Appl. Microbiol., Volume 5, Issue 2 (June 2025) – 19 articles

Microbially induced calcite precipitation (MICP) has attracted attention as an environmentally friendly soil stabilization method, with Sporosarcina pasteurii being a key ureolytic bacterium in this process. However, its behavior in oxygen-limited environments remains poorly understood, limiting the predictability of MICP outcomes in natural soils. This study investigated the population dynamics of Sporosarcina in compacted soil reactors operated under aerobic and anaerobic conditions, including saturated environments. Quantitative PCR and 16S rRNA gene sequencing revealed that Sporosarcina thrived and became dominant under aerobic, unsaturated conditions, but failed to maintain a high abundance under anaerobic or saturated conditions. These findings indicate that gas-phase oxygen—not merely its presence in the overlying atmosphere—is essential for effective Sporosarcina-driven MICP. The results highlight a critical environmental constraint that limits the application of biostimulation strategies relying on indigenous Sporosarcina in oxygen-poor soils. This study provides the first in situ evidence linking oxygen availability and microbial dominance in MICP systems, with implications for optimizing microbial soil stabilization in real-world conditions. Full article

The traditional fermentation of table olives is a complex and dynamic, process, carried out by a consortium of microorganisms that interact with each other and contribute to the uniqueness and attractiveness of the final product. Fermentation is conducted by yeasts and lactic acid bacteria (LAB) that coexist in olive fruits. The succession of one microbial population to the detriment of others depends on internal and external factors that affect the process, e.g., the maturation degree of fruits, cultivar, endophytic, or epiphytic state of microorganisms, pH, water activity, temperature, and salt concentration. Thus, studying microbiota evolution and their identification in natural table olive fermentations is paramount. This review aims to provide an overview of the knowledge on the natural fermentation of table olives, namely regarding microbial dynamics, as to report the main species involved in the fermentation process, highlight the influence of the olive oil ecosystem on the origin of the microbiota and consequently on the obtaining of the final product. The results report a total of 97 yeast species and 45 LAB species described in olives and brine over the last few decades. Full article

Beer lees (BL), a by-product of beer production, consist mainly of dead yeast cells with potential nutritional value. On the other hand, yeast extract (YE), obtained through the lysis of yeast cells, is commonly used as a nutrient-rich supplement for the growth of fastidious microorganisms such as lactic acid bacteria (LAB). However, YE is a high-cost ingredient. Therefore, the aim of this study was to optimize the use of BL as a low-cost alternative source of YE through different lysis treatments, evaluating its suitability to support the growth of UNQLpc 10 and UNQLp 11 strains in a whey permeate (WP)-based medium. Growth kinetics and cell viability were compared with those obtained in MRS broth. The best results were observed with sonicated BL, up to 10 logarithmic units, which supported LAB growth comparable to MRS. Although autolyzed BL promoted lower bacterial growth than sonicated BL, it showed greater cell disruption and higher levels of nitrogen, proteins, and amino acids (5.32%, 26.0%, and 277 nM, respectively). Additionally, autolyzed BL exhibited lower concentrations of reducing sugars and a higher presence of Maillard reaction products, as indicated by colorimetric analysis. These changes, which may be related to the formation of Maillard reaction products during the autolysis process, could have negatively affected the nutritional quality of the extract and, thus, reduced its effectiveness as a bacterial growth promoter. Full article

Sialidases are gradually entering various areas of human practice—in medicine and pharmacy, as antiviral, antitumor, diagnostic, and vaccine preparations; for the chemoenzymatic synthesis of regioselective sialoglycoconjugates; and for the structural analysis of sialoglycoproteins. Optimizing the synthesis conditions of these commercially important enzymes would be beneficial for enhancing their production and expanding potential applications. Since sialidase producers are often pathogenic microorganisms, the use of saprophytic bacteria could be an alternative to reduce the health risk when working with them. So far, the topic has not been widely discussed. By a single-factor optimization method, the most suitable fermentation conditions for achieving maximum sialidase production by the non-model strain Oerskovia paurometabola O129 were established. The dynamics of enzyme accumulation during the growth phases and the optimal physicochemical parameters for cultivation were determined (30 °C, pH 8.0, agitation at 200 rpm, for 28 h). The addition of various inducers and surfactants to improve enzyme yield was also investigated. The effect of surfactants on bacterial sialidase production was tested for the first time. Maximum enzyme production (98.3 U/mL), representing about a three-fold increase compared to non-optimized conditions, was obtained by culturing the strain under optimal conditions and by the synergistic action of glucomacropeptide and Tween 80. A new, simple, and cost-effective laboratory model for optimizing sialidase production by the saprophytic strain O. paurometabola O129 in submerged fermentation was proposed. Future work may involve scaling up the process and exploring genetic or metabolic enhancements for targeted biomedical and industrial applications. Full article

The study of bacteriocins has significantly enhanced our understanding of microbial interactions, notably within the genus Streptococcus. Among the most functionally diverse and clinically relevant bacteriocins are those belonging to the lantibiotic class, which exhibit potent antimicrobial properties and are central to the competitive dynamics of streptococcal species. This review focuses on the discovery and characterization of bacteriocins produced by Streptococcus pyogenes and Streptococcus salivarius, emphasizing their biological significance within their exclusive human host. A cornerstone of these studies has been the development and application of the pioneer agar culture-based bacteriocin detection methodology, known as streptococcal bacteriocin fingerprinting. This approach has proven invaluable for the initial detection and differentiation of a wide array of bacteriocin-like inhibitory substances (BLIS) in streptococcal populations. A central theme of this review is the diverse biological roles of lantibiotics in S. pyogenes and S. salivarius, particularly in relation to microbial competition, colonization dynamics, and host interactions. The expression of lantibiotic determinants provides distinct advantages to the producing strain, including enhanced niche establishment and the ability to suppress competing microbes. Furthermore, the presence of specific lantibiotic immunity mechanisms safeguards the producer from self-inhibition and potential antagonism from closely related competitors. In S. pyogenes, lantibiotic production has been implicated in virulence modulation, raising important questions about its role in pathogenicity and host immune evasion. Conversely, S. salivarius, a prominent commensal and probiotic candidate species, utilizes its lantibiotic arsenal to confer colonization benefits and mediate beneficial interactions, especially within the oral and upper respiratory tract microbiomes. The implications of in situ lantibiotic expression extend beyond microbial ecology, presenting opportunities for innovative probiotic and therapeutic applications. The potential for harnessing bacteriocin-producing streptococci in antimicrobial interventions, particularly in combating antibiotic-resistant pathogens, underscores the translational relevance of these findings. This review integrates historical and contemporary perspectives on streptococcal bacteriocin research, providing insights into future avenues for leveraging these bioactive peptides in clinical and biotechnological contexts. Full article

The biotechnological applications of chitinases are diverse. They are used in industrial sectors such as pharmaceuticals, textiles, and agriculture, including the use of recombinant chitinases for pest control, since traditional treatments affect and contaminate hive products. Bacillus licheniformis UV01 bacterium is of interest, as it expresses genes for different enzymes, including chitinase. The Chibluv01 gene was cloned into the pHTP8 vector with a His/tag for purification using affinity chromatography. It showed a specific activity of 115 U/m. The optimal pH and temperature were 7.5 and 42 °C, respectively. The choleoptericidal activity (ability to kill beetles) of the enzyme was evaluated in the larvae and adult beetles of Aethina tumida treated with immersion in a purified enzyme extract at different concentrations, and the mortality was verified at 24, 48, and 72 h. Within 24 h of application, the mortality increased by 50% in the larval stage and 56.6% in adult beetles compared to the control groups. The LC₅₀ and LC₉₀ were obtained: 104.05 U/mL and 234.36 U/mL in larvae and 92.99 U/mL and 211.14 U/mL in adults, respectively. These results indicate the potential of the application of ChiBlUV02 chitinase in pest control. Full article

This study evaluated the antimicrobial potential of a Bacillus subtilis spore-based probiotic cocktail to reduce foodborne pathogens in both nutrient-rich laboratory media and a complex food matrix (hummus). Three common foodborne pathogens—Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella Typhimurium—were cultured individually in full-strength, half-strength, and quarter-strength tryptic soy broth (TSB) with or without the probiotic spores (~7 log CFU/mL). Additionally, a commercial hummus formulation was inoculated with L. monocytogenes (~3 log CFU/g) and B. subtilis spores (~7 log CFU/g) and stored at 30 °C to simulate temperature abuse. In TSB, E. coli and Salmonella grew to ~8.2 log CFU/mL in full-strength media, with no significant inhibition by the probiotics. However, L. monocytogenes showed substantial suppression: in nutrient-limited TSB, viable counts dropped below the detection limit of 1.48 log CFU/mL by 24 h in the presence of probiotics. In hummus, L. monocytogenes grew to an average of 8.22 log CFU/g in the absence of probiotics but remained significantly lower at an average of 5.03 log CFU/g when co-inoculated with B. subtilis (p < 0.05). Germination of probiotic spores was confirmed within 6 h under all conditions. These findings suggest that B. subtilis spores selectively inhibit Listeria, particularly under nutrient stress or abuse conditions. While the probiotic had limited impact on Gram-negative pathogens, its application may serve as a clean-label strategy for suppressing L. monocytogenes in ready-to-eat (RTE) foods. This dual-model approach provides insights into both mechanistic activity and practical limitations of spore probiotics in complex food matrices. Full article

Cyanobacteria are gaining significant importance as potential biocontrol agents against phytopathogenic fungi. We evaluated the inhibitory effects of a suspension of Nostoc sp. BCAC 1226 on Penicillium sp., Phytophthora sp., and Stemphylium sp. in vitro using potato dextrose agar medium. On the 7th day of incubation, Phytophthora sp. showed a reduction in colony area from 18.30 ± 1.68 to 8.55 ± 0.74 cm² (53.6% inhibition). Similarly, Penicillium sp. showed a reduction from 17.64 ± 1.46 to 8.90 ± 0.36 cm² (49.4% inhibition), and Stemphylium sp. showed a reduction from 17.76 ± 1.28 to 13.5 ± 0.73 cm² (23.7% inhibition). The inhibitory effects were more significant on the 14th day, with the growth of Phytophthora sp. further reduced to 4.9 ± 0.40 cm² (72.8% inhibition), Penicillium sp. to 5.54 ± 0.32 cm² (68.8% inhibition), and Stemphylium sp. to 8.71 ± 0.31 cm² (50.8% inhibition). These results indicate the potential antifungal activity of Nostoc sp. suspension, with the highest reduction observed in Phytophthora sp., followed by Penicillium sp. and Stemphylium sp. Future research should focus on the chemical characterization of the antifungal metabolites produced by Nostoc sp. BCAC 1226 and in vivo evaluations on economically important crops to evaluate their practical efficiency under field conditions. Full article

If lettuce is contaminated in the field, Shiga toxin-producing E. coli (STEC) O157:H7 can survive through the distribution chain. Prolonged cold storage during transportation may impact pathogen physiology, affecting subsequent stress survival and virulence. Greenhouse-grown Romaine lettuce, inoculated with three STEC O157:H7 strains, was harvested after 24 h and stored at 2 °C for 5 d following 4 h at harvest temperature (9 °C or 17 °C). Culturable, persister, and viable but non-culturable (VBNC) cells were quantified. Virulence was evaluated using Galleria mellonella and acid tolerance at pH 2.5 and tolerance to 20–25 ppm free chlorine were quantified. Colder harvest temperature (9 °C) before cold storage led to greater transformation of STEC O157:H7 into dormant states and decreased virulence in most cases. Increasing length of cold storage led to decreased virulence and acid tolerance of STEC O157:H7 on lettuce, while having no significant effect on chlorine tolerance. These findings highlight that entry of STEC O157:H7 into dormant states during harvest and transportation at cold temperatures leads to decreased stress tolerance and virulence with increasing cold storage. Changes in STEC O157:H7 physiology on lettuce during cold storage can be integrated into risk assessment tools for producers, which can assist in identifying practices that minimize risk of STEC O157:H7 from consumption of lettuce. Full article

The escalating threats posed by plant pathogens and the environmental repercussions of conventional agrochemicals necessitate sustainable agricultural solutions. This review focuses on plant growth-promoting microorganisms (PGPMs) such as bacteria, filamentous fungi, and yeasts, which play a pivotal role as biocontrol agents. These organisms enhance plant growth and resilience through nutrient solubilization, phytohormone production, and antagonistic activities against pathogens, offering a dual benefit of disease suppression and growth enhancement. However, the effective application of PGPMs faces challenges, including variability in field performance, survival and colonization under field conditions, and regulatory hurdles. This paper discusses these challenges and explores recent advances in utilizing these bioagents in sustainable agriculture, underscoring the importance of integrated pest management systems that reduce chemical inputs, thus promoting ecological balance and sustainable farming practices. Full article

During cocoa bean fermentation, yeasts, particularly those with pectinolytic activity, contribute to pulp degradation, facilitating and accelerating fermentation. This study aimed to identify and evaluate pectinolytic yeast strains for their suitability as starter cultures in cocoa bean fermentation. A high-throughput screening of 1139 yeasts previously isolated from cocoa bean fermentations identified three strains of Wickerhamomyces pijperi with strong pectinolytic activity. These strains also reduced the viscosity of a pectin-enriched cocoa pulp simulation medium (mCPSMpc) from 23.06 ± 0.11 mPa·s (uninoculated sample) to 4.40 ± 0.14 mPa·s, 4.22 ± 0.13 mPa·s, and 4.77 ± 0.17 mPa·s after 24 h for samples inoculated with strains H312, H403, and H404, respectively. W. pijperi H403 and H404, applied in co-culture with Limosilactobacillus fermentum 223 and Saccharomyces cerevisiae H290 in 1 kg lab-scale fermentations, significantly enhanced pulp degradation, with runoff after 23.8 h reaching 12.6–13.3%, compared to 4.7% in uninoculated controls. In 20 kg fermentations in Costa Rica, the effect was less pronounced, likely due to lower inoculation rates and environmental factors. Quantitative PCR confirmed the persistence of W. pijperi H403 in fermentations. Additionally, trial cultivations in 15 L stirred-tank bioreactors successfully demonstrated the ability to produce larger biomass quantities for upscaled applications. These findings highlight W. pijperi H403 as a promising candidate for controlled cocoa fermentation, potentially accelerating biochemical changes and improving process stability. Full article

Gastrointestinal health is critical to the productivity and welfare of pigs. The transition from milk to plant-based feeds represents an intestinal challenge at wean that can result in dysbiosis and pathogen susceptibility. Prebiotic galacto-oligosaccharides (GOS) and xylo-oligosaccharides (XOS) are non-digestible carbohydrates that can reach the hind gut to promote gut health, either by enhancing the abundance of beneficial members of the intestinal microbiota or via direct interaction with the gut epithelium. Amongst the changes in the intestinal microbiota, GOS and XOS promote populations of short-chain fatty acid (SCFA)-producing bacteria of the genera Lactobacillus, Bifidobacterium and Streptococcus. SCFAs benefit the host by providing nutritional support for the gut, enhance intestinal barrier function and regulate inflammatory responses. By modifying the indigenous microbiota, prebiotics offer a sustainable alternative to the use of antimicrobial growth promoters that have led to the dissemination of antimicrobial resistance and represent a growing threat to public health. This review examines microbial and cellular mechanisms whereby prebiotic feed supplements can support the development of a diverse and robust microbiota associated with a healthy and productive digestive system over the lifetime of the animal, and which is in sharp contrast to the development of dysbiosis often associated with existing antimicrobial treatments. The application of prebiotic feed supplements should be tailored to their modes of action and the developmental challenges in production, such as the provision of GOS to late gestational sows, GOS and XOS to pre-weaning piglets and GOS and XOS to growing/fattening pigs. Full article

Vegetative compatibility groups (VCGs) in fungi like Verticillium dahliae are important for understanding genetic diversity and for informed plant disease management. This study utilized hyperspectral imagery (HSI) and machine learning to differentiate the VCGs of V. dahliae. A total of 194 isolates from VCGs 2B and 4A and 4B were cultured and imaged across the 533–1719 nm spectral range, and the spectral, textural, and morphological features were extracted. The study documented the spectral profiles of V. dahliae’s isolates and identified specific spectral features that can effectively differentiate among the VCGs. Multiple machine learning algorithms, including random forest and artificial neural networks (ANNs), were trained and evaluated on previously unseen isolates. The results showed that combining spectral, textural, and morphological data provided the highest classification accuracy. The ANN model achieved a 79.4% accuracy overall, with an 87% accuracy for VCG 2B and 88% for VCG 4A, but it had consistently low accuracies for VCG 4B. Although this work utilized only three of the nearly eight known VCGs, the findings underscore the potential of the HSI for fungal group classification. The study also highlights the need for future work to include a wider range of VCGs from multiple regions, larger sample sizes, and careful selection of feature sets to enhance model performance and generalizability. Full article

This study investigates the gut microbiome of Samia cynthia ricini, a domesticated silkworm species in Assam and Northeast India that is known for its Eri-silk production. Samples were collected at various growth stages and under different dietary conditions, generating 6341 features. The 5th instar larvae of the Eri-fed group exhibited the highest feature count, while moths from the same group had the lowest. The microbiome was characterized by 11 dominant taxa, mainly Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Notable differences were observed between larval and moth samples, with adult moths—particularly Eri-fed females—having a higher abundance of Bacteroidetes. Specific taxa such as Oscillospira, Sutterella, Succinivibrionaceae, and Prevotella were more abundant in adult moths. Eri-fed samples exhibited greater microbiome diversity, while Kesseru-fed samples were rich in Bifidobacterium. Interaction networks revealed unique species correlations in moths, including Clostridiales, Firmicutes, Gallibacterium, and Lachnospiraceae. Functional analysis highlighted diet-related differences, whereby Kesseru-fed samples showed more carbohydrate metabolism pathways, while larval microbiomes had distinct pathways for aromatic compound degradation and detoxification. Moth samples exhibited increased biosynthesis pathways, protein absorption, RNA transport, and immunogenic functions. This research enhances the understanding of microbiome dynamics in silkworms, offering insights for improved growth conditions and pest management strategies for this economically and ecologically significant species. Full article

The projected global population of 9.22 billion by 2075 necessitates sustainable food sources that provide health benefits beyond essential nutrition, as the relationship between food biochemistry and human well-being is becoming increasingly significant. Microalgae are simple microscopic organisms rich in various bioactive compounds, such as pigments, vitamins, polyunsaturated fatty acids, polysaccharides, bioactive peptides, and polyphenols, which can be used to develop novel foods with potential health benefits. Bioactive substances offer numerous health benefits, including anti-inflammatory, anticancer, antioxidant, anti-obesity, and heart-protective effects. However, incorporating microalgal biomass into functional food products presents several challenges, including species diversity, fluctuations in biomass production, factors affecting cultivation, suboptimal bioprocessing methods, inconclusive evidence regarding bioavailability and safety, and undesirable flavors and aromas in food formulations. Despite these challenges, significant opportunities exist for the future development of microalgae-derived functional food products. Extensive investigations are essential to overcome these challenges and enable the large-scale commercialization of nutritious microalgae-based food products. This review aims to examine the potential of microalgae as natural ingredients in functional food production, explore the factors limiting their industrial acceptance and utilization, and assess the safety issues associated with human consumption. Full article

Fungal infections are a major but often neglected global health challenge, affecting both human health and agricultural productivity. Current treatments are limited by few drug classes and increasing multidrug resistance, exacerbated by the widespread use of antifungal agents in clinical and agricultural settings. This study investigates the antifungal potential of a novel 8-hydroxyquinoline derivative with a triazole core at the 5-position, synthesized to improve both efficacy and mechanistic understanding as a fluorescent chemical probe. Biological assays demonstrated significant antifungal activity of compound 10 against a range of pathogens, which was active against all Candida species, dermatophytes, and Fusarium solani with MIC values ranging from 0.5 to 4 µg/mL. Confocal fluorescence microscopy of treated fungal cells was conducted and showed a high accumulation of compound 10 at the cell edge. To further investigate the mode of action, results from a sorbitol protection assay suggested a possible cell wall action, and scanning electron microscopy (SEM) revealed cell wall disruption, such as cell shrinkage and surface roughness, in treated fungal cells. These findings highlight the 8-hydroxyquinoline-triazole scaffold as a promising antifungal agent with cell wall damage properties, providing a basis for future therapeutic development against human and plant fungal pathogens. Full article

Microalgae are the primary producers in aquatic ecosystems, while simultaneously playing a vital role in various industrial sectors. Despite their significant ecological and bioeconomic importance, the impacts of oxidative stress on their populations remain poorly understood. In this mini-review, we summarize recent advancements in understanding oxidative stress modulation in microalgae, with a focus on responses to climate change-related stressors. Additionally, we compare the valuable insights obtained from multi-omics studies on specific biochemical pathways and genes, correlating the responses and mechanisms by which microalgae respond to oxidative stress among different species. Full article

There are approximately 130 reported medicinal effects attributed to mushrooms. We investigated the anti-inflammatory effects of hot-water extracts of 66 wild and cultivated fungi species (both edible and poisonous) by analyzing the inhibition of platelet aggregation and interleukin-8 (IL-8) gene expression induced by sodium arachidonate (A-Na), platelet-aggregating factor (PAF), and adenosine diphosphate (ADP). All species exhibited inhibitory effects: 38.3–98.1%, 37.3–96.8%, and 41.0–96.6% species inhibited platelet aggregation induced by A-Na, PAF, and ADP, respectively, while 17.0–97.0% inhibited IL-8 expression. Gyromitra esculenta showed the highest inhibition rate in all assays. High inhibition (≥80%) of A-Na-, PAF-, and ADP-induced platelet aggregation was observed in 29 (43.9%), 29 (43.9%) and 31 (47.0%) species, respectively. Half (33) of the species exhibited high inhibition of IL-8 expression. Four (6.1%), five (7.6%), and seven (10.6%) species exhibited inhibition rates of <50% for A-Na-, PAF-, and ADP-induced platelet aggregation, while nine (13.6%) exhibited low inhibition of IL-8 expression. The majority (87.5–100%) of poisonous species exhibited high inhibition. Our findings suggest that anti-inflammatory effects are universal among fungi, with poisonous species showing particular potential as raw materials for drug discovery. It can be inferred that many fungi contain universal or pleiotropic compounds with anti-inflammatory activities. Full article

The COVID-19 pandemic has underscored the need for efficient and non-invasive diagnostic tools for early detection and management. This study evaluated the TERA breath analyzer (TERA.Bio^®), a Real-Time High-Throughput Breathalyzer, for SARS-CoV-2 detection. It aimed to validate and implement the TERA.Bio^® for the detection of SARS-CoV-2 within a university population compared to RT-qPCR testing. Conducted at the University of Miami, this observational study consisted of two phases: a validation phase and a longitudinal monitoring phase, using cross-sectional and prospective cohort designs, respectively. Participants, including symptomatic individuals and those in close contact with confirmed cases, underwent simultaneous testing with the TERA.Bio^® and mid-nasal swab RT-qPCR tests. The study evaluated TERA.Bio^®’s accuracy, sensitivity, specificity, and its role for surveillance. A total of 27,445 breath samples were analyzed through the TERA.Bio^®. In the validation phase, the TERA.Bio^® demonstrated a sensitivity of 64% and a specificity of 85.1%. Longitudinal monitoring revealed no significant correlation between unclear TERA.Bio^® results and smoking status. The TERA.Bio^® is a viable tool for COVID-19 screening in university environments, providing rapid, cost-effective, apt extensive screening and monitoring in a dense academic setting. Its non-invasive nature, high throughput, and electronic health system compatibility make it an essential addition to existing COVID-19 diagnostic strategies. This study highlights the critical role of innovative diagnostic tools in pandemic management and suggests potential applications of TERA.Bio^® technology in broader public health scenarios. Full article