[object Object], [object Object], [object Object] et al.

Hygiene • 2026

The process of ensuring the safety of the food supply is dynamic. Both the possibility of contamination and the effectiveness of safety precautions are impacted by changes in the kinds of food consumed, the geographical origins of food products, and the methods by which these foods are processed. For instance, compared to earlier generations, consumers’ general understanding of safe food preparation and handling techniques has decreased due to a higher reliance on prepackaged convenience foods. Nowadays, consumers depend increasingly on other people to make sure the food they eat is safe. Growing consumption of minimally processed foods and growing imports of fresh products from other nations have resulted from changes in consumer tastes and food processing technologies. This review aims to critically synthesize existing knowledge on microbial risks in food, focusing on their sources, mechanisms of contamination, risk evaluation methodologies, and implementation of food safety measures. Major foodborne pathogens, including Salmonella, Escherichia coli, Listeria monocytogenes, and Norovirus, are discussed alongside factors influencing their survival and transmission. Today Clostridium botulinum, Staphylococcus aureus, and Salmonella spp. remain among the major foodborne pathogens, but during the last two decades food-borne diseases such as shigellosis, listeriosis, campylobacteriosis, and diseases caused by pathogenic strains of Escherichia coli have become increasingly salient. These new concerns necessitate continued investment in research and technology development to improve the safety of the food supply. The review highlights current approaches to microbiological risk assessment, regulatory frameworks, and control strategies, while also addressing emerging challenges such as antimicrobial resistance, biofilms, and ready-to-eat foods. By integrating risk evaluation with practical implementation strategies, this review provides valuable insights for researchers, regulators, and food industry stakeholders seeking to strengthen food safety systems and reduce the burden of foodborne diseases.

[object Object], [object Object], [object Object] et al.

bioRxiv (Cold Spring Harbor Laboratory) • 2026

Poorly soluble lanthanide minerals pose challenges for both a sustainable extraction of lanthanides as key resources for decarbonization and lanthanide-dependent microbial metabolism. Microbial use of lanthanides is widespread, yet bacteria's preference for light lanthanides requires differentiation mechanisms that enable downstream utilization. Whether lanthanide discrimination occurs during access, mobilization, uptake, or intracellular processing is mostly unknown and likely controlled by habitat and bioavailability. We studied microbial lanthanide mobilization and uptake from different lanthanide minerals, an alloy, and pure lanthanide compounds. Beijerinckiaceae bacterium RH AL1 served as a model organism for an integrated approach combining transcriptomics, analytics, and electron microscopy. This facultative methylotroph depends on light lanthanides for methanol oxidation and forms periplasmic lanthanide deposits. AL1 grew with all tested lanthanide sources and selectively enriched light lanthanides independent of source type, overall lanthanide content, and the proportion of light lanthanides. Transcriptomics revealed that the type of lanthanide source significantly influenced gene expression beyond lanthanide utilization. Lanthanide discrimination in Beijerinckiaceae bacterium RH AL1 is a multilayered process rooted in the complementary action of chelation, uptake mechanisms, and periplasmic storage. Adaptations that increase lanthanide bioavailability transform mineral-bound lanthanides into shared resources within microbial communities, with implications for sustainable lanthanide use.

[object Object], [object Object], [object Object] et al.

Innovaciencia • 2026

Introduction. Tejuino is an artisanal Mexican fermented corn beverage with limited shelf life, challenging industrial production. Research on microbial safety methods remains scarce despite their cultural importance. Objectives. This study aimed to evaluate the impact of Ultrasound-assisted thermal processing (USTP) on microbial safety and physicochemical properties on tejuino beverage. Materials and Methods. Commercial tejuino samples (200mL) underwent ultrasonic treatment at 0.5 kJ/mL at 20 °C, followed by thermal treatment at 45-65°C (USTP– USTP 65). Fresh, pasteurized (65°C/30 min), and ultrasound-treated samples served as controls. Analyses included microbiological [aerobic mesophilic bacteria (AMB), coliform bacteria (CB), molds and yeasts (MY), lactic acid bacteria (LAB)] and physicochemical parameters (pH, acidity, soluble solids, browning index, density, viscosity, conductivity, turbidity, color), as well as antioxidants [total soluble phenols (TSP), DPPH, ABTS, FRAP]. Results. AMB, CB, and MY counts decreased under USTP treatments while maintaining substantial LAB concentrations in a temperature-dependent response (USTP45–USTP65) compared to controls. All physicochemical properties except density were altered by USTP treatments in a temperature-dependent manner compared to fresh control. USTP45, USTP50, and USTP55 treatments showed similar TSP content and antioxidant activity by DPPH and ABTS compared to ultrasound-treated and fresh controls, while FRAP values decreased significantly in temperatures of 50°C. Conclusions. The ultrasound-assisted thermal processing can be a viable alternative for the industrial manufacturing of tejuino.

[object Object], [object Object], [object Object] et al.

Biology of Sex Differences • 2026

Abstract Background Parkinson’s disease (PD) is a neurodegenerative disorder with established sex differences in incidence and progression. Epidemiological evidence suggests nicotine may confer protection against PD, but its mechanisms, particularly regarding sex-specific effects, remain unclear. This study investigated the neuroprotective mechanisms of nicotine in a rotenone-induced PD rat model, with a specific focus on evaluating sex-dependent modulation across behavioral, pathological, and gut-related outcomes. Methods Male and female Sprague-Dawley rats were administered rotenone (2 mg/kg/day, s.c.) for four weeks to induce PD. Nicotine (0.5 mg/kg/day, s.c.) was administered 30 min after rotenone. Motor function was assessed using rotarod and CatWalk XT gait analysis. Neuropathology in the substantia nigra was evaluated via immunofluorescence for α-synuclein and tyrosine hydroxylase (TH). Gut pathology was analyzed through colon histopathology (H E staining) and ELISA for IL-6 and α-synuclein. Gut microbiota composition was assessed by 16 S rDNA sequencing, and serum metabolomics was performed using UPLC-MS/MS. Data were analyzed by two-way ANOVA with Tukey’s post-hoc test. Results Nicotine significantly attenuated rotenone-induced motor impairments: males showed a superior response in balance-related parameters, while females exhibited enhanced efficacy in dynamic gait metrics. Pathologically, nicotine reduced nigral α-synuclein accumulation and TH depletion in both sexes, with males showing greater α-synuclein accumulation following rotenone exposure. Crucially, nicotine exclusively ameliorated colon histopathology, reduced plasma α-synuclein, and suppressed colon IL-6 in females, while attenuating intestinal α-synuclein accumulation in both sexes. Microbiota analysis revealed sex-divergent taxonomic shifts with nicotine treatment. Metabolomics showed significantly more extensive metabolic reprogramming in females, particularly affecting indole derivatives. Pearson correlations revealed significant sex-specific associations between altered serum indole derivatives and gut microbiota genera. Conclusions Nicotine exerts neuroprotection in PD through sex-dependent modulation of multiple pathological pathways, primarily involving the gut-microbiota-metabolite axis. Females benefit from enhanced gastrointestinal protection and metabolic reprogramming, while males show preferential motor balance restoration. These findings underscore the critical importance of sex-stratified therapeutic strategies for PD.

[object Object], [object Object], [object Object] et al.

Journal of Science Innovation and Technology Research • 2026

This study focused on determining the Impact of some herbicides (glyphosate and butachlor) on soil physiochemical properties and microbial population in Mubi, Adamawa State, Nigeria. A field study was carried out from April to October 2025 in the research farm of Adamawa University Mubi. Two (2) different herbicides that include: butachlor, and glyphosate each at four different concentrations were used. The soil sample was collected prior and after application of the different concentrations of the two herbicides at two weeks interval and physiochemical properties using a standard procedures were analyzed. The results revealed that butachlor, and glyphosate  treated soils had no significant effect on most of the physiochemical properties of the soil sample at 0, 2, 4 and 6 weeks after treatment (WAT). A total of eight (8) fungal species, eight (8) Gram positive bacteria, and ten (10) Gram negative bacteria were identified in the treated soils. The concentration of the two different herbicides were found to only have a significant effect on the bacterial population. The 0, 2, 4 and 6 WAT sampling periods, however, had significant effects on both the bacterial and fungal populations. The study concluded that the two herbicides used at different concentrations had no significant effect on most of the physiochemical properties of the soils sampled analyzed at 0, 2, 4 and 6 WAT with the presence of fungi species, and Gram negative and positive bacteria. The herbicides had significant effect with soil sampled at 0 WAT having higher population than 2, 4 and 6 WAT prospectively.

[object Object], [object Object], [object Object]

BMC Biotechnology • 2026

Abstract Background Rising demand for rare earth elements (REEs) and the severe environmental impact of conventional extraction from phosphate minerals (monazite, apatite) have intensified the search for green alternatives. Microbial bioleaching offers a low-energy, low-waste, and a sustainable biotechnological alternative by exploiting the ability of fungi and bacteria to generate organic acids, siderophores, reducing agents, and other metabolites that solubilize REEs. Although interest in REE bioleaching has increased, a biotechnology-focused synthesis of microbial mechanisms, metabolic constraints, and process determinants specific to phosphate matrices remains limited. Methods A PRISMA-guided systematic review was conducted. Scopus, Web of Science, PubMed, and Google Scholar and other major databases were searched to identify peer-reviewed studies reporting microbial bioleaching of REEs from phosphate minerals. From 443 identified records, 25 studies met the inclusion criteria after screening and eligibility assessment. These studies were evaluated based on microbial species, metabolic mechanisms, culture conditions, mineral substrates, and REE solubilization performance. Results Fungal species, particularly Aspergillus , Penicillium and Paecilomyces demonstrated the highest REE mobilization efficiencies through intensive production of citric, oxalic, and gluconic acids, along with phosphatase activity. Bacterial strains, including Acidithiobacillus , Bacillus , Pantoea , Burkholderia , Pseudomonas , and Klebsiella contributed complementary mechanisms such as proton extrusion, siderophore secretion, and Fe(III) / Fe(II) redox cycling. Bioleaching performance was strongly influenced by media composition, carbon source, nitrogen assimilation, pH evolution, mineralogy of the phosphate substrate, pulp density, and particle size. Across studies, the lack of standardized conditions limited direct comparability, but organic acid dominated pathways consistently produced the most robust REE solubilization. Conclusions Microbial bioleaching is a promising biotechnological platform for REE recovery from phosphate minerals, driven by metabolically diverse acidogenic, chelating, enzymatic, and redox mechanisms. However, advancements remain constrained by heterogeneous methodologies, limited integration of mechanistic studies, and minimal use of engineered strains or controlled bioreactor systems. Future progress requires standardized experimental frameworks, improved mechanistic understanding of organism-specific roles, and rational design of optimized microbial systems. This review offers a biotechnology-centered foundation to guide next-generation research on sustainable REE mobilization from phosphate resources.

[object Object], [object Object], [object Object] et al.

Research Square • 2026

Abstract Allergen immunotherapy directly addresses the biological cause of allergies like those causing asthma. For perennial allergies, the treatment involves exposure to house dust mite (HDM) extracts that aim to block T helper 2 responses. Here, we investigate whether exposure to HDM extracts affects other aspects of innate host defenses against infection using the Drosophila genetic model organism. We find that pre-treatment of flies with HDM extract injection provides a degree of protection against several types of microbial infections, namely Gram-negative and Gram-positive bacterial infections as well as fungal infections. Interestingly, this protection appears to be achieved through distinct mechanisms. The priming afforded by HDM extracts against Gram-negative bacteria is mediated via a mild induction of the Immune deficiency pathway. In contrast, the protection against a Gram-positive bacterium, Staphylococcus aureus , and some Aspergillus fumigatus mycotoxins may involve the induction of host anti-oxidant defenses. We conclude that HDM extract appears to stimulate distinct host defenses that are differentially relevant according to the nature of the subsequent immune challenge. Future studies on the role of the host anti-oxidant responses in the Drosophila model will reveal how the host is able to cope with deleterious reactive oxygen species that may be generated during infections.

[object Object], [object Object], [object Object] et al.

Frontiers in Psychiatry • 2026

Theoretical framework Cigarette smoking is the leading preventable cause of death worldwide, with nicotine dependence notably common among individuals with Substance Use Disorders (SUD). Smoking exacerbates both physical and mental health issues, further complicating the treatment of SUD. Current therapeutic approaches for SUD often prove inadequate, indicating a need for new strategies. Recent advancements in metabolomics and gut microbiome research have provided valuable insights into the biological mechanisms underlying addiction, warranting further investigation. Objectives This study aims to investigate the therapeutic potential of smoking cessation for individuals with SUD, using a Cognitive-Behavioral Therapy (CBT) six-week group intervention within a therapeutic community. The research specifically explores the psychobehavioral, metabolic, and gut microbiome domains. It is hypothesized that smoking cessation will improve emotional regulation self-efficacy and reduce substance craving, mediated by changes in metabolic and microbiome profiles linked to brain systems of affect and reward. Methods A randomized controlled trial (N = 100) will be conducted, examining outcomes such as clinical relapse rates as well as microbial and metabolic markers, investigating pathways of short-chain fatty acids, oxidative stress and inflammation, lipid, tryptophan, and one-carbon metabolism. Participants will undergo a CBT smoking cessation intervention, with pre- and post-assessments, compared to a control group receiving treatment as usual. Metabolomic and microbiome analyses will be conducted using blood and stool samples, alongside psychological assessments via questionnaires. Covariate analyses will be undertaken to control for metabolic and gut microbial effects of long-term psychiatric medications (antidepressants, mood stabilizers, antipsychotics, and opioid substitutions) present in the sample. Behavioral assessments will be conducted at a 3-month follow-up. The study is registered at clinicaltrials.gov under NCT06803706. Level of originality This research will enhance our understanding of the complex interplay between smoking and mental health, offering potential for more effective treatment strategies for SUD. The current study’s focus on connections between metabolic and gut microbiome pathways with affect and reward is expected to yield valuable insights into addiction mechanisms and improve diagnostic and therapeutic practices. Clinical trial registration https://clinicaltrials.gov/study/NCT06803706?cond=metabolomic%20and%20microbial%20biomarkers%20in%20smoking%20cessation amp;rank=1 , identifier NCT06803706.

[object Object], [object Object], [object Object] et al.

bioRxiv (Cold Spring Harbor Laboratory) • 2026

The diversity of environmental microbial exposure is a key driver of immune maturation and host defense; however, its impact on brain immunity and neurodegenerative diseases remains poorly documented. Here, we show that controlled indoor rewilding, by introducing a natural farm-like environment into laboratory housing, reshapes peripheral and central nervous system (CNS) immune networks in wild-type (WT) and 5xFAD mice, a model of Alzheimer's disease (AD). Compared with traditional specific pathogen-free (SPF) housing, rewilded mice exhibited systemic shifts toward mature immune phenotypes, including increases in effector and memory B and T cells, expansion of plasma cell populations, and alterations in immunoglobulin isotypes. In the brain, indoor rewilding recalibrated microglial and astrocytic activation of SPF-5xFAD mice, attenuating pro-inflammatory transcriptional programs while enhancing homeostatic, complement, and phagocytic signatures. A strong transcriptional convergence was observed between rewilded and wild mice, with rewilded 5xFAD mice exhibiting greater similarity to human AD transcriptional profiles. Morphological and histochemical analyses confirmed that rewilded microglia adopt metabolically adaptable, homeostatic states that influence amyloid-β plaque binding and clearance. Collectively, these findings suggest that microbial diversity through »dirty» mouse modeling could enhance the translational relevance of neuroimmunology and neurodegenerative disease research.

[object Object], [object Object], [object Object] et al.

Microbiology Spectrum • 2026

ABSTRACT The tumor immune microenvironment and intratumoral microbiota play critical roles in cancer progression and immunotherapy response, yet their integrated functions in stomach adenocarcinoma (STAD) are not well understood. This study conducted a multi-omics analysis of transcriptomic and microbiome data from 348 patients with STAD. Using the ImmuCellAI algorithm, immune cell infiltration (ICI) was estimated, and non-negative matrix factorization classified samples into three immune subtypes (INC-1, INC-2, and INC-3). Differential expression analysis identified immune-related signature genes enriched in immune signaling pathways. Tumor mutational burden, microsatellite instability, immune checkpoint gene expression, and drug sensitivity were compared across subtypes. Microbiome clustering identified three subtypes (MC-1, MC-2, and MC-3), with associations to immune infiltration and microbial composition. The immune subtypes showed distinct patterns of ICI, clinical stage, and gene expression, with differentially expressed genes enriched in immune and tumor-related pathways. Microbiome subtypes exhibited unique diversity metrics and associations with the immune microenvironment. Integration of immune and microbial data improved immune checkpoint blockade (ICB) prediction, with genera like Staphylococcus and Ralstonia correlating with immune genes such as CD22, VIPR2, and FLT3. These findings provide insights into ICB response and support more precise immunotherapy strategies for STAD. IMPORTANCE Deciphering the interactions between the tumor immune microenvironment and the intratumoral microbiota is crucial for advancing precision immunotherapy in stomach adenocarcinoma (STAD). In this study, we present an integrative multi-omics framework that stratifies patients into distinct immune and microbial subtypes, uncovering their associations with immunogenomic profiles, immune cell infiltration patterns, and clinical features. Notably, we identify specific microbial genera correlated with immune-related gene expression and immune checkpoint blockade responsiveness. These findings provide novel insights into the immune–microbiome axis in STAD and underscore the potential of integrative multi-omics approaches to enhance patient stratification and guide more effective immunotherapeutic strategies.

[object Object], [object Object], [object Object] et al.

Current Microbiology • 2026

Abstract The production of high-quality Prunus seedling rootstocks in soilless systems requires optimizing the interaction between genetics, nutrient availability, and rhizosphere microbiology. This study evaluated the morphophysiological response of four peach rootstock genotypes (‘Capdeboscq’, “Okinawa Roxo”, “NR0060408”, and “NR0160305”) to inoculation with Trichoderma asperellum and a microbial consortium ( Bacillus amyloliquefaciens  +  Trichoderma harzianum ), under contrasting doses of controlled-release fertilizer (0 and 4 g dm − 3 of CRF). Longitudinal analysis (0-120 days) demonstrated that nutrient availability is the primary limiting factor; microbial bioinputs did not compensate for the absence of fertilization due to the metabolic cost of symbiosis. However, under nutrient sufficiency (4 g dm − 3 ), strong synergism was observed. The new selections (“NR0060408” and “NR0160305”) exhibited high phenotypic plasticity, maximizing the conversion of biostimulation into shoot biomass and outperforming the “Okinawa Roxo” genotype, which displayed a conservative growth strategy. The Bacillus - Trichoderma consortium was superior to single inoculation in responsive genotypes, potentiating seedling leaf area and height. Furthermore, inoculation promoted the “stay-green” effect, maintaining chlorophyll index stability until the end of the cycle. It is concluded that the use of bioinputs, especially in a consortium, acts as a metabolic catalyst in responsive genotypes, but their efficacy depends on adequate basal nutritional management.

[object Object], [object Object], [object Object] et al.

Animal Production Science • 2026

Context Methane emissions from ruminant livestock are a significant global greenhouse gas source, with 80% of New Zealand’s methane emissions from livestock production. There is increasing pressure to reduce this to meet reduction targets set by the Paris agreement. There are approximately 1 million farmed deer in New Zealand. While breeding for lower methane has proven successful in sheep, direct methane measurements in deer are prohibitively difficult and expensive. Proxies from sheep may enable selection of lower-emitting animals. High and low methane sheep differ in rumen size and microbial profiles. Aims This study investigated individual variation in deer rumen size and whether size differences were associated with specific microbial profiles. Associations between production phenotypes (eye muscle area, carcass fat and lean proportions estimated by computed tomography (CT) and microbial profiles were also examined. Methods Ten-month-old animals (n = 126) were CT-scanned to calculate rumen size, eye muscle area, and carcass fat/lean proportions. Rumen samples were processed into operational taxonomic units with 97% homology. Relationships between phenotypes and microbial profiles were estimated using linear mixed models in ASReml 3.0 and R software. Key results No association was found between deer rumen size and ruminotype profiles linked to low methane in sheep. However, three individual taxonomic groups showed associations with deer rumen size and eye muscle area: Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium, Fibrobacter, and Anoplodinium and Diplodinium. Conclusions While rumen size in deer does not currently show a clear link to low-methane ruminotypes identified in sheep, microbial composition exhibits notable associations with rumen size and production traits. Importantly, differences in taxonomic groups revealed that Methanobrevibacter gottschalkii and Methanobrevibacter ruminantium – previously thought to be competing species where one clade replaced the other – may not be in direct competition. The relationship between rumen size and methane-related microbial profiles warrants further study. Implications Understanding microbial associations in deer could inform breeding strategies aimed at reducing methane emissions. Identifying key taxa linked to rumen size and production traits may provide practical proxies for selecting low-emission animals without direct methane measurement.

[object Object], [object Object], [object Object] et al.

Microbiology Spectrum • 2026

ABSTRACT Reductive soil disinfestation (RSD) is an environmentally friendly method that can alleviate continuous cropping obstacles. Organic material application is crucial for ensuring RSD success. However, whether RSD treatment involving vegetable straw as organic material can alleviate continuous cropping obstacles in greenhouse cucumber remains unclear. Herein, we added 25 t∙ha −1 of tomato, bitter melon, and pepper straw to soil as organic material for RSD treatment of greenhouse soil, respectively. The results revealed that RSD treatment increased soil pH; organic matter, available nitrogen, and available potassium contents; and sucrase, urease, and catalase activities. Principal coordinate analyses revealed that the bacterial and fungal community compositions were greatly altered and that the fungal and bacterial Chao1 and Shannon indices decreased. The relative abundance of beneficial microorganisms such as Bacillus , Arthrobacter , Streptomyces , and Penicillium increased, whereas that of harmful microorganisms such as Fusarium decreased. RSD treatment promoted cucumber growth and development and significantly increased yield. On the basis of the RSD treatment effects on soil properties and cucumber growth and development, using pepper straw as organic material for RSD treatment was the most effective. A year of field trials revealed that adding vegetable straw as organic material for RSD treatment improved chemical properties and enzyme activities, altered the cucumber soil microbial community, and increased the cucumber yield. However, the long-term effects of RSD treatment on soil properties and microbial communities must be studied further. IMPORTANCE Driven by both economic benefits and market demand, intensive facility agriculture, characterized by uninterrupted monocultures, has become a significant aspect of contemporary agricultural practices. Reductive soil disinfestation (RSD) is an effective agricultural practice, and the application of organic material is crucial for achieving RSD success. Our research revealed that the use of vegetable straw as organic material for RSD treatment can effectively alleviate continuous cropping obstacles in greenhouse cucumber cultivation.

[object Object], [object Object], [object Object] et al.

Microbiology Spectrum • 2026

ABSTRACT The environmental microbiome in elderly care facilities plays a crucial role in the health of aging populations with immunosenescence; however, its composition and health associations remain underexplored. This study characterizes the microbial ecology of premium elderly care facilities, focusing on key functional spaces, environmental drivers, and implications for resident health. We conducted 16S rRNA gene sequencing (V3–V4 regions) on 320 surface and air samples from six functional spaces (dining areas, medical facilities, bedrooms, bathrooms, recreational rooms, and corridors) across four premium elderly care facilities. Environmental parameters (temperature, humidity, CO₂, and occupancy) were measured concurrently. Bioinformatics analysis (QIIME 2, DADA2, and Silva database) and statistical modeling (permutational multivariate analysis of variance, distance-based redundancy analysis, and PICRUSt2) were employed to assess microbial diversity, taxonomic composition, functional potential, and environmental correlations. Using 16S rRNA gene sequencing across four facilities in different geographic regions, we identified significant spatial heterogeneity in microbial diversity and composition, with dining areas and recreational rooms exhibiting higher richness (Shannon index: 6.07 ± 0.37) and human-associated taxa (e.g., Firmicutes), while medical facilities and bathrooms harbored lower diversity but elevated opportunistic pathogens ( Pseudomonas and Klebsiella ). Environmental parameters—particularly relative humidity (explaining 13.8% of community variation) and occupancy—strongly influenced the microbial structure. A core microbiome dominated by Proteobacteria, Firmicutes, and Actinobacteria was conserved across facilities, while functional predictions revealed space-specific traits, including predicted enrichment of antibiotic resistance genes in medical facilities (ARG Shannon diversity: 4.87 ± 0.42) and carbohydrate metabolism pathways in dining areas. Negative correlations between beneficial ( Lactobacillus ) and pathogenic taxa ( Staphylococcus aureus ) were consistent with potential ecological strategies for microbial balance, although validation with absolute quantification is needed. This study highlights the need for space-specific microbial management in elderly care environments, emphasizing humidity control, ventilation, and targeted hygiene to mitigate pathogen risks while preserving beneficial communities. Our findings suggest the potential value of ecologically informed stewardship over pathogen-centric approaches. Future research should integrate multi-omics and longitudinal health data to optimize microbiome-resident health interactions. IMPORTANCE As people age, their immune systems weaken, making the elderly especially vulnerable to germs in their surroundings. This study reveals that the types and amounts of bacteria living on surfaces and in the air within premium elderly care facilities differ significantly depending on the room's purpose—such as dining areas, medical rooms, or bathrooms. We found that humidity and how many people use a space strongly influence these bacterial communities. Crucially, areas like medical rooms had more bacteria linked to infections and antibiotic resistance, while social spaces hosted more diverse and potentially beneficial bacteria. This shows that a “one-size-fits-all” cleaning approach is not ideal. Instead, tailoring hygiene practices and environmental controls (like managing humidity) to specific spaces could better protect residents' health by reducing harmful germs while supporting helpful ones, offering a smarter way to manage these critical living environments for our aging population.

[object Object], [object Object], [object Object] et al.

Research Square • 2026

Abstract Background: The aging population faces increased risks of metabolic and cognitive decline, with emerging evidence linking gut microbiota to exercise-mediated health benefits. Senescence-accelerated mouse prone 6 (SAMP6) exhibits early aging phenotypes, while senescence-resistant 1 (SAMR1) serves as a healthy control. Methods: Thirty-six male SAMP6 and twelve SAMR1 mice (5- and 7-month-old) were assigned to eight groups (n = 6/group). Seven-month-old SAMP6 mice underwent 8 weeks of treadmill training: low-intensity continuous (12 m/min), moderate-intensity continuous (15 m/min), high-intensity interval training (HIIT; 12/20 m/min), or progressively intensified protocol (12→15 m/min). Fecal samples were collected post-intervention for 16S rRNA sequencing (V3–V4 region). Alpha diversity, beta diversity, and taxonomic composition were analyzed. Gut microbiome health index (GMHI) and microbial dysbiosis index (MDI) were calculated to assess health-associated microbial configuration. Results: Sedentary SAMR1 mice exhibited higher alpha diversity than SAMP6 controls, indicating a link between microbial richness and healthy aging. HIIT significantly restructured gut microbiota composition in SAMP6 mice, characterized by enrichment of Eggerthella lenta and Lactobacillus johnsonii , increased Proteobacteria abundance, and reduced overall alpha diversity. Moderate-intensity continuous training (MICT) enriched Faecalibaculum rodentium with milder compositional shifts. Progressively intensified training resulted in an intermediate microbial phenotype. GMHI was positive in SAMR1 and all exercised SAMP6 groups, with HIIT showing the highest score; sedentary SAMP6 groups exhibited negative GMHI. MDI values were consistent with these health-associated shifts. Conclusions: HIIT is associated with distinct compositional shifts and improved gut microbiome health indices in aging-prone mice, despite reduced alpha diversity. These findings highlight exercise intensity as a critical determinant of gut microbial ecology and support HIIT as a candidate precision exercise strategy for older adults. Future studies employing fecal microbiota transplantation are necessary to test causality.

[object Object], [object Object], [object Object] et al.

Frontiers in Microbiology • 2026

Background Sepsis and septic shock are severe complications for surgical malignancy patients. Conventional diagnostics often fail to capture the complex infectome in these populations. This study aimed to characterize the distinct microbial and resistome landscapes in cancer versus non-cancer patients using multi-site metagenomic next-generation sequencing (mNGS) to support specific antimicrobial strategies. Methods We conducted a single-center retrospective cohort study at the General Surgery ICU of Xuanwu Hospital, including 107 septic shock patients (52 cancer; 55 non-cancer). mNGS was performed on blood, bile, ascitic fluid, and bronchoalveolar lavage samples to identify pathogens and antibiotic resistance genes (ARGs). Findings were analyzed for their association with ICU length of stay and mortality. Results Cancer patients were significantly older (median 68 vs. 51 years, p   lt; 0.0001) with higher comorbidity scores (CCI: 7.0 vs. 4.0, p  = 0.006). However, mNGS revealed a lower pathogen detection rate in cancer patients (53.85% vs. 85.45%, p  = 0.0006) and a lower incidence of bacteremia (25.0% vs. 45.45%, p  = 0.0426). Cancer patients had shorter ICU LOS (9 vs. 13 days, p  = 0.0369) and antibiotic durations (7 vs. 11 days, p  = 0.0368). Dominant pathogens included Klebsiella pneumoniae and Enterococcus faecium , harboring diverse ARGs across beta-lactam and aminoglycoside categories. Multivariate Cox regression identified IL-6 ( p  = 0.018) was significant prognostic indicators for cancer patients. We also examined the distribution of virulence factors, despite their low detection rates. Conclusion Septic shock in cancer patients exhibits a unique resistome signature and distinct prognostic drivers. The identification of microbial targets via mNGS was associated with the implementation of targeted antimicrobial strategies and inflammation monitoring. These findings suggest that mNGS provides valuable molecular insights that may support clinical management and prognostic stratification for cancer patients in the surgical ICU.

[object Object], [object Object], [object Object] et al.

bioRxiv (Cold Spring Harbor Laboratory) • 2026

Microbially modified bile acids shape host physiology by regulating nutrient absorption, glucose homeostasis, circadian rhythms and thermoregulation. Here we identify a previously unrecognized drug-activating function of microbial bile acid conjugation. By systematically mining human LC-MS/MS datasets across public repositories and linking uncharacterized bile acid spectra to health-associated metadata, we discovered conjugates of the 75-year-old anti-inflammatory drug 5-aminosalicylic acid (5-ASA) with primary and secondary bile acids, including cholic, deoxycholic and lithocholic acids. These bile acid-drug conjugates were detected specifically in individuals treated with 5-ASA or its prodrugs. Multiple gut bacteria, including members of the Bacteroidota and Bacillota, generated cholyl-5-ASA in vitro, and bile salt hydrolase-associated transaminase activity was required for conjugate formation. In a mouse model of colitis, cholyl-5-ASA was associated with reduced intestinal inflammatory pathology and showed markedly enhanced activation of PPAR-g; in cell-based reporter assays compared with 5-ASA alone. Consistent with this activity, cholyl-5-ASA elicited selective immunophenotypic changes in CD4+; T cells in vitro, including increased Foxp3+ regulatory T cells. Together with prior evidence that 5-ASA efficacy depends on the microbiome, these findings support a model in which microbial bile acid conjugation represents a key activation step for 5-ASA therapy. More broadly, this work demonstrates how pan-repository metabolomics can uncover previously unrecognized microbiome-dependent chemical functions with direct therapeutic relevance.

[object Object], [object Object], [object Object] et al.

bioRxiv (Cold Spring Harbor Laboratory) • 2026

Metagenomic analysis of microbial communities relies significantly on the quality and completeness of reference genomes, which allow researchers to compare sequencing reads against reference genome collections to reveal essential community characteristics. However, the reliability of these analyses is often compromised by substantial discrepancies across existing reference resources, including differences in genome content, assembly fragmentation, taxonomic representation, and metadata completeness. While these inconsistencies are known to introduce bias, the extent of divergence between major databases remains largely unknown. Here, we present a comprehensive benchmark of discrepancies across multiple widely used microbial genome reference resources. We developed the Cross-DB Genomic Comparator (CDGC), which utilizes reference genome alignments to systematically capture discrepancies in genome assemblies across reference databases. Applying this framework, we found that 99% of viral genomes were identical across databases, indicating strong consistency in viral reference resources. In contrast, fungal genomes showed substantially greater variability: although 82% of assemblies exhibited at least 90% similarity, only 7% were identical across databases. More concerning, we identified a subset of 461 assemblies with less than 50% similarity, suggesting the presence of technical artifacts, incomplete assemblies, or damaged genome files that require closer examination. Collectively, these results demonstrate that systematic cross-database benchmarking provides a critical mechanism for refining the accuracy of individual reference databases and advancing efforts towards more unified and reliable universal reference genomes.

[object Object], [object Object], [object Object] et al.

Nutrients • 2026

Background: Gut microbiota dysbiosis is critically implicated in the pathogenesis of allergic airway inflammation (AAI) via the gut–lung axis. While Latilactobacillus curvatus is a promising probiotic candidate, its specific immunomodulatory mechanisms in respiratory diseases remain poorly understood. Objective: In this study, we investigated the protective effects and underlying mechanisms of L. curvatus IM01 in an ovalbumin (OVA)-induced murine AAI model using an integrated multi-omics approach. Results: Our results demonstrated that oral administration of L. curvatus IM01 significantly attenuated airway inflammation, suppressed Th2-type immune responses, and reduced serum IgE levels. Crucially, our multi-omics integration revealed a coherent gut–lung axis narrative driven by microbial and metabolic crosstalk. Specifically, 16S rRNA sequencing indicated that L. curvatus IM01 was closely linked to structural shifts in the gut microbial community, notably characterized by an enrichment trend for beneficial genera such as Odoribacter and Lactobacillus. This microbial restructuring was closely associated with a modulated cecal metabolic profile, as untargeted metabolomics exhibited a clear trend toward the restoration of key systemically active immunoregulatory metabolites, including indolelactic acid (ILA) and choline, which have been previously linked to the alleviation of AAI symptoms. Further linking this metabolic shift to respiratory immune tolerance, lung transcriptomic analysis showed that the treatment is strongly associated with the promotion of the differentiation of CD4+ T cells into Foxp3+ regulatory T cells (Tregs). Conclusions: Collectively, these findings suggest a novel potential pathway by which L. curvatus IM01 modulates the gut–lung axis through coordinated microbial and metabolic interventions, highlighting its potential as a therapeutic functional food ingredient for AAI.

[object Object], [object Object], [object Object] et al.

Fermentation • 2026

Proteins are fundamental to life and indispensable for human physiological activities. However, traditional proteins derived from natural sources such as animals and plants face challenges including low extraction efficiency and limited availability. Therefore, recombinant proteins produced via microbial manufacturing have emerged as a promising alternative. This review specifically focuses on the production of recombinant protein with certain specific functional characteristics, using microorganisms. Owing to their unique functional attributes, such proteins are in increasing demand in diverse fields, including food, medicine, and agriculture. Firstly, this review outlines the definition of recombinant protein and summarizes the microbial manufacturing and applications of nine typical proteins with certain specific functional characteristics. Secondly, the strategies of utilizing microorganisms for the efficient production and purification of recombinant proteins was systematically reviewed.

[object Object], [object Object], [object Object] et al.

Diabetologia • 2026

Abstract Aims/hypothesis Growing evidence implicates gut microbiota-derived metabolites in metabolic homeostasis. Indole, a microbial tryptophan metabolite, has been reported to enhance glucagon-like peptide-1 (GLP-1) secretion in vitro, and its derivatives have been inversely associated with risk of type 2 diabetes. We hypothesised that indole acts via the gastrointestinal tract to modulate glucose homeostasis, and tested this hypothesis using in vitro and in vivo models. Methods We measured GLP-1 secretion from cultured murine enteroendocrine cells, and evaluated intraperitoneal glucose tolerance and hormone secretion in mice following indole treatment. Subsequently, the impact of indole on intestinal epithelial cell fate and L cell number was examined using murine ileal organoid cultures and in vivo. Finally, we explored the effect of chronic indole administration on metabolic outcomes in a murine model of type 2 diabetes. Results Indole stimulated in vitro GLP-1 secretion in a concentration-dependent manner, and improved acute glucose management in vivo. Additionally, we demonstrate that indole drives enteroendocrine L cell differentiation in murine ileal organoids, resulting in increased L cell density and longer-term glucoregulatory benefits in vivo. Finally, sub-chronic indole administration improved glucose tolerance and insulin sensitivity in a diabetic mouse model. Conclusions/interpretation Our findings identify indole as a glucose-lowering molecule that acts on the gut, and raise the possibility of incorporating indole into nutraceutical supplements to aid in the treatment or prevention of type 2 diabetes. This study highlights the importance of gut microbiota-derived metabolites in metabolic health and opens new avenues for developing novel strategies to combat type 2 diabetes. Data availability RNA sequencing data are available from the Gene Expression Omnibus under accession number GSE306720. Graphical Abstract

[object Object], [object Object], [object Object] et al.

Biogeosciences • 2026

Abstract. Respiration is a key process in the organic carbon cycle of marine sediments, the understanding of which is key to future management decisions which aim to maximise sediment carbon storage. The microbial community is typically considered the dominant actor in overall sedimentary respiration, but knowledge is lacking about interactions with other components, particularly the macrofauna. The “inverted microbial loop” hypothesis suggests that macrofaunal activity stimulates the microbial respiration of organic carbon through the mixing of fresh organic carbon to depth, and subsequent priming (i.e. activation of refractory detritus by co-respiration with fresh detritus). We conducted experimental incubations to partition respiration amongst the microbial and macrofaunal components of the community and investigate interactions between them. We prepared sediment cores with native benthic communities, macrofauna only and microbial communities only. We added 13C labelled fresh organic matter to these cores and measured respiration over 7 d, quantifying both O2 consumption (reflecting remineralisation of all sedimentary organic C) and production of 13C dissolved inorganic C (DIC, reflecting remineralisation of labile organic C). Consumption of O2, which reflected remineralisation of ambient as well as added fresh organic C, showed greater rates when macrofaunal and microbial communities were present together than the sum of their separate rates. This provides direct experimental evidence that the inverted microbial loop mechanism stimulates mineralisation of less reactive, ambient organic C. Macrofaunal and microbial communities showed approximately equal contributions to the total community respiration, suggesting that faunal respiration should be more routinely included in carbon degradation modelling. The fate of the added fresh organic C in different treatments suggested competition for this resource between macrofauna and microbes, and some functional redundancy amongst different components of the benthic community. The enhanced understanding of sediment respiration generated by this study has implications for management of shelf seafloors to balance carbon storage with other human uses.

[object Object], [object Object], [object Object] et al.

Frontiers in Cellular and Infection Microbiology • 2026

Introduction Crohn’s disease (CD) is commonly treated with biologic therapies, including anti-TNFα agents, vedolizumab (VDZ), and ustekinumab (USTE), yet only a subset of patients respond to these treatments. This study aimed to evaluate the potential of the gut microbiome to predict treatment response. Methods Adult CD patients initiating anti-TNFα (infliximab or adalimumab), VDZ or USTE were enrolled. Pre-treatment ileal and/or colonic biopsies were collected endoscopically. Treatment response after 26–52 weeks was defined by ≥50% reduction in the simple endoscopic score for CD and either a corticosteroid-free clinical response (≥3-point HBI decrease or remission [HBI ≤4] without systemic steroids) or a biochemical response (≥50% or ≤5 mg/L CRP reduction and ≥50% or ≤250 μg/g faecal calprotectin reduction) versus baseline. Mucosal microbiota was profiled by 16S rRNA gene sequencing of biopsies. Machine learning models predicting treatment response were trained using ASV-level count data. The impact of heat-killed bacteria on anti-TNFα–induced CD14 + CD206 + macrophages was tested in mixed lymphocyte reactions (MLRs). Results A total of 125 patients were included: 39 on anti-TNFα, 47 on VDZ, and 39 on USTE. Clinical features were similar between responders and non-responders, aside from sex (USTE-colon) and CRP (USTE-ileum). No major microbial differences were observed in VDZ, USTE ileal or colon samples. However, in colonic biopsies, anti-TNFα responders had significantly higher pre-treatment α-diversity, and 3.9% of β-diversity variation associated with response. Among six models, the anti-TNFα colonic model performed significantly better than random (AUC = 0.90) to predict response. Mediterraneibacter gnavus ASVs associated with non-response, whereas Blautia ASVs associated with response, to anti-TNFα. When tested in MLRs, pretreatment with M. gnavus and B. luti led to a reduction in macrophage polarization, with a significantly stronger effect observed for M. gnavus compared with B. luti . Discussion Taken together, this study demonstrates that the colonic mucosal microbiome prior to anti-TNFα treatment can distinguish responders from non-responders in CD, supporting its potential as a predictive biomarker.

[object Object], [object Object], [object Object] et al.

Journal of Animal Science • 2026

Abstract Dairy cows experience oxidative stress, inflammation, and immune dysfunction during the transition from dry-off to early lactation. Postbiotics such as Saccharomyces cerevisiae fermentation product (SCFP), consisting of nonliving microorganisms with or without their components, have beneficial effects on the production efficiency and immune function of dairy cows. The objective of this study was to evaluate the effects of SCFP on milk production, milk composition, ruminal fermentation, blood metabolites, oxidative status, inflammatory responses, and the ruminal microbial community in Holstein dairy cows supplemented from the day of dry-off through early lactation. Two hundred cows were blocked on the basis of parity, BCS, milk yield and the time of dry-off, and were randomly allocated to specific treatment groups within each block. The treatments included the control group (CON, n = 100) receiving basal diets with no SCFP supplementation and the SCFP group (n = 100) receiving basal diets supplemented with 19 g/d of SCFP from d -60 to 60 relative to parturition. Milk yield—monitored for all 100 cows per treatment—was tracked until d 140 postpartum. In parallel, ruminal fluid, feces, milk, and blood samples were collected from a subset of cows (n = 20/treatment) during the treatment period for further analyses. Data were analyzed via the MIXED procedure in SAS (SAS Institute Inc.). The results revealed that the average milk yield of dairy cows in the SCFP group was greater than that in the CON group (43.93 vs. 42.08 kg/d, P = 0.04, n = 100) during the treatment period and remained greater (41.92 vs. 39.98 kg/d, P = 0.04, n = 100) throughout the 140 days postpartum recording period. Cows fed SCFP had significantly lower serum β-hydroxybutyrate and nonesterified fatty acid concentrations than did those in the CON group. Compared with the CON group, the SCFP group presented greater levels of superoxide dismutase and lower malonaldehyde concentrations. The SCFP group also presented a greater total antioxidant capacity prepartum and higher glutathione peroxidase levels postpartum. Additionally, the SCFP group had lower concentrations of proinflammatory factors, such as IL-1β, serum amyloid A, and haptoglobin, throughout the treatment period, indicating a stronger anti-inflammatory capability. Overall, SCFP supplementation improved the ruminal environment, reduced oxidative stress and the inflammatory status, and ultimately increased milk production.

[object Object], [object Object], [object Object] et al.

Frontiers in Microbiology • 2026

Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis , a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus , which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus , even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus , likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.

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Antibiot Khimioter = Antibiotics and Chemotherapy • 2026

The aim of the study was to compare the analytical sensitivity and microbial growth detection time using the BACT/ALERT 3D 120 (bioMérieux, France), YUNONА LABSTAR 100 (SCENKER, China), and Autobio BC 120 (Autobio, China) blood culture analyzers. Material and methods. The study was conducted in two stages. 1) In vitro: suspensions of 10 clinical strains at concentrations simulating bacteremia (30 CFU/ml, final dilution 1–2 CFU/vial). 2) Clinical phase: 197 blood cultures from 89 cardiothoracic surgery patients, tested in parallel using only the BACT/ALERT 3D 120 and YUNONA LABSTAR 100 systems. At both stages, samples were inoculated into pairs of aerobic and anaerobic vials, and the presence of growth and its detection time were assessed. Results . In the in vitro phase, the total sensitivity was 80.5%, 77.5%, and 74.5% for the YUNONA LABSTAR 100, BACT/ALERT 3D 120, and Autobio BC 120 systems, respectively. During aerobic cultivation of gram-negative bacteria, detection rates were high in all systems (90–100%). Under anaerobic conditions, the YUNONA LABSTAR 100 system showed the maximum sensitivity for this group (72.5%), while the Autobio BC 120 system showed the minimum sensitivity (45%). The efficacy profiles differed: the advantage of the Autobio BC 120 system in the detection speed of enterobacteria under aerobic conditions (median 11.5 h vs. 13–13.9 h for others) was combined with its lower sensitivity of anaerobic vials for gram-positive bacteria (77.5% vs. 100% for the BACT/ALERT 3D 120 and YUNONA LABSTAR 100 systems). A notable finding was the growth of P. aeruginosa in all anaerobic vials of the YUNONA LABSTAR 100 system. For Candida spp., all systems showed lower sensitivity and longer detection times compared to bacteria. In the clinical phase, growth was confirmed in 19 cases (9.6%). Under aerobic conditions, both systems detected growth in 73.7% of vials. In anaerobic vials (excluding obligate aerobes), growth was detected by the BACT/ALERT 3D 120 system in 75% of cases, which was more frequent than with the YUNONA LABSTAR 100 system (56.3%). The overall sensitivity for detecting a bacteremia episode was 89.5% (17/19) for the BACT/ALERT 3D 120 system versus 73.7% (14/19) for the YUNONA LABSTAR 100 system, meaning the BACT/ALERT 3D 120 system detected 3 more bacteremia cases. The analysis by pathogen groups showed that for enterobacteria and gram-positive cocci, the sensitivity of the BACT/ALERT 3D 120 system was higher. Complete agreement in identification between both systems was observed in only 47.4% of samples, with the overall discrepancy rate reaching 52.6%. Conclusion . The diagnostic efficacy of the compared systems is variable and depends on the type of microorganism and cultivation conditions. Superiority in individual in vitro parameters (e.g., speed) does not guarantee a similar result in clinical practice, where stable sensitivity in detecting a bacteremia episode is key. The high percentage of discrepancies between modern systems confirms the validity of recommendations for collecting multiple samples to improve bacteremia detection.

[object Object], [object Object], [object Object] et al.

Microbial Genomics • 2026

Background . Helicobacter pylori infection is a major risk factor for gastric cancer (GC), especially in East Asia. However, the mechanisms through which bacterial strain heterogeneity contributes to GC risk remain poorly understood. This study aims to elucidate the roles of specific virulence factors, antibiotic resistance profiles and genetic variations in H. pylori in GC development. Methods. We integrated host clinical data with phenotypic and genomic analyses of 31 clinical H. pylori isolates. Genomic analysis was performed to determine phylogenetic lineage and virulence markers. Antibiotic susceptibility and biofilm-forming ability of the clinical isolates were also assessed, and a genome-wide association study (GWAS) was employed to identify genetic polymorphisms linked to GC risk. Results. Among the isolates, 93.5 % of isolates belonged to the East Asian lineage and carried high-risk virulence markers ( cagA EPIYA-ABD, vacA s1m1). However, multidrug resistance was observed in 64.5 % of isolates, with high resistance rates to metronidazole (71.0%) and levofloxacin (48.4%) exceeding global averages. Strong biofilm-forming strains were significantly associated with tetracycline resistance compared to weak biofilm-forming strains. Additionally, GWAS identified five SNPs significantly associated with GC risk, with variants in hemC , babB and C694_RS04850 being enriched in high-risk strains. Conclusions. This study demonstrates the critical impact of H. pylori strain diversity in GC development, emphasizing the necessity for region-specific surveillance and innovative therapeutic strategies.

[object Object], [object Object], [object Object] et al.

Microorganisms • 2026

Functional microbial inoculation is widely applied in soil restoration; however, its effects on aggregate-scale nutrient cycling remain unclear. Based on ecological stoichiometry theory, we conducted 1-year and 3-year pot experiments using Bacillus thuringiensis (NL-11) and Gongronella butleri (NL-15) under plant-present and plant-absent conditions, with only NL-11 applied in the 1-year experiment. Aggregate size distribution, mean weight diameter (MWD), soil nutrients, microbial biomass, and enzyme activities were evaluated across aggregate classes. The results demonstrated that microbial effects were dependent on both time and plant presence. Under 3-year plant-present conditions, NL-11 and NL-15 significantly increased macroaggregate proportions and MWD, thereby enhancing aggregate stability. Under 3-year no-plant conditions, NL-15 increased organic carbon and total nitrogen in macro- and meso-aggregates by 55–59% and elevated soil C/P and N/P ratios, whereas NL-11 primarily enhanced total nitrogen. In 1-year no-plant macroaggregates, NL-11 increased microbial biomass phosphorus and reduced microbial biomass C/P and N/P ratios. Both inoculants enhanced invertase activity under plant-absent conditions, whereas plant presence stimulated acid phosphatase activity, with NAG activity increasing only under NL-15. Overall, microbial inoculation altered nutrient availability and microbial metabolic characteristics, promoted coordinated C–N–P stoichiometry, and facilitated the recovery of aggregate-scale nutrient cycling.

[object Object], [object Object], [object Object] et al.

Microbiology Research Journal International • 2026

Background and Aims: Crohn’s disease (CD) is a chronic inflammatory bowel disease characterized by gastrointestinal inflammation, with gut microbiota dysbiosis playing a key role in its onset and progression. This study aimed to evaluate whether 1-kestose supplementation modulates gut microbiota composition and mucin degradation–related biomarkers in patients with clinically inactive to mild CD, and to explore plausible ecological mechanisms in vitro. Study Design: Single-arm pilot intervention study with exploratory laboratory experiments. Place and Duration of Study: Samples were collected at Tokai University Hospital (Japan), and microbiome/qPCR analyses and in vitro assays were performed at Fujita Health University (Japan). The supplementation period was four months. Methodology: Nineteen patients with clinically inactive to mild CD (CDAI ≤ 220) received 1-kestose (3 g) twice daily for 4 months. Fecal microbiota composition was assessed by 16S rRNA gene sequencing, and qPCR quantified nanA homologs (nan levels) as a functional marker related to mucin-degrading potential. Clinical biomarkers (CDAI, fecal calprotectin, CRP, albumin) were monitored. To investigate potential mechanisms, in vitro cultures of Ruminococcus gnavus and Bifidobacterium longum were performed under sugar-supplemented conditions, including 1-kestose, and growth responses were evaluated; short-chain fatty acids (SCFAs) were descriptively assessed in pooled culture supernatants. Results: Clinical biomarkers remained stable throughout supplementation. 1-kestose intake was associated with an increased relative abundance of Bifidobacterium and a decreased abundance of Blautia, along with reduced fecal nan levels. In vitro, B. longum showed enhanced early growth with 1-kestose compared with other sugars, whereas R. gnavus exhibited impaired growth under acidic conditions. Exploratory SCFA measurements suggested higher acetate in sugar-supplemented B. longum cultures. Conclusion: In this single-arm pilot cohort of patients with clinically inactive to mild CD, 1-kestose supplementation was associated with shifts toward potentially beneficial taxa and a reduction in nan levels, a functional marker linked to mucin-degrading potential. These findings, supported by exploratory in vitro observations, suggest that 1-kestose may modulate gut ecological conditions; however, clinical efficacy and causality require confirmation in randomized, placebo-controlled trials with detailed dietary and medication monitoring.

[object Object], [object Object], [object Object] et al.

Research Square • 2026

Abstract Background Handling, preparation and sale of roadside roasted meats often predispose and may compromise such products leading to microbial contamination of both raw and ready-to-eat meat. This study assessed effects of handling roadside roasted meats on levels of microbial contamination sold at Namawojjolo and Lukaya Highway Food Markets in Uganda. Methods A total of 89 samples comprising of raw and ready-to-eat beef, chicken, and goat meats were collected using simple random sampling and analyzed for contamination by five key pathogens: Staphylococcus aureus , Escherichia coli, Campylobacter, Listeria, and Salmonella . Microbiological analysis was performed using standard culture and quantification technique and data were statistically analyzed using ANOVA and Bonferroni post-hoc tests. Results Raw samples exhibited highest contamination across all pathogens, where S. aureus in raw chicken (8 ± 0.56 log₁₀ CFU/g) and raw goat (8 ± 0.97 log₁₀ CFU/g) far exceeded Uganda’s National Bureau of Standards (UNBS) limits. Similarly, most of cold samples matched or surpassed hot samples in contamination. For example, cold beef showed higher Listeria counts (5 ± 1.93 log₁₀ CFU/g) than hot beef (3 ± 2.71 log₁₀ CFU/g). All tested meat types showed microbial contamination above UNBS safety limits for the five microbes examined which is ≤ 2 log₁₀ CFU/g for S.aureus and E.coli or completely absent for Salmonella , Lysteria and Campylobacter . However, S. aureus was consistently highest for all three meat types; for example, 8.4 ± 9.0 log₁₀ CFU/g for goat meat compared to 5.5 ± 5.7 shown for Salmonella in goat meat. Conclusion The findings highlight food safety gaps in the informal meat vending sector in Uganda. The pervasive microbial contamination, especially with pathogens of significant public health concern, underscores an urgent need for improved hygiene practices and regulatory oversight to safeguard consumer health. This study provides empirical evidence for targeted interventions to reduce foodborne disease risks associated with roadside meat consumption in Uganda and possibly, elsewhere.

[object Object], [object Object], [object Object] et al.

bioRxiv (Cold Spring Harbor Laboratory) • 2026

Microbial fuel cell offers a promising approach to improve wastewater quality and generate bioenergy from dark fermented effluents. In this study, the use of dark-fermented palm oil mill effluent as an electron donor for bioelectricity generation was investigated using a double-chambered microbial fuel cell (MFC). The MFCs were operated at room temperature (29 2℃), anode electrolytes adjusted to pH 7, and a chemical catholyte as the oxidizing agent. The maximum power and current densities of 63.31 8.07 mW/m2 and 155.16 12.88 mA/m2, respectively, were generated from the MFCs inoculated with sludge, which was 5.9 times higher than control without inoculum. Microbial community analysis revealed the enrichment of fermentative and electrogenic representative taxa from the phyla Bacillota, Bacteroidota and Pseudomonadota on the anode electrodes. Optimizations of the running conditions were carried out, suggesting the optimum parameters of 0.5 kΩ external resistance, anolyte initial pH 9, and 75% DFPOME substrate concentration. Operation under the optimized conditions increased current production, wastewater treatment, and Coulombic efficiency compared to the non-optimized conditions. Multiple configurations were also evaluated, showing higher cumulative voltage, power, and current densities with the stacked MFC connections, compared to single MFC units. Parallel circuit connection produced higher power and current density than serial connection. This study demonstrated the feasibility of MFC as a promising downstream treatment for biohydrogen production processes, towards higher treatment efficiency and resource recovery.

[object Object], [object Object], [object Object] et al.

Dentistry Journal • 2026

Background: This in vitro study compared color stability, surface properties, and microbial adhesion of four gingival epithesis materials (silicone: Gingivamoll®; nylon: Valplast®; PETG-based high-performance polymer: Eldy Plus®; PMMA: Palapress®) after staining. Methods: Standardized specimens (10 × 10 × 2 mm; n = 18/material) underwent 15 or 30 staining cycles (sequential immersion in coffee, curry, tea, and 40% alcohol). Color (CIELAB) and color difference (ΔE00), gloss (G), and surface roughness (Ra) were measured at baseline and after 15 and 30 cycles; surface morphology was assessed by SEM. Microbial adhesion was assessed using a six-species biofilm model and quantified as log CFU at baseline and after 15 and 30 cycles. Results: All materials showed clinically relevant discoloration (ΔE00 2). Valplast® exhibited the greatest color change (p 0.05), while color change in other materials remained lower. Gingivamoll® showed the lowest gloss and highest roughness, whereas other materials remained smoother; roughness increased significantly over time (p 0.05). SEM revealed a coating on the hard materials and nodular agglomerates on silicone. Biofilm CFU did not differ over time or between materials (all p 0.05). Conclusions: Staining induced material-dependent changes in color and surface properties, with Valplast® most prone to discoloration and silicone showing high roughness and nodular surface changes, contrasting with coatings on hard materials. Microbial adhesion analysis yielded pilot-level results, intended to inform the design of future investigations.

[object Object], [object Object], [object Object] et al.

Water, Air, & Soil Pollution • 2026

Summary The Tietê River is an anthropogenically disturbed urban water body polluted by a combination of untreated domestic sewage releasing (carbon, nitrogen and phosphorus pollution) and diffuse pollution that cross São Paulo State in Southeast of Brazil. Along its course, it presents contrasting sites showing elevated levels of nutrients and contaminants (eutrophic sites) and oligotrophic environments, in both water and sediments. In this study, we investigated how pollution influences the taxonomic and functional diversity of microbial communities in the Tietê River watershed, with the aim of understanding their role in pollutant transformation during downstream transport. Four sampling sites along a pollution gradient—from São Paulo city to a relatively pristine area near the river mouth—were evaluated. Results indicated that diversity differences were primarily linked to water quality, with higher diversity observed in less contaminated sites. Heterotrophic metabolism was more prominent in polluted regions, whereas photoautotrophic and lithotrophic microorganisms were more abundant in clean areas. Additionally, genes associated with the metabolism of aromatic compounds and virulence factors were more prevalent in environments with higher anthropogenic influence, suggesting a functional shift geared toward environmental adaptation and bioremediation. We propose that, in areas with high organic matter concentrations, microbial communities tend to adopt an r-strategy lifestyle, characterized by rapid growth and reproduction, while in oligotrophic, less polluted sites, more competitive k-strategists predominate. Although the following hypothesis was not extensively studied, the lower abundance of genes involved in secondary metabolic synthesis in eutrophic sites suggests that pollution may reduce the availability of novel species or traits relevant for biotechnological applications. Additionally, community shifts appear to be influenced by "conditionally rare taxa," which temporarily alter their activity and abundance in response to environmental constraints, playing a critical role in water self-purification processes. Overall, these findings offer new insights into the environmental factors driving self-purification in the Tietê River and shed light on the ecological mechanisms underpinning river resilience.

[object Object], [object Object], [object Object] et al.

Antibiot Khimioter = Antibiotics and Chemotherapy • 2026

Background . Modern military conflicts are characterized by an increase in the incidence of mine-blast wounds (MBWs). Bacterial infection may lead to severe purulent complications. The microbial landscape and antibiotic susceptibility of bacteria in MBWs are poorly understood and remain a subject of debate. The aim of this study was to analyze the species composition and antibiotic resistance of bacteria in patients with lower extremity MBWs. Material and methods . The results of examination and treatment of 575 patients with lower extremity MBWs were retrospectively analyzed. The median age of the wounded was 35 years [IQR: 18–60], and the median time since the injury was 16 days [IQR: 4–62]. Microbiological examination included qualitative analysis of bacterial flora and determination of antibiotic susceptibility. Wound discharge and tissues obtained during surgical debridement (SD) were examined. Antibiotic susceptibility testing was performed using the disk diffusion method. Results . Co-infection was predominant and amounted to 70.1% of the cases. Among gram-positive microorganisms, Enterococcus faecalis was most common at 43.9%. Among gram-negative bacteria, the most common were: Acinetobacter spp. — 39.3%, Pseudomonas aeruginosa — 19.9%, Klebsiella pneumoniae — 18.9%, Escherichia coli — 12.2%, Enterobacter spp. — 11.4%. The longer the time since the injury, the more frequently gram-negative microorganisms were isolated. The highest polyantibiotic resistance was noted among Acinetobacter spp. (69.6%), K. pneumoniae (66.5%) and P. aeruginosa (40.1%). The need for repeated chemical wound ablation was observed more often when Acinetobacter spp. and P. aeruginosa were isolated (69.8% and 42.5%). Conclusion . MBWs are characterized by high levels of microbial associations and gram-negative flora, the number of which increased over time after the wound formation. This demonstrates the importance of controlling wound contamination with hospital-acquired, polyantibiotic-resistant microflora.

[object Object], [object Object], [object Object] et al.

Microbiology Spectrum • 2026

ABSTRACT Dyslipidemia, characterized by abnormal blood lipid levels, constitutes a significant risk factor for cardiovascular disease. Emerging evidence indicates that the gut microbiota influences lipid metabolism, although findings across studies have been inconsistent. In this cross-sectional investigation, we analyzed the composition of gut microbiota, associated metabolic pathways, predicted gut metabolites, and the resistome in 1,384 participants (including 895 individuals with dyslipidemia and 489 controls) through shotgun metagenomic sequencing. Our findings demonstrated that Bacteroides caccae was enriched among dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism. Conversely, Coprococcus eutactus and Coprococcus catus , recognized producers of short-chain fatty acids (SCFAs) involved in lipid regulation, as well as Blautia obeum , known to be positively affected by SCFAs, were more prevalent in the control group. Additionally, we identified an enrichment of the gene family responsible for dTDP-beta-D-fucofuranose biosynthesis, associated with bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris serving as a major contributor. Dyslipidemia cases also exhibited depletion of glycogen and peptidoglycan biosynthesis pathways, which may compromise energy storage and immune function, alongside decreased levels of pseudouridine, a molecule involved in RNA metabolism. Furthermore, a marginal increase in abundance of antibiotic-resistance genes, tetQ , was observed in dyslipidemia cases, suggesting a potential link between the gut resistome and metabolic dysregulation. These results offer novel insights into the role of gut microbiota in the pathophysiology of dyslipidemia and underscore potential microbiome-targeted interventions for metabolic disease management. IMPORTANCE Dyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. This study analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and antimicrobial resistance genes in 1,384 participants using shotgun metagenomic sequencing. Individuals with dyslipidemia exhibited an imbalance in gut bacteria, including an increase in Bacteroides caccae , a species associated with inflammation, and a decrease in short-chain fatty acid-producing bacteria such as Coprococcus eutactus and Blautia obeum , which support metabolic health. Furthermore, we identified significant changes in microbial metabolic pathways related to energy storage and immune function, as well as an increased abundance of tetracycline resistance genes ( tetQ ), suggesting a potential link between dyslipidemia and antimicrobial resistance. Our study provides a comprehensive overview of dyslipidemia-associated gut microbial alterations, highlighting potential mechanistic links and therapeutic targets.

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Research Square • 2026

Abstract It has long been debated in ecology whether communities behave as cohesive units or as loose collections of independent species. Here, we study this question in the context of community coalescence, the mixing of previously isolated communities, using bacterial microcosm experiments combined with ecological modeling. Our results demonstrate that interspecies interaction strength determines whether communities or species are the units of selection during coalescence. When interactions are moderate to strong, one parental community consistently outcompetes the other, indicating community-level selection. In contrast, under weak interactions, species fates are uncorrelated and the two communities contribute equally to the coalesced outcome, indicating the absence of community-level selection. These patterns extend to communities derived from natural samples with greater taxonomic diversity and richness. Furthermore, we identify two distinct regimes underlying community-level selection in experiments with different media conditions: an emergent regime in which collective dynamics shape outcomes that cannot be predicted from species traits alone, and a top-down regime where dominant species determine the winning community. Together, these results reconcile conflicting observations on community-level selection during community coalescence by demonstrating that communities behave as cohesive units only when interactions are sufficiently strong.

[object Object], [object Object]

Research Square • 2026

Abstract Oncoids are widespread components of Phanerozoic carbonate systems, however, their occurrence in the Ordovician of Baltoscandia has remained poorly documented. This study presents the first detailed description of oncoids from the Upper Ordovician (Katian–Hirnantian) of Estonia, based on a unique historical collection assembled over nearly three decades by the Estonian scientist L. Põlma that has not previously been available for detailed scientific analysis. The material originates from northern and central Estonia. Macroscopically, the oncoids occur within lenticular interlayers of oncolitic grainstones and are predominantly spheroidal to ellipsoidal in shape, with typical diameters of 1–2 cm and rare specimens reaching up to 10 cm. Petrographic analysis indicates that the oncoids belong to the porostromatic type. Well-preserved filamentous and tubular microstructures attributable to the calcareous cyanobacteria Girvanella were identified. Oncoid nuclei consist mainly of strongly micritized fragments of skeletal fauna. The extreme rarity of oncoids in the Katian–Hirnantian successions of Estonia is interpreted not as an environmental limitation, but rather as a consequence of preservation bias related to platform morphology and sediment bypass on Ordovician shoals. The association of Girvanella oncoids with peloids and cortoids indicates an intense microbial activity and suggests the operation of a microbial carbonate factory on shallow, high-energy platform highs prior to the Hirnantian glaciation. These findings provide new insights into Late Ordovician carbonate production on the Baltoscandian platform and highlight the importance of unique legacy collections for reconstructing underrepresented depositional environments.

[object Object], [object Object], [object Object] et al.

Frontiers in Neuroscience • 2026

Background Gut dysbiosis is hypothesized to be a potential pathological mechanism in patients across the Alzheimer’s disease (AD) spectrum. Nevertheless, despite growing interest, existing findings remain largely inconsistent. Purpose This systematic review and meta-analysis aimed to compare the composition of gut microbiota (GM) between patients with mild cognitive impairment (MCI) or AD and healthy controls (HC). Methods PubMed, Embase, MEDLINE and Web of science were searched from January 2022 to November 2025. Eligible studies included observational studies and pre-intervention arms of interventional trials reporting GM abundance in AD spectrum patients vs. HC. Two reviewers independently screened articles, extracted data, and assessed bias risk. Effect sizes were pooled using an inverse-variance weighted random-effects model. Results Twenty studies (1,025 HC and 456 AD spectrum patients) were analyzed. AD patients demonstrated reduced GM diversity vs. HC cohort. The abundances of Megamonas and Bacteroides were elevated in AD patients, while Firmicutes and Proteobacteria were reduced. When stratified by clinical stage, Fusobacteria and Lactobacillus abundances showed gradient shift from MCI to AD. Conclusion Individuals within the AD spectrum exhibit altered GM abundance, with these differences influenced by clinical stage. The present study did not identify any significant trends; it reports only findings that have been statistically substantiated.

[object Object], [object Object], [object Object] et al.

Microorganisms • 2026

Climate change is reshaping Antarctic ecosystems, where the resilience of Deschampsia antarctica and Colobanthus quitensis is mediated by endophytic microbial communities assembled under strong abiotic drivers. This study explores the temperature-dependent biofilm development in two Antarctic endophytic microbial communities (ALS and LS). Multivariate analysis revealed a fundamental trade-off between planktonic expansion and biofilm matrix investment as a function of thermal cues. While moderate warming (15–25 °C) optimized cell viability and turbidity, extreme thermal stress at 37–42 °C in nutrient-rich conditions triggered a significant shift toward a matrix-rich signature, characterized by a synergistic increase in total DNA and cellulose. Crucially, at the thermal extreme of 42 °C, we observed a decoupling of optical density from culturable biomass, where high turbidity did not translate into viable cells, signaling a state of severe environmental stress. These results identify 25 °C as the quantitative threshold for optimal growth, while temperatures of 37–42 °C act as a specific trigger for protective matrix production. Such thermal plasticity suggests that Antarctic endophytes are evolutionarily primed for persistence not only in cold native niches but also during bird-mediated dispersal at endothermic host temperatures.

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Frontiers in Microbiology • 2026

Introduction Crop rotation promotes ecological effects and production by regulating belowground processes, particularly the shaping of the rhizosphere soil microbiome. Rhizosphere metabolites are a key driver of belowground processes and play a crucial role in shaping soil microbial community composition. However, the rhizosphere metabolites of different potato rotations have rarely been reported, and the regulation of key metabolites on the rhizosphere soil microbiome remains unclear. Methods This study measured agronomic traits of potatoes, collected potato rhizosphere soils from three crop rotations, including potato monoculture (P-P), maize ( Zea mays )-potato rotation (M-P), cowpea ( Vigna unguiculata )-potato rotation (V-P), to determine rhizosphere soil metabolites and analyze defense metabolites, and assess the soil bacterial and fungal diversity and community composition. Results Compared to monoculture, the potato rotations had positive effects on growth and yield. Potato rotations had more primary metabolites, such as amino acids and carbohydrates and conjugates, but significantly reduced secondary metabolites with defensive functions in rhizosphere soils including phenols and other benzene derivatives, flavonoids, alkaloids and other N-containing compounds, and terpenoids. Potato rotation systems supported higher diversity of bacteria and fungi and enriched beneficial bacteria such as biocontrol, nitrogen fixation, C degradation, denitrification, and pollutant degradation bacteria, while suppressing pathogenic fungi in the rhizosphere soils. Rhizosphere soil metabolites strongly correlated with the microbial community composition. The secondary metabolites, which are predominantly alkaloids, terpenoids, and flavonoids, exerted a dominant regulatory effect on the composition of soil microbial community. Discussion These results demonstrate the important regulation of rhizosphere metabolites on soil microbial community composition, deepening our understanding of the benefits of crop rotation via the belowground effect.