacterial physiology and pathogenesis. The type III secretion system (T3SS) of Pseudomonas aeruginosa is a virulence factor that contributes to acute infections. It has been demonstrated that bacterial metabolism affects the T3SS. Meanwhile, expression of T3SS [...] Read more.
Carbon metabolism plays an important role in bacterial physiology and pathogenesis. The type III secretion system (T3SS) of Pseudomonas aeruginosa is a virulence factor that contributes to acute infections. It has been demonstrated that bacterial metabolism affects the T3SS. Meanwhile, expression of T3SS genes is negatively regulated by the small RNAs RsmY and RsmZ. In this study, we studied the relationship between the dihydrolipoamide acetyltransferase gene aceF and the T3SS. Our results reveal an upregulation of RsmY and RsmZ in the aceF mutant, which represses the expression of the T3SS genes. Meanwhile, the aceF mutant is more tolerant to hydrogen peroxide. We demonstrate that the expression levels of the catalase KatB and the alkyl hydroperoxide reductase AhpB are increased in the aceF mutant. The simultaneous deletion of rsmY and rsmZ in the aceF mutant restored the expression levels of katB and ahpB, as well as bacterial susceptibility to hydrogen peroxide. Thus, we identify a novel role of AceF in the virulence and oxidative response of P. aeruginosa. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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13 pages, 302 KiB  
Review
The Gut Microbiota Influenced by the Intake of Probiotics and Functional Foods with Prebiotics Can Sustain Wellness and Alleviate Certain Ailments like Gut-Inflammation and Colon-Cancer
by Divakar Dahiya and Poonam Singh Nigam
Microorganisms 2022, 10(3), 665; https://doi.org/10.3390/microorganisms10030665 - 20 Mar 2022
Cited by 53 | Viewed by 8315
Abstract
The gut microbiota is composed of several microbial strains, with diverse and variable combinations in healthy and sick persons, changing at different stages of life. A healthy balance between host and gut microorganisms must be maintained in order to perform the normal physiological, [...] Read more.
The gut microbiota is composed of several microbial strains, with diverse and variable combinations in healthy and sick persons, changing at different stages of life. A healthy balance between host and gut microorganisms must be maintained in order to perform the normal physiological, metabolic, and immune functions and prevent disease development. Disturbances in the balance of the gut microbiota by diverse reasons initiate several health issues and promote the progression of certain diseases. This review is based on published research and reports that describe the role of probiotic microorganisms in the sustainability of health and the alleviation of certain diseases. Information is presented on the GRAS strains that are used as probiotics in the food industry for the production of fermented milk, yogurt, fermented food, functional foods, and probiotic drinks. To maintain a healthy microbiota, probiotic supplements in the form of freeze-dried live cells of probiotic strains are also available in different forms to consumers. The health benefits of lactic acid bacteria and other microorganisms and their role in the control of certain diseases such as gut inflammation, diabetes, and bowel cancer and in the safeguarding of the gut epithelial permeability from the invasion of pathogens are discussed. Full article
(This article belongs to the Special Issue Gut Microbiota and Nutrients)
13 pages, 2502 KiB  
Article
Typing of the Gut Microbiota Community in Japanese Subjects
by Tomohisa Takagi, Ryo Inoue, Akira Oshima, Hiroshi Sakazume, Kenta Ogawa, Tomo Tominaga, Yoichi Mihara, Takeshi Sugaya, Katsura Mizushima, Kazuhiko Uchiyama, Yoshito Itoh and Yuji Naito
Microorganisms 2022, 10(3), 664; https://doi.org/10.3390/microorganisms10030664 - 20 Mar 2022
Cited by 15 | Viewed by 9491
Abstract
Gut microbiota are involved in both host health and disease and can be stratified based on bacteriological composition. However, gut microbiota clustering data are limited for Asians. In this study, fecal microbiota of 1803 Japanese subjects, including 283 healthy individuals, were analyzed by [...] Read more.
Gut microbiota are involved in both host health and disease and can be stratified based on bacteriological composition. However, gut microbiota clustering data are limited for Asians. In this study, fecal microbiota of 1803 Japanese subjects, including 283 healthy individuals, were analyzed by 16S rRNA sequencing and clustered using two models. The association of various diseases with each community type was also assessed. Five and fifteen communities were identified using partitioning around medoids (PAM) and the Dirichlet multinominal mixtures model, respectively. Bacteria exhibiting characteristically high abundance among the PAM-identified types were of the family Ruminococcaceae (Type A) and genera Bacteroides, Blautia, and Faecalibacterium (Type B); Bacteroides, Fusobacterium, and Proteus (Type C); and Bifidobacterium (Type D), and Prevotella (Type E). The most noteworthy community found in the Japanese subjects was the Bifidobacterium-rich community. The odds ratio based on type E, which had the largest population of healthy subjects, revealed that other types (especially types A, C, and D) were highly associated with various diseases, including inflammatory bowel disease, functional gastrointestinal disorder, and lifestyle-related diseases. Gut microbiota community typing reproducibly identified organisms that may represent enterotypes peculiar to Japanese individuals and that are partly different from those of indivuals from Western countries. Full article
(This article belongs to the Special Issue State-of-the-Art Gut Microbiota Research in Asia)
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17 pages, 1803 KiB  
Article
Effects of Perchlorate and Other Groundwater Inorganic Co-Contaminants on Aerobic RDX Degradation
by Amit Yadav, Swati Gupta, Paula Istvan and Zeev Ronen
Microorganisms 2022, 10(3), 663; https://doi.org/10.3390/microorganisms10030663 - 20 Mar 2022
Cited by 2 | Viewed by 2202
Abstract
Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) pollution is accompanied by other co-contaminants, such as perchlorate and chlorates, which can retard biodegradation. The effects of perchlorate and chlorate on aerobic RDX degradation remain unclear. We hypothesized that they have a negative or no impact on aerobic RDX-degrading bacteria. [...] Read more.
Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) pollution is accompanied by other co-contaminants, such as perchlorate and chlorates, which can retard biodegradation. The effects of perchlorate and chlorate on aerobic RDX degradation remain unclear. We hypothesized that they have a negative or no impact on aerobic RDX-degrading bacteria. We used three aerobic RDX-degrading strains—Rhodococcus strains YH1 and T7 and Gordonia YY1—to examine this hypothesis. The strains were exposed to perchlorate, chlorate, and nitrate as single components or in a mixture. Their growth, degradation activity, and gene expression were monitored. Strain-specific responses to the co-contaminants were observed: enhanced growth of strain YH1 and inhibition of strain T7. Vmax and Km of cytochrome P450 (XplA) in the presence of the co-contaminants were not significantly different from the control, suggesting no direct influence on cytochrome P450. Surprisingly, xplA expression increased fourfold in cultures pre-grown on RDX and, after washing, transferred to a medium containing only perchlorate. This culture did not grow, but xplA was translated and active, albeit at lower levels than in the control. We explained this observation as being due to nitrogen limitation in the culture and not due to perchlorate induction. Our results suggest that the aerobic strain YH1 is effective for aerobic remediation of RDX in groundwater. Full article
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15 pages, 1016 KiB  
Communication
Genomic Profiling of Antibiotic-Resistant Escherichia coli Isolates from Surface Water of Agricultural Drainage in North-Western Mexico: Detection of the International High-Risk Lineages ST410 and ST617
by José Antonio Magaña-Lizárraga, Bruno Gómez-Gil, José Guadalupe Rendón-Maldonado, Francisco Delgado-Vargas, Inés Fernando Vega-López and María Elena Báez-Flores
Microorganisms 2022, 10(3), 662; https://doi.org/10.3390/microorganisms10030662 - 20 Mar 2022
Cited by 10 | Viewed by 3980
Abstract
Aquatic environments are recognized as one of the main reservoirs for the emergence and dissemination of high-risk lineages of multidrug-resistant (MDR) bacteria of public health concern. However, the genomic characteristics of antibiotic-resistant Escherichia coli isolates from aquatic origins remain limited. Herein, we examined [...] Read more.
Aquatic environments are recognized as one of the main reservoirs for the emergence and dissemination of high-risk lineages of multidrug-resistant (MDR) bacteria of public health concern. However, the genomic characteristics of antibiotic-resistant Escherichia coli isolates from aquatic origins remain limited. Herein, we examined the antibiotic resistance and virulence genomic profiles of three E. coli recovered from surface water in northwest Mexico. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), and in-depth in silico analysis were performed. Two E. coli exhibited MDR phenotypes. WGS-based typing revealed genetic diversity, and phylogenetic analysis corroborated a notable divergent relationship among the studied E. coli. One E. coli strain, harboring enterotoxigenic and extraintestinal pathogenic-associated virulence genes, was assigned to the ST4 lineage. MDR E. coli, belonging to the international high-risk clones ST410 and ST617, carried genes and mutations conferring resistance to aminoglycosides, β-lactams, quinolones, sulfonamides, tetracyclines, and trimethoprim. This study describes, for the first time, the detection and genomic profiling of high-risk lineages of E. coli ST410 and ST617 from surface water in Mexico. Additionally, our results underscore the role of surface water as a reservoir for critical pathogenic and MDR E. coli clones and the need for the surveillance and monitoring of aquatic environments via WGS from the One Health perspective. Full article
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20 pages, 1882 KiB  
Article
A Farm-to-Fork Quantitative Microbial Exposure Assessment of β-Lactam-Resistant Escherichia coli among U.S. Beef Consumers
by Yangjunna Zhang, John W. Schmidt, Terrance M. Arthur, Tommy L. Wheeler, Qi Zhang and Bing Wang
Microorganisms 2022, 10(3), 661; https://doi.org/10.3390/microorganisms10030661 - 19 Mar 2022
Cited by 3 | Viewed by 2707
Abstract
Integrated quantitative descriptions of the transmission of β-lactam-resistant Escherichia coli (BR-EC) from commercial beef products to consumers are not available. Here, a quantitative microbial exposure assessment model was established to simulate the fate of BR-EC in a farm-to-fork continuum and provide an estimate [...] Read more.
Integrated quantitative descriptions of the transmission of β-lactam-resistant Escherichia coli (BR-EC) from commercial beef products to consumers are not available. Here, a quantitative microbial exposure assessment model was established to simulate the fate of BR-EC in a farm-to-fork continuum and provide an estimate of BR-EC exposure among beef consumers in the U.S. The model compared the per-serving exposures from the consumption of intact beef cuts, non-intact beef cuts, and ground beef. Additionally, scenario analysis was performed to evaluate the relative contribution of antibiotic use during beef cattle production to the level of human exposure to BR-EC. The model predicted mean numbers of BR-EC of 1.7 × 10−4, 8.7 × 10−4, and 6.9 × 10−1 CFU/serving for intact beef cuts, non-intact beef cuts, and ground beef, respectively, at the time of consumption. Sensitivity analyses using the baseline model suggested that factors related to sectors along the supply chain, i.e., feedlots, processing plants, retailers, and consumers, were all important for controlling human exposure to BR-EC. Interventions at the processing and post-processing stages are expected to be most effective. Simulation results showed that a decrease in antibiotic use among beef cattle might be associated with a reduction in exposure to BR-EC from beef consumption. However, the absolute reduction was moderate, indicating that the effectiveness of restricting antibiotic use as a standalone strategy for mitigating human exposure to BR-EC through beef consumption is still uncertain. Good cooking and hygiene practices at home and advanced safety management practices in the beef processing and post-processing continuum are more powerful approaches for reducing human exposure to antibiotic-resistant bacteria in beef products. Full article
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17 pages, 3312 KiB  
Article
Interplay between Arabidopsis thaliana Genotype, Plant Growth and Rhizosphere Colonization by Phytobeneficial Phenazine-Producing Pseudomonas chlororaphis
by Antoine Zboralski, Hara Saadia, Amy Novinscak and Martin Filion
Microorganisms 2022, 10(3), 660; https://doi.org/10.3390/microorganisms10030660 - 19 Mar 2022
Cited by 3 | Viewed by 2758
Abstract
Rhizosphere colonization by phytobeneficial Pseudomonas spp. is pivotal in triggering their positive effects on plant health. Many Pseudomonas spp. Determinants, involved in rhizosphere colonization, have already been deciphered. However, few studies have explored the role played by specific plant genes in rhizosphere colonization [...] Read more.
Rhizosphere colonization by phytobeneficial Pseudomonas spp. is pivotal in triggering their positive effects on plant health. Many Pseudomonas spp. Determinants, involved in rhizosphere colonization, have already been deciphered. However, few studies have explored the role played by specific plant genes in rhizosphere colonization by these bacteria. Using isogenic Arabidopsis thaliana mutants, we studied the effect of 20 distinct plant genes on rhizosphere colonization by two phenazine-producing P. chlororaphis strains of biocontrol interest, differing in their colonization abilities: DTR133, a strong rhizosphere colonizer and ToZa7, which displays lower rhizocompetence. The investigated plant mutations were related to root exudation, immunity, and root system architecture. Mutations in smb and shv3, both involved in root architecture, were shown to positively affect rhizosphere colonization by ToZa7, but not DTR133. While these strains were not promoting plant growth in wild-type plants, increased plant biomass was measured in inoculated plants lacking fez, wrky70, cbp60g, pft1 and rlp30, genes mostly involved in plant immunity. These results point to an interplay between plant genotype, plant growth and rhizosphere colonization by phytobeneficial Pseudomonas spp. Some of the studied genes could become targets for plant breeding programs to improve plant-beneficial Pseudomonas rhizocompetence and biocontrol efficiency in the field. Full article
(This article belongs to the Special Issue Interactions between Plant Beneficial Pseudomonas spp. and Their Host)
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19 pages, 3358 KiB  
Article
Photoinactivation of Phage Phi6 as a SARS-CoV-2 Model in Wastewater: Evidence of Efficacy and Safety
by Marta Gomes, Maria Bartolomeu, Cátia Vieira, Ana T. P. C. Gomes, Maria Amparo F. Faustino, Maria Graça P. M. S. Neves and Adelaide Almeida
Microorganisms 2022, 10(3), 659; https://doi.org/10.3390/microorganisms10030659 - 19 Mar 2022
Cited by 14 | Viewed by 2953
Abstract
The last two years have been marked by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. This virus is found in the intestinal tract; it reaches wastewater systems and, consequently, the natural receiving water bodies. As such, inefficiently treated wastewater (WW) can [...] Read more.
The last two years have been marked by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. This virus is found in the intestinal tract; it reaches wastewater systems and, consequently, the natural receiving water bodies. As such, inefficiently treated wastewater (WW) can be a means of contamination. The currently used methods for the disinfection of WW can lead to the formation of toxic compounds and can be expensive or inefficient. As such, new and alternative approaches must be considered, namely, photodynamic inactivation (PDI). In this work, the bacteriophage φ6 (or, simply, phage φ6), which has been used as a suitable model for enveloped RNA viruses, such as coronaviruses (CoVs), was used as a model of SARS-CoV-2. Firstly, to understand the virus’s survival in the environment, phage φ6 was subjected to different laboratory-controlled environmental conditions (temperature, pH, salinity, and solar and UV-B irradiation), and its persistence over time was assessed. Second, to assess the efficiency of PDI towards the virus, assays were performed in both phosphate-buffered saline (PBS), a commonly used aqueous matrix, and a secondarily treated WW (a real WW matrix). Third, as WW is generally discharged into the marine environment after treatment, the safety of PDI-treated WW was assessed through the determination of the viability of native marine water microorganisms after their contact with the PDI-treated effluent. Overall, the results showed that, when used as a surrogate for SARS-CoV-2, phage φ6 remains viable in different environmental conditions for a considerable period. Moreover, PDI proved to be an efficient approach in the inactivation of the viruses, and the PDI-treated effluent showed no toxicity to native aquatic microorganisms under realistic dilution conditions, thus endorsing PDI as an efficient and safe tertiary WW disinfection method. Although all studies were performed with phage φ6, which is considered a suitable model of SARS-CoV-2, further studies using SARS-CoV-2 are necessary; nevertheless, the findings show the potential of PDI for controlling SARS-CoV-2 in WW. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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11 pages, 1246 KiB  
Article
Only Low Effects of Water Filters on the Enteric Carriage of Gastrointestinal Pathogen DNA in Colombian Indigenous People
by Simone Kann, Gustavo Concha, Maria Hartmann, Thomas Köller, Juliane Alker, Ulrich Schotte, Lothar Kreienbrock, Hagen Frickmann and Philipp Warnke
Microorganisms 2022, 10(3), 658; https://doi.org/10.3390/microorganisms10030658 - 19 Mar 2022
Cited by 4 | Viewed by 2043
Abstract
Water filtration is a common strategy of water sanitation in resource-poor tropical settings. Here, we assessed the intermediate term effect of this preventive procedure including specific filter-related as well as general hygiene training on the molecular detection of enteric pathogens in stool samples [...] Read more.
Water filtration is a common strategy of water sanitation in resource-poor tropical settings. Here, we assessed the intermediate term effect of this preventive procedure including specific filter-related as well as general hygiene training on the molecular detection of enteric pathogens in stool samples from Colombian Indigenous people. From a total of 89 individuals from an Indigenous tribe called Wiwa, stool samples were assessed by real-time PCR for enteropathogenic microorganisms prior to the implementation of water filtration-based infection prevention. Three years after the onset of the preventive strategy, a follow-up assessment was performed. A significantly beneficial effect of water filtration could be shown for Ascaris spp. only (p = 0.035) and a tendency (p = 0.059) for Hymenolepis nana. No hints for effects on the gastrointestinal shedding of Giardia duodenalis, Entamoeba histolytica, Cryptosporidium spp., Campylobacter spp., Shigella spp./enteroinvasive Escherichia coli, Necator americanus, Strongyloides stercoralis, Trichuris trichiura, and Taenia spp. were seen. In conclusion, the study indicates that water filtration can only be an element of a multi-modal hygiene concept to reduce enteric pathogen carriage in inhabitants of resource-poor tropical settings in spite of tendencies of beneficial effects. Full article
(This article belongs to the Special Issue Detection and Epidemiology of Foodborne Pathogens)
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18 pages, 564 KiB  
Review
Setting a Plausible Route for Saline Soil-Based Crop Cultivations by Application of Beneficial Halophyte-Associated Bacteria: A Review
by Han Meng Teo, Aziz A., Wahizatul A. A., Kesaven Bhubalan, Siti Nordahliawate M. S., Muhamad Syazlie C. I. and Lee Chuen Ng
Microorganisms 2022, 10(3), 657; https://doi.org/10.3390/microorganisms10030657 - 19 Mar 2022
Cited by 15 | Viewed by 3413
Abstract
The global scale of land salinization has always been a considerable concern for human livelihoods, mainly regarding the food-producing agricultural industries. The latest update suggested that the perpetual salinity problem claimed up to 900 million hectares of agricultural land worldwide, inducing salinity stress [...] Read more.
The global scale of land salinization has always been a considerable concern for human livelihoods, mainly regarding the food-producing agricultural industries. The latest update suggested that the perpetual salinity problem claimed up to 900 million hectares of agricultural land worldwide, inducing salinity stress among salt-sensitive crops and ultimately reducing productivity and yield. Moreover, with the constant growth of the human population, sustainable solutions are vital to ensure food security and social welfare. Despite that, the current method of crop augmentations via selective breeding and genetic engineering only resulted in mild success. Therefore, using the biological approach of halotolerant plant growth-promoting bacteria (HT-PGPB) as bio-inoculants provides a promising crop enhancement strategy. HT-PGPB has been proven capable of forming a symbiotic relationship with the host plant by instilling induced salinity tolerance (IST) and multiple plant growth-promoting traits (PGP). Nevertheless, the mechanisms and prospects of HT-PGPB application of glycophytic rice crops remains incomprehensively reported. Thus, this review describes a plausible strategy of halophyte-associated HT-PGPB as the future catalyst for rice crop production in salt-dominated land and aims to meet the global Sustainable Development Goals (SDGs) of zero hunger. Full article
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10 pages, 1506 KiB  
Article
Short-Term Exposure to Thermophilic Temperatures Facilitates CO Uptake by Thermophiles Maintained under Predominantly Mesophilic Conditions
by Caitlin K. Wilson and Gary M. King
Microorganisms 2022, 10(3), 656; https://doi.org/10.3390/microorganisms10030656 - 18 Mar 2022
Cited by 3 | Viewed by 1980
Abstract
Three phylogenetically and phenotypically distinct CO-oxidizing thermophiles (Alicyclobacillus macrosporangiidus CPP55 (Firmicutes), Meiothermus ruber PS4 (Deinococcus-Thermus) and Thermogemmatispora carboxidovorans PM5T (Chloroflexi)) and one CO-oxidizing mesophile (Paraburkholderia paradisi WAT (Betaproteobacteria)) isolated from volcanic soils were used to assess [...] Read more.
Three phylogenetically and phenotypically distinct CO-oxidizing thermophiles (Alicyclobacillus macrosporangiidus CPP55 (Firmicutes), Meiothermus ruber PS4 (Deinococcus-Thermus) and Thermogemmatispora carboxidovorans PM5T (Chloroflexi)) and one CO-oxidizing mesophile (Paraburkholderia paradisi WAT (Betaproteobacteria)) isolated from volcanic soils were used to assess growth responses and CO uptake rates during incubations with constant temperatures (25 °C and 55 °C) and during multi-day incubations with a temperature regime that cycled between 20 °C and 55 °C on a diurnal basis (alternating mesophilic and thermophilic temperatures, AMTT). The results were used to test a conjecture that some thermophiles can survive in mesothermal habitats that experience occasional thermophilic temperatures. Meiothermus ruber PS4, which does not form spores, was able to grow and oxidize CO under all conditions, while the spore-forming Alicyclobacillus macrosporangiidus CPP55 grew and oxidized CO during the AMTT regime and at 55 °C, but was not active at 25 °C. Thermogemmatispora carboxidovorans PM5T, also a spore former, only grew at 55 °C but oxidized CO during AMTT and 55 °C incubations. In contrast, the non-sporing mesophile, Paraburkholderia paradisi WAT, was only able to grow and oxidize CO at 25 °C; growth and CO uptake ceased during the AMTT incubations after exposure to the initial round of thermophilic temperatures. Collectively, these results suggest that temporary, periodic exposure to permissive growth temperatures could help maintain populations of thermophiles in mesothermal habitats after deposition from the atmosphere or other sources. Full article
(This article belongs to the Special Issue Microbial Adaptation and Tolerance to Environmental Stresses)
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17 pages, 1647 KiB  
Article
Characterization of Bifidobacterium asteroides Isolates
by Alessandra Pino, Bachir Benkaddour, Rosanna Inturri, Pietro Amico, Susanna C. Vaccaro, Nunziatina Russo, Amanda Vaccalluzzo, Gianluigi Agolino, Cinzia Caggia, Hadadji Miloud and Cinzia L. Randazzo
Microorganisms 2022, 10(3), 655; https://doi.org/10.3390/microorganisms10030655 - 18 Mar 2022
Cited by 7 | Viewed by 3335
Abstract
Bifidobacteria have long been recognized as bacteria with probiotic and therapeutic features. The aim of this work is to characterize the Bifidobacterium asteroides BA15 and BA17 strains, isolated from honeybee gut, to evaluate its safety for human use. An in-depth assessment was carried [...] Read more.
Bifidobacteria have long been recognized as bacteria with probiotic and therapeutic features. The aim of this work is to characterize the Bifidobacterium asteroides BA15 and BA17 strains, isolated from honeybee gut, to evaluate its safety for human use. An in-depth assessment was carried out on safety properties (antibiotic resistance profiling, β-hemolytic, DNase and gelatinase activities and virulence factor presence) and other properties (antimicrobial activity, auto-aggregation, co-aggregation and hydrophobicity). Based on phenotypic and genotypic characterization, both strains satisfied all the safety requirements. More specifically, genome analysis showed the absence of genes encoding for glycopeptide (vanA, vanB, vanC-1, vanC-2, vanD, vanE, vanG), resistance to tetracycline (tetM, tetL and tetO) and virulence genes (asa1, gelE, cylA, esp, hyl). Full article
(This article belongs to the Section Veterinary Microbiology)
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15 pages, 1202 KiB  
Article
Isolation and Characterization of Commensal Bifidobacteria Strains in Gut Microbiota of Neonates Born Preterm: A Prospective Longitudinal Study
by Sandra Wydau-Dematteis, Johanne Delannoy, Anne-Claire Téolis, Agnès Giuseppi, Florence Campeotto, Alexandre Lapillonne, Marie-José Butel and Julio Aires
Microorganisms 2022, 10(3), 654; https://doi.org/10.3390/microorganisms10030654 - 18 Mar 2022
Cited by 5 | Viewed by 2389
Abstract
Bifidobacterial population dynamics were investigated using a longitudinal analysis of dominant species isolated from feces of neonates born preterm (singletons (n = 10), pairs of twins (n = 11)) from birth up to 16 months of age. We performed quantification, isolation, [...] Read more.
Bifidobacterial population dynamics were investigated using a longitudinal analysis of dominant species isolated from feces of neonates born preterm (singletons (n = 10), pairs of twins (n = 11)) from birth up to 16 months of age. We performed quantification, isolation, and identification of the dominant bifidobacteria strains. The genetic relationship of the isolates was investigated via pulsed field gel electrophoresis (PFGE) genotyping, and PCR was used to screen the specific genetic marker tet genes. Additionally, all of the isolated strains were phenotypically characterized by their response to gastro-intestinal stresses and the MIC determination of tetracycline. In the same individual, our results showed a turnover of the bifidobacteria dominant population not only at species but also at strain levels. In addition, we found clonally related strains between twins. A minority of strains were tolerant to gastric (6%) and intestinal (16%) stresses. Thirteen percent of the strains were resistant to tetracycline. This work is original as it provides insights at the strain level of the early life in vivo dynamics of gut microbiota bifidobacteria in preterm neonates. It highlights the need to take into consideration the fluctuation of bifidobacteria populations that may occur for one individual. Full article
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25 pages, 3617 KiB  
Article
YfiB: An Outer Membrane Protein Involved in the Virulence of Shigella flexneri
by Tanuka Sen and Naresh K. Verma
Microorganisms 2022, 10(3), 653; https://doi.org/10.3390/microorganisms10030653 - 18 Mar 2022
Cited by 1 | Viewed by 3099
Abstract
The intracellular pathogen Shigella flexneri, which is the causative agent of bacillary dysentery, significantly influences the worldwide implication of diarrheal infections, consequentially causing about 1.1 million deaths each year. Due to a nonavailability of an authorized vaccine and the upsurge of multidrug [...] Read more.
The intracellular pathogen Shigella flexneri, which is the causative agent of bacillary dysentery, significantly influences the worldwide implication of diarrheal infections, consequentially causing about 1.1 million deaths each year. Due to a nonavailability of an authorized vaccine and the upsurge of multidrug resistance amongst Shigella strains, there has been a huge demand for further genetic analyses which could help in the advancement of new/improved drugs, and finding vaccine candidates against the pathogen. The present study aims to illustrate the role of the yfiB gene in Shigella virulence, part of the periplasmic YfiBNR tripartite signalling system. This system is involved in the regulation of cyclic-di-GMP levels inside the bacterial cells, a vital messenger molecule impacting varied cellular processes such as biofilm formation, cytotoxicity, motility, synthesis of exopolysaccharide, and other virulence mechanisms such as adhesion and invasion of the bacteria. Through a combination of genetic, biochemical, and virulence assays, we show how knocking out the yfiB gene can disrupt the entire YfiBNR system and affect the native c-di-GMP levels. We found that this subsequently causes a negative effect on the biofilm formation, bacterial invasion, host–surface attachment, and the overall virulence of Shigella. This study also carried out a structural and functional assessment of the YfiB protein and determined critical amino acid residues, essential for proper functioning of this signalling system. The present work improves our understanding of the in vivo persistence and survival of Shigella, brings light to the c-di-GMP led regulation of Shigella virulence, and provides a prospective new target to design anti-infection drugs and vaccines against S. flexneri and other bacterial pathogens. Full article
(This article belongs to the Section Medical Microbiology)
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10 pages, 1737 KiB  
Communication
Virological Characterization of Pigs with Erythema Multiforme
by Sabrina Halecker, Vasileios Papatsiros, Dimitra Psalla, Ludwig Krabben, Benedikt Kaufer and Joachim Denner
Microorganisms 2022, 10(3), 652; https://doi.org/10.3390/microorganisms10030652 - 18 Mar 2022
Cited by 5 | Viewed by 2820
Abstract
Erythema multiforme in pigs is an acute, self-limiting disease characterized by red skin areas and often associated with anorexia, fever and respiratory problems. The cause of the disease remains unknown. In a recent study, animals of a commercial breeding herd in Greece were [...] Read more.
Erythema multiforme in pigs is an acute, self-limiting disease characterized by red skin areas and often associated with anorexia, fever and respiratory problems. The cause of the disease remains unknown. In a recent study, animals of a commercial breeding herd in Greece were examined, and all animals were found seropositive for porcine reproductive and respiratory syndrome virus (PRRSV). However, neither PRRSV and porcine circovirus type 2 (PCV2) viremia nor antibodies against Aujeszky’s disease virus, African swine fever virus and classical swine fever virus were detected. Here, an extended examination of these pigs was performed on a wide range of porcine viruses using highly sensitive polymerase chain reaction (PCR)-based methods. Affected skin of five animals revealed the presence of porcine lymphotropic herpesvirus-1 (PLHV-1) in all cases, PLHV-2 in one animal and PLHV-3 in four animals. However, neither porcine cytomegalovirus (PCMV) nor porcine circoviruses (PCV1, PCV2, PCV3 and PCV4) were detected. In blood samples, PLHV-1 was present in two animals and PLHV-2, PCV2 and PCV3 in one individual, with PCMV, PCV1 and PCV4 in none of the animals. In one animal, four viruses were found in the blood (PLHV-1, PLHV-2, PCV2 and PCV3). A PRRSV viremia was also not detected. All animals carried porcine endogenous retrovirus C (PERV-C) in their genome, but recombinant PERV-A/C was not detected. The results suggest that porcine viruses may be involved in erythema multiforme in these animals and that further studies are needed to assess the role of these pathogens in the disease. Full article
(This article belongs to the Section Medical Microbiology)
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13 pages, 1697 KiB  
Article
The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules
by Petar Pujic, Nicole Alloisio, Guylaine Miotello, Jean Armengaud, Danis Abrouk, Pascale Fournier and Philippe Normand
Microorganisms 2022, 10(3), 651; https://doi.org/10.3390/microorganisms10030651 - 18 Mar 2022
Cited by 4 | Viewed by 1913 | Correction
Abstract
Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic Frankia. A proteogenomic analysis of symbiotic Frankia alni was done by comparing those proteins more and less abundant in Alnus glutinosa nodules relative [...] Read more.
Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic Frankia. A proteogenomic analysis of symbiotic Frankia alni was done by comparing those proteins more and less abundant in Alnus glutinosa nodules relative to N-replete pure cultures with propionate as the carbon source and ammonium as the nitrogen-source. There were 250 proteins that were significantly overabundant in nodules at a fold change (FC) ≥ 2 threshold, and 1429 with the same characteristics in in vitro nitrogen-replete pure culture. Nitrogenase, SuF (Fe–Su biogenesis) and hopanoid lipids synthesis determinants were the most overabundant proteins in symbiosis. Nitrogenase was found to constitute 3% of all Frankia proteins in nodules. Sod (superoxide dismutase) was overabundant, indicating a continued oxidative stress, while Kats (catalase) were not. Several transporters were overabundant including one for dicarboxylates and one for branched amino acids. The present results confirm the centrality of nitrogenase in the actinorhizal symbiosis. Full article
(This article belongs to the Section Plant Microbe Interactions)
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20 pages, 3367 KiB  
Article
Organelle Engineering in Yeast: Enhanced Production of Protopanaxadiol through Manipulation of Peroxisome Proliferation in Saccharomyces cerevisiae
by Bo Hyun Choi, Hyun Joon Kang, Sun Chang Kim and Pyung Cheon Lee
Microorganisms 2022, 10(3), 650; https://doi.org/10.3390/microorganisms10030650 - 18 Mar 2022
Cited by 16 | Viewed by 3405
Abstract
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may [...] Read more.
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may consequently reduce the desired yield of the target isoprenoid. As a strategy to overcome this suggested limitation, we selected peroxisome membranes as depots for the additional storage of biosynthesized isoprenoids to facilitate increased isoprenoid production in Saccharomyces cerevisiae. To maximize the peroxisome membrane storage capacity of S.cerevisiae, the copy number and size of peroxisomes were increased through genetic engineering of the expression of three peroxisome biogenesis-related peroxins (Pex11p, Pex34p, and Atg36p). The genetically enlarged and high copied peroxisomes in S.cerevisiae were stably maintained under a bioreactor fermentation condition. The peroxisome-engineered S.cerevisiae strains were then utilized as host strains for metabolic engineering of heterologous protopanaxadiol pathway. The yields of protopanaxadiol from the engineered peroxisome strains were ca 78% higher than those of the parent strain, which strongly supports the rationale for harnessing the storage capacity of the peroxisome membrane to accommodate the biosynthesized compounds. Consequently, this study presents in-depth knowledge on peroxisome biogenesis engineering in S.cerevisiae and could serve as basic information for improvement in ginsenosides production and as a potential platform to be utilized for other isoprenoids. Full article
(This article belongs to the Special Issue Microbial Genetics and Evolution)
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15 pages, 2858 KiB  
Article
Comparative Genome Analysis of the Photosynthetic Betaproteobacteria of the Genus Rhodocyclus: Heterogeneity within Strains Assigned to Rhodocyclus tenuis and Description of Rhodocyclus gracilis sp. nov. as a New Species
by John A. Kyndt, Fabiola A. Aviles, Johannes F. Imhoff, Sven Künzel, Sven C. Neulinger and Terrance E. Meyer
Microorganisms 2022, 10(3), 649; https://doi.org/10.3390/microorganisms10030649 - 18 Mar 2022
Cited by 5 | Viewed by 2284
Abstract
The genome sequences for Rhodocyclus purpureus DSM 168T and four strains assigned to Rhodocyclus tenuis (DSM 110, DSM 111, DSM 112, and IM 230) have been determined. One of the strains studied (IM 230) has an average nucleotide identity (ANI) of 97% [...] Read more.
The genome sequences for Rhodocyclus purpureus DSM 168T and four strains assigned to Rhodocyclus tenuis (DSM 110, DSM 111, DSM 112, and IM 230) have been determined. One of the strains studied (IM 230) has an average nucleotide identity (ANI) of 97% to the recently reported genome of the type strain DSM 109 of Rcy. tenuis and is regarded as virtually identical at the species level. The ANI of 80% for three other strains (DSM 110, DSM 111, DSM 112) to the type strain of Rcy. tenuis points to a differentiation of these at the species level. Rcy. purpureus is equidistant from Rcy. tenuis and the new species, based on both ANI (78–80%) and complete proteome comparisons (70% AAI). Strains DSM 110, DSM 111, and DSM 112 are very closely related to each other based on ANI, whole genome, and proteome comparisons but clearly distinct from the Rcy. tenuis type strain DSM 109. In addition to the whole genome differentiation, these three strains also contain unique genetic differences in cytochrome genes and contain genes for an anaerobic cobalamin synthesis pathway that is lacking from both Rcy. tenuis and Rcy. purpureus. Based on genomic and genetic differences, these three strains should be considered to represent a new species, which is distinctly different from both Rcy. purpureus and Rcy. tenuis, for which the new name Rhodocyclus gracilis sp. nov. is proposed. Full article
(This article belongs to the Special Issue Phototrophic Bacteria)
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15 pages, 2114 KiB  
Article
Harnessing Paenarthrobacter ureafaciens YL1 and Pseudomonas koreensis YL2 Interactions to Improve Degradation of Sulfamethoxazole
by Lan Yu, Yingning Wang, Xiaoqing Shan, Fang Ma and Haijuan Guo
Microorganisms 2022, 10(3), 648; https://doi.org/10.3390/microorganisms10030648 - 18 Mar 2022
Cited by 9 | Viewed by 2329
Abstract
Sulfamethoxazole (SMX) is a widespread and persistent pollutant in the environment. Although the screening and analysis of SMX-degrading bacteria have been documented, the interaction mechanisms of functional microorganisms are still poorly understood. This study constructed a consortium with strain YL1 and YL2 supplied [...] Read more.
Sulfamethoxazole (SMX) is a widespread and persistent pollutant in the environment. Although the screening and analysis of SMX-degrading bacteria have been documented, the interaction mechanisms of functional microorganisms are still poorly understood. This study constructed a consortium with strain YL1 and YL2 supplied with SMX as the sole carbon and energy source. The coexisting mechanism and the removal of SMX of the consortium were investigated. The total oxidizable carbon (TOC) removal rate of the combined bacterial system was 38.94% compared to 29.45% for the single bacterial system at the same biomass. The mixed bacterial consortium was able to resist SMX at concentrations up to 400 mg/L and maintained a stable microbial structure at different culture conditions. The optimum conditions found for SMX degradation were 30 °C, pH 7.0, a shaking speed of 160 r·min−1, and an initial SMX concentration of 200 mg·L−1. The degradation of SMX was accelerated by the addition of YL2 for its ability to metabolize the key intermediate, 4-aminophenol. The removal rate of 4-aminophenol by strain YL2 reached 19.54% after 5 days. Genome analysis revealed that adding riboflavin and enhancing the reducing capacity might contribute to the degradation of SMX. These results indicated that it is important for the bioremediation of antibiotic-contaminated aquatic systems to understand the metabolism of bacterial communities. Full article
(This article belongs to the Special Issue Biodegradation and Environmental Microbiomes)
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21 pages, 10114 KiB  
Article
The Escherichia coli Amino Acid Uptake Protein CycA: Regulation of Its Synthesis and Practical Application in l-Isoleucine Production
by Christine Hook, Natalya Eremina, Petr Zaytsev, Daria Varlamova and Nataliya Stoynova
Microorganisms 2022, 10(3), 647; https://doi.org/10.3390/microorganisms10030647 - 17 Mar 2022
Cited by 4 | Viewed by 2694
Abstract
Amino acid transport systems perform important physiological functions; their role should certainly be considered in microbial production of amino acids. Typically, in the context of metabolic engineering, efforts are focused on the search for and application of specific amino acid efflux pumps. However, [...] Read more.
Amino acid transport systems perform important physiological functions; their role should certainly be considered in microbial production of amino acids. Typically, in the context of metabolic engineering, efforts are focused on the search for and application of specific amino acid efflux pumps. However, in addition, importers can also be used to improve the industrial process as a whole. In this study, the protein CycA, which is known for uptake of nonpolar amino acids, was characterized from the viewpoint of regulating its expression and range of substrates. We prepared a cycA-overexpressing strain and found that it exhibited high sensitivity to branched-chain amino acids and their structural analogues, with relatively increased consumption of these amino acids, suggesting that they are imported by CycA. The expression of cycA was found to be dependent on the extracellular concentrations of substrate amino acids. The role of some transcription factors in cycA expression, including of Lrp and Crp, was studied using a reporter gene construct. Evidence for the direct binding of Crp to the cycA regulatory region was obtained using a gel-retardation assay. The enhanced import of named amino acids due to cycA overexpression in the l-isoleucine-producing strain resulted in a significant reduction in the generation of undesirable impurities. This work demonstrates the importance of uptake systems with respect to their application in metabolic engineering. Full article
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18 pages, 11240 KiB  
Article
Biological Control of Diamondback Moth—Increased Efficacy with Mixtures of Beauveria Fungi
by Sereyboth Soth, Travis R. Glare, John G. Hampton, Stuart D. Card and Jenny J. Brookes
Microorganisms 2022, 10(3), 646; https://doi.org/10.3390/microorganisms10030646 - 17 Mar 2022
Cited by 8 | Viewed by 3813
Abstract
Diamondback moth (DBM) is an important horticultural pest worldwide as the larvae of these moths feed on the leaves of cruciferous vegetables. As DBM has developed resistance to more than 100 classes of synthetic insecticides, new biological control options are urgently required. Beauveria [...] Read more.
Diamondback moth (DBM) is an important horticultural pest worldwide as the larvae of these moths feed on the leaves of cruciferous vegetables. As DBM has developed resistance to more than 100 classes of synthetic insecticides, new biological control options are urgently required. Beauveria species are entomopathogenic fungi recognized as the most important fungal genus for controlling a wide range of agricultural, forestry, and veterinary arthropod pests. Previous research, aimed at developing new Beauveria-based biopesticides for DBM, has focused on screening single isolates of Beauveria bassiana. However, these fungal isolates have individual requirements, which may limit their effectiveness in some environments. This current study separately assessed 14 Beauveria isolates, from a range of habitats and aligned to four different species (Beauveria bassiana, B. caledonica, B. malawiensis, and B. pseudobassiana), to determine the most effective isolate for the control of DBM. Further assays then assessed whether selected combinations of these fungal isolates could increase the overall efficacy against DBM. Six Beauveria isolates (three B. bassiana and three B. pseudobassiana) achieved high DBM mortality at a low application rate with the first documented report of B. pseudobassiana able to kill 100% of DBM larvae. Further research determined that applications of low-virulent Beauveria isolates improved the control of DBM compared to mixtures containing high-virulent isolates. This novel approach increased the DBM pest mortality and shortened the time to kill. Full article
(This article belongs to the Section Environmental Microbiology)
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15 pages, 355 KiB  
Article
Characterization of Uropathogenic Escherichia coli Reveals Hybrid Isolates of Uropathogenic and Diarrheagenic (UPEC/DEC) E. coli
by Rodrigo H. S. Tanabe, Regiane C. B. Dias, Henrique Orsi, Daiany R. P. de Lira, Melissa A. Vieira, Luís F. dos Santos, Adriano M. Ferreira, Vera L. M. Rall, Alessandro L. Mondelli, Tânia A. T. Gomes, Carlos H. Camargo and Rodrigo T. Hernandes
Microorganisms 2022, 10(3), 645; https://doi.org/10.3390/microorganisms10030645 - 17 Mar 2022
Cited by 14 | Viewed by 4061
Abstract
(1) Background: Pathogenic Escherichia coli are divided into two groups: diarrheagenic (DEC) and extraintestinal pathogenic (ExPEC) E. coli. ExPEC causing urinary tract infections (UTIs) are termed uropathogenic E. coli (UPEC) and are the most common cause of UTIs worldwide. (2) Methods: Here, [...] Read more.
(1) Background: Pathogenic Escherichia coli are divided into two groups: diarrheagenic (DEC) and extraintestinal pathogenic (ExPEC) E. coli. ExPEC causing urinary tract infections (UTIs) are termed uropathogenic E. coli (UPEC) and are the most common cause of UTIs worldwide. (2) Methods: Here, we characterized 112 UPEC in terms of phylogroup, serotype, the presence of virulence factor-encoding genes, and antimicrobial resistance. (3) Results: The majority of the isolates were assigned into the phylogroup B2 (41.07%), and the serogroups O6 (12.5%) and O25 (8.9%) were the most frequent. Five hybrid UPEC (4.5%), with markers from two DEC pathotypes, i.e., atypical enteropathogenic (aEPEC) and enteroaggregative (EAEC) E. coli, were identified, and designated UPEC/aEPEC (one isolate) and UPEC/EAEC (four isolates), respectively. Three UPEC/EAEC harbored genes from the pap operon, and the UPEC/aEPEC carried ibeA. The highest resistance rates were observed for ampicillin (46.4%) and trimethoprim/sulfamethoxazole (34.8%), while 99.1% of the isolates were susceptible to nitrofurantoin and/or fosfomycin. Moreover, 9.8% of the isolates were identified as Extended Spectrum β-Lactamase producers, including one hybrid UPEC/EAEC. (4) Conclusion: Our data reinforce that hybrid UPEC/DEC are circulating in the city of Botucatu, Brazil, as uropathogens. However, how and whether these combinations of genes influence their pathogenicity is a question that remains to be elucidated. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
15 pages, 12893 KiB  
Article
Characterization of Some Salt-Tolerant Bacterial Hydrolases with Potential Utility in Cultural Heritage Bio-Cleaning
by Robert Ruginescu, Madalin Enache, Octavian Popescu, Ioana Gomoiu, Roxana Cojoc, Costin Batrinescu-Moteau, Gabriel Maria, Maria Dumbravician and Simona Neagu
Microorganisms 2022, 10(3), 644; https://doi.org/10.3390/microorganisms10030644 - 17 Mar 2022
Cited by 14 | Viewed by 2578
Abstract
Salt-tolerant enzymes produced by halophilic and halotolerant microorganisms have been proposed to be used in various applications that involve high saline conditions. Considering their biotechnological significance and the current need for more efficient producers of such catalysts, the present study aimed to evaluate [...] Read more.
Salt-tolerant enzymes produced by halophilic and halotolerant microorganisms have been proposed to be used in various applications that involve high saline conditions. Considering their biotechnological significance and the current need for more efficient producers of such catalysts, the present study aimed to evaluate the extracellular proteolytic, esterolytic, cellulolytic and xylanolytic activities of some halotolerant strains, and to characterize their functional parameters. A total of 21 bacterial and fungal strains belonging to the genera Bacillus, Virgibacillus, Salinivibrio, Salinicoccus, Psychrobacter, Nocardiopsis, Penicillium, Aspergillus, and Emericellopsis were assayed by quantitative methods. Among them, the members of the Bacillus genus exhibited the highest catalytic activities. The exoenzymes produced by three selected Bacillus strains were active over wide ranges of salinity, temperature and pH. Proteases were active at 20–80 °C, pH 6–10, and 0–1 M NaCl, while esterases showed good catalytic activities at 20–80 °C, pH 7.5–10, and 0–4 M NaCl. Cellulases and xylanases were active at 20–80 °C, pH 5–10, and 0–5 M NaCl. Due to such properties, these hydrolases could be used in a newly proposed application, namely to clean aged consolidants and organic deposits accumulated over time from the surfaces of salt-loaded wall paintings. Full article
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15 pages, 2003 KiB  
Article
Geo-Spatial Characteristics of 567 Places of Tick-Borne Encephalitis Infection in Southern Germany, 2018–2020
by Amelie M. Friedsam, Oliver J. Brady, Antonia Pilic, Gerhard Dobler, Wiebke Hellenbrand and Teresa M. Nygren
Microorganisms 2022, 10(3), 643; https://doi.org/10.3390/microorganisms10030643 - 17 Mar 2022
Cited by 7 | Viewed by 2388
Abstract
Tick-borne encephalitis (TBE) is a growing public health problem with increasing incidence and expanding risk areas. Improved prevention requires better understanding of the spatial distribution and ecological determinants of TBE transmission. However, a TBE risk map at sub-district level is still missing for [...] Read more.
Tick-borne encephalitis (TBE) is a growing public health problem with increasing incidence and expanding risk areas. Improved prevention requires better understanding of the spatial distribution and ecological determinants of TBE transmission. However, a TBE risk map at sub-district level is still missing for Germany. We investigated the distribution and geo-spatial characteristics of 567 self-reported places of probable TBE infection (POI) from 359 cases notified in 2018–2020 in the study area of Bavaria and Baden-Wuerttemberg, compared to 41 confirmed TBE foci and 1701 random comparator places. We built an ecological niche model to interpolate TBE risk to the entire study area. POI were distributed heterogeneously at sub-district level, as predicted probabilities varied markedly across regions (range 0–93%). POI were spatially associated with abiotic, biotic, and anthropogenic geo-spatial characteristics, including summer precipitation, population density, and annual frost days. The model performed with 69% sensitivity and 63% specificity at an optimised probability threshold (0.28) and an area under the curve of 0.73. We observed high predictive probabilities in small-scale areas, consistent with the known circulation of the TBE virus in spatially restricted microfoci. Supported by further field work, our findings may help identify new TBE foci. Our fine-grained risk map could supplement targeted prevention in risk areas. Full article
(This article belongs to the Special Issue Epidemiology, Surveillance and Prevention of Tick-Borne Diseases)
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10 pages, 1152 KiB  
Article
Molecular Typing, Antibiotic Resistance and Enterotoxin Gene Profiles of Staphylococcus aureus Isolated from Humans in South Korea
by Sunghyun Yoon, Yon Kyoung Park, Tae Sung Jung and Seong Bin Park
Microorganisms 2022, 10(3), 642; https://doi.org/10.3390/microorganisms10030642 - 17 Mar 2022
Cited by 3 | Viewed by 2117
Abstract
The emergence of antimicrobial-resistant Staphylococcus aureus has become a grave concern worldwide. In this study, 95 strains of S. aureus isolated from stool samples were collected from Busan, South Korea to characterize their antimicrobial susceptibility, enterotoxin genes, and molecular typing using matrix-assisted laser [...] Read more.
The emergence of antimicrobial-resistant Staphylococcus aureus has become a grave concern worldwide. In this study, 95 strains of S. aureus isolated from stool samples were collected from Busan, South Korea to characterize their antimicrobial susceptibility, enterotoxin genes, and molecular typing using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and random amplification of polymorphic DNA (RAPD) assay. Only two strains showed no drug resistance, whereas resistance to three or more antibiotics was observed in 87.4% of strains. Ampicillin resistance was the most common at 90% and all strains were susceptible to vancomycin. The distribution of enterotoxin genes encoded in isolates was sea (32.6%), sec (11.6%), seg (19%), sea & sec (2.1%), and sec & seg (34.7%). Molecular typing using both MALDI-TOF MS and RAPD indicated that S. aureus exhibited diverse clonal lineages and no correlations were observed among the profiling of enterotoxin, MALDI-TOF MS, and RAPD. This investigation provides useful information on foodborne pathogenic S. aureus that has a significant public health impact in South Korea. Full article
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16 pages, 2227 KiB  
Article
Phthalate Esters Metabolic Strain Gordonia sp. GZ-YC7, a Potential Soil Degrader for High Concentration Di-(2-ethylhexyl) Phthalate
by Tong Hu, Chen Yang, Zhengyu Hou, Tengfei Liu, Xiaotong Mei, Lianbao Zheng and Weihong Zhong
Microorganisms 2022, 10(3), 641; https://doi.org/10.3390/microorganisms10030641 - 17 Mar 2022
Cited by 13 | Viewed by 2577
Abstract
As commonly used chemical plasticizers in plastic products, phthalate esters have become a serious ubiquitous environmental pollutant, such as in soil of plastic film mulch culture. Microbial degradation or transformation was regarded as a suitable strategy to solve the phthalate esters pollution. Thus, [...] Read more.
As commonly used chemical plasticizers in plastic products, phthalate esters have become a serious ubiquitous environmental pollutant, such as in soil of plastic film mulch culture. Microbial degradation or transformation was regarded as a suitable strategy to solve the phthalate esters pollution. Thus, a new phthalate esters degrading strain Gordonia sp. GZ-YC7 was isolated in this study, which exhibited the highest di-(2-ethylhexyl) phthalate degradation efficiency under 1000 mg/L and the strongest tolerance to 4000 mg/L. The comparative genomic analysis results showed that there exist diverse esterases for various phthalate esters such as di-(2-ethylhexyl) phthalate and dibutyl phthalate in Gordonia sp. GZ-YC7. This genome characteristic possibly contributes to its broad substrate spectrum, high degrading efficiency, and high tolerance to phthalate esters. Gordonia sp. GZ-YC7 has potential for the bioremediation of phthalate esters in polluted soil environments. Full article
(This article belongs to the Section Environmental Microbiology)
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17 pages, 5945 KiB  
Article
Comparison of Fermentation Behaviors and Characteristics of Tomato Sour Soup between Natural Fermentation and Dominant Bacteria-Enhanced Fermentation
by Juan Li, Xiaoyu Wang, Wenyan Wu, Jingzhu Jiang, Dandan Feng, Yuanyuan Shi and Ping Hu
Microorganisms 2022, 10(3), 640; https://doi.org/10.3390/microorganisms10030640 - 17 Mar 2022
Cited by 10 | Viewed by 2774
Abstract
In this study, the correlations between microbial communities with physicochemical properties and volatile flavor compounds (VFCs) during the fermentation of traditional tomato sour soup (CTN) are explored. The results of high-throughput sequencing (HTS) of CTN showed that Lacticaseibacillus (28.67%), Enterobacter (12.37%), and Providencia [...] Read more.
In this study, the correlations between microbial communities with physicochemical properties and volatile flavor compounds (VFCs) during the fermentation of traditional tomato sour soup (CTN) are explored. The results of high-throughput sequencing (HTS) of CTN showed that Lacticaseibacillus (28.67%), Enterobacter (12.37%), and Providencia (12.19%) were the dominant bacteria in the first round of fermentation, while Lacticaseibacillus (50.11%), Enterobacter (13.86%), and Providencia (8.61%) were the dominant bacteria in the second round of fermentation. Additionally, the dominant fungi genera of the first fermentation were Pichia (65.89%) and Geotrichum (30.56%), and the dominant fungi genera of the second fermentation were Pichia (73.68%), Geotrichum (13.99%), and Brettanomyces (5.15%). These results indicate that Lacticaseibacillus is one of the main dominant bacteria in CTN. Then, the dominant strain Lacticaseibacillus casei H1 isolated from CTN was used as a culture to ferment tomato sour soup to monitor dynamic changes in the physicochemical properties and VFCs during enhanced fermentation of tomato sour soup (TN). The physicochemical analysis showed that, compared with CTN, the TN group not only produced acid faster but also had an earlier peak of nitrite and a lower height. The results of the GC–IMS analysis showed that the ester and alcohol contents in the TN group were 1.26 times and 1.8 times that of the CTN group, respectively. Using an O2PLS-DA analysis, 11 bacterial genera and 18 fungal genera were identified as the functional core flora of the CTN group flavor production, further verifying the importance of dominant bacteria for the production of VFCs. This study proved that enhanced fermentation not only shortens the fermentation cycle of tomato sour soup, but also significantly improves its flavor quality, which has great value in the industrial production of tomato sour soup and in the development of a vegetable fermentation starter. Full article
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