Journal Description
Applied Microbiology
Applied Microbiology
is an international, peer-reviewed, open access journal on application of microorganisms published quarterly online by MDPI.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 13.3 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.
- Applied Microbiology is a companion journal of Microorganisms.
Latest Articles
Porphyromonas gingivalis Strain W83 Infection Induces Liver Injury in Experimental Alcohol-Associated Liver Disease (ALD) in Mice
Appl. Microbiol. 2024, 4(2), 620-634; https://doi.org/10.3390/applmicrobiol4020043 - 27 Mar 2024
Abstract
The liver plays a vital role in the defense against infections. Porphyromonas gingivalis (P. gingivalis), a dominant etiologic oral bacterium implicated in periodontal disease (PD), has been associated with various systemic diseases. This study aimed to investigate the influence of P.
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The liver plays a vital role in the defense against infections. Porphyromonas gingivalis (P. gingivalis), a dominant etiologic oral bacterium implicated in periodontal disease (PD), has been associated with various systemic diseases. This study aimed to investigate the influence of P. gingivalis on alcohol-associated liver diseases (ALD). Mice were fed a Lieber–DeCarli liquid diet containing 5% ethanol for 10 days after an initial adaptation period on a diet with lower ethanol content for 7 days. Two days before tissue sample collection, the mice were administered P. gingivalis strain W83 (Pg) through intraperitoneal injection (IP). Pair-fed mice with Pg infection (PF+Pg) exhibited an activated immune response to combat infections. However, alcohol-fed mice with Pg infection (AF+Pg) showed liver injury with noticeable abscess lesions and elevated serum alanine aminotransferase (ALT) levels. Additionally, these mice displayed liver infiltration of inflammatory monocytes and significant downregulation of proinflammatory cytokine gene expression levels; and AF+Pg mice also demonstrated increased intrahepatic neutrophil infiltration, as confirmed by chloroacetate esterase (CAE) staining, along with elevated gene expression levels of neutrophil cytosol factor 1 (Ncf1), neutrophilic inflammation driver lipocalin 2 (Lcn2), and complement component C5a receptor 1 (C5ar1), which are associated with neutrophilic inflammation. Interestingly, compared to PF+Pg mice, the livers of AF+Pg mice exhibited downregulation of gene expression levels of NADPH oxidase 2 (Cybb), the leukocyte adhesion molecule Cd18, and the Toll-like receptor adaptor Myd88. Consequently, impaired clearance of P. gingivalis and other bacteria in the liver, increased susceptibility to infections, and inflammation-associated hepatic necrotic cell death were observed in AF+Pg mice, which is likely to have facilitated immune cell infiltration and contributed to liver injury. Furthermore, in addition to the Srebf1/Fasn pathway induced by alcohol feeding, Pg infection also activated carbohydrate response element-binding protein (ChREBP) in AF+Pg mice. In summary, this study demonstrates that P. gingivalis infection, acting as a “second hit”, induces dysfunction of immune response and impairs the clearance of bacteria and infections in alcohol-sensitized livers. This process drives the development of liver injury.
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(This article belongs to the Special Issue Human Microbiota Influence on Human Health Status 2.0)
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Open AccessArticle
In Silico Prophage Analysis of Halobacterium salinarum ATCC 33170
by
Danielle L. Peters, Bassel Akache, Wangxue Chen and Michael J. McCluskie
Appl. Microbiol. 2024, 4(2), 607-619; https://doi.org/10.3390/applmicrobiol4020042 - 26 Mar 2024
Abstract
The extremophile Halobacterium salinarum is an aerobic archaeon that has adapted to thrive in high-salt environments such as salted fish, hypersaline lakes, and salterns. Halophiles have garnered significant interest due to their unique interactions with bacteriophages known as haloarchaeophages. Studies have identified and
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The extremophile Halobacterium salinarum is an aerobic archaeon that has adapted to thrive in high-salt environments such as salted fish, hypersaline lakes, and salterns. Halophiles have garnered significant interest due to their unique interactions with bacteriophages known as haloarchaeophages. Studies have identified and characterized prophages in halophilic archaea, such as Haloferax volcanii, Haloquadratum walsbyi, and Haloarcula marismortui. Still, an investigation has yet to be conducted into the presence of prophage elements on Halobacterium salinarum ATCC 33170. This is of particular interest to us as we are using this strain as a source of archaeol, as one of the components of our sulfated lactosyl archaeol (SLA) archaeosome adjuvant. Genomic contigs of strain 33170 were bioinformatically assessed for prophage-like features using BLAST, PHASTER, InterProScan, and PHYRE2. A 7 kb region encoding six genes was identified as an incomplete prophage, and the proteins were further analyzed, revealing high homology to proteins encoded by bacteria, archaea, and an IS200 transposon. Restricting the BLASTp database to viruses resulted in hits to both myo- and siphoviral proteins, which would be unusual for an intact prophage. Additionally, no known phage structural proteins were identified in the search, suggesting a low chance that H. salinarum ATCC 33170 harbors a latent prophage.
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Open AccessReview
The Influence of Technological Shifts in the Food Chain on the Emergence of Foodborne Pathogens: An Overview
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Saja Hamaideh, Amin N. Olaimat, Murad A. Al-Holy, Ahmad Ababneh, Hafiz Muhammad Shahbaz, Mahmoud Abughoush, Anas Al-Nabulsi, Tareq Osaili, Mutamed Ayyash and Richard A. Holley
Appl. Microbiol. 2024, 4(2), 594-606; https://doi.org/10.3390/applmicrobiol4020041 - 25 Mar 2024
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The transformation of the food chain due to technological advances has had significant implications in regard to food safety. A noteworthy trend in this evolution relates to the emergence of new or previously unseen pathogens within products, thereby altering the landscape of foodborne
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The transformation of the food chain due to technological advances has had significant implications in regard to food safety. A noteworthy trend in this evolution relates to the emergence of new or previously unseen pathogens within products, thereby altering the landscape of foodborne illness epidemiology. The escalating frequency of these events underscores the need for a comprehensive re-evaluation of preventive strategies. The occurrence of novel species of bacteria, viruses, parasites, and unusual biotoxins from unexpected sources has challenged the previous limits that had been set to prevent foodborne illness outbreaks. The repercussions, ranging from detrimental effects on public health to economic burden, are influenced by a myriad of factors affecting the evolution of foodborne pathogens and emerging ailments. Among these factors are shifts in population demographics and behaviors, especially dietary patterns, as well as climate extremes, advances in more precise pathogen detection, microbial adaptation, evolving agricultural practices, and transformative changes within the food industry. This review critically examines the impact of technological metamorphosis along the food chain, encompassing production, processing, handling, packaging, storage, transportation, and industry demographics on the dynamics influencing the emergence of foodborne pathogens. Additionally, potential solutions to mitigate and manage this escalating issue are proposed.
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Open AccessArticle
Breaking the Mold: Towards Rapid and Cost-Effective Microbial Contamination Detection in Paints and Cosmetics Using ATP-Bioluminescence
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Mira Mutschlechner, Daniela Chisté and Harald Schöbel
Appl. Microbiol. 2024, 4(2), 582-593; https://doi.org/10.3390/applmicrobiol4020040 - 22 Mar 2024
Abstract
Traditional culture-based methods, though a “gold standard” for bacterial detection in various industrial sectors, do often not fulfill today’s high requirements regarding rapidity, on-site applicability, and cost-efficiency both during operation and evaluation. Here, the feasibility of using an adenosine triphosphate (ATP)-based assay for
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Traditional culture-based methods, though a “gold standard” for bacterial detection in various industrial sectors, do often not fulfill today’s high requirements regarding rapidity, on-site applicability, and cost-efficiency both during operation and evaluation. Here, the feasibility of using an adenosine triphosphate (ATP)-based assay for determining microbial contaminations in paints and cosmetics was investigated and compared with standard plate count techniques and dipslides. Therefore, we initially determined the level of sensitivity and assessed the accuracy and concordance among the different methods via spiking tests using a mix of frequently abundant bacterial species to simulate microbial contamination. Bioluminescence intensity was linearly proportional to log colony counts over five orders of magnitude (R2 = 0.99), indicating a high level of sensitivity. Overall, the accuracy varied depending on the test specimen, most probably due to matrix-related quenching effects. Although the degree of conformity was consistently higher at target concentrations ≥ 105 CFU·mL−1, microbial contaminations were detectable down to 103 CFU·mL−1, thus meeting the high requirements of various industries. ATP-based results tended to be within an order of magnitude lower than the reference. However, bearing that in mind, the developed assay serves as a rapid, real-time alternative for routine quality control and hygiene monitoring.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Green Macroalgae Hydrolysate for Biofuel Production: Potential of Ulva rigida
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Walaa Sayed, Audrey Cabrol, Alaa Salma, Abdeltif Amrane, Maud Benoit, Ronan Pierre and Hayet Djelal
Appl. Microbiol. 2024, 4(2), 563-581; https://doi.org/10.3390/applmicrobiol4020039 - 22 Mar 2024
Abstract
In this study, the green macroalgae Ulva rigida, which contains 34.9% carbohydrates, underwent treatment with commercial hydrolytic enzymes. This treatment yielded a hydrolysate that contained 23 ± 0.6 g·L−1 of glucose, which was subsequently fermented with Saccharomyces cerevisiae. The fermentation process
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In this study, the green macroalgae Ulva rigida, which contains 34.9% carbohydrates, underwent treatment with commercial hydrolytic enzymes. This treatment yielded a hydrolysate that contained 23 ± 0.6 g·L−1 of glucose, which was subsequently fermented with Saccharomyces cerevisiae. The fermentation process resulted in an ethanol concentration of 9.55 ± 0.20 g·L−1. The optimal conditions for ethanol production by S. cerevisiae were identified as follows: non-sterilized conditions, an absence of enrichment, and using an inoculum size of 118 mg·L−1. Under these conditions, the fermentation of the green macroalgal hydrolysate achieved a remarkable conversion efficiency of 80.78%. The ethanol o/t ratio, namely the ratios of the experimental to theoretical ethanol produced, for Scheffersomyces stipitis, Candida guilliermondii, Kluyveromyces marxianus, and S. cerevisiae after 48 h of fermentation were 52.25, 63.20, 70.49, and 82.87%, respectively. Furthermore, S. cerevisiae exhibited the best outcomes in terms of ethanol production (9.35 g·L−1) and conversion efficiency (80.78%) after 24 h (optimal time) of fermentation.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Biogenic Amine Formation in Artisan Galotyri PDO Acid-Curd Cheeses Fermented with Greek Indigenous Starter and Adjunct Lactic Acid Bacteria Strain Combinations: Effects of Cold (4 °C) Ripening and Biotic Factors Compromising Cheese Safety
by
Charikleia Tsanasidou, Loulouda Bosnea, Athanasia Kakouri and John Samelis
Appl. Microbiol. 2024, 4(1), 536-562; https://doi.org/10.3390/applmicrobiol4010038 - 18 Mar 2024
Abstract
The formation of biogenic amines (BAs) in artisan Galotyri PDO cheeses fermented with Sterptococcus thermophilus ST1 and the Greek indigenous nisin A-producing Lactococcus lactis spp. cremoris M78 (A1cheese), or with the A1 starter supplemented with either the enterocin A-B-P-producing Enterococcus faecium KE82 (A2cheese)
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The formation of biogenic amines (BAs) in artisan Galotyri PDO cheeses fermented with Sterptococcus thermophilus ST1 and the Greek indigenous nisin A-producing Lactococcus lactis spp. cremoris M78 (A1cheese), or with the A1 starter supplemented with either the enterocin A-B-P-producing Enterococcus faecium KE82 (A2cheese) or the multi-functional Lactiplantibacillus plantarum H25 (A4cheese) adjunct strains was evaluated. Three pilot-scale cheese trials, GL1, GL2, and GL3, made from boiled ewes’ milk, were analyzed for their BA contents before and after cold ripening at 4 °C for 30 days. Total BAs of the fresh GL1 and GL3 cheeses (pH 4.3–4.5) were below 50 mg/kg, except for the A1/GL1 and A1/GL3 cheeses, which contained ca. 300 mg/kg (81.2% histamine) and 1250 mg/kg (45.6% putrescine) BAs, respectively. Whereas due to an outgrowth (>7 log cfu/g) of post-thermal Gram-negative bacteria contaminants during fermentation, most fresh GL2 cheeses (pH 4.7–5.0) accumulated more than 1500 mg/kg of total BAs, which exceeded 3800 mg/kg in all GL2 cold-ripened cheeses due to major increases in cadaverine and putrescine. Tyramine and histamine exceeded 500 mg/kg in the fresh A1/GL2cheeses. Conversely, total BAs remained or declined below 50 mg/kg in all cold-ripened GL3 cheeses. None of the starter or adjunct cultures could be correlated with a specific BA increase, despite E. faecium KE82, which increased at 7.6–9.2 log cfu/g in the A2 cheeses is a strong tyramine producer in culture BA broth with 1% tyrosine in vitro. The adoption of strict hygienic measures during artisan Galotyri PDO cheese production (trial GL3) enabled the best performance of all starter LAB strain combinations and reduced BA formation, whereas the high presence of Gram-negative decarboxylating bacteria contaminants compromised cheese (trial GL2) safety.
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(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)
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Open AccessArticle
PluMu—A Mu-like Bacteriophage Infecting Actinobacillus pleuropneumoniae
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Lee Julia Bartsch, Roberto Fernandez Crespo, Yunfei Wang, Michael A. Skinner, Andrew N. Rycroft, William Cooley, David J. Everest, Yanwen Li, Janine T. Bossé and Paul R. Langford
Appl. Microbiol. 2024, 4(1), 520-535; https://doi.org/10.3390/applmicrobiol4010037 - 17 Mar 2024
Abstract
Actinobacillus pleuropneumoniae is the causative agent of pleuropneumonia, an economically important lung disease in pigs. In draft genomes of two Cypriot clinical A. pleuropneumoniae isolates (MIDG3457 and MIDG3459), we previously identified single genomic regions with homology to Mu-like bacteriophage and presented preliminary evidence
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Actinobacillus pleuropneumoniae is the causative agent of pleuropneumonia, an economically important lung disease in pigs. In draft genomes of two Cypriot clinical A. pleuropneumoniae isolates (MIDG3457 and MIDG3459), we previously identified single genomic regions with homology to Mu-like bacteriophage and presented preliminary evidence of active phage. Here, updated Phastest genomic analysis identified two loci in both MIDG3457 and MIDG3459 that were predicted to encode proteins with high homology to, and whose organisation was characteristic of, Mu-like phages. Phylogenetically, the closest matches were with Mannheimia Vb and Glaesserella SuMu phages. Phastest scored the loci as “complete”, indicating they produced active phage. PCR amplification of the Mu-like phage c and tail genes from DNase-treated polyethylene glycol 8000 (PEG)-precipitated supernatants of MIDG3457 and MIDG3459 (grown in either Brain Heart Infusion-NAD or Grace’s Insect Medium-NAD broth) indicated the presence of intact virions. The phages from MIDG3457 and MIDG3459 were named PluMu 3457-1, 3457-2, and PluMu 3459-1 and PluMu 3459-2, respectively. Transmission electron microscopy (TEM) of the PEG-precipitated supernatants of broth-grown MIDG3459 identified virions with icosahedral heads and tails, consistent with other Mu-like phages. We conclude that MIDG3459 produces an active Mu-like phage.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Thermal Inactivation of the Heat-Resistant Pathogens Salmonella Senftenberg 775W and Escherichia coli AW1.7 in Whey Concentrate
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Gregor Fiedler, Stefan Nöbel, Sönke Matzen, Meike Samtlebe and Charles M. A. P. Franz
Appl. Microbiol. 2024, 4(1), 510-519; https://doi.org/10.3390/applmicrobiol4010036 - 15 Mar 2024
Abstract
Pasteurized whey concentrate is used as a base for the production of ingredients for various food products. Whey concentrate (30% dry matter) was used to assess the thermal inactivation of Salmonella (S.) enterica serovar Senftenberg 775W (DSM 10062) and Escherichia (
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Pasteurized whey concentrate is used as a base for the production of ingredients for various food products. Whey concentrate (30% dry matter) was used to assess the thermal inactivation of Salmonella (S.) enterica serovar Senftenberg 775W (DSM 10062) and Escherichia (E.) coli AW1.7 (DSM 108612) strains in a pilot-scale pasteurizer mimicking industrial heat processing. These strains, chosen for their exceptional heat resistance, represent the most challenging scenario for pasteurization within the context of S. enterica and E. coli. Heat resistance was tested at temperatures of 56, 60, 64, 68, and 72 °C at an average holding time of 17.5 s. These exceptionally heat-resistant strains showed a relatively low reduction in numbers of between 0 and 4.2 log10 CFU/mL at lower inactivation temperatures of ≤68 °C. A reduction of at least 5 log10 CFU/mL, as required for adequate heat processing, was achieved for both species after heating at 72 °C for 17.5 s. This study shows that whey concentrate should not lead to contamination of food ingredients and can be considered safe after pasteurization at 72 °C for at least 17.5 s with respect to the pathogens tested.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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The Tale of Staphylococcus aureus Isolated from Mastitis Infections: The Effect of Antimicrobials and Bacterial Relatedness
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Angela Perdomo, Maria Salazar, Rasmi Janardhanan and Alexandra Calle
Appl. Microbiol. 2024, 4(1), 496-509; https://doi.org/10.3390/applmicrobiol4010035 - 09 Mar 2024
Abstract
Staphylococcus aureus is a common causative agent of mastitis in dairy cattle, posing a substantial threat to animal health and resulting in significant economic losses. Preventive measures are usually in place to control the spread of the organism between animals and around the
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Staphylococcus aureus is a common causative agent of mastitis in dairy cattle, posing a substantial threat to animal health and resulting in significant economic losses. Preventive measures are usually in place to control the spread of the organism between animals and around the dairy environment; however, mastitis outbreaks can still be recurrent. During this investigation, a total of 30 S. aureus isolates were obtained from six deceased cows, all diagnosed with chronic mastitis during an outbreak in West Texas. The aim of this study was to evaluate the response of the S. aureus isolates causing severe mastitis infections to iodine treatments and their antibiotic susceptibility, planktonic growth, and biofilm formation. Udder skin was inoculated with S. aureus and subjected to various iodine concentrations of 0.25%, 0.38%, 0.50%, 0.75%, and 1.00%, with exposure times of 15 s, 10 s, and 60 s. The same concentrations were tested on S. aureus’s biofilm formation. The results of the antimicrobial susceptibility test indicate that the exposure time did not influence the treatment. Lower iodine concentrations were compared with 1.00%, as the standard treatment used by the dairy for teat disinfection, and statistical difference (p < 0.001) was evident in the 0.00% iodine treatment compared to the other iodine concentrations. Moreover, a significant difference (p < 0.001) emerged when comparing the 0.25% and 0.38% iodine concentrations with 1.00%. No difference (p > 0.161) was detected between 0.50%, 0.75%, and 1.00%. These results suggest that, under the conditions investigated, iodine can be lowered to around 50% of the currently used dose without negatively impacting microbial control. On the other hand, S. aureus strains were susceptible to the tested antibiotics, demonstrating that antimicrobial resistance does not always play a role in the persistent mastitis infections caused by S. aureus. Further microbial phenotypic typing conducted on S. aureus strains indicated a possible common source of the infections, demonstrating the potential of there being resident S. aureus strains at this dairy farm.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Evaluation of the Antibacterial Activity of Isatin against Campylobacter jejuni and Campylobacter coli Strains
by
Claudia B. Barroso, Liliane M. Seki, Wagner T. C. Esteves, Michele C. Nascimento and Aurea Echevarria
Appl. Microbiol. 2024, 4(1), 486-495; https://doi.org/10.3390/applmicrobiol4010034 - 08 Mar 2024
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Antibiotic resistance, particularly against fluoroquinolones and macrolides, has emerged globally among thermophilic Campylobacters (Campylobacter jejuni and Campylobacter coli), giving rise to concerns about the efficacy of antibiotic treatment of these bacteria. Thus, developing new antibacterials with excellent activity is important. Isatin
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Antibiotic resistance, particularly against fluoroquinolones and macrolides, has emerged globally among thermophilic Campylobacters (Campylobacter jejuni and Campylobacter coli), giving rise to concerns about the efficacy of antibiotic treatment of these bacteria. Thus, developing new antibacterials with excellent activity is important. Isatin (IST) and its derivatives have exhibited promising antibacterial activities in several pathogenic bacteria. However, its activity against Campylobacter is unknown. Therefore, this study was conducted to evaluate the antibacterial activity of isatin against 29-Campylobacter strains (C. jejuni-17 and C. coli-12) and investigate the effects at the cellular level. The minimal inhibitory concentrations (MICs) of isatin were between <1.0 and 16.0 µg/mL in Campylobacter strains. Most strains presented with MIC = 8.0 µg/mL (76%). The minimal bactericidal concentration (MBC) was determined to be 16.0 µg/mL for 72% of the Campylobacter strains tested. The 50% inhibitory concentration (IC50) value for isatin was 125.63 µg/mL on the MRC-5 normal cell line, suggesting that isatin can be considered a safe substance in terms of cytotoxicity. In this study, we demonstrated the potential of isatin based on its low toxicity and effectiveness in vitro against antibiotic-resistant Campylobacter strains, which indicates that this compound could be an attractive candidate for future use in multidrug-resistant Campylobacter treatment.
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Open AccessCommunication
Surveillance of Bacterial Meningitis in the Italian Hospital of Desio: A Twenty-Year Retrospective Study
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Jari Intra, Davide Carcione, Roberta Maria Sala, Claudia Siracusa, Paolo Brambilla and Valerio Leoni
Appl. Microbiol. 2024, 4(1), 481-485; https://doi.org/10.3390/applmicrobiol4010033 - 05 Mar 2024
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Bacterial meningitis is a severe infection with a high fatality rate, and affects children in particular. Three vaccines against the most common bacterial causatives of meningitis, Haemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitides, exist. Monitoring the type and incidence
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Bacterial meningitis is a severe infection with a high fatality rate, and affects children in particular. Three vaccines against the most common bacterial causatives of meningitis, Haemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitides, exist. Monitoring the type and incidence of bacterial meningitis is important for making future prevention and control plans. In this study, we retrospectively analyzed data regarding bacterial meningitis recovered in the Italian Hospital of Desio from 2000 to 2019. Samples from a total of 128 patients were included. Streptococcus pneumoniae was the most common microorganism, isolated in 45 cases, followed by Neisseria meningitidis (14), Listeria monocytogenes (8), Streptococcus agalactiae (group B) (4), and Haemophilus influenzae type b (2). The implementation of vaccination schedules decreased the number of bacterial meningitis cases caused by H. influenzae type b, S. pneumoniae, and N. meningitidis. Considering the bacterial meningitis cases in subjects aged 0–12 years, no H. influenzae type b strain was isolated, five cases of N. meningitidis were identified before the introduction of vaccination, and seven S. pneumoniae strains were isolated before the introduction of the PCV13 vaccination. Surveillance studies allowed us to monitor changes in bacteria distribution and to guide vaccination strategies.
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Open AccessArticle
Complementation of an Escherichia coli K-12 Mutant Strain Deficient in KDO Synthesis by Forming D-Arabinose 5-Phosphate from Glycolaldehyde with Fructose 6-Phosphate Aldolase (FSA)
by
Emma Guitart Font and Georg A. Sprenger
Appl. Microbiol. 2024, 4(1), 470-480; https://doi.org/10.3390/applmicrobiol4010032 - 03 Mar 2024
Abstract
KDO (2-keto-3-deoxy-D-manno-octulosonate) is a landmark molecule of the Gram-negative outer membrane. Mutants without KDO formation are known to be barely viable. Arabinose 5-phosphate (A5P) is a precursor of KDO biosynthesis and is normally derived from ribulose 5-phosphate by A5P isomerases, encoded
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KDO (2-keto-3-deoxy-D-manno-octulosonate) is a landmark molecule of the Gram-negative outer membrane. Mutants without KDO formation are known to be barely viable. Arabinose 5-phosphate (A5P) is a precursor of KDO biosynthesis and is normally derived from ribulose 5-phosphate by A5P isomerases, encoded by kdsD and gutQ genes in E. coli K-12. We created a kdsD gutQ-deficient double mutant of strain BW25113 and confirmed that these cells are A5P auxotrophs. Fructose 6-phosphate aldolase (FSA) is known to utilize (among other donors such as dihydroxyacetone or hydroxyacetone) glycolaldehyde (GoA) as a donor compound and to provide A5P in vitro when glyceraldehyde 3-phosphate is the acceptor. We show here that this FSA function in vivo fully reverses the growth defect and the A5P deficiency in kdsD gutQ double mutants. Expression of both plasmid-encoded fsaA, fsaAA129S, or fsaB genes as well as a chromosomally integrated form of fsaAA129S led to maximal OD600 values of >2.2 when GoA was added exogenously (together with glucose as a C source) at a concentration of 100 µM (Ks values in the range of 4–10 µM). Thus, a novel bio-orthogonal bypass to overcome an A5P deficiency was opened. Lower GoA concentrations led to lower growth yields. Interestingly, mutant strains with recombinant fsa genes showed considerable growth yields even without exogenous GoA addition, pointing to yet unknown endogenous GoA sources in E. coli metabolism. This is a further example of the usefulness of FSA in rewiring central metabolic pathways in E. coli.
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(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))
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Open AccessArticle
Auxotrophy-Independent Plasmid Shuttle Vectors for Applications in Diverse Yeasts
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Jeremy R. Smith, Christine D. Sislak, Pedro Fernandez Mendoza, Laurin Carmichael, Alisha G. Lewis, Anqi Chen, Glycine Z. Jiang and Patrick A. Gibney
Appl. Microbiol. 2024, 4(1), 453-469; https://doi.org/10.3390/applmicrobiol4010031 - 28 Feb 2024
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Plasmid shuttle vectors are a common tool used to study yeast physiology. The majority of yeast plasmids have been optimized for Saccharomyces cerevisiae lab strain compatibility, relying on auxotrophic complementation as their selective property. We sought to construct a series of plasmid shuttle
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Plasmid shuttle vectors are a common tool used to study yeast physiology. The majority of yeast plasmids have been optimized for Saccharomyces cerevisiae lab strain compatibility, relying on auxotrophic complementation as their selective property. We sought to construct a series of plasmid shuttle vectors to extend functionality beyond strains with auxotrophic requirements, and test compatibility across a diverse panel of yeasts. We constructed 18 plasmids which were successfully maintained by yeasts from several genera. From a panel of 24 yeast strains, these plasmids were maintained by 18 yeasts, spanning 11 species within the genera Lachancea, Metschnikowia, Pichia, Saccharomyces, and Torulaspora. Additionally, an integrated gene expression reporter was assayed for functional compatibility with the 18 strains. Plasmid-derived gene expression was observed for 13 strains, spanning five species within the Saccharomyces genus, in addition to Torulaspora delbrueckii. These results indicate that this plasmid series is broadly useful for advancements and applications within academia, biotechnology, and the food and fermentation industries for research utilizing diverse Saccharomyces and non-Saccharomyces yeasts.
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Open AccessArticle
Transfer and Inactivation of Listeria monocytogenes during Pilot-Scale Dicing and Flume Washing of Onions
by
Andrew M. Scollon, Haiqiang Wang and Elliot T. Ryser
Appl. Microbiol. 2024, 4(1), 439-452; https://doi.org/10.3390/applmicrobiol4010030 - 27 Feb 2024
Abstract
This study assessed the extent of L. monocytogenes transfer from onions to the surface of a commercial dicer, from inoculated onions to uninoculated onions, and the efficacy of various sanitizers during the subsequent flume washing of diced onions. Spanish yellow onions (Allium
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This study assessed the extent of L. monocytogenes transfer from onions to the surface of a commercial dicer, from inoculated onions to uninoculated onions, and the efficacy of various sanitizers during the subsequent flume washing of diced onions. Spanish yellow onions (Allium cepa L.) were dip-inoculated in a 3-strain avirulent L. monocytogenes cocktail (5.9 or 4.2 log CFU/50 g) and air-dried. After dicing one 2.2 kg batch of onions inoculated at ~5.9 log CFU/50 g followed by ten uninoculated batches of 2.2 kg each, L. monocytogenes progressively decreased from 4.6 to 2.6 log CFU/50 g in baches 1 through 10, respectively. After onions inoculated at ~4.0 log CFU/g were diced and flume washed for 2 min in tap water, electrolyzed water containing 55 ppm free chlorine, 80 ppm free chlorine from a commercial sanitizer, or 80 ppm peroxyacetic acid and dewatered on a mechanical shaker table, L. monocytogenes populations decreased 0.4, 0.3, 1.4, and 1.0 log, respectively, with populations of ~1.2 log CFU/mL in water for all three sanitizers. These findings should be useful in future risk assessments and aid in the development of improved industry guidelines to better enhance the safety of diced onions.
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(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)
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Open AccessReview
Sustainability of Biogas Production from Anaerobic Digestion of Food Waste and Animal Manure
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Sharath Kumar Ankathi, Utkarsh S. Chaudhari, Robert M. Handler and David R. Shonnard
Appl. Microbiol. 2024, 4(1), 418-438; https://doi.org/10.3390/applmicrobiol4010029 - 21 Feb 2024
Abstract
Anaerobic digestion (AD) involves a set of microbiological reactions and physio-chemical processes to generate biogas, a mixture of predominantly CH4 and CO2. It is commercialized globally; however, AD has limited commercial applications in the U.S. compared to other regions of
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Anaerobic digestion (AD) involves a set of microbiological reactions and physio-chemical processes to generate biogas, a mixture of predominantly CH4 and CO2. It is commercialized globally; however, AD has limited commercial applications in the U.S. compared to other regions of the world. The main objective of this article is to review different studies on socio-economic and environmental aspects and policies of biogas/biomethane production and to focus on resource availability. The key outcome from this review shows that the anaerobic digestion of food waste and animal manure has great potential to achieve economic and environmental benefits compared to other waste management techniques such as landfilling or conventional manure management. The 12 life cycle assessment (LCA) studies reviewed showed lower impacts for biogas systems and indicated a need for standardization of methodology so that alternative production concepts can be objectively compared. Similarly, economic analyses showed higher profitability for a biogas combined heat and power facility compared to a biomethane facility. By considering a review of the sustainability of biogas, we presented a new multi-criteria sustainable assessment framework that includes three domains: i. resource availability and logistics, ii. process modeling, and iii. impact assessment with primary application to the optimum location and installation of sustainable biogas/biomethane plants in the U.S.
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A Major Facilitator Superfamily Transporter Contributes to Ergot Alkaloid Accumulation but Not Secretion in Aspergillus leporis
by
Abigail M. Jones, Kyle A. Davis and Daniel G. Panaccione
Appl. Microbiol. 2024, 4(1), 406-417; https://doi.org/10.3390/applmicrobiol4010028 - 20 Feb 2024
Abstract
Ergot alkaloids are fungal natural products with important roles in agriculture and medicine. We used heterologous expression and gene knockout approaches to investigate potential roles for the product of a major facilitator superfamily transporter gene (easT) recently found in an ergot
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Ergot alkaloids are fungal natural products with important roles in agriculture and medicine. We used heterologous expression and gene knockout approaches to investigate potential roles for the product of a major facilitator superfamily transporter gene (easT) recently found in an ergot alkaloid biosynthetic gene cluster in Aspergillus leporis. A strain of Aspergillus fumigatus previously engineered to accumulate lysergic acid, but which did not convert the precursor agroclavine to lysergic acid efficiently or secrete lysergic acid well, was chosen as an expression host for easT. Expression of easT in this strain resulted in accumulation of significantly more pathway intermediates but no detectable lysergic acid. Secretion of ergot alkaloids was reduced in the easT-expressing strain. EasT localized to discrete vesicle-like structures in the cytosol of A. fumigatus, with no localization detected in the plasma membrane. When easT was knocked out in A. leporis, accumulation of lysergic acid amides was reduced relative to the wild type. There was no negative effect on secretion of ergot alkaloids in the knockout mutant. The data indicate that easT encodes a product that contributes to accumulation of ergot alkaloids, perhaps by transporting intermediates between cellular compartments, but does not have a significant role in secreting ergot alkaloids.
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Transcriptional Response of Salmonella enterica to Bacteriophage Treatments with Differential Multiplicities of Infection
by
Catherine W. Y. Wong and Siyun Wang
Appl. Microbiol. 2024, 4(1), 390-405; https://doi.org/10.3390/applmicrobiol4010027 - 16 Feb 2024
Abstract
Salmonella enterica (S. enterica) is a causative agent of numerous foodborne outbreaks, as current industrial measures may be <90% effective. Therefore, bacteriophages have been suggested as an antimicrobial treatment against S. enterica, but it is currently unclear if there is
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Salmonella enterica (S. enterica) is a causative agent of numerous foodborne outbreaks, as current industrial measures may be <90% effective. Therefore, bacteriophages have been suggested as an antimicrobial treatment against S. enterica, but it is currently unclear if there is an optimal bacteriophage multiplicity of infection (MOI) against S. enterica. Two bacteriophage cocktails at MOIs 1, 10, 100, 1000 and 10,000 were co-inoculated against four S. enterica strains (S. Enteritidis, S. Newport, S. Muenchen and S. Typhimurium), and populations were estimated on days 0–3. The transcriptional profiles of 20 genes previously indicated to be differentially expressed after bacteriophage treatment were studied by extracting RNA from all four S. enterica strains after bacteriophage SE14, SF5 and SF6 treatment on days 0, 1 and 3, and RT-qPCR was conducted to determine the expression of the 20 selected genes. The results showed that an MOI of 1000 was the most optimal in reducing S. Enteritidis populations to undetectable levels from day 0 to 3. The cas1 (SOS response) and mod (DNA modification and recombination) genes were highly upregulated between 2.5- and 5-fold on day 0 for S. Enteritidis S5-483 and S. Typhimurium S5-536 at MOIs of 1000 and 10,000. On day 3, hsdS (DNA modification and recombination) was upregulated by ~1-fold for S. enteritidis S5-483 after an MOI of 1000. Understanding an optimal bacteriophage MOI can be beneficial to implementing effective and optimal bacteriophage treatments in the industry. Knowledge of S. enterica’s transcriptional response after bacteriophage treatment provides further insight into how S. enterica can survive bacteriophage infection.
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Utilizing a Metagenome Assembled Genome Approach Revealed Further Insights into Microbially Mediated Heavy-Metal Resistance in Soils from a Former Nuclear Materials Production Facility
by
Navya Kommu, Paul Stothard, Christian Chukwujindu, Ashish Pathak and Ashvini Chauhan
Appl. Microbiol. 2024, 4(1), 376-389; https://doi.org/10.3390/applmicrobiol4010026 - 13 Feb 2024
Abstract
Soils and sediments from the Savannah River Site (SRS), located in the USA are known to have a long history of co-contamination with radionuclides (mainly uranium) and heavy metals. To better understand the bacterial taxonomic and genomic characteristic of the SRS soil habitat,
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Soils and sediments from the Savannah River Site (SRS), located in the USA are known to have a long history of co-contamination with radionuclides (mainly uranium) and heavy metals. To better understand the bacterial taxonomic and genomic characteristic of the SRS soil habitat, shotgun metagenomes were obtained from three different levels of contaminated soil—high, medium, and low. Sequences were then assembled and annotated to generate metagenome-assembled genomes (MAGs) using toolkits within the nf-core/mag. The initial analysis resulted in a total of 254 MAGs. After bin refinement and de-replication, 55 MAGs which met the quality standard with a completeness > 75% and contamination < 25%, accounting for 21.67% of all the MAGs, were reconstructed. Further refinement with completeness > 90% and contamination < 10% yielded 24 MAGs (18 from the winter season and 6 from the summer season) spanning 6 bacterial phyla, predominantly Actinomycetota, Proteobacteriota, Bacteroidota, and Cyanobacteria. Overall, the Arthrobacter MAG was found to be robust for further analysis, with over 1749 genes putatively involved in the crucial metabolism of elements viz. nitrogen, phosphorous, and sulfur, and 598 genes encoding enzymes for the resistance of metals including cadmium, zinc, chromium, arsenic, and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium-contaminated soils.
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Antibiotic-Resistant Bacteria across a Wastewater Treatment Plant
by
Ofélia Godinho, Olga Maria Lage and Sandra Quinteira
Appl. Microbiol. 2024, 4(1), 364-375; https://doi.org/10.3390/applmicrobiol4010025 - 12 Feb 2024
Abstract
Antimicrobial resistance is presently one of the leading causes of death worldwide. The surveillance of different environments, namely, wastewater treatment plants (WWTPs), as hotspots of antibiotic-resistant bacteria, has become crucial under the One Health approach. This study aimed to characterize, phenotypically and genotypically,
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Antimicrobial resistance is presently one of the leading causes of death worldwide. The surveillance of different environments, namely, wastewater treatment plants (WWTPs), as hotspots of antibiotic-resistant bacteria, has become crucial under the One Health approach. This study aimed to characterize, phenotypically and genotypically, antibiotic-resistant bacteria along a WWTP receiving domestic and industrial sewage. Four sampling sites, representing distinct treatment points of the WWTP, were selected for sampling bacterial isolation in selective media supplemented, or not, with antibiotics, and subsequent antimicrobial susceptibility testing. Antibiotic resistance encoding genes were screened by molecular methods. A total of 50 bacterial isolates were obtained, 50% of which were affiliated with the genus Enterococcus. The antimicrobial susceptibility testing revealed antibiotic phenotypic resistance in isolates obtained from all the four treatment points of the wastewater samples, with resistance to tetracycline (32.5%) and ampicillin (25%) being the most common. Three isolates were found to be multidrug resistant and were affiliated with the genera Citrobacter, Shigella and Klebsiella. Molecular screening revealed the presence of tet(M), blaTEM, blaSHV and blaCTX-M, as well as class 1 integrons carrying dfrA25, ANT(3″)-IIa and aadA6 genes. This study highlights the relevance of bacterial isolation and their antimicrobial susceptibility evaluation in WWTP systems since antibiotic-resistant strains were found from the raw influent to the final effluent discharged into the environment, denoting the need for surveillance and containment measures.
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Inhibitory Effects of Bacillus subtilis Isolated from Meju (Fermented Soybean Brick) on the Growth of Aspergillus parasiticus
by
Jong-Gyu Kim and Jeong-Yeong Park
Appl. Microbiol. 2024, 4(1), 354-363; https://doi.org/10.3390/applmicrobiol4010024 - 12 Feb 2024
Abstract
Background: Meju is a base material for making soy sauce, soybean paste, and red chili pepper paste, which are representative ingredients of Korean cuisine. Objectives: This study aimed to isolate a predominant bacterial strain of B. subtilis from meju and to observe its inhibitory
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Background: Meju is a base material for making soy sauce, soybean paste, and red chili pepper paste, which are representative ingredients of Korean cuisine. Objectives: This study aimed to isolate a predominant bacterial strain of B. subtilis from meju and to observe its inhibitory effects on an aflatoxigenic mold. Methods: We used yellow soybeans (Glycine max (L.) Merr.) grown in South Korea, and meju was produced according to the recommended methods of the Korea Food Research Institute. The identification of the strain was conducted based on its morphological and biochemical characteristics and 16S rDNA sequence. Evaluation of the bacterial effect against A. parasiticus ATCC 15517 was done in yeast extract–sucrose broth at 28 °C. Its inhibitory effect was evaluated using two approaches: mycelial weight and aflatoxin production. Aflatoxins were determined using high-performance liquid chromatography. Results: In the meju samples fermented for three months, a B. subtilis strain, K-0924 was identified. At the end of the incubation period of A. parasiticus, dry mycelial weight was significantly reduced by more than 80% (p < 0.01) and total aflatoxin production was inhibited by more than 63% (p < 0.05) in the presence of B. subtilis. Conclusions: These results indicate that B. subtilis K-0924 inhibits the growth and aflatoxin production of toxigenic Aspergillus, which can be contaminated with meju. We could expect more inhibition by other bacteria related to fermentation of meju, and further examination is necessary on species other than B. subtilis.
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