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Appl. Microbiol., Volume 5, Issue 4 (December 2025) – 14 articles

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18 pages, 3395 KB  
Article
Identification of Filamentous Fungi Present in Prolonged Fermentations of Coffea arabica L. var. Castillo
by Camila Buitrago-Zuluaga, Carol Vanessa Osorio-Giraldo and Aida Esther Peñuela-Martínez
Appl. Microbiol. 2025, 5(4), 114; https://doi.org/10.3390/applmicrobiol5040114 - 15 Oct 2025
Abstract
In efforts to enhance the sensory profile of coffee, fermentation variations have been implemented, including extending the process for prolonged periods. Such practices create imbalances among the microbial groups involved and increase populations of filamentous fungi, compromising product safety. To identify the filamentous [...] Read more.
In efforts to enhance the sensory profile of coffee, fermentation variations have been implemented, including extending the process for prolonged periods. Such practices create imbalances among the microbial groups involved and increase populations of filamentous fungi, compromising product safety. To identify the filamentous fungi present in fermentations for up to 192 h, coffee samples were collected from fermentations conducted under semi-anaerobic (SA) and self-induced anaerobic fermentation (SIAF) conditions. Microscopic, metabolic, and rDNA sequencing techniques were applied to identify the filamentous fungi. Relative abundance and taxonomic classification were obtained through High-Throughput Sequencing of the ITS region. In addition, the presence of Ochratoxin A (OTA) was evaluated through HPLC/FLD. The most abundant genera identified was Aspergillus in SA fermentations, and Fusarium in SIAFs both at 192 h. 3438 OTUs of filamentous fungi were obtained, distributed across 11 orders, 20 families, and 17 genera. The results suggest a greater presence of mycotoxin-producing genera in fermentations with longer processing times, particularly under semi-anaerobic conditions. However, OTA levels remained below 0.8 ppb (µg/kg). These findings provide essential information for microbiological control of fermentation, supporting the maintenance of product safety in subsequent stages and ensuring the safety of the final product. Full article
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21 pages, 1315 KB  
Review
Synergies in Green Bioprocessing: A Comprehensive Review of Heterologous Protein Expression and the Transformative Potential of Natural Deep Eutectic Solvents
by José Agustín Martínez-Olivares and Victor Coca-Ruiz
Appl. Microbiol. 2025, 5(4), 113; https://doi.org/10.3390/applmicrobiol5040113 - 15 Oct 2025
Abstract
Heterologous protein expression underpins the production of therapeutics, industrial enzymes, and diagnostic reagents, yet persistent challenges remain in enhancing yields, achieving correct folding, and reducing the costs and environmental burdens of downstream processing. Natural Deep Eutectic Solvents (NADESs)—a class of biocompatible, sustainable, and [...] Read more.
Heterologous protein expression underpins the production of therapeutics, industrial enzymes, and diagnostic reagents, yet persistent challenges remain in enhancing yields, achieving correct folding, and reducing the costs and environmental burdens of downstream processing. Natural Deep Eutectic Solvents (NADESs)—a class of biocompatible, sustainable, and highly tunable solvents—have recently emerged as promising tools to overcome these limitations. This review systematically examines the intersection of recombinant protein production and NADES technology, assessing their applications across the full workflow, from host strain expression to purification and final formulation. Literature analysis highlights the potential of NADESs as media additives that mitigate cellular stress and improve soluble protein yields, as gentle solubilizing and refolding agents for inclusion bodies, as phase-forming components in aqueous two-phase systems for green purification, and as stabilizing excipients for long-term storage. Key constituents such as betaine, proline, urea, and arginine are identified as functional agents whose eutectic mixtures often deliver synergistic benefits that differ mechanistically from the action of the individual components. The integration of NADESs into recombinant protein production offers a path toward more sustainable and economically viable biomanufacturing. Critical gaps remain, including in vivo validation and techno-economic assessment. Future opportunities include high-throughput NADES screening and computational design of application-specific solvents. Full article
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19 pages, 5571 KB  
Article
Eco-Efficient Intensification of Potato with Bacillus subtilis and Trichoderma viride Under NPK Fertilization
by Miguel Tueros, Melina Vilcapoma, Guido Pillaca, José Velásquez, Henry Campos, Hector Cántaro-Segura, Omar Paitamala and Daniel Matsusaka
Appl. Microbiol. 2025, 5(4), 112; https://doi.org/10.3390/applmicrobiol5040112 - 15 Oct 2025
Abstract
Potato production in the Andean highlands demands strategies that reduce dependence on synthetic inputs without sacrificing yield. We evaluated two microbial bioinputs—Bacillus subtilis and Trichoderma viride—applied once pre-plant to seed tubers, under three organo-mineral fertilization regimes (0%, 50%, and 100% of [...] Read more.
Potato production in the Andean highlands demands strategies that reduce dependence on synthetic inputs without sacrificing yield. We evaluated two microbial bioinputs—Bacillus subtilis and Trichoderma viride—applied once pre-plant to seed tubers, under three organo-mineral fertilization regimes (0%, 50%, and 100% of the recommended NPK rate) in two cultivars (INIA 303-Canchán and Yungay) in field conditions in Ayacucho, Peru, using a randomized complete block, split-plot design (three replicates). Agronomic traits (plant height, root dry weight, stems per plant, tubers per plant, and plot-level yield) were analyzed with robust two-way ANOVA and multivariate methods. Combining microbial inoculation with 50% NPK sustained growth responses comparable to 100% NPK for key traits: in Yungay with T. viride, plant height at 50% NPK (≈96.15 ± 1.71 cm) was not different from 100% NPK (≈98.87 ± 1.70 cm), and root dry weight at 50% NPK (≈28.50 ± 0.28 g) matched or exceeded 100% NPK (≈16.97–22.62 g depending on cultivar–treatment). Notably, T. viride increased root biomass even without mineral fertilizer (≈27.62 ± 0.29 g in Yungay), while B. subtilis enhanced canopy vigor and stem number at full NPK (≈4.5 ± 0.29 stems). Yungay out-yielded INIA 303-Canchán overall (≈57.5 ± 2.5 kg vs. ≈42.7 ± 2.5 kg per plot). The highest yields occurred with B. subtilis + 100% NPK (≈62.88 ± 6.07 kg per plot), followed by B. subtilis + 50% NPK (≈51.7 ± 6.07 kg per plot). Plant height was the strongest correlate of yield (Spearman ρ ≈ 0.60), underscoring its value as a proxy for productivity. Overall, a single pre-plant inoculation with B. subtilis or T. viride can halve mineral fertilizer inputs while maintaining growth and sustaining high, cultivar-dependent yields in highland potato systems. Full article
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13 pages, 2698 KB  
Article
Adopting Biochar as Immobilization Support for Hyper Ammonia-Producing Bacteria Proliferation
by Christiana Bitrus, Ademola Hammed, Tawakalt Ayodele, Kudirat Alarape, Niloy Chandra Sarker, Clairmont Clementson and Ewumbua Monono
Appl. Microbiol. 2025, 5(4), 111; https://doi.org/10.3390/applmicrobiol5040111 - 14 Oct 2025
Abstract
The many uses of biochar extend to microbial enhancement in fermentation processes because it acts as a catalyst and a support medium in agricultural industries, particularly for biofertilizer production. This study explores how three key biochar parameters, concentration (0.05–0.25% w/v), [...] Read more.
The many uses of biochar extend to microbial enhancement in fermentation processes because it acts as a catalyst and a support medium in agricultural industries, particularly for biofertilizer production. This study explores how three key biochar parameters, concentration (0.05–0.25% w/v), temperature (30–50 °C), and particle size (250 μm–1.40 mm) affect hyper-ammonia-producing bacteria (HAB) growth during fermentation using commercially sourced pine wood-derived biochar. Fermentation experiments utilized enriched cow rumen fluid under controlled conditions, monitoring bacterial growth via optical density (OD600) over 48 h. Microbial proliferation was strongly influenced by all tested parameters (concentration, temperature, particle size). Highest growth occurred at 0.15% biochar concentration, 45 °C, and 250 μm particle size within the tested parameter ranges. Lower concentrations and smaller particles promoted microbial adhesion and colonization. Higher biochar levels hindered growth due to surface saturation and reduced pore accessibility. SEM imaging supported these findings by revealing structural changes on the biochar surface at different concentrations. Regression analysis demonstrated strong correlation between biochar parameters and microbial activity (R2 = 0.9931), though multicollinearity limited individual variable significance. These findings support biochar optimization for enhanced microbial processing in biotechnological applications. Full article
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22 pages, 1877 KB  
Article
Bifidobacterium Longum subsp. infantis and Lacticaseibacillus Rhamnosus GG Protect Intestinal Epithelium Against Inflammation-Mediated Damage in an Immunocompetent In-Vitro Model
by Ilia Belotserkovsky, Cecile Vernochet, Maroussia Roelens, Benoît Beitz, Bouthaina Ben Abdallah, Sophiane Poissonnier, Samuel Bellais, Amy Hesketh, Jazmin Meza Torres, Manal Mouharib, Justine Sunshine, Mike Shaffer, Janie Parrino, Jared Silverman, COSIPOP Study Group, Romain Daillère and Christophe Vedrine
Appl. Microbiol. 2025, 5(4), 110; https://doi.org/10.3390/applmicrobiol5040110 - 13 Oct 2025
Abstract
Impairment of the intestinal epithelial barrier, accompanied by local and systemic inflammation, underlies numerous human pathologies, including inflammatory bowel diseases, celiac disease, sepsis, as well as severe acute malnutrition. Bifidobacterium longum subsp. infantis and Lacticaseibacillus rhamnosus GG (LGG®) have been shown [...] Read more.
Impairment of the intestinal epithelial barrier, accompanied by local and systemic inflammation, underlies numerous human pathologies, including inflammatory bowel diseases, celiac disease, sepsis, as well as severe acute malnutrition. Bifidobacterium longum subsp. infantis and Lacticaseibacillus rhamnosus GG (LGG®) have been shown in preclinical studies to strengthen the gut epithelial barrier and attenuate inflammation. This study aimed to compare the ability of four commercial strains of B. infantis, LGG, and their combination to mitigate inflammation-mediated epithelial damage using an in vitro immunocompetent intestinal model. A microfluidic mid-throughput platform OrganoPlate® was used to co-culture intestinal epithelial cells (Caco-2) with peripheral blood mononuclear cells (PBMCs). Epithelial damage was induced by stimulating PBMCs with lipopolysaccharide (LPS), and probiotic-conditioned media were applied to the apical side of Caco-2 cells to assess effects on barrier integrity, cytokine secretion, and gene transcription. All tested probiotics significantly protected the epithelium by modulating tight junction protein expression and promoting transcription of homeostatic cytokines, resulting in a “leak-tight” phenotype. These findings indicate that metabolites produced by B. infantis and/or LGG can protect the intestinal epithelium in vitro, warranting further in vivo studies to evaluate the translational relevance of this effect. Full article
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12 pages, 1201 KB  
Article
Knockouts of Yeast Plasma Membrane Phosphate Transporters Alter Resistance to Heavy Metals
by Larisa Ledova, Lubov Ryazanova, Ludmila Trilisenko, Vladimir Ostroumov and Tatiana Kulakovskaya
Appl. Microbiol. 2025, 5(4), 109; https://doi.org/10.3390/applmicrobiol5040109 - 11 Oct 2025
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Abstract
Mutant yeast strains with altered sensitivity to heavy metals are crucial for revealing the mechanisms of metal absorption and detoxification, as well as for bioremediation of these pollutants. Here, we show that a knockout of the PHO87 gene encoding the low-affinity phosphate transporter [...] Read more.
Mutant yeast strains with altered sensitivity to heavy metals are crucial for revealing the mechanisms of metal absorption and detoxification, as well as for bioremediation of these pollutants. Here, we show that a knockout of the PHO87 gene encoding the low-affinity phosphate transporter of the cytoplasmic membrane of S. cerevisiae increased resistance to manganese, silver, and vanadate ions. However, a knockout of PHO90 (PHO87 paralog) did not affect the sensitivity to silver and vanadate ions but increased sensitivity to manganese ions. The Δpho87 cells accumulated 10 times less manganese compared to the wild-type cells, while the Δpho90 cells accumulated two times more manganese compared to the wild-type cells, when grown in YPD with 2 mM MnSO4. The polyphosphate content of the Δpho84, Δpho87, and Δpho90 cells cultivated at high phosphate concentration did not differ from that of the wild-type strain. In the presence of 2 mM MnSO4, Δpho87 cells contained several times less polyphosphates, and Δpho90 cells contained more short-chain polyphosphates than the cells of the wild-type strain. We hypothesize that phosphate carriers participate in the regulation of heavy metal uptake, and the respective knockouts are useful in bioremediation and bioassay of these pollutants. Full article
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25 pages, 6855 KB  
Article
Survey of Thirteen Novel Pseudomonas putida Bacteriophages
by Simon Anderson, Rachel Persinger, Akaash Patel, Easton Rupe, Johnathan Osu, Katherine I. Cooper, Susan M. Lehman, Rohit Kongari, James D. Jaryenneh, Catherine M. Mageeney, Steven G. Cresawn and Louise Temple
Appl. Microbiol. 2025, 5(4), 108; https://doi.org/10.3390/applmicrobiol5040108 - 7 Oct 2025
Viewed by 291
Abstract
Bacteriophages have been widely investigated as a promising treatment of food, medical equipment, and humans colonized by antibiotic-resistant bacteria. Phages pose particular interest in combating those bacteria which form biofilms, such as the medically important human pathogen Pseudomonas aeruginosa and several plant pathogens, [...] Read more.
Bacteriophages have been widely investigated as a promising treatment of food, medical equipment, and humans colonized by antibiotic-resistant bacteria. Phages pose particular interest in combating those bacteria which form biofilms, such as the medically important human pathogen Pseudomonas aeruginosa and several plant pathogens, including P. syringae. In an undergraduate lab course, P. putida was used as the host to isolate novel anti-pseudomonal bacteriophages. Environmental samples of soil and water were collected, and purified phage isolates were obtained. After Illumina sequencing, genomes of these phages were assembled de novo and annotated. Assembled genomes were compared with known genomes in the literature and GenBank to identify taxonomic relations and to refine their functional annotations. The thirteen phages described are sipho-, myo-, and podoviruses in several families of Caudoviricetes, spanning several novel genera, with genomes ranging from 40,000 to 96,000 bp. One phage (DDSR119) is unique and is the first reported P. putida siphovirus. The remaining 12 can be clustered into four distinct groups. Six are highly related to each other and to previously described Autotranscriptaviridae phages: Waldo5, PlaquesPlease, and Laces98 all belong to the Waldovirus genus, whereas Stalingrad, Bosely, and Stamos belong to the Troedvirus genus. Zuri was previously classified as the founding member of a new genus Zurivirus within the family Schitoviridae. Ebordelon and Holyagarpour each represent different species within Zurivirus, whereas Meara is a more distantly related member of the Schitoviridae. Dolphis and Jeremy are similar enough to form a genus but have only a few distant relatives among sequenced phages and are notable for being temperate. We identified the lysis cassettes in all 13 phages, compared tail spike structures, and found auxiliary metabolic genes in several. Studies like these, which isolate and characterize infectious virions, enable the identification of novel proteins and molecular systems and also provide the raw materials for further study, evaluation, and manipulation of phage proteins and their hosts. Full article
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8 pages, 801 KB  
Opinion
Probiotics, Placebos, or Profits? Reclaiming Scientific Language in the Age of Commercialized Microbes
by Gerrit A. Stuivenberg
Appl. Microbiol. 2025, 5(4), 107; https://doi.org/10.3390/applmicrobiol5040107 - 7 Oct 2025
Viewed by 365
Abstract
The prevalence of probiotic-labeled products with no evidence of improved health outcomes associated with their consumption has perturbed both the trust of clinicians and the public perception of microbial therapeutics. While probiotics are clearly defined as live microorganisms that, when administered in adequate [...] Read more.
The prevalence of probiotic-labeled products with no evidence of improved health outcomes associated with their consumption has perturbed both the trust of clinicians and the public perception of microbial therapeutics. While probiotics are clearly defined as live microorganisms that, when administered in adequate amounts, confer a health benefit on the host, it is often ignored in the microbial marketplace. Many products including household cleaners, cosmetics, and pet foods attach probiotic to their labels without supplying viable strains, clinically effective doses, or proven outcomes. Evidence from metagenomic studies and compositional analyses suggest that many probiotics on the market are mischaracterized or mislabeled, a problem that is only exacerbated by weak regulatory standards. In contrast, there are a limited collection of strain-specific interventions such as Lactobacillus rhamnosus GG, L. rhamnosus GR1, Saccharomyces boulardii, and Escherichia coli Nissle 1917 that have demonstrated beneficial effects in randomized clinical trials. Considering that the consumption of commercial probiotics often lacks measurable health benefits, it is unreasonable to group proven microbial therapeutics under the same umbrella term of “probiotic”. This paper proposes a strict enforcement of semantic distinction: reserving “probiotics” for less regulated microbial-rich products whereas microbe-containing products that have demonstrated clinical benefit following robust regulatory oversight should be considered for reclassification. Full article
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15 pages, 3975 KB  
Article
Acid Adaptation Leads to Sensitization of Salmonella Challenge Cultures During Processing of Air-Dried Beef (Biltong, Droëwors)
by Pratikchhya Adhikari, Cailtin E. Karolenko, Jade Wilkinson and Peter M. Muriana
Appl. Microbiol. 2025, 5(4), 106; https://doi.org/10.3390/applmicrobiol5040106 - 6 Oct 2025
Viewed by 248
Abstract
US food regulatory agencies have adopted a preference for researchers and testing labs to use ‘acid-adapted challenge cultures’ when performing inoculated validation studies of food processes that involve acidic treatments to accustom the cultures to acidic pH so that they will not be [...] Read more.
US food regulatory agencies have adopted a preference for researchers and testing labs to use ‘acid-adapted challenge cultures’ when performing inoculated validation studies of food processes that involve acidic treatments to accustom the cultures to acidic pH so that they will not be easily affected during processing. We evaluated acid adaptation in regard to the processing of South African style air-dried beef, notably biltong and droëwors, using a mixture of five serovars of Salmonella as well as a unique serovar isolated from dried beef (Salmonella Typhimurium 1,4,[5],12:i:-). Acid adaptation was obtained by growing cultures in tryptic soy (TS) broth containing 1% glucose. Non-adapted cultures were obtained by growth in TS broth without glucose or in TS broth with 1% glucose but buffered with 0.2 M phosphate buffer. Processes included biltong (dried solid beef) and droëwors (ground, sausage-style). Each trial was performed twice and triplicate samples were examined at each sampling point (i.e., n = 6). Statistical analysis was applied using analysis of variance (ANOVA) or one-way repeated measures (RM-ANOVA) and the Holm–Sidak test for pairwise multiple comparisons to determine significant differences (p < 0.05). We observed that in all processes examined (eight trials), treatments using acid-adapted cultures were more sensitive to the biltong and droëwors processes, giving greater reductions (5.3-log reduction) than when non-adapted cultures were used (3.8-log reduction). Acid adaptation leads to stressed conditions in Salmonella resulting in sensitization to the multiple hurdles found in biltong and droëwors processing (acid/vinegar, salt, desiccation). Based on our data, the use of non-adapted Salmonella cultures to achieve desired challenge culture process lethality could result in more robust processing conditions and a greater level of safety in these products as intended by US regulatory guidance. Full article
(This article belongs to the Special Issue Applied Microbiology of Foods, 3rd Edition)
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21 pages, 3648 KB  
Article
BioLumCity: 3D-Printed Bioluminescent Urban Tiles Employing Aliivibrio fischeri Bioink as Passive Urban Light
by Yomna K. Abdallah, Alberto T. Estévez, Aranzazu Balfagón Martin and Marta Serra Soriano
Appl. Microbiol. 2025, 5(4), 105; https://doi.org/10.3390/applmicrobiol5040105 - 5 Oct 2025
Viewed by 307
Abstract
Integrating bioluminescent organisms as passive lighting sources in the built environment is currently a hot topic. However, there are several limitations facing the implementation and up-scaling of these naturally bioluminescent organisms in the built environment on architectural and urban scales, such as the [...] Read more.
Integrating bioluminescent organisms as passive lighting sources in the built environment is currently a hot topic. However, there are several limitations facing the implementation and up-scaling of these naturally bioluminescent organisms in the built environment on architectural and urban scales, such as the scale, sensitivity, enclosure, and difficulty of maintenance. Moreover, there are complex technicalities and operational aspects of conventional bioreactors that host these bioluminescent agents, especially in terms of managing their recharge and effluent, not to mention their high maintenance cost. The current work offers a sustainable, stand-alone, bioluminescent urban screen system employing Aliivibrio fischeri CECT 524 bioink on 3D-printed customized scaffolds as bioreceptive panel design based on a field-diffusion pattern to host the bioluminescent bacterial bioink. The field-diffusion pattern was employed thanks to its proven efficiency in entrapment of the various microbial cultures. Three different growth media were tested for culturing Aliivibrio fischeri CECT 524, including Luria Bertani Broth (LB), the Tryptone Soy Broth (TSB), and the standard Marine Broth (MB). The results revealed that the Marine Broth (MB) media achieved the highest bioluminescent intensity and duration. The maximum light emission typically in range of ~490 nm of blue–green light captured by a conventional reflex camera (human eye vision) was observed for 10 consecutive days in complete darkness after 3–10 s, at a room temperature of 25 °C. This was visible mainly at the thin curvilinear peaks of the 3D-printed field pattern. P1 achieved the highest performance in terms of visible blue–green light, and a duration of 10 days of active bioluminescence was achieved without the need for refilling, thanks to the high number of peaks and narrow wells at <0.5 cm of its field-diffusion pattern. This study proves the efficiency of this biomimetic pattern in terms of the bioreceptivity of the bioluminescent bacterial bioink. Furthermore, the proposed 3D-printed urban screens proved their economic sustainability in terms of affordability and their minimized production processes, in addition to their easy maintenance and recharge. These results qualify these 3D-printed bioluminescent urban screens for easy and decentralized adoption and application on an architectural and urban scale. Full article
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8 pages, 476 KB  
Communication
Brucella Diagnostics in Endemic Areas: Evaluation of Point-of-Care Kits and the Need for Alternative Diagnostic Tests
by Aggrey Keya, Pauline Gitonga, Daniel Wanjohi, Esther Lemarkoko, Joseph Sankok, Brian Ogoti, Angela Bosco-Lauth, Marybeth Maritim, George Gitao, Joshua Onono, Julius Oyugi and Richard Bowen
Appl. Microbiol. 2025, 5(4), 104; https://doi.org/10.3390/applmicrobiol5040104 - 29 Sep 2025
Viewed by 265
Abstract
Brucellosis is a significant public health challenge in Kenya, particularly in pastoralist communities where the disease is endemic. Reliable and accurate point-of-care diagnostics are essential for timely case identification and effective disease management. The Febrile Brucella Agglutination Test (FBAT) is commonly used for [...] Read more.
Brucellosis is a significant public health challenge in Kenya, particularly in pastoralist communities where the disease is endemic. Reliable and accurate point-of-care diagnostics are essential for timely case identification and effective disease management. The Febrile Brucella Agglutination Test (FBAT) is commonly used for diagnosis of brucellosis in Kenya, but concerns have been noted about its diagnostic accuracy, prompting an independent evaluation. The aim of this study was to compare the diagnostic performance of five FBAT kits with a commercial Enzyme-Linked Immunosorbent Assay (ELISA) as the reference standard, and to build local laboratory capacity for in-house kit validation for the Kajiado County laboratory staff. A total of 200 serum samples (100 ELISA-confirmed positives and 100 negatives) were tested using the FBAT kits. Each kit was evaluated for its ability to detect antibodies to both B. abortus and B. melitensis antigens. Diagnostic performance indicators, including sensitivity, specificity, and Cohen’s Kappa, were calculated, and McNemar’s test was applied to assess concordance with the ELISA results. Overall, none of the FBAT kits proved to have acceptable sensitivity and specificity compared to ELISA. We conclude that FBAT kits are not sufficient for the diagnosis of brucellosis and that alternative diagnostics should be considered. Full article
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6 pages, 189 KB  
Editorial
Current Trends in the Applications of Probiotics and Other Beneficial Microbes: Expanding Horizons
by Sabina Fijan and Tamara Fijan
Appl. Microbiol. 2025, 5(4), 103; https://doi.org/10.3390/applmicrobiol5040103 - 26 Sep 2025
Viewed by 490
Abstract
While pathogenic microbes, such as Yersinia pestis, Mycobacterium tuberculosis, Clostridium tetani, influenza A virus, and many others, have historically been the focus of scientific attention due to their role in causing severe diseases, beneficial microorganisms are being increasingly recognized for [...] Read more.
While pathogenic microbes, such as Yersinia pestis, Mycobacterium tuberculosis, Clostridium tetani, influenza A virus, and many others, have historically been the focus of scientific attention due to their role in causing severe diseases, beneficial microorganisms are being increasingly recognized for their essential contributions to human, animal, and plant health within the One Health framework, as well as their contributions to nutrition and the stability of ecosystems [...] Full article
23 pages, 2125 KB  
Article
Development and Evaluation of an Exogenous Bioaugmentation Framework Using an Immobilized Mixed Bacterial Consortium for the Remediation of Hydrocarbon-Contaminated Soils
by Emerance Jessica Claire D’Assise Goma-Tchimbakala, Ilaria Pietrini, Alessandro Conte, Neria Costa and Stefano Paolo Corgnati
Appl. Microbiol. 2025, 5(4), 102; https://doi.org/10.3390/applmicrobiol5040102 - 25 Sep 2025
Viewed by 342
Abstract
Improving the quality of oil-contaminated soils remains a critical challenge, and bioaugmentation using allochthonous bacteria offers promising perspectives. This study proposes a framework for exogenous bioaugmentation using a bacterial consortium, composed of strains from diverse climates, immobilized in alginate beads and combined with [...] Read more.
Improving the quality of oil-contaminated soils remains a critical challenge, and bioaugmentation using allochthonous bacteria offers promising perspectives. This study proposes a framework for exogenous bioaugmentation using a bacterial consortium, composed of strains from diverse climates, immobilized in alginate beads and combined with calcium peroxide as an oxygen-releasing compound. Two conditions were tested: freshly prepared beads (BA) and lyophilized beads (LA). Their performance was compared to natural attenuation (NA) and to landfarming coupled with bioaugmentation using a free autochthonous consortium. Hydrocarbon degradation was assessed through total petroleum hydrocarbon (TPH) and alkane depletion (GC-MS), microbial community dynamics (amplicon sequencing), and abundance of the alkB gene (qPCR). In three months, the BA treatment achieved a 44% TPH reduction, outperforming LA (34%) and NA (10% less than BA). However, LA induced a marked increase in alkB gene copies and microbial biomass at the end of the experiment, suggesting greater long-term potential. Dominant genera varied across treatments: Rhodococcus in NA, Gordonia in BA, and Pseudomonas in LA. In parallel, the autochthonous consortium achieved up to 80% oil degradation. This study demonstrates the viability of lyophilized microbial consortia in scalable, ready-to-use formulations and provides an operational methodology for exogenous bioaugmentation as a tool for the remediation of hydrocarbon-contaminated soils. Full article
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23 pages, 1444 KB  
Review
Streptococcus thermophilus: Metabolic Properties, Functional Features, and Useful Applications
by Alyaa Zaidan Ghailan and Alaa Kareem Niamah
Appl. Microbiol. 2025, 5(4), 101; https://doi.org/10.3390/applmicrobiol5040101 - 23 Sep 2025
Viewed by 974
Abstract
Streptococcus thermophilus is a Gram-positive, homofermentative lactic acid bacterium classified within the Firmicutes phylum, recognized for its probiotic properties and significant role in promoting human health. This review consolidates existing understanding of its metabolic pathways, functional metabolites, and diverse applications, highlighting evidence-based insights [...] Read more.
Streptococcus thermophilus is a Gram-positive, homofermentative lactic acid bacterium classified within the Firmicutes phylum, recognized for its probiotic properties and significant role in promoting human health. This review consolidates existing understanding of its metabolic pathways, functional metabolites, and diverse applications, highlighting evidence-based insights to enhance scientific integrity. S. thermophilus predominantly ferments lactose through the Embden-Meyerhof-Parnas pathway, resulting in L(+)-lactic acid as the primary end-product, along with secondary metabolites including acetic acid, formic acid, and pyruvate derivatives. Exopolysaccharides (EPS) are composed of repeating units of glucose, galactose, rhamnose, and N-acetylgalactosamine. They display strain-specific molecular weights ranging from 10 to 2000 kDa and contribute to the viscosity of fermented products, while also providing antioxidant and immunomodulatory benefits. Aromatic compounds such as acetaldehyde and phenylacetic acid are products of amino acid catabolism and carbohydrate metabolism, playing a significant role in the sensory characteristics observed in dairy fermentations. Bacteriocins, such as thermophilins (e.g., Thermophilin 13, 110), exhibit extensive antimicrobial efficacy against pathogens including Listeria monocytogenes and Bacillus cereus. Their activity is modulated by quorum-sensing mechanisms that involve the blp gene cluster, and they possess significant stability under heat and pH variations, making them suitable for biopreservation applications. In food applications, S. thermophilus functions as a Generally Recognized as Safe (GRAS) starter culture in the production of yogurt and cheese, working in conjunction with Lactobacillus delbrueckii subsp. bulgaricus to enhance acidification and improve texture. Specific strains have been identified to mitigate lactose intolerance, antibiotic-related diarrhea, and inflammatory bowel diseases through the modulation of gut microbiota, the production of short-chain fatty acids, and the inhibition of Helicobacter pylori. The genome, characterized by a G + C content of approximately 37 mol%, facilitates advancements in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas technology and heterologous protein expression, with applications extending to non-dairy fermentations and the development of postbiotics. This review emphasizes the adaptability of S. thermophilus, showcasing the variability among strains and the necessity for thorough preclinical and clinical validation to fully utilize its potential in health, sustainable agriculture, and innovation. It also addresses challenges such as susceptibility to bacteriophages and limitations in proteolytic activity. Full article
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