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Appl. Microbiol., Volume 2, Issue 4 (December 2022) – 24 articles

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12 pages, 1223 KiB  
Review
Impacts of the Green Revolution on Rhizosphere Microbiology Related to Nutrient Acquisition
by Mary Dixon, Carley Rohrbaugh, Antisar Afkairin and Jorge Vivanco
Appl. Microbiol. 2022, 2(4), 992-1003; https://doi.org/10.3390/applmicrobiol2040076 - 30 Nov 2022
Cited by 3 | Viewed by 2825
Abstract
The Green Revolution (GR) involved selective breeding of cereals and the use of high fertilizer inputs with the goal of increasing crop yields to alleviate hunger. As a result of both greater use of inorganic fertilizers and the introduction of semi-dwarf cultivars, grain [...] Read more.
The Green Revolution (GR) involved selective breeding of cereals and the use of high fertilizer inputs with the goal of increasing crop yields to alleviate hunger. As a result of both greater use of inorganic fertilizers and the introduction of semi-dwarf cultivars, grain yield increased globally and hunger was alleviated in certain areas of the world. However, these changes in varietal selection and fertilization regimes have impacted soil fertility and the root-associated microbiome. Higher rates of inorganic fertilizer application resulted in reduced rhizosphere microbial diversity, while semi-dwarf varieties displayed a greater abundance of rhizosphere microbes associated with nitrogen utilization. Ultimately, selection for beneficial aboveground traits during the GR led to healthier belowground traits and nutrient uptake capabilities. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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11 pages, 2920 KiB  
Review
Biocontrol of Grapevine Crown Gall Performed Using Allorhizobium vitis Strain ARK-1
by Akira Kawaguchi
Appl. Microbiol. 2022, 2(4), 981-991; https://doi.org/10.3390/applmicrobiol2040075 - 19 Nov 2022
Cited by 3 | Viewed by 1766
Abstract
Grapevine crown gall (GCG), which is caused by tumorigenic Allorhizobium vitis (=Rhizobium vitis), is the most important bacterial disease in grapevine, and its economic impact on grapevine is very high. When young vines develop GCG, they often die, whereas older vines [...] Read more.
Grapevine crown gall (GCG), which is caused by tumorigenic Allorhizobium vitis (=Rhizobium vitis), is the most important bacterial disease in grapevine, and its economic impact on grapevine is very high. When young vines develop GCG, they often die, whereas older vines may show stress and poor growth depending on the severity of GCG, because GCG interferes with the vascular system of the grapevine trunk and prevents nutrient flow, leading to inferior growth and death. Viticultural practices and chemical control designed to inhibit GCG are only partially effective presently; thus, a biocontrol procedure could be a desirable and effective approach for GCG prevention. This article reviews the practical use of biocontrol options for GCG inhibition that involve using nonpathogenic and antagonistic A. vitis strains. In these studies, screening tests of biocontrol agents discovered nonpathogenic A. vitis strains VAR03-1, ARK-1, ARK-2, and ARK-3. After dipping grapevine roots in a suspension of candidate strains prior to planting in the field, treatment using ARK-1 was shown to significantly reduce the number of plants with GCG. A meta-analysis indicated that ARK-1 is very useful for controlling crown gall in various plant species, including grapevine. It was reported that when a mixture of ARK-1 and a tumorigenic strain was examined in grapevines, the expression levels of several virulence genes of the virulent strain were significantly lower. ARK-1 can reduce the pathogen population in grapevines and gall incidence. Moreover, ARK-1 can prime the induction of certain defense genes of grapevine. These results indicate that ARK-1 has a unique biocontrol mechanism and that it is a promising new biocontrol agent to control GCG. Full article
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16 pages, 2960 KiB  
Article
Phosphorus Recycling, Biocontrol, and Growth Promotion Capabilities of Soil Bacterial Isolates from Mexican Oak Forests: An Alternative to Reduce the Use of Agrochemicals in Maize Cultivation
by Rocío Hernández-León, Antonio González-Rodríguez and Yunuen Tapia-Torres
Appl. Microbiol. 2022, 2(4), 965-980; https://doi.org/10.3390/applmicrobiol2040074 - 16 Nov 2022
Cited by 1 | Viewed by 1910
Abstract
Six bacteria (Bacillus velezensis 13, Bacillus subtillis 42, Pseudomonas fluorescens E221, Pseudomonas Poae EE12, Rahnella sp. EM1, and Serratia sp. EM2) isolated from the soil and litter of Mexican oak forests were characterized by identifying their ability to acquire phosphorus from different [...] Read more.
Six bacteria (Bacillus velezensis 13, Bacillus subtillis 42, Pseudomonas fluorescens E221, Pseudomonas Poae EE12, Rahnella sp. EM1, and Serratia sp. EM2) isolated from the soil and litter of Mexican oak forests were characterized by identifying their ability to acquire phosphorus from different sources, analyzed for their biocontrol capabilities against two different phytopathogenic fungi, and finally tested for their ability to stimulate the germination of maize seeds and promotion of maize seedling growth. The greatest capacity to biocontrol the mycelial growth of phytopathogenic fungi Botrytis cinerea and Fusarium oxysporum was found in B. velezensis 13 and B. subtillis 42. P. poae EE12 and P. fluorescens E221 significantly promoted germination and the length of the primary root in Zea mays. Rahnella sp. EM1 and Serratia sp. EM2 could produce indole compounds related to auxin synthesis and increased the fresh weight of the maize seedlings. Together, these isolates represent an alternative to reduce the use of agrochemicals in maize cultivation. In general, soil microorganisms from Mexican oak forests represent a source of genetic resources for the sustainable management and conservation of soils for agricultural use. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)
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9 pages, 840 KiB  
Article
The Development of a Real-Time PCR Assay for Specific Detection of the NISKHI Sheep Pox Vaccine Virus Strain DNA
by Alexander Sprygin, Ali Mazloum, Antoinette Van Schalkwyk, Alena Krotova, Kseniya Shalina, Marko Dmitric, Olga Byadovskaya, Larisa Prokhvatilova and Ilya Chvala
Appl. Microbiol. 2022, 2(4), 956-964; https://doi.org/10.3390/applmicrobiol2040073 - 15 Nov 2022
Cited by 2 | Viewed by 1296
Abstract
Sheep pox (SPP) constitutes a global animal health scourge, despite the numerous efforts targeting the eradication of the disease implemented in affected countries. An efficient control and eradication strategy incorporates the use of live attenuated vaccines, which in turn requires a method for [...] Read more.
Sheep pox (SPP) constitutes a global animal health scourge, despite the numerous efforts targeting the eradication of the disease implemented in affected countries. An efficient control and eradication strategy incorporates the use of live attenuated vaccines, which in turn requires a method for differentiation between vaccinated and infected sheep. The NISKHI live attenuated SPP vaccine (LAV) is abundantly used in Russia, Kazakhstan and other Central Asian countries. This study describes the development and evaluation of a real-time PCR with a high-resolution melting assay, capable of differentiating the NISKHI vaccine virus from circulating virulent field strains. The RNA polymerase subunit RPO132 gene contains a unique single nucleotide polymorphism (SNP) capable of altering the melting curves of amplicons from LAV and virulent field isolates circulating in the region. The melting temperature (Tm) of field isolates ranged from 75.47 °C ± 0.04 to 75.86 °C ± 0.08, while the vaccine strain averaged 76.46 °C ± 0.12. Subsequent evaluation of this assay demonstrated that the recent SPP outbreaks in central Russia may be attributed to virulent field isolates. This robust assay was proven to consistently and differentially detect the NISKHI LAV strain when analyzing clinical samples from affected sheep. Full article
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6 pages, 282 KiB  
Article
Validation of a Lateral Flow Assay for Rapid Diagnosis of Histoplasmosis in Advanced HIV Disease, Buenos Aires, Argentina
by Mariana Andreani, Claudia E. Frola, Diego H. Caceres, Cristina E. Canteros, María J. Rolón, Tom Chiller and Liliana Guelfand
Appl. Microbiol. 2022, 2(4), 950-955; https://doi.org/10.3390/applmicrobiol2040072 - 15 Nov 2022
Cited by 2 | Viewed by 1514
Abstract
Histoplasmosis is a major cause of mortality in individuals with advanced human immunodeficiency virus (HIV) disease (AHD). We evaluated in patients with AHD a lateral flow assay (LFA) developed by MiraVista® Diagnostics (MVD LFA). Histoplasmosis was defined based on the European Organization [...] Read more.
Histoplasmosis is a major cause of mortality in individuals with advanced human immunodeficiency virus (HIV) disease (AHD). We evaluated in patients with AHD a lateral flow assay (LFA) developed by MiraVista® Diagnostics (MVD LFA). Histoplasmosis was defined based on the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) case definitions. We also compared the results of this LFA with those obtained using a commercial enzyme immunoassay (EIA) developed by IMMY, Clarus Histoplasma GM EIA, IMMY (HGM EIA). A retrospective observational study was conducted at Hospital Juan A. Fernández, located in Buenos Aires, Argentina. The study included 48 urine specimens from patients aged >18 years with AHD. Urine specimens included 17 patients with disseminated histoplasmosis and 31 specimens from patients without evidence of histoplasmosis. Specimens were tested using the MVD LFA and the HGM EIA. The MVD LFA and the HGM EIA had similar analytical performance, with a sensitivity of 94%, specificity of 100%, positive predictive value of 100%, negative predictive value of 97%, and an accuracy of 98%. Comparison of the MVD LFA with the HGM EIA demonstrated a Kappa agreement index of 0.906. The LFA evaluated in this study had high analytical performance; it provided rapid diagnosis of histoplasmosis with minimal requirements for laboratory training, equipment, and laboratory infrastructure. Full article
16 pages, 2277 KiB  
Article
Globally Disseminated Multidrug Resistance Plasmids Revealed by Complete Assembly of Multidrug Resistant Escherichia coli and Klebsiella pneumoniae Genomes from Diarrheal Disease in Botswana
by Teddie O. Rahube, Andrew D. S. Cameron, Nicole A. Lerminiaux, Supriya V. Bhat and Kathleen A. Alexander
Appl. Microbiol. 2022, 2(4), 934-949; https://doi.org/10.3390/applmicrobiol2040071 - 11 Nov 2022
Cited by 3 | Viewed by 1905
Abstract
Antimicrobial resistance is a disseminated global health challenge because many of the genes that cause resistance can transfer horizontally between bacteria. Despite the central role of extrachromosomal DNA elements called plasmids in driving the spread of resistance, the detection and surveillance of plasmids [...] Read more.
Antimicrobial resistance is a disseminated global health challenge because many of the genes that cause resistance can transfer horizontally between bacteria. Despite the central role of extrachromosomal DNA elements called plasmids in driving the spread of resistance, the detection and surveillance of plasmids remains a significant barrier in molecular epidemiology. We assessed two DNA sequencing platforms alone and in combination for laboratory diagnostics in Botswana by annotating antibiotic resistance genes and plasmids in extensively drug resistant bacteria from diarrhea in Botswana. Long-read Nanopore DNA sequencing and high accuracy basecalling effectively estimated the architecture and gene content of three plasmids in Escherichia coli HUM3355 and two plasmids in Klebsiella pneumoniae HUM7199. Polishing the assemblies with Illumina reads increased base calling precision with small improvements to gene prediction. All five plasmids encoded one or more antibiotic resistance genes, usually within gene islands containing multiple antibiotic and metal resistance genes, and four plasmids encoded genes associated with conjugative transfer. Two plasmids were almost identical to antibiotic resistance plasmids sequenced in Europe and North America from human infection and a pig farm. These One Health connections demonstrate how low-, middle-, and high-income countries collectively benefit from increased whole genome sequencing capacity for surveillance and tracking of infectious diseases and antibiotic resistance genes that can transfer between animal hosts and move across continents. Full article
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13 pages, 2159 KiB  
Article
Selection of Listeria monocytogenes InlA-Binding Peptides Using Phage Display—Novel Compounds for Diagnostic Applications?
by Julia Kenzel, Dagmar Adeline Brüggemann and Susanne Aileen Funke
Appl. Microbiol. 2022, 2(4), 921-933; https://doi.org/10.3390/applmicrobiol2040070 - 10 Nov 2022
Viewed by 1538
Abstract
Listeria monocytogenes is a pathogenic, gram-positive bacterium causing foodborne infections and listeriosis, an infection responsible for serious medical conditions, especially for pregnant women, newborns, or people with a weak immune system. Even after antibiotic treatment, 30% of clinical infections result in death. L. [...] Read more.
Listeria monocytogenes is a pathogenic, gram-positive bacterium causing foodborne infections and listeriosis, an infection responsible for serious medical conditions, especially for pregnant women, newborns, or people with a weak immune system. Even after antibiotic treatment, 30% of clinical infections result in death. L. monocytogenes is able to enter and multiply in mammalian cells. Invasion into epithelial cells in the human intestine is mediated by the interaction of the bacterial surface protein internalin A (InlA) with the host cell receptor E-cadherin (E-cad). We have used phage display to select InlA-specific peptides consisting of 12 amino acids using a randomized, recombinant peptide library. We could demonstrate that the selected peptides bound to recombinant InlA protein as well as to L. monocytogenes cells. In vitro, some of the peptides inhibited the interaction between recombinant InlA and human E-cad. As far as we know, this is the first publication on the development of InlA-specific peptide ligands. In the future, our peptides might be used for the development of innovative diagnostic tools or even therapeutic approaches. Full article
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16 pages, 10439 KiB  
Article
The Baseline Gut Microbiota Enterotype Directs Lifestyle-Induced Amelioration of Pollen Allergy Severity: A Self Controlled Case-Series Study
by Satoshi Watanabe, Takayoshi Fukushima, Yusuke Matsuo, Takahito Morimoto, Tsuneo Deguchi, Keisuke Fukumuro and Yu Sawai
Appl. Microbiol. 2022, 2(4), 905-920; https://doi.org/10.3390/applmicrobiol2040069 - 10 Nov 2022
Viewed by 2282
Abstract
Deciphering the key factors underlying individual responses to a habitual diet is important in implementing personalized nutrition strategies to treat allergic diseases. This prospective randomized cohort study aimed to identify key factors determining individual pollen allergy (PA) trajectories in a natural setting. Baseline [...] Read more.
Deciphering the key factors underlying individual responses to a habitual diet is important in implementing personalized nutrition strategies to treat allergic diseases. This prospective randomized cohort study aimed to identify key factors determining individual pollen allergy (PA) trajectories in a natural setting. Baseline data on fecal microbiota composition, lifestyle activities, and diet habits of 190 participants with PA and 92 healthy controls were collected, followed by a SOMPO-guided intestinal activity program. Three enterotypes enriched in Bacteroides, Prevotella, and Ruminococcus and four subenterotypes for enterotypes Bacteroides and Prevotella enriched with Faecalibacterium, Megamonas, and Fusobacterium were identified at baseline. PA severity was significantly negatively correlated with the daily intake of fermented plants and no weekly intake of meat, but positively correlated with poor sleep quality. Interactions between enterotype and lifestyle factors affected PA severity, and intestinal activity intervention based on the baseline enterotype reduced the PA severity score. In conclusion, the findings of this study demonstrated that the baseline gut enterotype plays a crucial role in PA. This study suggests combining enterotype data with habitual diet can improve PA severity. Full article
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23 pages, 4521 KiB  
Article
Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation
by Adrian Jones, Steven E. Massey, Daoyu Zhang, Yuri Deigin and Steven C. Quay
Appl. Microbiol. 2022, 2(4), 882-904; https://doi.org/10.3390/applmicrobiol2040068 - 07 Nov 2022
Viewed by 9446
Abstract
Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University [...] Read more.
Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University in 2022, and find that sections of the partial genome phylogenetically group with Guangxi pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, it is also found in 10 additional NGS datasets from 5 separate mammalian species and is likely related to contamination by a laboratory researched virus. Absence of bat mitochondrial sequences from the datasets, the fragmentary nature of the virus sequence and the presence of a partial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has been cloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated with significant Homo sapiens genetic material, and numerous viruses not associated with the host animals sampled. We further identify the dominant human haplogroup of the contaminating H. sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association of this novel SARS2r-CoV with both bat CoV and the GX PCoV clades is an important step towards identifying the origin of the GX PCoVs. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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9 pages, 286 KiB  
Article
Evaluation of STANDARDTM M10 SARS-CoV-2, a Novel Cartridge-Based Real-Time PCR Assay for the Rapid Identification of Severe Acute Respiratory Syndrome Coronavirus 2
by Laura Grumiro, Martina Brandolini, Giulia Gatti, Agata Scalcione, Francesca Taddei, Giorgio Dirani, Andrea Mancini, Agnese Denicolò, Martina Manera, Silvia Zannoli, Maria Michela Marino, Manuela Morotti, Valentina Arfilli, Arianna Battisti, Monica Cricca and Vittorio Sambri
Appl. Microbiol. 2022, 2(4), 873-881; https://doi.org/10.3390/applmicrobiol2040067 - 04 Nov 2022
Cited by 2 | Viewed by 1397
Abstract
Since the beginning of the pandemic, SARS-CoV-2 has caused problems for all of world’s population, not only in terms of deaths but also in terms of overloading healthcare facilities in all countries. Diagnosis is one of the key aspects of controlling the spread [...] Read more.
Since the beginning of the pandemic, SARS-CoV-2 has caused problems for all of world’s population, not only in terms of deaths but also in terms of overloading healthcare facilities in all countries. Diagnosis is one of the key aspects of controlling the spread of SARS-CoV-2, and among the current molecular techniques, real-time PCR is considered as the gold standard. The availability of tests that allow for the rapid and accurate identification of SARS-CoV-2 is therefore of considerable importance. Moreover, if these tests allow for even minimal intervention by the operator, any risk of contamination is reduced. In this study, the performances of the new STANDARDTM M10 SARS-CoV-2 (SD Biosensor Inc., Suwon, Korea) rapid molecular test, which incorporates the above-mentioned features, were characterized. The clinical and analytical performances measured by testing different variants circulating in Italy of STANDARDTM M10 SARS-CoV-2 were compared to the test already on the market and recognized as the gold standard: Xpert Xpress SARS-CoV-2 (Cepheid, Sunnyvale, CA, USA). The results obtained between the two tests are largely comparable, suggesting that STANDARDTM M10 SARS-CoV-2 can be used with excellent results in the fight against the global spread of SARS-CoV-2. Full article
12 pages, 1555 KiB  
Article
Influence of Culture Media and Environmental Factors (Water Potential and Temperature) on Mycelial Growth of Phytopythium vexans (de Bary), the Causal Agent of Dieback Disease in Apple Trees
by Salma Jabiri, Hajar El Hamss, Mohammed Bendriss Amraoui and Rachid Lahlali
Appl. Microbiol. 2022, 2(4), 861-872; https://doi.org/10.3390/applmicrobiol2040066 - 02 Nov 2022
Cited by 3 | Viewed by 1439
Abstract
This study aimed at evaluating the effects of culture media and environmental factors (temperature and water potential (Ψw)) on the growth of the pathogenic fungus Phytopythium vexans (de Bary) associated with root rot and dieback disease in apple trees. Tomato agar, potato dextrose [...] Read more.
This study aimed at evaluating the effects of culture media and environmental factors (temperature and water potential (Ψw)) on the growth of the pathogenic fungus Phytopythium vexans (de Bary) associated with root rot and dieback disease in apple trees. Tomato agar, potato dextrose agar (PDA), and soybean agar were the most favourable for rapid mycelial growth, with optimum growth recorded for PDA medium. To determine the environmental conditions that promoted the development of this phytopathogen, the effects of temperature (5–30 °C), water potential (Ψw) (−15.54; −0.67 MPa) (0.89–0.995 aw), and their interaction were evaluated on the in vitro radial growth rates of the five isolates of P. vexans and on their latency phase (time period prior to growth). The results of this study showed that temperature, water potential, and their interaction had significant effects (p < 0.001) on the radial growth rates and latency phases of all tested P. vexans isolates. All isolates were able to grow throughout the temperature range (5 to 30 °C), with the maximum radial growth rate being observed at the highest temperatures, 25–30 °C. Growth was seen to be faster at −0.67 MPa (0.995 aw) at 25 °C and 30 °C. No growth was observed at Ψw < −5.44 MPa (0.96 aw), regardless of the temperature. It was found that the length of the latency phase depended significantly on both environmental factors. The longest latency phases (5 days on average) were recorded at a temperature of 5 °C and Ψw of −0.67 MPa (0.995 aw) and −2.69 MPa (0.98 aw), while the shortest latency phases were observed at a temperature of 30 °C and a Ψw of −0.67 MPa (0.995 aw), with an average of 0.2 days. The findings from this study could help to understand the impact of these environmental factors on the occurrence of diseases caused by P. vexans and more likely to design a reliable preventive control strategy based on the avoidance of conditions that play in favour of the phytopathogen. Full article
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6 pages, 845 KiB  
Article
Comparison of Fourteen Rapid Point-of-Care Antigen Tests for SARS-CoV-2: Use and Sensitivity
by Zulema Pérez-Martínez, Gabriel Martín, Marta Sandoval, Cristian Castelló-Abiétar, Susana Rojo-Alba, Jose Antonio Boga, Santiago Melón and Marta Elena Álvarez-Argüelles
Appl. Microbiol. 2022, 2(4), 855-860; https://doi.org/10.3390/applmicrobiol2040065 - 30 Oct 2022
Viewed by 1011
Abstract
Fast, sensitive techniques are advisable for SARS-CoV-2 detection. Various rapid SARS-CoV-2 antigen detection tests have been developed, but type and quality of the sample, stage of the disease and viral load can all have an impact on their sensitivity. For this study, a [...] Read more.
Fast, sensitive techniques are advisable for SARS-CoV-2 detection. Various rapid SARS-CoV-2 antigen detection tests have been developed, but type and quality of the sample, stage of the disease and viral load can all have an impact on their sensitivity. For this study, a total of 486 swabs were processed and checked with various commercially available tests and then compared with q(RT)-PCR (the gold-standard method). Total sensitivity varied considerably; for example, 42.10% (nal von minden and Tody Laboratories), 68.42% (Cahnos) and 84.78% (PCL). Sensitivity reached 100% when the cycle threshold (Ct) was lower than 22 in almost all tests, although this dropped considerably when the Ct was higher above 30, where only 3 tests identified 40% or more positive samples and in 5 cases it was 0%. What is more, only 2 cases were 100% accurate when viral load was higher than 5 log/103 cells and accuracy was 0% in 12 cases when viral load was lower than 4 log/103 cells. These results, particularly taking into consideration the fact that they used normalized viral load, suggest that antigen detection tests have their role in the fast triage of positive patients, but that considerable care should be taken with negative results, which is even more important if they are used for massive screening. Full article
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18 pages, 1722 KiB  
Review
Lactic Acid Bacteria as Mucosal Immunity Enhancers and Antivirals through Oral Delivery
by Assad Moon, Yuan Sun, Yanjin Wang, Jingshan Huang, Muhammad Umar Zafar Khan and Hua-Ji Qiu
Appl. Microbiol. 2022, 2(4), 837-854; https://doi.org/10.3390/applmicrobiol2040064 - 26 Oct 2022
Cited by 1 | Viewed by 2744
Abstract
Mucosal vaccination offer an advantage over systemic inoculation from the immunological viewpoint. The development of an efficient vaccine is now a priority for emerging diseases such as COVID-19, that was declared a pandemic in 2020 and caused millions of deaths globally. Lactic acid [...] Read more.
Mucosal vaccination offer an advantage over systemic inoculation from the immunological viewpoint. The development of an efficient vaccine is now a priority for emerging diseases such as COVID-19, that was declared a pandemic in 2020 and caused millions of deaths globally. Lactic acid bacteria (LAB) especially Lactobacillus are the vital microbiota of the gut, which is observed as having valuable effects on animals’ and human health. LAB produce lactic acid as the major by-product of carbohydrate degradation and play a significant role in innate immunity enhancement. LAB have significant characteristics to mimic pathogen infections and intrinsically possess adjuvant properties to enhance mucosal immunity. Increasing demand and deliberations are being substantially focused on probiotic organisms that can enhance mucosal immunity against viral diseases. LAB can also strengthen their host’s antiviral defense system by producing antiviral peptides, and releasing metabolites that prevent viral infections and adhesion to mucosal surfaces. From the perspectives of “one health” and the use of probiotics, conventional belief has opened up a new horizon on the use of LAB as antivirals. The major interest of this review is to depict the beneficial use of LAB as antivirals and mucosal immunity enhancers against viral diseases. Full article
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10 pages, 1783 KiB  
Article
Agrobacterium tumefaciens-Mediated Gene Transfer in a Major Human Skin Commensal Fungus, Malassezia globosa
by Otomi Cho, Yasuhiko Matsumoto, Tsuyoshi Yamada and Takashi Sugita
Appl. Microbiol. 2022, 2(4), 827-836; https://doi.org/10.3390/applmicrobiol2040063 - 25 Oct 2022
Viewed by 1602
Abstract
Although the fungal microbiome in human skin mainly comprises lipophilic yeasts, including Malassezia species, these microorganisms can cause various dermatitis conditions, including pityriasis versicolor, seborrheic dermatitis, folliculitis, and atopic dermatitis, depending on the host condition. Both Malassezia globosa and Malassezia restricta are major [...] Read more.
Although the fungal microbiome in human skin mainly comprises lipophilic yeasts, including Malassezia species, these microorganisms can cause various dermatitis conditions, including pityriasis versicolor, seborrheic dermatitis, folliculitis, and atopic dermatitis, depending on the host condition. Both Malassezia globosa and Malassezia restricta are major species implicated in Malassezia-related dermatitis. However, the pathogenicity of these microorganisms has not been revealed at the genetic level owing to the lack of a genetic recombination system. Therefore, we developed a gene recombination system for M. globosa using Agrobacterium tumefaciens-mediated gene transfer of the target gene FKB1, which encodes the FKBP12 protein that binds the calcineurin inhibitor tacrolimus. The wild-type strain of M. globosa was sensitive to tacrolimus, whereas the FKB1 deletion mutant was resistant to tacrolimus. Reintroduction of FKB1 into the FKB1 deletion mutant restored wild-type levels of susceptibility to tacrolimus. Moreover, an FKB1-eGFP fusion gene was generated and expression of this fusion protein was observed in the cytoplasm. This newly developed gene recombination system for M. globosa will help further our understanding of the pathogenesis of M. globosa-related dermatitis at the genetic level. Full article
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9 pages, 1575 KiB  
Article
Detection of Hepatitis E Virus (HEV) in Pigs and in the Wild Boar (Sus scrofa) Population of Chieti Province, Abruzzo Region, Italy
by Fabrizio De Massis, Giuseppe Aprea, Silvia Scattolini, Daniela D’Angelantonio, Alexandra Chiaverini, Iolanda Mangone, Margherita Perilli, Giulia Colacicco, Sabrina Olivieri, Francesco Pomilio, Adriano Di Pasquale, Giacomo Migliorati, Giovanni Di Paolo, Chiara Morgani and Angelo Giammarino
Appl. Microbiol. 2022, 2(4), 818-826; https://doi.org/10.3390/applmicrobiol2040062 - 19 Oct 2022
Cited by 3 | Viewed by 1771
Abstract
Hepatitis E virus (HEV) is a zoonotic pathogen, causing infectious hepatitis in man. Pigs and wild boars are the natural asymptomatic reservoirs, while the disease in humans could be either asymptomatic or evolve in hepatitis. In Europe, an increasing number of human infections [...] Read more.
Hepatitis E virus (HEV) is a zoonotic pathogen, causing infectious hepatitis in man. Pigs and wild boars are the natural asymptomatic reservoirs, while the disease in humans could be either asymptomatic or evolve in hepatitis. In Europe, an increasing number of human infections from HEV have been reported over the last few years. The main route of transmission is through contaminated food, by direct or indirect consumption of raw or undercooked pork and wild boar meat and meat products. Up to now, HEV prevalence in Italian northern regions has been extensively determined in wild boars and pigs, while less data have been collected from the southern ones. There is a need to report more data about HEV prevalence from wild boars and pigs in southern Italy in consideration of the potential risk posed by some specific traditional food products manufactured in these areas and produced from pig and wild boar livers (e.g., sausages and salami). The aim of this study was to demonstrate the circulation of the Hepatitis E virus (HEV) in pigs and in the wild boar population of the province of Chieti, Abruzzo Region, Central Italy. Moreover, potential HEV seroprevalence in hunters from that area was also assessed. The overall prevalence of HEV RNA in wild boars was 9.5% (CI 5.4–16.2%), but no HEV RNA was detected in samples from pigs. Full article
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13 pages, 939 KiB  
Article
Evaluation of Environmental Lactococcus lactis Strains Reveals Their Potential for Biotransformation of Lignocellulosic Feedstocks
by Desirée Román Naranjo, Michael Callanan, Anne Thierry and Olivia McAuliffe
Appl. Microbiol. 2022, 2(4), 805-817; https://doi.org/10.3390/applmicrobiol2040061 - 12 Oct 2022
Viewed by 1362
Abstract
In this study, the potential for a collection of wild-type L. lactis strains to metabolize the breakdown products of lignocellulose was investigated. The strains, isolated from a variety of environmental sources including grass and vegetables, were analyzed for their ability to ferment pentose [...] Read more.
In this study, the potential for a collection of wild-type L. lactis strains to metabolize the breakdown products of lignocellulose was investigated. The strains, isolated from a variety of environmental sources including grass and vegetables, were analyzed for their ability to ferment pentose sugars and their cellulolytic ability. In total, 21 environment-derived L. lactis strains were evaluated. Eleven of the 21 L. lactis isolates were found to have the potential to ferment pentose sugars commonly produced by lignocellulose breakdown. A 3,5-dinitrosalicylic acid (DNS)-based cellulase assay was performed, and 10 of the 21 L. lactis isolates showed cellulolytic activity. Six strains were able to both metabolize pentose sugars and showed cellulolytic activity: these included green pea isolates DPC 6754, DPC 6755, DPC 6756, and DPC 6758, the grass isolate DPC 6760, and the mung bean sprouts isolate KF147. For the first time, certain wild-type non-engineered L. lactis were found to possess cellulolytic activity. Moreover, these two abilities do not appear to be correlated. These findings highlight that environment-derived L. lactis, a species with a history of safe use in food production, has the potential for second-generation bioconversion processes, and the potential to re-utilize plant biomass found in waste streams. Full article
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5 pages, 388 KiB  
Brief Report
Utilization of Microwaves: A Novel Approach to SARS-CoV-2 Genome Extraction
by Marta Elena Álvarez-Argüelles, Susana Rojo-Alba, Gabriel Martín, Zulema Pérez-Martínez, Cristian Castelló-Abietar, Jose Antonio Boga and Santiago Melón
Appl. Microbiol. 2022, 2(4), 800-804; https://doi.org/10.3390/applmicrobiol2040060 - 12 Oct 2022
Viewed by 1020
Abstract
In this study, an innovative approach to the heat extraction method has been tested: the use of microwaves, which can dramatically decrease the time that is needed to do the genome extraction. The method can obtain the virus with enough quality to assure [...] Read more.
In this study, an innovative approach to the heat extraction method has been tested: the use of microwaves, which can dramatically decrease the time that is needed to do the genome extraction. The method can obtain the virus with enough quality to assure the identification by RT-qPCR and minimize procedures and contaminations. Full article
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18 pages, 1638 KiB  
Review
Zika Virus Infection and Development of Drug Therapeutics
by Jiao Guo, Xi Ma, Xi Xu, Yan Guo, Bixuan Li, Meihua Wang and Yang Wang
Appl. Microbiol. 2022, 2(4), 782-799; https://doi.org/10.3390/applmicrobiol2040059 - 09 Oct 2022
Cited by 2 | Viewed by 3800
Abstract
Zika virus (ZIKV) is an emerging flavivirus that is associated with neurological complications, such as neuroinflammatory Guillain Barré Syndrome in adults and microcephaly in newborns, and remains a potentially significant and international public health concern. The World Health Organization is urging the development [...] Read more.
Zika virus (ZIKV) is an emerging flavivirus that is associated with neurological complications, such as neuroinflammatory Guillain Barré Syndrome in adults and microcephaly in newborns, and remains a potentially significant and international public health concern. The World Health Organization is urging the development of novel antiviral therapeutic strategies against ZIKV, as there are no clinically approved vaccines or drugs against this virus. Given the public health crisis that is related to ZIKV cases in the last decade, efficient strategies should be identified rapidly to combat or treat ZIKV infection. Several promising strategies have been reported through drug repurposing studies, de novo design, and the high-throughput screening of compound libraries in only a few years. This review summarizes the genome and structure of ZIKV, viral life cycle, transmission cycle, clinical manifestations, cellular and animal models, and antiviral drug developments, with the goal of increasing our understanding of ZIKV and ultimately defeating it. Full article
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16 pages, 1927 KiB  
Article
The Growth Medium Affects the Viability of IPEC-J2 Animal Cell Line in the Presence of Probiotic Bacteria
by Marie-Josée Lemay, Yves Raymond, Claude P. Champagne and Julie Brassard
Appl. Microbiol. 2022, 2(4), 766-781; https://doi.org/10.3390/applmicrobiol2040058 - 06 Oct 2022
Viewed by 1778
Abstract
Background: The IPEC-J2 cell line is frequently used as an in vitro model to study the bioactivity of live probiotics. However, lactic acid bacteria (LB) acidify the medium, and the impact of pH and lactic acid accumulation on cell viability seem to be [...] Read more.
Background: The IPEC-J2 cell line is frequently used as an in vitro model to study the bioactivity of live probiotics. However, lactic acid bacteria (LB) acidify the medium, and the impact of pH and lactic acid accumulation on cell viability seem to be underestimated. Methods: IPEC-J2 viability was assessed by neutral red and flow cytometry in the presence of eight probiotics at concentrations between 106 and 109 bacteria/mL in maintenance and buffered media. Results: It was shown that a high inoculation level led to higher cytotoxic effects on IPEC-J2 cells after 22 h of incubation and that viability losses were more related to a combination of low pH and lactic acid than to the probiotics themselves. Furthermore, with LB at 106 and 107 bacteria/mL, the addition of phosphates to the media significantly reduced the drop in the pH and preserved the IPEC-J2 viability between 100% and 69%, compared to a highly variable viability between 100% and 17.5% in the unbuffered media. Conclusions: Under certain in vitro conditions, probiotics can lead to the deterioration of animal cells, and pH neutralization is an essential parameter in the cell–probiotic system in order to preserve cell viability and to better evaluate the bioactive properties of live probiotics. Full article
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17 pages, 1839 KiB  
Article
Genomic Features of Pseudomonas putida PCL1760: A Biocontrol Agent Acting via Competition for Nutrient and Niche
by Daniel Mawuena Afordoanyi, Roderic Gilles Claret Diabankana, Aynur Kamilevich Miftakhov, Evgenii Sergeyevich Kuchaev and Shamil Zavdatovich Validov
Appl. Microbiol. 2022, 2(4), 749-765; https://doi.org/10.3390/applmicrobiol2040057 - 02 Oct 2022
Cited by 1 | Viewed by 1802
Abstract
Pseudomonasputida strain PCL1760 is a biocontrol agent protecting plants from pathogens via the mechanism of competition for nutrients and niches (CNN). To confirm this mechanism as well as to adapt the strain for biotechnological applications, full genome analysis was compared with the [...] Read more.
Pseudomonasputida strain PCL1760 is a biocontrol agent protecting plants from pathogens via the mechanism of competition for nutrients and niches (CNN). To confirm this mechanism as well as to adapt the strain for biotechnological applications, full genome analysis was compared with the known biotechnological model, P. putida S12, and other related species, which were analyzed on different genomic databases. Moreover, the antibacterial activity of PCL1760 was tested against Staphylococcus aureus, Pseudomonas aeruginosa, and Pseudomonas syringae. No genetic systems involved in antibiosis were revealed among the secondary metabolite clusters of the strain of PCL1760. The only antagonistic effect was observed against P. syringae, which might be because of siderophore (yellow-greenish fluorescence), although less than 19% pyoverdin biosynthesis clusters were predicted using the AntiSMASH server. P. putida PCL1760 in comparison with the Pseudomonas simiae strain PCL1751, another biocontrol agent acting solely via CNN, which lost its ‘luxury’ genes necessary for antibiosis or parasitism/predation mechanisms, but carries genetic systems providing motility. Interestingly, immunity genes (CRISPR/Cas and prophages) showed PCL1760 to be robust in comparison with S12, while annotation on OrthoVenn2 showed PCL1760 to be amenable for genetic manipulations. It is tempting to state that rhizobacteria using the mechanism of CNN are distinguishable from biocontrol agents acting via antibiosis or parasitism/predation at the genomic level. This confirms the CNN of PCL1760 as the sole mechanism for biocontrol and we suggest the strain as a new model for genetic engineering. Full article
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14 pages, 2308 KiB  
Article
Degradation of Polycyclic Aromatic Hydrocarbons by Co-Culture of Pleurotus ostreatus Florida and Azospirillum brasilense
by Natalia Pozdnyakova, Anna Muratova and Olga Turkovskaya
Appl. Microbiol. 2022, 2(4), 735-748; https://doi.org/10.3390/applmicrobiol2040056 - 30 Sep 2022
Cited by 2 | Viewed by 1525
Abstract
Bacterial-fungal interactions are important in the functioning of natural ecosystems. We examined possible synergistic or antagonistic effects during the degradation of polycyclic aromatic hydrocarbons (PAHs) by a fungal–bacterial co-culture. Bacteria and fungi were grown in a liquid nutrient medium supplemented with PAH substrates. [...] Read more.
Bacterial-fungal interactions are important in the functioning of natural ecosystems. We examined possible synergistic or antagonistic effects during the degradation of polycyclic aromatic hydrocarbons (PAHs) by a fungal–bacterial co-culture. Bacteria and fungi were grown in a liquid nutrient medium supplemented with PAH substrates. The degradation of PAHs and the identification of metabolites were checked by HPLC. Enzyme activities were spectrophotometrically measured with test substrates. Compared to monocultures, the co-culture yielded higher mycelium dry weights and higher numbers of bacterial colony-forming units (CFUs). Both organisms and their co-culture transformed three- and four-ring PAHs into the corresponding quinones. The degradation of PAHs was accompanied by the production of fungal extracellular laccase and versatile peroxidase, whose activities were higher in the co-culture than they were in the monocultures. The presence of exogenous indole-3-acetic acid (IAA) boosted PAH degradation and enzyme production. The xylotrophic basidiomycete Pleurotus ostreatus Florida and the plant-growth-promoting rhizobacterium Azospirillum brasilense exerted a positive mutual effect, including increases in mycelium dry weight, number of CFUs, degradation of PAHs, and production of fungal extracellular enzymes. IAA may be a factor in the interactions of P. ostreatus Florida with A. brasilense. Full article
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19 pages, 954 KiB  
Review
Combined Biological and Chemical/Physicochemical Pretreatment Methods of Lignocellulosic Biomass for Bioethanol and Biomethane Energy Production—A Review
by Shruthi Meenakshisundaram, Antoine Fayeulle, Estelle Léonard, Claire Ceballos, Xiaojun Liu and André Pauss
Appl. Microbiol. 2022, 2(4), 716-734; https://doi.org/10.3390/applmicrobiol2040055 - 30 Sep 2022
Cited by 7 | Viewed by 2735
Abstract
Lignocellulosic biomass is a low-cost and environmentally-friendly resource that can be used to produce biofuels such as bioethanol and biogas, which are the leading candidates for the partial substitution of fossil fuels. However, the main challenge of using lignocellulosic materials for biofuel production [...] Read more.
Lignocellulosic biomass is a low-cost and environmentally-friendly resource that can be used to produce biofuels such as bioethanol and biogas, which are the leading candidates for the partial substitution of fossil fuels. However, the main challenge of using lignocellulosic materials for biofuel production is the low accessibility to cellulose for hydrolysis of enzymes and microorganisms, which can be overcome by pretreatment. Biological and chemical pretreatments have their own disadvantages, which could be reduced by combining the two methods. In this article, we review biological–chemical combined pretreatment strategies for biogas and bioethanol production. The synergy of fungal/enzyme–NaOH pretreatment is the only biological–chemical combination studied for biogas production and has proven to be effective. The use of enzyme, which is relatively expensive, has the advantage of hydrolysis efficiency compared to fungi. Nonetheless, there is vast scope for research and development of other chemical–biological combinations for biogas production. With respect to ethanol production, fungal–organosolv combination is widely studied and can achieve a maximum of 82% theoretical yield. Order of pretreatment is also important, as fungi may reduce the accessibility of cellulose made available by prior chemical strategies and suppress lignin degradation. The biofuel yield of similarly pretreated biomass can vary depending on the downstream process. Therefore, new strategies, such as bioaugmentation and genetically engineered strains, could help to further intensify biofuel yields. Full article
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15 pages, 27173 KiB  
Review
Photocatalytic Inactivation of Viruses and Prions: Multilevel Approach with Other Disinfectants
by Takashi Onodera, Katsuaki Sugiura, Makoto Haritani, Tohru Suzuki, Morikazu Imamura, Yoshifumi Iwamaru, Yasuhisa Ano, Hiroyuki Nakayama and Akikazu Sakudo
Appl. Microbiol. 2022, 2(4), 701-715; https://doi.org/10.3390/applmicrobiol2040054 - 23 Sep 2022
Cited by 2 | Viewed by 1435
Abstract
Ag, Cu, Zn, Ti, and Au nanoparticles show enhanced photocatalytic properties. Efficient indoor disinfection strategies are imperative to manage the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Virucidal agents, such as ethanol, sodium hypochlorite, 222-nm UV light, and electrolyzed water inactivate SARS-CoV-2 [...] Read more.
Ag, Cu, Zn, Ti, and Au nanoparticles show enhanced photocatalytic properties. Efficient indoor disinfection strategies are imperative to manage the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Virucidal agents, such as ethanol, sodium hypochlorite, 222-nm UV light, and electrolyzed water inactivate SARS-CoV-2 in indoor environments. Tungsten trioxide (WO3) photocatalyst and visible light disinfect abiotic surfaces against SARS-CoV-2. The titanium dioxide (TiO2)/UV system inactivates SARS-CoV-2 in aerosols and on deliberately contaminated TiO2-coated glass slide surfaces in photocatalytic chambers, wherein 405-nm UV light treatment for 20 min sterilizes the environment and generates reactive oxygen species (ROS) that inactivate the virus by targeting S and envelope proteins and viral RNA. Mesoscopic calcium bicarbonate solution (CAC-717) inactivates pathogens, such as prions, influenza virus, SARS-CoV-2, and noroviruses, in fluids; it presumably acts similarly on human and animal skin. The molecular complexity of cementitious materials promotes the photocatalysis of microorganisms. In combination, the two methods can reduce the pathogen load in the environment. As photocatalysts and CAC-717 are potent disinfectants for prions, disinfectants against prionoids could be developed by combining photocatalysis, gas plasma methodology, and CAC-717 treatment, especially for surgical devices and instruments. Full article
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13 pages, 793 KiB  
Article
Selected Antimicrobial Peptides Inhibit In Vitro Growth of Campylobacter spp.
by John Eric Line, Bruce S. Seal and Johnna K. Garrish
Appl. Microbiol. 2022, 2(4), 688-700; https://doi.org/10.3390/applmicrobiol2040053 - 21 Sep 2022
Cited by 1 | Viewed by 1712
Abstract
Campylobacter is a major cause of acute human diarrheal illness. Broiler chickens constitute a primary reservoir for C. jejuni leading to human infection. Consequently, there is a need for developing novel intervention methods. Antimicrobial peptides (AMP) are small proteins which have evolved in [...] Read more.
Campylobacter is a major cause of acute human diarrheal illness. Broiler chickens constitute a primary reservoir for C. jejuni leading to human infection. Consequently, there is a need for developing novel intervention methods. Antimicrobial peptides (AMP) are small proteins which have evolved in most lifeforms to provide defense against microbial infections. To date, over 3000 AMP have been discovered; however, few of them have been analyzed specifically for ability to kill campylobacters. We selected and evaluated a set of 11 unique chemically synthesized AMP for ability to inhibit growth of C. jejuni. Six of the AMP we tested produced zones of inhibition on lawns of C. jejuni. These AMP included: NRC-13, RL-37, Temporin L, Cecropin–Magainin, Dermaseptin, and C12K-2β12. In addition, MIC were determined for Cecropin–Magainin, RL-37 and C12K-2β12 against 15 isolates of Campylobacter representing the three most common pathogenic strains. MIC for campylobacters were approximately 3.1 µg/mL for AMP RL-37 and C12K-2β12. MIC were slightly higher for the Cecropin–Magainin AMP in the range of 12.5 to 100 µg/mL. These AMP are attractive subjects for future study and potential in vivo delivery to poultry to reduce Campylobacter spp. populations. Full article
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