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Appl. Microbiol., Volume 4, Issue 1 (March 2024) – 38 articles

Cover Story (view full-size image): Applied Microbiology (ISSN 2673-8007) provides an advanced forum for studies related to the application of microorganisms, with a strong emphasis on biotechnology, environment, medicine, and food. It publishes original scientific research articles, comprehensive reviews, comments, commentaries, perspectives, etc. Our aim is to encourage scientists to publish their experimental and theoretical results in as much detail as possible. There is no restriction on the maximum length of the papers. The full experimental details must be provided so that the results can be reproduced. Electronic files and software regarding the full details of the calculation or experimental procedure, if unable to be published in a normal way, can be deposited as supplementary electronic material.
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27 pages, 1238 KiB  
Article
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
Viewed by 492
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) [...] Read more.
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. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)
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16 pages, 14072 KiB  
Article
PluMu—A Mu-like Bacteriophage Infecting Actinobacillus pleuropneumoniae
by 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
Viewed by 354
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 [...] Read more.
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. Full article
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10 pages, 727 KiB  
Article
Thermal Inactivation of the Heat-Resistant Pathogens Salmonella Senftenberg 775W and Escherichia coli AW1.7 in Whey Concentrate
by 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
Viewed by 399
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 ( [...] Read more.
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. Full article
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14 pages, 1423 KiB  
Article
The Tale of Staphylococcus aureus Isolated from Mastitis Infections: The Effect of Antimicrobials and Bacterial Relatedness
by 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
Viewed by 545
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 [...] Read more.
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. Full article
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10 pages, 700 KiB  
Article
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
Viewed by 510
Abstract
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 [...] Read more.
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. Full article
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5 pages, 565 KiB  
Communication
Surveillance of Bacterial Meningitis in the Italian Hospital of Desio: A Twenty-Year Retrospective Study
by 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
Viewed by 494
Abstract
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 [...] Read more.
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. Full article
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11 pages, 1235 KiB  
Article
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
Viewed by 367
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 [...] Read more.
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. Full article
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17 pages, 951 KiB  
Article
Auxotrophy-Independent Plasmid Shuttle Vectors for Applications in Diverse Yeasts
by 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
Viewed by 589
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)
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14 pages, 3735 KiB  
Article
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
Viewed by 428
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods 2.0)
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21 pages, 1481 KiB  
Review
Sustainability of Biogas Production from Anaerobic Digestion of Food Waste and Animal Manure
by 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
Viewed by 1277
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 [...] Read more.
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. Full article
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12 pages, 1281 KiB  
Article
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
Viewed by 349
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 [...] Read more.
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. Full article
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16 pages, 6769 KiB  
Article
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
Viewed by 581
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 [...] Read more.
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. Full article
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14 pages, 3969 KiB  
Article
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
Viewed by 713
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, [...] Read more.
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. Full article
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12 pages, 316 KiB  
Article
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
Viewed by 737
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, [...] Read more.
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. Full article
10 pages, 1822 KiB  
Article
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
Viewed by 528
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 [...] Read more.
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. Full article
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13 pages, 477 KiB  
Article
Detecting Closer to Care: Combining Phage and LAMP to Detect Tuberculosis, Bovine TB and Johne’s Disease
by Christopher G. Shield, Alexandra E. M. Bartlett, Pranabashis Haldar and Benjamin M. C. Swift
Appl. Microbiol. 2024, 4(1), 341-353; https://doi.org/10.3390/applmicrobiol4010023 - 01 Feb 2024
Viewed by 684
Abstract
Mycobacterial diseases impact millions in the human and veterinary fields each year. Their diagnosis is long and laborious, often only sensitive in the late stages of disease. This has created an unmet need for new diagnostics that are effective in the earlier stages [...] Read more.
Mycobacterial diseases impact millions in the human and veterinary fields each year. Their diagnosis is long and laborious, often only sensitive in the late stages of disease. This has created an unmet need for new diagnostics that are effective in the earlier stages of infection and are quick and easy to perform. This study details the optimization of LAMP assays for the detection of M. tuberculosis, M. bovis and M. avium subsp. paratuberculosis combined with phage-mediated lysis to meet the needs of a novel diagnostic—termed phage-LAMP. The optimized phage-LAMP assay had a limit of detection of less than 10 mycobacteria per ml and no cross-reaction was seen between assays. The phage-LAMP method was then tested on a small number of clinical blood samples from suspected TB patients and herds suspected of Johne’s disease. The phage-LAMP assay could detect viable Mycobacterium tuberculosis and M. avium subsp. paratuberculosis in these samples. Full article
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12 pages, 1970 KiB  
Article
Structural Characterization and Immunomodulatory Activity of an Exopolysaccharide Produced by Probiotic Leuconostoc mesenteroides 201607 Isolated from Fermented Food
by Selvakumar Vijayalakshmi, Jong-Rai Kim, Ramachandran Chelliah, Kaliyan Barathikannan, Abdurahman Hajinur Hirad and Deog-Hwan Oh
Appl. Microbiol. 2024, 4(1), 329-340; https://doi.org/10.3390/applmicrobiol4010022 - 31 Jan 2024
Viewed by 840
Abstract
Fermented foods containing probiotic Leuconostoc mesenteroides 201607 (LM) were used to extract exopolysaccharides. An incomplete understanding exists regarding the immunomodulatory characteristics of exopolysaccharides (EPSs), which are important constituents of bacterial biofilms. In this instance, we examined the immunomodulatory capacity of EPSs from fermented [...] Read more.
Fermented foods containing probiotic Leuconostoc mesenteroides 201607 (LM) were used to extract exopolysaccharides. An incomplete understanding exists regarding the immunomodulatory characteristics of exopolysaccharides (EPSs), which are important constituents of bacterial biofilms. In this instance, we examined the immunomodulatory capacity of EPSs from fermented food extracted from L. mesenteroides 201607. Partially purified exopolysaccharide from L. mesenteroides 201607 (PP-LMEPS) consists of glucose (57.1%), rhamnose (29.53%), and galactose (13.36%). The maximum EPS yield was attained after 30 h of incubation at 37 °C and an initial pH of 7.0. When lipopolysaccharide-stimulated RAW264.7 was exposed to PP-LMEPS, the inflammatory cytokines were considerably decreased or elevated dose-dependently. Upon the exposure of lipopolysaccharide-stimulated RAW264.7 cells to PP-LMEPS, a dose-dependent modulation of inflammatory cytokines was observed. This suggests that the extracted EPS possesses immunomodulatory characteristics, as evidenced by a significant decrease or increase in inflammatory cytokine levels. However, further research is warranted to fully elucidate the precise mechanisms and potential therapeutic implications of the immunomodulatory properties of PP-LMEPS. Full article
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17 pages, 4108 KiB  
Article
Mapping Selected Emergent Marine Toxin-Producing Organisms Using Historical Samples with Two Methods (Biosensors and Real-Time PCR): A Comparison of Resolution
by Gerado Mengs, Rowena F. Stern, Jessica L. Clarke, Matthew Faith and Linda K. Medlin
Appl. Microbiol. 2024, 4(1), 312-328; https://doi.org/10.3390/applmicrobiol4010021 - 30 Jan 2024
Viewed by 667
Abstract
The Continuous Plankton Recorder (CPR) survey is a valuable resource for mapping changes in plankton distribution and understanding harmful algal ecology because of its breadth and longevity. Preservation methods with formalin degrade DNA, making it difficult to use as a molecular tool for [...] Read more.
The Continuous Plankton Recorder (CPR) survey is a valuable resource for mapping changes in plankton distribution and understanding harmful algal ecology because of its breadth and longevity. Preservation methods with formalin degrade DNA, making it difficult to use as a molecular tool for archived marine samples. DNA was extracted from CPR samples immediately after collection, seven months later and after nine years of storage from a cruise track along the Iberian Peninsula. PCR reactions performed from the nine-year timepoint were hybridized to probes in an electrochemical biosensor and compared to results obtained from RT-PCR performed at two earlier time points. The successful identification of Pseudo-nitzschia spp., Prorocentrum lima, Alexandrium minutum, Alexandrium ostenfeldii, Gambierdiscus spp. and Coolia spp. was documented. The biosensor analysis outperformed RT-PCR, allowing us to document certain tropical toxic dinoflagellates, viz., Gambierdiscus and Coolia, that produce human ciguatoxins and Coolia toxins, respectively. These non-native algal toxins can accumulate, pervade the food web and negatively impact human food security. This supports the northerly movement of microalgae with climate change in offshore Iberian peninsular waters. This study highlights biosensors as a cost-effective tool for the offshore monitoring of HAB species and advances molecular technologies for long-term CPR datasets that have limited records of harmful algae. DNA from formalin-preserved CPR samples is degraded, so the use of a short, multiprobe biosensor can augment historical plankton records with contemporary methods that also capture infrequently occurring benthic taxa carried in surface waters. The integration of probe-based biosensor technologies offers a promising avenue for exploring plankton dynamics in response to environmental changes. Full article
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15 pages, 311 KiB  
Article
The Impact of In-Water vs. In-Feed Chlortetracycline and Tiamulin Administration in Piglets on the Fecal Prevalence and Antimicrobial Resistance of Salmonella
by Victor L. Ishengoma, Raghavendra G. Amachawadi, Mike D. Tokach, Qing Kang, Robert D. Goodband, Joel DeRouchey, Jason Woodworth and Tiruvoor G. Nagaraja
Appl. Microbiol. 2024, 4(1), 297-311; https://doi.org/10.3390/applmicrobiol4010020 - 28 Jan 2024
Viewed by 597
Abstract
Antimicrobial Resistance (AMR) in bacteria is a growing public health concern in the US and around the world threatening the continual use of antimicrobials. In pigs, the oral route, either in-feed or in-water, is by far the most common route of administration of [...] Read more.
Antimicrobial Resistance (AMR) in bacteria is a growing public health concern in the US and around the world threatening the continual use of antimicrobials. In pigs, the oral route, either in-feed or in-water, is by far the most common route of administration of antimicrobials. Because the distribution of the antibiotic in the gut and the dosages are different, the impact of in-feed vs. in-water administration of antibiotics on the prevalence of pathogens, such as Salmonella, and the development of AMR are likely to be different. Therefore, a study was conducted to compare in-feed vs. in-water administrations of chlortetracycline (CTC) and/or tiamulin on the fecal prevalence and AMR profiles of Salmonella in nursery piglets. A total of 1296 weaned piglets, housed in 48 pens (27 piglets per pen), were assigned randomly to six treatment groups: Control (no antibiotic), in-feed CTC, in-water CTC, in-feed tiamulin, in-water tiamulin, or in-feed CTC and tiamulin. Fecal samples (n = 1440) were collected randomly from five piglets from each pen during the pre-treatment (days 7, 0), treatment (days 7, 14), and post-treatment (days 21, 28) phases. Salmonella enterica isolation and identification were completed by culture and PCR methods. The microbroth dilution method with SensititreTM (ThermoFisher Scientific, Lenexa, KS, USA) plates was used to determine the antimicrobial susceptibility and resistance of Salmonella strains. The susceptibility and resistance were interpreted based on the Clinical and Laboratory Standards Institute guidelines. The overall prevalence of Salmonella was 3.0% (43/1440). All isolates belonged to Salmonella enterica subsp. enterica serovar Typhimurium. Salmonella isolates were susceptible to azithromycin and resistant (100%) to ampicillin, streptomycin, sulfisoxazole, tiamulin, and tetracycline. Neither antibiotic, CTC or tiamulin, nor the route of administration, in-feed or in-water, had an effect (p > 0.05) on the occurrence of resistant Salmonella in the feces of piglets. Full article
13 pages, 3500 KiB  
Article
Culture-Independent Quantification of Legionella pneumophila in Evaporative Cooling Systems Using Immunomagnetic Separation Coupled with Flow Cytometry
by Philipp Streich, Johannes Redwitz, Sandra Walser-Reichenbach, Caroline E. W. Herr, Martin Elsner and Michael Seidel
Appl. Microbiol. 2024, 4(1), 284-296; https://doi.org/10.3390/applmicrobiol4010019 - 27 Jan 2024
Viewed by 659
Abstract
Legionella pneumophila are pathogenic bacteria that repeatedly occur in high concentrations in the process water of evaporative cooling systems (ECS). When released into the environment, the resulting bioaerosols can cause outbreaks with fatal consequences. The official, internationally accepted detection method for Legionella spp. [...] Read more.
Legionella pneumophila are pathogenic bacteria that repeatedly occur in high concentrations in the process water of evaporative cooling systems (ECS). When released into the environment, the resulting bioaerosols can cause outbreaks with fatal consequences. The official, internationally accepted detection method for Legionella spp. in water samples is based on cultivation. However, cultivation is time-consuming and may underestimate the total count of viable L. pneumophila in ECS. Therefore, culture-independent methods are receiving attention for rapid monitoring. Cartridge-based immunomagnetic separation (IMS) coupled with flow cytometry (FCM) is an innovative, antibody-based method for the culture-independent quantification of L. pneumophila, using a panel of antibodies against serogroup (Sg) 1–15. We characterized the IMS-FCM method as a quantitative rapid test by general analytical procedures. Viable cryopreserved L. pneumophila standards were used in calibration experiments for the method. We achieved detection limits for Sg 1, Sg 4, and Sg 6 of 100, 105 and 88 viable cells per 100 mL, respectively. Furthermore, we demonstrated the practical applicability of IMS-FCM with real ECS samples and compared the performance against cultivation. Cultivation showed here no positive results, but IMS-FCM evidenced L. pneumophila in a range of 0–80,000 viable cells per 100 mL. This work demonstrates that IMS-FCM is a suitable, culture-independent, quantitative method for rapidly monitoring L. pneumophila. Full article
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9 pages, 1482 KiB  
Communication
First Description of Simplicillium lanosoniveum, a Potential Antagonist of the Coffee Leaf Rust from Cuba
by Yamilé Baró Robaina, Isel González Marrero, María Elena Lorenzo Nicao, Rafael F. Castañeda Ruiz, De-Wei Li, Amaia Ponce de la Cal, Haifa Ben Gharsa, Romina G. Manfrino, Christina Schuster and Andreas Leclerque
Appl. Microbiol. 2024, 4(1), 275-283; https://doi.org/10.3390/applmicrobiol4010018 - 26 Jan 2024
Viewed by 459
Abstract
(1) The fungal genus Simplicillium (Cordycipitaceae: Hypocreales) has an extensive distribution and a broad spectrum of hosts and substrates. The species Simplicillium lanosoniveum is a mycoparasite with potential for biological control of coffee leaf rust, Hemileia vastatrix. Morphologically, Simplicillium closely resembles mycoparasitic [...] Read more.
(1) The fungal genus Simplicillium (Cordycipitaceae: Hypocreales) has an extensive distribution and a broad spectrum of hosts and substrates. The species Simplicillium lanosoniveum is a mycoparasite with potential for biological control of coffee leaf rust, Hemileia vastatrix. Morphologically, Simplicillium closely resembles mycoparasitic and entomopathogenic Lecanicillium fungi, often resulting in misidentification. A fungal isolate was obtained from leaf-rust-infested coffee plants from Cienfuegos Province, Cuba. (2) Combined analyses of morphology and molecular markers (ITS, LSU, EF-1alpha) were used for fungal identification. (3) In the NJ, ML, and BI phylogenies which were reconstructed, the isolate LBSim-01 was located in the Simplicillium lanosoniveum clade. This species-level identification was supported by morphological features. (4) The isolate LBSim-01 was assigned to the species Simplicillium lanosoniveum. This is the first description of a Simplicillium fungus associated with coffee leaf rust in Cuba. The presented results hold implications for the biological control of this economically relevant plant disease. Full article
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25 pages, 3237 KiB  
Review
Role of Bacteria-Derived Exopolysaccharides in Inflammatory Bowel Disease with a Special Focus on Cyanobacterial Exopolysaccharides
by Devaprakash Manoharan, Sivakumar Natesan, Muriel Billamboz and Samir Jawhara
Appl. Microbiol. 2024, 4(1), 250-274; https://doi.org/10.3390/applmicrobiol4010017 - 23 Jan 2024
Viewed by 968
Abstract
Instances of inflammatory bowel disease (IBD), a chronic inflammatory condition of the gastrointestinal tract, are rapidly increasing in western and newly industrialized countries. Exopolysaccharides (EPSs) are one of the strategies to enhance the gut microbiota and modulate the immune-inflammatory response deregulation in IBD [...] Read more.
Instances of inflammatory bowel disease (IBD), a chronic inflammatory condition of the gastrointestinal tract, are rapidly increasing in western and newly industrialized countries. Exopolysaccharides (EPSs) are one of the strategies to enhance the gut microbiota and modulate the immune-inflammatory response deregulation in IBD patients. EPSs are produced by commensal bacteria such as Lactobacillus and Bifidobacterium. Additionally, Cyanobacteria species are promising sources of novel EPS and have potential pharmaceutical and therapeutic applications. The presence of uronic acids and sulphate groups in Cyanobacterial EPSs is an important factor that gives EPSs an anionic charge that is not seen in other prokaryotic species. This feature may impact their physico-chemical characteristics and biological properties. Additionally, Cyanobacterial EPSs have a wide range of biotechnological applications that include use as thickeners, stabilizers, and gelling agents in the food and pharmaceutical sectors. The present review focuses on the role of EPSs in IBD, with a special focus on EPSs derived from Cyanobacteria. This review also covers the biological properties of Cyanobacterial EPS in immuno-inflammatory responses and against pathogens as well as its role in biotechnological applications. Overall, Cyanobacterial EPSs have therapeutic potential against IBD due to their anti-inflammatory and immunoregulatory properties that can reduce inflammation and regulate the immune response and restore the gut microbiota of patients. Full article
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13 pages, 2314 KiB  
Article
Combination Screening of a Naïve Antibody Library Using E. coli Display and Single-Step Colony Assay
by Mieko Kato and Yoshiro Hanyu
Appl. Microbiol. 2024, 4(1), 237-249; https://doi.org/10.3390/applmicrobiol4010016 - 23 Jan 2024
Viewed by 672
Abstract
The use of single-domain camelid antibodies, termed VHHs or nanobodies, has found increasing application in diagnosis, pharmaceutical development, and research because of their superior properties, such as small size, elevated stability, high water solubility, and excellent affinity for the antigen. Antigen-specific VHHs are [...] Read more.
The use of single-domain camelid antibodies, termed VHHs or nanobodies, has found increasing application in diagnosis, pharmaceutical development, and research because of their superior properties, such as small size, elevated stability, high water solubility, and excellent affinity for the antigen. Antigen-specific VHHs are generated by screening VHH display libraries via bio-panning. However, the bio-panning step needs to be repeated multiple times, which is time-consuming and laborious. Here, we developed a simple and rapid screening method that combined Escherichia coli display and a single-step colony assay to successfully identify positive clones from a naïve VHH library. The library was constructed from peripheral blood mononuclear cells of alpaca, and VHHs were displayed on the surface of E. coli using the inverse autotransporter intimin. Libraries enriched by magnetic cell sorting were screened directly using a single-step colony assay. Colonies formed on the hydrophilic filter and antigen-coated membrane. The expression of VHHs was induced, and those bound to the antigen on the membrane were detected as positive clones. Screening and identification of positive clones required only two days, which saves considerable time and resources compared to existing protocols. Full article
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22 pages, 2350 KiB  
Article
Toward Effects of Hydrophobicity on Biosurfactant Production by Bacillus subtilis Isolates from Crude-Oil-Exposed Environments
by Seyedeh Zahra Hashemi, Jamshid Fooladi, Maliheh Vahidinasab, Philipp Hubel, Jens Pfannstiel, Evelina Pillai, Holger Hrenn, Rudolf Hausmann and Lars Lilge
Appl. Microbiol. 2024, 4(1), 215-236; https://doi.org/10.3390/applmicrobiol4010015 - 18 Jan 2024
Viewed by 773
Abstract
Background: Due to their structural features, biosurfactants reveal promising physicochemical properties, making them interesting for various applications in different fields, such as the food, cosmetics, agriculture, and bioremediation sectors. In particular, the bioproduction of surfactin, one of the most potent microbially synthesized biosurfactant [...] Read more.
Background: Due to their structural features, biosurfactants reveal promising physicochemical properties, making them interesting for various applications in different fields, such as the food, cosmetics, agriculture, and bioremediation sectors. In particular, the bioproduction of surfactin, one of the most potent microbially synthesized biosurfactant molecules, is of great interest. However, since the wild-type productivities are comparably low, stimulatory environmental conditions have to be identified for improved bioproduction This study aims to find a correlation between the hydrophobicity and production of the biosurfactant surfactin by B. subtilis isolates from crude-oil-contaminated soil and water. Methods: The surfactin production yield was characterized in adapted batch cultivations using high-performance thin-layer liquid chromatography (HPTLC). Defined hydrophobic environmental conditions were achieved by supplementation with hexadecane or polystyrene beads, and the effects on biosurfactant production were measured. Adaptations at the protein level were analyzed using mass spectrometry measurements. Results: The correlation between hydrophobicity and surfactin production was characterized using Bacillus subtilis strains ZH1 and P7 isolated from crude-oil-contaminated soil and water. Since these isolates show the biodegradation of crude oil and hexadecane as hydrophobic substrates, respectively, a first-time approach, using polystyrene beads, was applied to provide a hydrophobic environment. Interestingly, contrary to popular opinion, reduced biosurfactant production was determined. Using mass spectrometric approaches, the physiological effects of co-cultivation and the cellular response at the protein level were investigated, resulting in altered quantities of stress proteins and proteins involved in the carbon metabolism counter to polystyrene beads. Conclusions: Contrary to common opinion, increasing hydrophobicity does not have a stimulating effect, and even reduces the effect on the bioproduction of surfactin as the main biosurfactant using selected B. subtilis strains. Full article
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21 pages, 2787 KiB  
Article
Development of a Standardised International Protocol for Evaluation of the Disinfection Efficacy of Healthcare Laundry Wash Processes
by Lucy Owen, Caroline Cayrou, Georgina Page, Martin Grootveld and Katie Laird
Appl. Microbiol. 2024, 4(1), 194-214; https://doi.org/10.3390/applmicrobiol4010014 - 18 Jan 2024
Viewed by 680
Abstract
This research aims to develop a standardised protocol for monitoring the disinfection efficacy of healthcare laundry processes in view of numerous differential methodologies currently being employed within the healthcare laundry sector, including agitation and surface sampling for post-laundering decontamination assessment and swatch and [...] Read more.
This research aims to develop a standardised protocol for monitoring the disinfection efficacy of healthcare laundry processes in view of numerous differential methodologies currently being employed within the healthcare laundry sector, including agitation and surface sampling for post-laundering decontamination assessment and swatch and bioindicator testing for in-wash-process efficacy. Enterococcus faecium as an indicator species within industrial wash systems is preferable due to its high thermal and disinfectant tolerance. Methods for measuring laundry disinfection were compared; commercially available E. faecium bioindicators and contaminated cotton swatches (loose, in cloth bags or within nylon membranes) were laundered industrially at ambient temperature and microbial recovery determined. E. faecium was lost from cotton during laundering but retained by the bioindicator membrane, which allows disinfection efficacy to be measured without loss of microorganisms from the test swatch. Commercially available bioindicators were only permeable to disinfectants and detergents at ≥60 °C. Subsequently, polyethersulphone membranes for enclosing contaminated swatches were developed for low-temperature laundering, with permeability to industrial laundry chemistries at below ≤60 °C. This study demonstrates that bioindicators are the recommended methodology for laundry disinfection validation. The use of a universal healthcare laundry disinfection methodology will lead to standardised microbiological testing across the industry and improvements in infection control. Full article
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13 pages, 1693 KiB  
Article
16S rRNA Gene Sequencing-Based Identification and Comparative Analysis of the Fecal Microbiota of Five Syntopic Lizard Species from a Low-Mountain Area in Western Bulgaria
by Irina Lazarkevich, Stephan Engibarov, Simona Mitova, Emiliya Vacheva, Steliyana Popova, Nikola Stanchev, Rumyana Eneva, Yana Gocheva, Ivanka Boyadzhieva and Maria Gerginova
Appl. Microbiol. 2024, 4(1), 181-193; https://doi.org/10.3390/applmicrobiol4010013 - 18 Jan 2024
Viewed by 527
Abstract
Studies on the gut microbiome of free-living reptiles in Europe are generally fragmentary and still missing in Bulgaria. We aimed to identify and compare the fecal microbiota profiles of five syntopic lizard species from three families: the European green lizard (Lacerta viridis [...] Read more.
Studies on the gut microbiome of free-living reptiles in Europe are generally fragmentary and still missing in Bulgaria. We aimed to identify and compare the fecal microbiota profiles of five syntopic lizard species from three families: the European green lizard (Lacerta viridis), the common wall lizard (Podarcis muralis), the meadow lizard (Darevskia praticola) (Lacertidae), the European snake-eyed skink (Ablepharus kitaibelii) (Scincidae), and the European slow worm (Anguis fragilis) (Anguidae), which coinhabit a low mountainous area in the western part of the country. A high-throughput sequencing of the hypervariable V3-V4 region of the 16S rRNA gene, performed on the Illumina HiSeq2500 platform, was used. The core microbiota of lizard hosts seems to be species-specific. A dynamic phyla proportion between hosts was found. The richest alpha diversity was observed in D. praticola, and the lowest alpha diversity was observed in P. muralis and A. fragilis. Within the three lacertids, the microbiota of D. praticola and L. viridis were more closely related to each other than they were to those of P. muralis. Sharing a largely common trophic resource (all species except A. fragilis are mainly insectivorous) was not an indication of similarity in their gut microbial communities. Full article
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19 pages, 2833 KiB  
Article
Methanogenic Archaea Quantification in the Human Gut Microbiome with F420 Autofluorescence-Based Flow Cytometry
by Yorick Minnebo, Kim De Paepe, Ruben Props, Tim Lacoere, Nico Boon and Tom Van de Wiele
Appl. Microbiol. 2024, 4(1), 162-180; https://doi.org/10.3390/applmicrobiol4010012 - 17 Jan 2024
Viewed by 867
Abstract
Methane-producing Archaea can be found in a variety of habitats, including the gastrointestinal tract, where they are linked to various diseases. The majority of current monitoring methods can be slow and laborious. To facilitate gut methanogenic Archaea detection, we investigated flow cytometry for [...] Read more.
Methane-producing Archaea can be found in a variety of habitats, including the gastrointestinal tract, where they are linked to various diseases. The majority of current monitoring methods can be slow and laborious. To facilitate gut methanogenic Archaea detection, we investigated flow cytometry for rapid quantification based on the autofluorescent F420 cofactor, an essential coenzyme in methanogenesis. The methanogenic population was distinguishable from the SYBR green (SG) and SYBR green/propidium iodide (SGPI) stained background microbiome based on elevated 452 nm emission in Methanobrevibacter smithii spiked controls. As a proof-of-concept, elevated F420-autofluorescence was used to detect and quantify methanogens in 10 faecal samples and 241 in vitro incubated faecal samples. The methanogenic population in faeces, determined through Archaea-specific 16S rRNA gene amplicon sequencing, consisted of Methanobrevibacter and Methanomassiliicoccus. F420-based methanogen quantification in SG and SGPI-stained faecal samples showed an accuracy of 90 and 100% against Archaea proportions determined with universal primers. When compared to methane and Archaea presence, methanogen categorisation in in vitro incubated faeces exhibited an accuracy of 71 and 75%, with a precision of 42 and 70%, respectively. To conclude, flow cytometry is a reproducible and fast method for the detection and quantification of gut methanogenic Archaea. Full article
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15 pages, 3038 KiB  
Article
Effect of kuratsuki Bacillus and Priestia on Taste of Sake
by Karin Kobayashi and Hiromi Nishida
Appl. Microbiol. 2024, 4(1), 147-161; https://doi.org/10.3390/applmicrobiol4010011 - 15 Jan 2024
Viewed by 587
Abstract
The co-cultivation of sake yeast (AK25, K901, K1401, or K1801 strain) and the kuratsuki Bacillus A-10 and/or Priestia B-12 strains in koji solution was performed to demonstrate the effects of these two kuratsuki bacteria on sake taste. The results showed that the Brix [...] Read more.
The co-cultivation of sake yeast (AK25, K901, K1401, or K1801 strain) and the kuratsuki Bacillus A-10 and/or Priestia B-12 strains in koji solution was performed to demonstrate the effects of these two kuratsuki bacteria on sake taste. The results showed that the Brix and acidity patterns of sake preparations produced with and without these kuratsuki bacteria were very similar. This indicated that the addition of these kuratsuki bacteria did not inhibit ethanol fermentation or organic acid production by sake yeast. A taste recognition device showed that the effects of these kuratsuki bacteria on the saltiness and sourness of sake were greater than those on other taste properties. Astringency stimulation and saltiness of sake produced using the sake yeast K901 were increased by Bacillus A-10 and decreased by Priestia B-12. Except for these two cases, the taste intensities of sake preparations produced with the Bacillus A-10 and Priestia B-12 strains were very similar, but differed from those of sake produced with kuratsuki Kocuria. These results support our hypothesis that the flavor and taste of sake can be controlled by utilizing the interactions between kuratsuki bacteria and sake yeast. For crating the desired sake taste, a combination of kuratsuki bacteria and sake yeast should be considered. Full article
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14 pages, 3737 KiB  
Article
Genetic Analysis and Epidemiological Impact of SARS-CoV-2: A Multinational Study of 1000 Samples Using RT-PCR
by Talib Banser, Zainularifeen Abduljaleel, Kamal H. Alzabeedi, Adil A. Alzahrani, Asim Abdulaziz Khogeer, Fadel Hassan Qabbani, Ahmed T. Almutairi, Sami Melebari and Naiyer Shahzad
Appl. Microbiol. 2024, 4(1), 133-146; https://doi.org/10.3390/applmicrobiol4010010 - 15 Jan 2024
Viewed by 679
Abstract
The ongoing global public health challenge posed by the COVID-19 pandemic necessitates continuous research and surveillance efforts. In this study, we comprehensively analyzed over 1000 COVID-19 RT-PCR tests conducted on a cohort of 1200 patients in Saudi Arabia. Our primary goal was to [...] Read more.
The ongoing global public health challenge posed by the COVID-19 pandemic necessitates continuous research and surveillance efforts. In this study, we comprehensively analyzed over 1000 COVID-19 RT-PCR tests conducted on a cohort of 1200 patients in Saudi Arabia. Our primary goal was to investigate mutations in specific genes RdRp, N, and E different infection and recovery stages in Saudi patients with SARS-CoV-2. We also extended our analysis to include patients of various nationalities residing in Saudi Arabia, with the overarching objective of assessing these genes as markers for COVID-19 presence and progression. To diagnose and investigate potential genetic variations in COVID-19, we engaged RT-PCR. Our study primarily focused on detecting mutations in the RdRp, N, and E genes in Saudi patients with SARS-CoV-2, as well as individuals from various national residing in Saudi Arabia. This molecular technique provided valuable insights into the virus’s genetic makeup during infection and recovery. In our analysis of 671 positive COVID-19 cases, diverse gene involvement patterns were observed. Specifically, 55.91% had mutations in all three genes (RdRp, N, and E), 62.33% in both N and E genes, and 67.16% in RdRp and N genes. Additionally, 30.75% exhibited mutations exclusively in the RdRp gene, and 51.58% had mutations in the N gene. The N gene, in particular, showed high sensitivity as a marker for identifying active viral circulation. Regarding the temporal dynamics of the disease, the median duration between a positive and a subsequent negative COVID-19 RT-PCR test result was approximately 33.86 days for 44% of cases, 14.31 days for 30%, and 22.67 days for 4%. The insights from this study hold significant implications for managing COVID-19 patients during the ongoing pandemic. The N gene shows promise as a marker for detecting active viral circulation, potentially improving patient care and containment strategies. Establishing a defined positive threshold for diagnostic methods and correlating it with a low risk of infection remains a challenge. Further research is needed to address these complexities and enhance our understanding of COVID-19 epidemiology and diagnostics. Full article
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9 pages, 991 KiB  
Communication
Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks
by Luc Cornet, Valérian Lupo, Stéphane Declerck and Denis Baurain
Appl. Microbiol. 2024, 4(1), 124-132; https://doi.org/10.3390/applmicrobiol4010009 - 10 Jan 2024
Viewed by 686
Abstract
Genomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of horizontal gene transfer [...] Read more.
Genomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of horizontal gene transfer on the detection of genomic contamination has been little studied. In this study, we evaluated the efficiency of detection of six widely used contamination detection tools. To this end, we developed a simulation framework using orthologous group inference as a robust basis for the simulation of contamination. Additionally, we implemented a variable mutation rate to simulate horizontal transfer. Our simulations covered six distinct taxonomic ranks, ranging from phylum to species. The evaluation of contamination levels revealed the suboptimal precision of the tools, attributed to significant cases of both over-detection and under-detection, particularly at the genus and species levels. Notably, only so-called “redundant” contamination was reliably estimated. Our findings underscore the necessity of employing a combination of tools, including Kraken2, for accurate contamination level assessment. We also demonstrate that none of the assayed tools confused contamination and horizontal gene transfer. Finally, we release CRACOT, a freely accessible contamination simulation framework, which holds promise in evaluating the efficacy of future algorithms. Full article
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