Applied Microbiology

Schizophrenia is a complex psychiatric disorder traditionally linked to neurotransmitter dysregulation, particularly within dopamine and glutamate pathways. However, recent evidence implicates the gut–brain axis as a potential contributor to its pathophysiology. This perspective article proposes a systems-level understanding of schizophrenia that incorporates the role of gut microbial dysbiosis specifically, reductions in short-chain fatty acid (SCFA)-producing taxa, and elevations in pro-inflammatory microbes. These imbalances may compromise gut barrier integrity, stimulate systemic inflammation, and disrupt neurochemical signaling in the brain. We synthesize findings from animal models, clinical cohorts, and microbial intervention trials, highlighting mechanisms such as SCFA regulation, altered tryptophan–kynurenine metabolism, and microbial impacts on neurotransmitters. We also explore microbiome-targeted interventions like probiotics, prebiotics, dietary strategies, and fecal microbiota transplantation (FMT) and their potential as adjunctive therapies. While challenges remain in causality and translation, integrating gut–brain axis insights may support more personalized and biologically informed models of schizophrenia care. Full article

Alkalihalophilus marmarensis is an obligate alkaliphile with exceptional tolerance to high-pH environments, making it a promising candidate for industrial bioprocesses that require contamination-resistant and extremophilic production platforms. However, its practical deployment is hindered by limited biomass formation under extreme conditions, which constrains overall productivity. This study presents a model-driven investigation of how pH (8.8 and 10.5), culture duration (24 and 48 h), and nitrogen source composition (peptone and meat extract) affect cell dry mass, lactate, and protease synthesis. Using the response surface methodology and multi-objective optimization, we established predictive models (R² up to 0.92) and uncovered key trade-offs in biomass and metabolite yields. Our findings reveal that peptone concentration critically shapes the metabolic output, with low levels inhibiting growth and high levels suppressing protease activity. Maximum cell dry mass (4.5 g/L), lactate (19.3 g/L), and protease activity (43.5 U/mL) were achieved under distinct conditions, highlighting the potential for targeted process tuning. While the model validation confirmed predictions for lactate, deviations in cell dry mass and protease outputs underscore the complexity of growth–product interdependencies under nutrient-limited regimes. This work delivers a foundational framework for developing fermentations with A. marmarensis and advancing its application in sustainable, high-pH industrial bioprocesses. The insights gained here can be further leveraged through synthetic biology and bioprocess engineering to fully exploit the metabolic potential of obligate alkaliphiles like A. marmarensis. Full article

Anaerobes, the oldest evolutionary life forms, have been unexplored for their potential to produce secondary metabolites due to the difficulties observed in their cultivation. Antimicrobials derived from anaerobic bacteria are an emerging and valuable source of novel therapeutic agents. The urgent need for new antimicrobial agents due to rising antibiotic resistance has prompted an investigation into anaerobic bacteria. The conventional method of antimicrobial discovery is based on cultivation and extraction methods. Antibacterial and antifungal substances are produced by anaerobic bacteria, but reports are limited due to oxygen-deficient growth requirements. The genome mining approach revealed the presence of biosynthetic gene clusters involved in various antimicrobial compound synthesis. Thus, the current review is focused on antimicrobials derived from anaerobes to unravel the potential of anaerobic bacteria as an emerging valuable source of therapeutic agents. These substances frequently consist of peptides, lipopeptides, and other secondary metabolites. Many of these antimicrobials have distinct modes of action that may be able to go around established resistance pathways. To this effect, we discuss diverse antimicrobial compounds produced by anaerobic bacteria, their biosynthesis, heterologous production, and activity. The findings suggest that anaerobic bacteria harbor significant biosynthetic potential, warranting further exploration through recombinant production for developing new antibiotics. Full article

This exploratory study presents the first metagenomic assessment of the gut microbiome in domestic cats from Cali, Colombia. Fecal samples were collected from 10 healthy, sterilized domestic cats, aged 8 months to over 2 years, with variation in sex (7 females, 3 males), diet (processed or raw), and outdoor access (5 with, 5 without). Using 16S rRNA gene metabarcoding and pooled shotgun metagenomic sequencing, the study characterized the taxonomic composition and functional potential of the feline gut microbiome. Dominant phyla included Bacillota and Bacteroidota, with substantial inter-individual variation. Peptoclostridium was the most consistently abundant genus, while Megamonas and Megasphaera showed higher variability. Shotgun analysis detected antibiotic resistance genes (ErmG, ErmQ) and virulence factors (pfoA, plc, colA, nanJ, nagI) in Clostridium perfringens, highlighting potential zoonotic risk. The composition of the gut microbiota was influenced primarily by diet and outdoor access, while age and gender had more moderate effects. The study concludes that lifestyle and environmental factors play a key role in shaping the gut microbiome of domestic cats. We recommend further longitudinal and larger-scale studies to better understand the dynamics of feline microbiota and their implications for animal and public health within a One Health framework. Full article

Fruit rot seriously damages pomelo production. Given concerns regarding the safety of chemical agents, biological alternatives are becoming more preferable. Therefore, the experiment aimed to (i) identify the pathogens causing pomelo fruit rot disease and (ii) select Trichoderma spp. strains controlling the determined pathogens in Ben Tre, Vietnam. Three pathogenic fungal strains isolated from diseased pomelo fruits were selected. The three pathogenic fungal strains were randomly injected into 9 healthy pomelo fruits. The strain PCP-B02-A2 led to a completely rotten fruit on day 17 after infection, while strains PCP-B02-B2 and PCP-B03-A1 had infected spots whose lengths were 17.5 and 28.1 mm, became larger, and eventually led to the whole fruit rot. The pathogens were identified by the internal transcribed spacer (ITS) technique as Colletotrichum gloeosporioides PCP-B02-A2, Pseudopestalotiopsis camelliae sinensis PCP-B03-A1, and P. chinensis PCP-B02-B2. Twenty-five Trichoderma spp. strains were isolated. The ITS technique identified four strains, including Trichoderma asperellum TP-B01, T. harzianum TP-B08, T. harzianum TP-B09, and T. asperellum TP-C25. The PCP-B02-A2 strain had antagonism at 66.7–68.7%, while those of PCP-B02-B2 and PCP-B03-A1 were 64.2–71.1% and 55.7–57.4%, respectively. Full article

Cheese ripening involves microbial changes, with starter lactic acid bacteria (SLAB) initiating fermentation and nonstarter lactic acid bacteria (NSLAB) driving flavor and texture development. However, heat-resistant spores of Clostridium and Bacillus can survive pasteurization and cause spoilage during ripening. This study evaluated NSLAB dynamics in the presence of spores during cheese ripening. Cheddar cheese samples at pilot-scale level (110 L) with four treatments, namely control, with spores of B. licheniformis (T1), with spores of Cl. tyrobutyricum (T2), and both spores (T3) at 2.0 Log₁₀ CFU/mL, were ripened at 7 °C for six months. SLAB declined from 8.0 to 0.2 Log₁₀ CFU/g, while NSLAB increased from 2.0 to 8.5 Log₁₀ CFU/g by month three and maintained their counts up to six months, unaffected by spore presence. Spore counts were ≤1.45 Log₁₀ CFU/g in controls but reached 2.94 ± 0.02 (T2) and 2.48 ± 0.03 (T3), correlating with spoilage signs after five months. MALDI-TOF identified L. rhamnosus (up to 37%) and L. paracasei (up to 25%) as dominant NSLAB across treatments. Physicochemical parameters were not significantly affected by higher spore levels. While NSLAB dominated, they were inadequate to prevent spoilage in spore-inoculated samples exceeding 2.0 logs during cheese ripening. Full article

A key feature that differentiates Gram-positive and Gram-negative bacteria is the outer membrane, an asymmetric membrane composed of lipopolysaccharides, phospholipids, lipoproteins and integral proteins, including the outer-membrane proteins (OMPs). By being in direct contact with the extracellular milieu, the outer membrane and OMPs participate in multiple functions in Gram-negative bacteria, including controlling nutrient and molecule access to the cytoplasm, membrane vesicle formation and resistance to environmental stresses. OMPs have a characteristic barrel shape formed by antiparallel β-strands, with or without channels that allow diffusion of substrates through the outer membrane. The marine bacterium Vibrio cholerae is responsible for non-invasive gastroenteritis and cholera disease by consumption of contaminated water or food. Its OMPs, besides having a porin function, contribute to resistance to osmotic pressure and antimicrobial agents, intracellular signaling, adhesion to host cells and biofilm formation, amongst other functions. In this review, in addition to quickly reviewing the general structure of the outer membrane, the OMPs and how they reach the outer membrane, the functions attributed to these proteins are compiled. The mechanisms used by each of the described OMP to accomplish these functions in the marine pathogenic bacterium V. cholerae are discussed. Potential clinical and bioengineering applications of OMPs, such as diagnostic tools, vaccine development, and targeted antimicrobial or anti-virulence strategies are presented. What is known about the OMPs of V. cholerae is presented below. Full article

Antimicrobial use in food animals selects for antimicrobial-resistant (AMR) bacteria, which most commonly reach humans via the food chain. However, AMR bacteria can also escape the feedyard via agricultural runoff, manure used as crop fertilizer, and even dust. A study published in 2015 reported AMR genes in dust from cattle feedyards; however, one of the study’s major limitations was the failure to investigate gene presence in viable bacteria, or more importantly, viable bacteria of importance to human health. Our main objective was to investigate the presence and quantity of viable bacteria and antimicrobial-resistant (AMR) determinants in fugitive bioaerosols from cattle feedyards in the downwind environment. Six bioaerosol sampling campaigns were conducted at three commercial beef cattle feedyards to assess variability in viable bacteria and AMR determinants associated with geographic location, meteorological conditions, and season. Dust samples were collected using four different sampling methods, and spiral plated in triplicate on both non-selective and antibiotic-selective media. Colonies of total aerobic bacteria, Enterococcus spp., Salmonella enterica, and Escherichia coli were enumerated. Viable bacteria, including AMR bacteria, were identified in dust from cattle feedyards. Bacteria and antimicrobial resistance genes (ARGs via qPCR) were mainly found in downwind samples. Total suspended particles (TSPs) and impinger samples yielded the highest bacterial counts. Genes encoding beta-lactam resistance (bla_CMY-2 and bla_CTX-M) were detected while the most common ARG was tet(M). The predominant Salmonella serovar identified was Lubbock. Further research is needed to assess how far viable AMR bacteria can travel in the ambient environment downwind from cattle feedyards, to model potential public health risks. Full article

The EAT-Lancet diet is an outstanding model of a healthy, environmentally sustainable diet. However, its effects on the gut microbiota remain poorly explored. This study assessed the asso-ciation between adherence to the EAT-Lancet diet in habitual intake and the relative abundance of selected gut bacteria in a Mexican subpopulation. Fifty-four young adults (18–35 years) completed a validated Food Frequency Questionnaire (FFQ) and were nutritionally assessed. Participants were grouped into low, moderate, and high adherence levels to the EAT-Lancet diet. Blood samples were analysed for glucose and lipid profiles, and gDNA from faecal samples was analysed using Real-time qPCR to quantify gut bacteria. While no significant differences in bacterial abundance were observed across adherence levels, correlations emerged with increased adherence. Notably, Bifidobacterium negatively correlated with beef and lamb intake (rho −0.5, p < 0.05), and Akkermansia muciniphila negatively correlated with fish intake (rho −0.8, p < 0.05). Bilophila wadsworthia positively correlated with triglycerides, while Prevotella copri and Faecalibacterium prausnitzii negatively correlated with body fat and blood pressure, respectively. In addition, a non-significant trend toward a higher abundance of Firmicutes, Akkermansia muciniphila, and Prevotella copri was observed in the high-adherence group, whereas Lactobacillus tended to be more abundant in participants with low and moderate adherence. These findings suggest that adherence to the EAT-Lancet diet modulates gut microbiota composition. However, further controlled interventional studies are needed to confirm these effects and their implications for human health. Full article

The growing threat of antibiotic-resistant Gram-negative bacteria highlights the urgent need for innovative, non-bactericidal therapeutic strategies. Quorum-sensing (QS) inhibition has emerged as a promising approach to attenuate bacterial virulence without exerting selective pressure. This study evaluated the antimicrobial, anti-QS, and antibiofilm properties of aqueous extracts from five medicinal plants native to northeastern Mexico: Gymnosperma glutinosum, Ibervillea sonorae, Larrea tridentata, Olea europaea, and Tecoma stans. Disk diffusion and violacein quantification assays using Chromobacterium violaceum demonstrated significant QS inhibition by G. glutinosum and T. stans, with violacein reductions of 60.02% and 52.72%, respectively, at 40 mg/mL. While L. tridentata and O. europaea exhibited antibacterial activity, I. sonorae showed no growth or pigment inhibition but achieved the highest biofilm disruption (89.89%) against Salmonella typhimurium. UPLC-MS analysis identified chlorogenic acid, kaempferol, and D-(−)-quinic acid as major constituents, compounds previously associated with QS modulation. These findings highlight the potential of traditional Mexican plant species as sources of QS inhibitors and bio-film-disrupting agents, supporting their further development as alternatives to conventional antibiotics. Full article

The whole-genome sequencing of lactic acid bacteria provides a valuable resource for identifying the genetic determinants underlying molecular mechanisms related to their probiotic properties. Analysis of draft genome sequences relies on bioinformatics tools for genetic data processing and in silico analytical methods to pinpoint the genetic determinants encoding biologically active compounds. The aim of this study was to perform the phenotypic determination of the antibiotic sensitivity and bioinformatics analyses on whole-genome assemblies from LAB from the human oral microbiome, and determine the presence of acquired antibiotic resistance genes, peptidases, adhesion proteins, and bacteriocins. Bioinformatics processing was performed in order to establish the molecular mechanisms responsible for the previously observed probiotic properties. The tested LAB strains exhibited a broad spectrum of antibiotic multiresistance, but did not possess acquired antibiotic resistance genes. The detected genes for peptidase activity were from the Pep family of hydrolase enzymes. Genetic determinants for adhesion proteins contained LPxTG, YSIRK, KxYKxGKxW, and SEC 10/PgrA domains, as well as MucBP domains. Lectins were found for five of the strains with the presence of WxL domains from the CscC protein family and L-type lectin domains. The in silico analyses show that some of the tested strains possessed mechanisms for bacteriocin production. Full article

Background: Clinical features of asthma are associated with differences in the lower airway microbiome. However, knowledge is limited on whether airway microbiota composition differs between individuals residing in different geographic regions and if asthma-associated differences in lower airway microbiota are similar between distinct populations. Methods: Existing 16S rRNA gene sequence data, generated from sputum collected from adults with or without asthma (n = 74) from two single-center cohort studies in the U.S. and United Arab Emirates, were re-processed for merged computational analysis using standard available tools. Potential differences between study sites, asthma status and specific clinical factors (inhaled corticosteroid use, ICS; obesity) were examined. Results: Differences in sputum bacterial composition, assessed by alpha- and beta-diversity measures, were associated with study site. Despite this, asthma-related differences were discerned in both cohorts. Specifically, sputum microbiota of asthmatic patients on ICS treatment displayed reduced bacterial phylogenetic diversity, compared to those not on ICS treatment (p = 0.006). Sputum bacterial composition also differed by obesity status (unweighted Unifrac distance PERMANOVA, p = 0.004). Specific genera were identified in both cohorts that were differentially enriched between obese vs. non-obese subjects, including Rothia and Veillonella (obesity-associated) and Campylobacter (non-obesity-associated). Conclusions: Our findings suggest clinical factors associated with differences in the lower airway microbiome in asthma may transcend variation related to geographic area of residence. Full article

E. coli attaches to, and forms biofilms on various surfaces, including latex and polystyrene, contributing to nosocomial spread. E. coli responds to both exogenous and endogenous insulin, which induces behavioral changes. Human insulin, a quorum signal surrogate for microbial insulin, may affect the ability of E. coli to interact with latex and polystyrene in the presence of various sugars. E. coli ATCC 25923 was grown in peptone (1%) yeast nitrogen base broth to either the logarithmic or stationary growth phase. Adherence to latex was determined using 6 × 6 mm latex squares placed in a suspension of washed cells (10³ CFU/mL; 30 min; 37 °C) in buffer containing insulin at 2, 20, and 200 µU/mL (Humulin^® R; Lilly) with and without mannose, galactose, fructose, sorbose, arabinose, xylose, lactose, maltose, melibiose, glucose-6-phosphate, glucose-1-phosphate, and glucosamine at concentrations reported to affect behavioral response. Attachment levels to latex were determined by the press plate method. Biofilm levels were measured in a similar fashion but with overnight cultures in flat bottom uncoated polystyrene plates. Controls were media, insulin, sugar, or buffer alone. Glucose served as the positive control. Overall, the stationary phase cells’ adherence to latex was greater, regardless of the test condition, than was measured for the logarithmic phase cells. The effect of insulin on adherence to latex was insulin and sugar concentration dependent. The addition of insulin (200 µU/mL) resulted in a significantly (p < 0.05) increased adherence to latex and biofilm formation on polystyrene compared with sugar alone for 12 of the 13 sugars tested with stationary phase bacteria and 10 of the 13 sugars tested with logarithmic phase bacteria. Adherence in response to sorbose was the only sugar tested that was unaffected by insulin. These findings show that insulin enhances E. coli’s association with materials in common usage in medical environments in a nutrition-dependent manner. Full article

Overuse of antibiotics is a concern in ‘culture-negative sepsis’ but it is unclear whether this is due to infection with viruses, fungi or other microbes that are not easily cultured, or whether it results from inflammatory processes. In a prospective study, we enrolled 50 preterm neonates with culture-positive sepsis (CP), culture-negative sepsis (CN), and asymptomatic preterm controls (CO). The microbiome of stool, skin, and blood, including bacterial, viral and fungal components and serum cytokine profiles were evaluated. The microbiome alpha or beta diversity did not differ between CN and CO groups. A MaAsLin analysis revealed increased relative abundances of specific bacterial and fungal genera in stool and skin samples in the CN group compared to CO. The virome analysis identified 24 viruses from skin samples, but they were not statistically different among the three groups. The cytokine and chemokine biomarker profiles were elevated in the CP group but were not statistically different between the CN and CO groups. Although the CN group had a longer hospital stay and higher BPD rates than the controls in unadjusted analyses, these differences were not significant after adjusting for gestational age and birth weight. The CN infants demonstrated microbial shifts without systemic immune activation or significantly worse clinical outcomes, supporting the rationale for discontinuing antibiotics in the absence of positive cultures. Full article

The rumen microbiome impacts beef cattle feed efficiency, a key economic factor in production systems. This study investigated the rumen microbiome of Charolais bulls with divergent residual feed intake-expected progeny difference (RFI-EPD) values to identify microbial taxa associated with feed efficiency. Forty Charolais bulls were evaluated for feed intake and growth over 60 days, and RFI values were determined. The 10 most efficient (NegRFI) and 10 least efficient (PosRFI) bulls were selected for microbiome analysis. Rumen fluid samples were collected and analyzed via 16S rRNA gene sequencing. Microbial analysis revealed no significant differences in alpha or beta diversity between groups, but differential abundance analysis identified 20 operational taxonomic units (OTUs) as more prevalent in NegRFI bulls, while 15 OTUs were more abundant in PosRFI bulls. Two OTUs from the key genus Prevotella showed different relative abundances in the two RFI-EPD groups. NegRFI bulls had a higher relative abundance of Prevotella OTU 109358, while PosRFI bulls had more Prevotella OTU 626329. Additionally, OTUs from Ruminococcus, a genus involved in fiber degradation and volatile fatty acid (VFA) production, were more abundant in NegRFI bulls. In contrast, PosRFI bulls had a higher abundance of OTUs from Oscillospira and F16, both linked to butyrate production. The results of this study support the need for further exploration into the role of microbial taxa associated with feed efficiency. A deeper understanding of the functional profile of the microbiota could aid in the development of microbiome-informed strategies to enhance nutrient utilization and performance in beef cattle. Full article

Significant heavy metals contamination is often caused by rapid industrialization, which is devastating to both public health and the environment. Conventional processes of metal removal also result in the accumulation of secondary waste. This work proposes the use of a novel fungal biomass (microwave heat dried) from Arthrinium malaysianum for the biosorption of toxic chromium. We have meticulously explored and investigated the interactions of hexavalent chromium with dried biomass using several cutting-edge techniques like FTIR for studying the involvement of functional groups on the biomass surface, XRD for the surface architecture changes after metal binding, XPS to unravel the reduction of hexavalent chromium into its non-toxic form, and FESEM-EDX for the visualization of the ultra-structure of fungal cell surface. The Langmuir isotherm demonstrates that the maximum removal capacity Q_max of Cr(VI) is 102.310 mgg⁻¹, at a pH of 3.5 with 100% removal of Cr(VI). There were substantial changes in the surface architecture during adsorption, confirmed by FESEM and AFM studies. FTIR and XPS data analysis indicated that carbonyl, hydroxyl, phosphate, and amine groups were responsible for the conversion of Cr(VI) (toxic) to Cr(III) (non-toxic). The IR spectra of biomass treated with Cr showed a decreased C-O stretching intensity and slight shriveling of the -OH band, and the bands in the FTIR spectra at 1642 cm⁻¹ to 1635 cm⁻¹ and at 1549 cm⁻¹ to 1547 cm⁻¹ shifted and appeared quite distinct. XRD revealed that the chromium-treated biomass had greater crystalline features and also the appearance of a wide peak where 2θ = 20°, approximately, indicating an amorphous nature at 576.0 eV and in highly loaded chromium (500 mg/L) biomass, with the Cr2p level displaying a slight shift, eventually terminating in a (576.0 eV) Cr₂O₃ to Cr(III) peak. Since the FTIR and XPS data obtained revealed that Cr(VI) reduces to Cr(III), this fungal biomass can also be used for generating metallic nanoparticles during biosorption. Thus, we suggest that the above-mentioned fungal biomass could be a very useful biomaterial for future translational research. We are in the process of fabricating beads with powdered biomass for further studies. Full article

In this study, pigment-producing yeast (Rhodotorula alborubescens) was isolated from the soil sample, demonstrating the potential for carotenoid biosynthesis. Physiological, morphological, biochemical, and molecular characterization confirmed the identity of the isolate. Optimization of the physical parameters for carotenoid production was achieved through batch shake flask experiments. The optimal conditions were determined to be 84 h of incubation at pH 6.0 and 28 °C under white light irradiation, utilizing the Yeast Peptone Dextrose (YPD) medium composed of 10 g/L yeast extract, 5 g/L of peptone, and 5 g/L dextrose, resulting in maximum carotenoid content. Further, the presence of β-carotene was confirmed using High-Performance Liquid Chromatography and Fourier Transform Infrared Spectroscopy. These findings highlight the potential of the isolated soil yeast (R. alborubescens) as a potential source of carotenoids, offering natural alternatives for various industrial applications. Full article

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