@article {pmid42573249,
year = {2026},
author = {Hansen, SC and Hamm, CW and Singer, JR and Weaver, CT and Gray, MJ},
title = {Ecology of protection: probiotic biogeography and sepsis prevention in the neonatal intestine.},
journal = {mBio},
volume = {},
number = {},
pages = {e0112726},
doi = {10.1128/mbio.01127-26},
pmid = {42573249},
issn = {2150-7511},
abstract = {Neonatal infection is a leading cause of morbidity and mortality worldwide, particularly among preterm and low birth weight infants. Probiotic bacteria are widely used in peri- and postnatal care and can reduce neonatal intestinal dysbiosis. However, formulations and efficacy remain highly variable, highlighting a critical gap in our understanding of the mechanisms that drive successful interventions in this population. Furthermore, current studies on probiotic efficacy rely on indirect or relative measures of intestinal bacterial burden. Here, we directly mapped the biogeography of intestinal colonization and quantified the probiotic effects of Escherichia coli Nissle 1917 (EcN) and Ligilactobacillus murinus strain V10 against Klebsiella pneumoniae dysbiosis across the neonatal murine intestine. Despite substantial differences in their spatial distribution along the intestine, both EcN and L. murinus V10 significantly reduced K. pneumoniae colonization and mortality from K. pneumoniae sepsis, with EcN providing greater protection. EcN's probiotic activity was partially dependent on high-affinity oxygen respiration, implicating luminal oxygen availability as a key ecological determinant of probiotic efficacy. Contrary to the common assumption that multi-strain probiotics are inherently superior, simultaneous administration of EcN and L. murinus V10 was less effective than EcN treatment alone at preventing sepsis-related death. These findings identify intestinal niche occupancy, oxygen utilization, and strain-strain interactions as critical variables which should inform the rational design of future probiotic interventions for high-risk neonates.IMPORTANCELate-onset sepsis (LOS) remains a devastating and difficult-to-treat complication of prematurity, and probiotics are increasingly used to reduce dysbiosis and infection risk in this vulnerable population. Probiotic regimens, however, are highly heterogeneous, and their mechanisms of action in the neonatal intestine are poorly defined, complicating efforts to design safe, effective, and regulatable interventions. In this work, we use a neonatal mouse model of LOS to rigorously test fundamental assumptions underlying the current paradigm for understanding the impact of probiotics on intestinal disease. We demonstrate that two distantly related probiotic bacteria, Escherichia coli Nissle 1917 and Ligilactobacillus murinus V10, each reduce intestinal colonization and mortality caused by the LOS pathobiont Klebsiella pneumoniae, but do so through distinct ecological and molecular mechanisms. These findings highlight ecological principles, including spatial niche occupancy, resource competition, and strain-strain interactions, as critical determinants of probiotic efficacy, and provide mechanistic insight that will be important for guiding rational probiotic strategies for high-risk neonates.},
}

@article {pmid42573621,
year = {2026},
author = {Tang, J and Zhang, S and Xu, G and Cui, M and Ge, X and Gao, H and Zhang, F},
title = {Enterococcus in herbal fermentation: a genus-specific perspective on enzymatic capability, biotransformation outcomes and safety.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42573621},
issn = {1432-072X},
support = {Grant No. 2025YFC3509000//National Key Research and Development Program of China/ ; },
mesh = {Biotransformation ; *Fermentation ; *Enterococcus/enzymology/metabolism/genetics/classification ; *Plants, Medicinal/microbiology/metabolism ; },
abstract = {Although Enterococcus species are consistently detected in traditional herbal fermentations, their functional contributions to medicinal plant biotransformation remain poorly characterised at the genus level. This review provides the first genus-specific synthesis of Enterococcus in medicinal and food-medicinal plant fermentation, integrating evidence across historical fermentation systems, microbial ecology, enzymatic capability, phytochemical transformation, and safety assessment. Enterococcus species frequently occupy an early-to-middle ecological niche in fermented herbal matrices, sustained by exceptional tolerance to acidic, saline, and polyphenol-rich conditions. This ecological fitness is coupled to a functionally diverse enzymatic repertoire-encompassing β-glucosidases, α-rhamnosidases, ferulic acid esterases, tannases, bile salt hydrolases, and phenolic acid decarboxylases-capable of targeting the major glycosidic, ester, amide, and carboxylate linkages present in plant secondary metabolite conjugates. Documented biotransformations include ginsenoside Rb1-to-F2 conversion, sequential flavonoid diglycoside hydrolysis, ellagic acid-to-urolithin A transformation, gallotannin degradation, and oxalate catabolism-reactions that collectively parallel key TCMs processing objectives of bioavailability enhancement, pharmacological activation, and toxicity reduction. Safety challenges, particularly the concentration of virulence factors and transferable antibiotic resistance in E. faecalis and E. faecium, are critically evaluated. Mitigation strategies-including whole-genome-based strain screening, heat-inactivated postbiotic preparations, and recombinant enzyme platforms-are discussed as viable pathways toward controlled, safety-validated medicinal applications. The evidence supports a fundamental reappraisal of Enterococcus as a mechanistically distinctive contributor to herbal fermentation. Future progress will require strain-resolved functional characterisation, multi-omics-guided analysis, and safety-validated bioprocess design. This review is intended for researchers in fermentation microbiology, natural-product biotransformation, and the modernisation of traditional medicine, as well as for those engaged in the safety evaluation of fermentation-associated bacteria.},
}

Biotransformation
*Fermentation
*Enterococcus/enzymology/metabolism/genetics/classification
*Plants, Medicinal/microbiology/metabolism

@article {pmid42573712,
year = {2026},
author = {Guo, Y and Wang, B and Ren, C and Xin, S and Gao, H and Liu, X and Hua, R and Wang, H and Zhao, J and Wang, Y and Shi, W and Lu, X and Gao, L and Li, S and Xu, J},
title = {Bidirectional influences and clinical implications of psychological factors and oral health during orthodontic treatment.},
journal = {The Saudi dental journal},
volume = {38},
number = {8},
pages = {},
pmid = {42573712},
issn = {1013-9052},
abstract = {INTRODUCTION: Psychological factors such as anxiety and stress frequently affect orthodontic treatment outcomes, but the underlying mechanisms remain unclear. To review evidence on how psychological factors influence orthodontic outcomes and to describe the biological pathways involved.

METHODS: We conducted a narrative review of Web of Science and PubMed up to January 2025, including 102 peer-reviewed studies on orthodontics, psychology, oral microbiota, taste, and inflammatory markers.

RESULTS: Psychological factors affect orthodontic treatment through three pathways: First, nervous system activation (HPA axis and autonomic nervous system); Second, alterations in oral microbiota and salivary biomarkers (cortisol, α-amylase, s-IgA), and third, modulation of alveolar bone remodeling via pro-inflammatory cytokines (IL-1β, IL-6, IL-8). Taste changes under stress may indirectly alter dietary habits and oral microbial ecology. Most evidence is cross-sectional, limiting causal inference.

CONCLUSION: Psychological factors significantly influence orthodontic outcomes via measurable biological mechanisms. Routine psychological assessment and patient education should be integrated into orthodontic practice.},
}

@article {pmid42573928,
year = {2026},
author = {Sheiber, J and Duque, A and Ranjan, A and Diokno, AC and Swana, H},
title = {Characterizing the role of the urobiome in the pathogenesis of recurrent urinary tract infections (rUTIs): a systematic review.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {42573928},
issn = {1573-2584},
abstract = {PURPOSE: Recurrent urinary tract infections (rUTIs) are associated with substantial morbidity, repeated antibiotic exposure, and increasing antimicrobial resistance. Emerging evidence suggests that alterations in the urinary microbiome (urobiome) may contribute to rUTI pathogenesis. This systematic review evaluated the role of the urobiome in the development and recurrence of rUTIs.

METHODS: This systematic review was conducted in accordance with the PRISMA 2020 guidelines. Literature searches were conducted and managed using Covidence systematic review software (Veritas Health Innovation, Melbourne, Australia). Searches included Web of Science, MEDLINE, PubMed, and CINAHL and covered studies published from 2014 through 2026. The final search was conducted on February 1, 2026. The search incorporated terms related to 'urobiome,' 'urinary microbiome,' 'urinary tract infection,' and 'recurrent urinary tract infection.' Searches were restricted to English-language studies and human participants. After deduplication, 213 unique records underwent title and abstract screening, and 62 articles were assessed in full text. 21 studies that directly evaluated recurrent or chronic UTI populations, or reported an rUTI-specific subgroup, were included in the qualitative synthesis. Data extraction included study design, patient population characteristics, definitions of rUTI, urine collection methods, microbiome assessment methodology (including 16S rRNA sequencing and enhanced quantitative urine culture), reported microbial diversity measures, taxonomic findings, and associations between microbiome characteristics and rUTI outcomes. Given heterogeneity in study design, sequencing platforms, urine collection techniques, and definitions of rUTI across studies, a quantitative meta-analysis was not performed. Findings were synthesized descriptively, with emphasis on recurring microbial patterns, diversity measures, and clinically relevant urobiome alterations associated with recurrent infection.

RESULTS: 21 studies met inclusion criteria. Recurrent urinary tract infection was associated with altered urinary microbial ecology although the direction of diversity changes varied across studies. Commonly reported differences included altered Lactobacillus abundance and enrichment of taxa, such as Gardnerella, Prevotella, and Enterobacterales. Mechanistic studies implicated intracellular bacterial persistence, biofilm formation, ecological shifts, and metabolite-microbiome interactions. Hormonal status and antibiotic exposure also influenced urobiome composition. Substantial methodological heterogeneity remained across studies.

CONCLUSION: Current evidence supports a potential role for the urobiome in rUTI pathogenesis. Altered microbial diversity, loss of protective organisms, and persistent bacterial reservoirs may contribute to recurrence. Further standardized longitudinal and mechanistic studies are needed to clarify causality and guide microbiome-targeted therapeutic strategies.},
}

@article {pmid42574048,
year = {2026},
author = {Dey, R and Beach, R and Hambrick, KM and Sgouralis, I and Frémont, P and Demory, D and Carr, E and Beckett, SJ and Weitz, JS and Talmy, D},
title = {Microbial Primer: Bayesian learning of traits from microbial time series data.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {8},
pages = {},
pmid = {42574048},
issn = {1465-2080},
mesh = {Bayes Theorem ; Ecosystem ; Markov Chains ; *Models, Biological ; Population Dynamics ; *Haptophyta/physiology ; },
abstract = {Mathematical models are increasingly used to infer traits, interactions and functional dynamics of microbial systems. One common example is a rate-based ordinary differential equation model parameterized with microbial traits. However, fitting such models with associated parameters to data requires a principled approach to extract information from time series while accounting for prior knowledge and measurement noise. These principles often remain implicit and not necessarily well defined. Here, we make the implicit, explicit: introducing Bayesian inference of ecological models for microbial time series, including three detailed case studies of algal population dynamics that follow a birth-death process. Complementing this primer, we provide an online tutorial on Bayesian inverse modelling with cross-programming language support via Python (PyMC) and Julia (Turing). By connecting theory, code, data and a series of hands-on educational modules, this primer aims to bring the utility of Bayesian learning to the broader microbial ecology research community.},
}

Bayes Theorem
Ecosystem
Markov Chains
*Models, Biological
Population Dynamics
*Haptophyta/physiology

@article {pmid42575094,
year = {2026},
author = {Zhai, J and Li, Y and Liu, J and Su, X and Cui, R and Zheng, D and Sun, Y and Yu, J and Dai, C},
title = {Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102974},
doi = {10.1016/j.xcrm.2026.102974},
pmid = {42575094},
issn = {2666-3791},
abstract = {The global rise of inflammatory bowel disease (IBD) reflects environmental shifts, yet how these changes are embedded in the gut microbial ecology remains unclear. We construct a microbiome atlas comprising 245,627 profiles. By classifying countries into three epidemiologic stages, we establish a framework. As the IBD burden increases, the gut microbial alpha diversity declines, and community structures form distinct clusters. This transition is characterized by a gradient of core genera. Integrating six shotgun metagenomic cohorts, we identify the depletion of anabolic pathways in IBD patients. Strain-level analysis reveals that epidemiologic staging shapes genetic architecture within species, identifying an IBD-enriched subclade of Eisenbergiella associated with elevated fecal cholic acid. We develop a microbial inflammatory risk score (MIRS), based on 19 genera, that discriminates IBD from controls (area under the curve [AUC] = 0.92). MIRS correlates with IBD prevalence. Our study provides an atlas linking epidemiology to microbiome ecology and strain evolution, offering a foundation for population-level surveillance and interventions in IBD.},
}

@article {pmid42576567,
year = {2026},
author = {Hernández, SR and Bueno-Camilo, FG and Olivares Ponce, PN and Palma-Vázquez, JR and Soimu, G and Maldonado-Álvarez, MA and Baasch, A and Brisson-Suárez, K and Roldán, LA and Vilas-Navós, B and Oyarzabal-Eula, S and Rendón, J and Martin, G and Campello, AF and Alves, FRF and Rôças, IN and Siqueira, JF},
title = {Prevalence of Apical Periodontitis in Eight Hispanic American Countries.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70254},
pmid = {42576567},
issn = {1365-2591},
abstract = {AIM: This multicenter cross-sectional study evaluated the prevalence and variables statistically associated with primary and post-treatment apical periodontitis (AP) in subjects from eight Hispanic American countries.

METHODOLOGY: Digital panoramic radiographs from subjects living in Argentina, Colombia, Ecuador, Guatemala, Mexico, Dominican Republic, Uruguay and Venezuela were analyzed. Teeth were evaluated for diverse factors, including the periapical status and presence of root canal treatment, caries, coronal restoration, intraradicular post, root resorption and periodontal involvement. Quality of root canal treatment and coronal restorations was also recorded. Associations between these diverse variables and AP were evaluated using chi-square tests and multivariable mixed-effects logistic regression with a random intercept for patient to account for within-patient clustering of teeth.

RESULTS: Overall, 11 850 subjects (294 662 teeth) were included; 51.5% of the subjects and 5.5% of the examined teeth had AP. Ecuador (62%) and Argentina (61%) had the highest AP prevalence per subject, whereas Mexico had the lowest (37%). Intermediate values were observed in Venezuela (57%), Guatemala (57%), Colombia (47%), Dominican Republic (46%) and Uruguay (45%). In general, 43% of the subjects had at least one root canal-treated tooth. Primary and post-treatment AP were observed in 3% and 42% of the teeth, respectively. Of the teeth with primary AP, 51% showed coronal restorations, and 32% had caries. Post-treatment AP was significantly associated with inadequate root canal fillings, inadequate coronal restorations and inadequate intraradicular posts (p < 0.05).

CONCLUSIONS: The prevalence of AP in the Hispanic American countries evaluated was high, affecting nearly half of the population. Post-treatment AP was highly prevalent and predominantly linked to inadequate root canal fillings, deficient or absent coronal restorations and intraradicular posts. These findings emphasize the importance of strengthening caries prevention strategies and improving the quality of endodontic and restorative care to reduce the burden of apical periodontitis in these regions.},
}

@article {pmid42576817,
year = {2024},
author = {Kunselman, E and Manrique, D and Burge, CA and Allard, S and Daniel, Z and Mitta, G and Petton, B and Gilbert, JA},
title = {Temperature and microbe mediated impacts of the San Diego Bay ostreid herpesvirus (OsHV-1) microvariant on juvenile Pacific oysters.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae014},
pmid = {42576817},
issn = {2755-1970},
abstract = {The ostreid herpesvirus (OsHV-1) was recently detected in San Diego Bay for the first time in farmed juvenile Pacific oysters (Crassostrea gigas). Due to the virus' ability to cause mass mortality (50%-100%), it is important to determine the factors that promote infection as well as the consequences of infection. Here, we assess the role of temperature in controlling OsHV-1 induced mortality. Pacific oysters were exposed to the San Diego Bay microvariant of OsHV-1 at four different temperatures (15°C, 18°C, 21°C, and 24°C). While OsHV-1 was able to replicate in oyster tissues at all temperatures, it did not induce mortality at 15°C, only at the higher temperatures. Additionally, we examined oyster tissue-associated bacterial response to OsHV-1 infection. As shown previously, bacterial richness increased following OsHV-1 exposure and then decreased as the oysters became sick and died. Four bacterial taxa linked to the San Diego Bay microvariant infection, including Arcobacter, Vibrio, Amphritea, and Pseudoalteromonas, were the same as those shown for other microvariant infections in other studies from globally distributed oysters, suggesting a similar spectrum of co-infection irrespective of geography and microvariant type. The significant shift in the bacterial community following exposure suggests a weakening of the host defenses as a result of OsHV-1 infection, which potentially leads to adverse opportunistic bacterial infection.},
}

@article {pmid42576819,
year = {2025},
author = {Williams, A and Lynch, J},
title = {Bridging research gaps and advancing policy for healthy soils.},
journal = {Sustainable microbiology},
volume = {2},
number = {3},
pages = {qvaf017},
pmid = {42576819},
issn = {2755-1970},
abstract = {The policy framework previously presented by Neale and colleagues in Sustainable Microbiology highlights the central role of soil microorganisms in sustainable agriculture and global food security, offering actionable interventions grounded in emerging scientific advances. However, the translation of soil science and ecology into impactful policy and practice remains limited. This opinion article revisits the longstanding concept of soil biotechnology, and regulatory/societal barriers to progress. We emphasize that the soil microbiome holds untapped potential for improving plant health, reducing agrochemical reliance, and promoting sustainable food systems through continued research. Interkingdom microbial interactions, especially those involving root exudation as a mechanism for microbial recruitment, are proposed as pivotal but underexplored areas of study. Phenotype-driven, trait-based approaches are advocated over traditional phylogenetic methods to better identify functionally relevant microbial consortia and intervention strategies. Furthermore, we stress the need to integrate ecological, agronomic, and economic insights to develop soil-centric food systems. This includes monetizing ecosystem services provided by healthy soils and implementing incentivized conservation schemes. Unlocking the potential of soil microbial ecology requires coordinated, interdisciplinary efforts and a paradigm shift in policy, funding, and public perception.},
}

@article {pmid42576821,
year = {2026},
author = {Faggionato, D and Muñoz-García, M and Kostic, T and Ferrari, ML and Vonaesch, P and Poyet, M and Portier, P and Ryan, MJ and Djeddour, D and Stumptner, C and Varese, GC and Zuzuarregui, A and Groussin, M and Schloter, M and Finn, RD and Haas, AS and Probert, I and Verkley, G and Overmann, J and Scholz, AH},
title = {Policy Briefing: from access to use-untangling the international legal frameworks that govern microbial resources.},
journal = {Sustainable microbiology},
volume = {3},
number = {1},
pages = {qvag005},
pmid = {42576821},
issn = {2755-1970},
abstract = {The wide geographic distribution of microorganisms, combined with their vast taxonomic and functional diversity, make them indispensable reservoirs of genetic variation that sustain ecosystem resilience and fuel biotechnological innovation. However, to use this diversity, microbiologists must navigate a complex legal and regulatory landscape governed by multiple United Nations treaties and their respective access and benefit-sharing frameworks as well as regulatory frameworks specific to particular ecosystems, biosecurity, pathogens, and intellectual property. This complex regulatory web is also actively growing and changing, which makes it immensely challenging for a "regular" microbiologist to navigate. For policymakers and negotiators, it is also difficult to appreciate the full complexity that practitioners experience. This policy briefing provides a concise regulatory guide for practitioners and policymakers alike, summarized in a graphical overview, to provide more clarity and understanding for those at the edge of decision-making and practice.},
}

@article {pmid42576822,
year = {2026},
author = {Faggionato, D and Muñoz-García, M and Kostic, T and Ferrari, ML and Vonaesch, P and Poyet, M and Portier, P and Ryan, MJ and Djeddour, D and Stumptner, C and Varese, GC and Zuzuarregui, A and Groussin, M and Schloter, M and Finn, RD and Haas, AS and Probert, I and Verkley, G and Overmann, J and Scholz, AH},
title = {Policy in Practice: How to do the Nagoya Protocol: common misconceptions, challenges and best practices for access and benefit-sharing compliance.},
journal = {Sustainable microbiology},
volume = {3},
number = {2},
pages = {qvag007},
pmid = {42576822},
issn = {2755-1970},
abstract = {The Nagoya Protocol establishes an international framework for access and benefit-sharing including for microbial research. Yet many microbiologists have only a vague understanding of what the Nagoya Protocol requires and are unsure how to navigate its complexities, despite the fact that non-compliance can have significant legal consequences and far-reaching reputational and legal impacts. This paper discusses common misconceptions and practical challenges that microbiologists may encounter when complying with the Nagoya Protocol and a step-by-step guide on how to "do" the Nagoya Protocol. We present three case studies to showcase real-life experiences and provide best practice principles for access and benefit-sharing while fostering biodiversity conservation, equitable collaboration, and sustainable innovation.},
}

@article {pmid42576838,
year = {2024},
author = {Kunselman, E and Wiggin, K and Diner, RE and Gilbert, JA and Allard, SM},
title = {Microbial threats and sustainable solutions for molluscan aquaculture.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae002},
pmid = {42576838},
issn = {2755-1970},
abstract = {Aquaculture is responsible for producing almost half of the world's seafood. As the global climate changes and population continues to increase, we must prepare for increased disease in aquatic animals, a risk compounded by high-density aquafarms that are necessary to keep up with demand. This review will highlight major microbial threats to aquaculture and current and alternative solutions to these threats with consideration for the accessibility of the proposed solutions. Molluscs are ideal for sustainable aquaculture because they require less inputs than most other protein sources, and through filter feeding, they improve local ecosystem health. However, they are also plagued by microbial diseases, and rising water temperatures will only exacerbate this problem by enhancing pathogen survival, range, and growth. At the same time, microbial treatments hold great promise for reducing disease burden and increasing yield and food safety. In order to combat threats to sustainable aquaculture, it is critical to monitor and predict microbial behavior in coastal water and animal populations, explore sustainable microbial treatment options such as probiotics and phage therapy, reduce reliance on antimicrobials, and develop mitigation strategies through partnership with mollusc farmers, government regulators, industry, academic researchers, and indigenous peoples.},
}

@article {pmid42576842,
year = {2025},
author = {Gilbert, JA and Scholz, AH and Bello, MGD and Korsten, L and Berg, G and Singh, BK and Boetius, A and Wang, F and Greening, C and Wrighton, K and Bordenstein, SR and Jansson, J and Lennon, JT and Souza, V and Allard, SM and Thomas, T and Cowan, D and Crowther, TW and Nguyen, N and Harper, L and Haraoui, LP and Ishaq, SL and McFall-Ngai, M and Redford, KH and Peixoto, R},
title = {Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature.},
journal = {Sustainable microbiology},
volume = {2},
number = {4},
pages = {qvaf024},
pmid = {42576842},
issn = {2755-1970},
abstract = {As the first and dominant life forms on the planet, microorganisms underpin all ecological and organismal systems that drive planetary functioning, ecosystem health, and human wellbeing. Microbial communities are affected by anthropogenic pressures, and some microbial ecosystems may be at risk of permanent disruption, but microbiology remains conspicuously underrepresented in global conservation frameworks. This article provides a comprehensive overview of the Microbial Conservation Specialist Group (MCSG) of the International Union for Conservation of Nature, including its goals, operational framework, and broader relevance. The MCSG provides the first formal global structure dedicated to the assessment, monitoring, and protection of microbial life across ecosystems. We outline its core mission, strategic framework, and planned activities to integrate microbial conservation into international biodiversity agendas, One Health/planetary policies, and ecological restoration initiatives. We also make a call for all key stakeholders to get involved in this initiative; the microbial world is vast, and we need "all experts on deck" to drive effective solutions.},
}

@article {pmid42576854,
year = {2024},
author = {Neale, D and Cullen, L and Ranout, AS},
title = {Improving soil health in the UK: why a microbial approach is indispensable in attaining sustainable soils.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae026},
pmid = {42576854},
issn = {2755-1970},
abstract = {Current agricultural approaches in the UK-and across much of the world-are unsustainable, particularly due to their impacts on soil health. With evidence already showing diminishing returns in productivity, which are only predicted to get worse with the climate crisis, restoring the health of soils and soil-dwelling microbes is an essential prerequisite for a thriving planet. This report proposes taking a new approach to soil health based on the soil microbiome. The complex community of soil microbes and their interactions are known to underpin soil health and consequently food security, resilience to climate change, global health, biodiversity, and more. As such, an approach that holistically takes soil into account is needed, rather than the siloed approaches used to date. This report therefore highlights the opportunity to take a microbiome approach to soil and how such an approach could be implemented in the UK going forward, whilst also recommending microbial solutions that can be deployed to improve the UK's soils now.},
}

@article {pmid42576858,
year = {2024},
author = {Alfahl, Z and Chueiri, A and Carolan, S and Darcy, G and Hussain, N and Cahill, N and O'Connor, L},
title = {Antimicrobial resistance detection methods in water environments: a scoping review.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae034},
pmid = {42576858},
issn = {2755-1970},
abstract = {Antimicrobial resistance (AMR) in water environments poses a significant threat to public health, ecosystem stability, and the effectiveness of antimicrobial treatments. This review aims to provide a comprehensive overview of the methods used to detect AMR in various water environments. A literature search was conducted following the PRISMA guidelines. Original articles published in English relating to AMR in water environments were included. Reviews, protocols, and abstracts were excluded. A total of 115 publications were selected for full-text evaluation. Overall, river water samples were the most commonly assessed samples across all of the reviewed studies (49/115 studies, 42%). The top 3 countries investigating AMR genes in water samples were the USA (19 studies, 17%), China (11 studies, 10%), and Brazil (10 studies, 9%). The review revealed that polymerase chain reaction and metagenomic methods are increasingly preferred for their high sensitivity, specificity, and comprehensive detection capabilities, appearing in 65/115 (57%) and 31/115 (27%) studies, respectively. Despite higher costs and technical complexity, these methods provide valuable insights into the resistome of water environments. Culture-dependent methods, while most cost effective and straightforward, are limited by their time-consuming nature and inability to detect non-viable resistant organisms, reducing their effectiveness in comprehensive AMR surveillance. The review addresses the challenges and limitations of current detection methods and proposes directions for future research to develop more robust, cost-effective, and user-friendly detection methods. The review highlights the urgent need for integrated approaches to monitor and mitigate AMR in water environments, ensuring better public health and environmental protection.},
}

@article {pmid42576874,
year = {2024},
author = {Cowan, DA and Babenko, D and Bird, R and Botha, A and Breecker, DO and Clarke, CE and Francis, ML and Gallagher, T and Lebre, PH and Nel, T and Potts, AJ and Trindade, M and Van Zyl, L},
title = {Oxalate and oxalotrophy: an environmental perspective.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvad004},
pmid = {42576874},
issn = {2755-1970},
abstract = {Oxalic acid is one of the most abundant organic acids produced by plants. Much of the global production of oxalic acid is deposited on soil surfaces in leaf litter to be oxidized by microorganisms, resulting in a pH increase and shifting the carbonate equilibria. In what is known as the oxalate-carbonate pathway, calcium oxalate metabolism results in CO2 being sequestered into soils as insoluble calcite (CaCO3). There is a growing appreciation that the global scale of this process is sufficiently large to be an important contribution to global carbon turnover budgets. The microbiomics, genetics, and enzymology of oxalotrophy are all soundly established, although a more detailed understanding of the landscape-scale kinetics of the process would be needed to incorporate oxalotrophy as an element of process models informing the relevant Sustainable Development Goals. Here, we review the current state of knowledge of oxalotrophs and oxalotrophy and the role they play in terrestrial ecosystem services and functions in terms of carbon sequestration and nutrient cycling. We emphasize the relevance of these to the Sustainability Development Goals (SDGs) and highlight the importance of recognizing oxalotrophy, when accounting for the natural capital value of an ecosystem.},
}

@article {pmid42576885,
year = {2025},
author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK},
title = {Microbes without borders: uniting societies for climate action.},
journal = {Sustainable microbiology},
volume = {2},
number = {3},
pages = {qvaf021},
pmid = {42576885},
issn = {2755-1970},
abstract = {The climate crisis is one of the greatest challenges of our time, yet the role of microorganisms remains underrecognized in climate science and policy. Microbes are highly sensitive to environmental change and regulate essential biogeochemical processes, while also offering solutions for reducing emissions, restoring ecosystems, and enhancing resilience. Microbiology societies from five continents recently convened in Washington, DC, for the inaugural Global Strategy Meeting on Microbes and Climate Change. The gathering launched a global alliance to position microbial science as a pillar of climate action and identified four priorities: building a coalition, embedding microbes in climate frameworks, transforming communication, and advancing real-world demonstration projects. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.},
}

@article {pmid42567435,
year = {2026},
author = {Cicirelli, V and Peruzzo, A and Burgio, M and Bramante, G and Fabbri, G and Toscan, E and Losasso, C and Rizzo, A},
title = {Evaluation of neonatal oral and rectal microbiota in dogs delivered by c-section, from birth to weaning.},
journal = {Veterinary journal (London, England : 1997)},
volume = {319},
number = {},
pages = {106816},
doi = {10.1016/j.tvjl.2026.106816},
pmid = {42567435},
issn = {1532-2971},
abstract = {In recent years, the role of the microbiota in early-life health has gained increasing attention; however, data on the initial phases of microbial colonization in dogs remain limited. This study investigated the development of oral and rectal microbiota in puppies delivered by cesarean section from birth to weaning, and the contribution of maternal microbial sources. Four French Bulldog dams and their litters (18 puppies) were enrolled under uniform management conditions. Oral and rectal swabs were collected from puppies at birth and at 15, 30, 45, and 60 days of age, together with maternal oral, teat-skin, and rectal samples, and analyzed by 16S rRNA gene sequencing. Longitudinal analyses revealed a marked, time-dependent increase in microbial richness and diversity in both oral and rectal niches, reflecting a clear ecological succession from pioneer facultative anaerobes to taxa associated with a mature microbiota. Alpha diversity significantly increased from birth to weaning in both oral and rectal samples (p < 0.001), while beta diversity analyses showed progressive convergence toward maternal microbial profiles over time, particularly after the dietary transition from milk to solid food. Source tracking analysis identified maternal teat-skin microbiota as the primary contributor during early life, while maternal oral and rectal sources became increasingly dominant as puppies matured. These findings demonstrate that microbial colonization in dogs begins very early and undergoes dynamic, site-specific maturation throughout the neonatal period. From a One Health perspective, the observed mother-offspring microbial interactions highlight the translational value of canine models for studying early-life microbiota development.},
}

@article {pmid42568410,
year = {2026},
author = {Amano, C and Willhelm, U and Koch, T and Reinthaler, T and Hansman, RL and Sintes, E and Herndl, GJ and González, JM and Baltar, F},
title = {Major contribution of anaplerosis to inorganic carbon fixation in the dark ocean.},
journal = {Nature geoscience},
volume = {19},
number = {8},
pages = {938-944},
pmid = {42568410},
issn = {1752-0894},
abstract = {While CO2 fixation by photo- and chemolithoautotrophs is a central process of the global carbon cycle, many organisms also incorporate inorganic carbon into organic compounds through anaplerotic carbon fixation, a process that replenishes intermediates of central metabolic pathways. However, the active drivers and quantitative importance of anaplerotic carbon fixation in the oceanic carbon cycling remain poorly understood. Here, through analysis of global ocean multi-omics datasets, we identified widespread expression of enzymes involved in this process, especially phosphoenolpyruvate carboxylase. The heterotrophic bacterial genus Alteromonas, a globally distributed marine taxon lacking genes for autotrophic carbon fixation pathways, exhibited particularly high transcriptional and proteomic activity for this enzyme. Laboratory incubations confirmed that Alteromonas assimilated dissolved inorganic carbon (DIC) into biomass, with rates regulated by temperature and organic matter availability. Single-cell tracer analyses of the deep ocean microbial communities quantified Alteromonas's contribution at about 17% of total dark DIC fixation (median; confidence interval, 10-28%), equivalent to a potential global flux of about 0.2 PgC yr[-1]. These results reveal substantial DIC fixation via anaplerosis, indicating that dark carbon fixation is partly supported by heterotrophic metabolism and modulated by environmental conditions, with responses that may differ from those of canonical autotrophic processes.},
}

@article {pmid42570393,
year = {2026},
author = {McCarthy, FMG and Patterson, RT and Pendea, F},
title = {Meeting report: 11th international symposium on testate amoebae (ISTA-11 Niagara), Brock University, Canada, June 22-27, 2025.},
journal = {Protist},
volume = {182},
number = {},
pages = {126177},
doi = {10.1016/j.protis.2026.126177},
pmid = {42570393},
issn = {1618-0941},
abstract = {An international group of 49 scientists from 12 countries assembled at Brock University, St. Catharines, Ontario, Canada, from June 22-27, 2025, for the 11th International Symposium on Testate Amoebae (ISTA-11 Niagara). The meeting, jointly organized by the International Society of Testate Amoebae Research (ISTAR) and the Canadian Association of Palynologists (CAP), marked a significant milestone as the first ISTA meeting held in North America. Participation included 19 students, underscoring strong engagement from early-career researchers. The largest national delegation was from Canada (17 participants), followed by China, Switzerland, and the United States (six participants each). The scientific program comprised 41 oral and 12 poster presentations, reflecting the continued growth and diversification of research on testate amoebae.},
}

@article {pmid42570687,
year = {2026},
author = {Xu, X and Fan, K and Ling, N and Li, J and Yang, T and Gao, GF and Ma, Y and Nie, L and Zhang, J and Chu, H},
title = {Soil pH regulates organic carbon pool by changing microbial life-history strategy.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.08.028},
pmid = {42570687},
issn = {2090-1224},
abstract = {INTRODUCTION: The stability of the vast soil carbon pool, crucial for climate regulation, depends on microbial processes that govern carbon loss as CO2 or its stabilization in soil. Microbial life-history strategies, representing tradeoffs between resource acquisition (A-strategy) and growth yield (Y-strategy), are central to soil organic carbon (SOC) dynamics. However, how abiotic factors modulate these strategies and, in turn SOC fate remains unclear.

OBJECTIVES: Using the black soil region of Northeast China, which harbors substantial yet vulnerable SOC reserves, this study aimed to identify the dominant abiotic driver shaping microbial life-history strategies and to elucidate how this driver influences SOC stabilization pathways.

METHODS: We conducted a field survey combining metagenomic profiling of microbial attributes (diversity, functional potential, and inferred life-history strategy) with measurements of soil properties including extracellular enzyme activities and SOC fractions. This integrative approach traced the pathway from abiotic drivers to microbial traits and ultimately to carbon allocation.

RESULTS: Soil pH emerged as the key environmental gradient, with a threshold at pH 6.43 marking a systemic shift in microbial ecology and carbon processing. Acidic soils (pH 4.60-6.43) favored A-strategists, characterized by large genomes, enriched carbohydrate-active enzymes, and high extracellular enzyme activity, enabling polymer degradation and humification but limiting mineral-associated organic carbon (MAOC) formation. In contrast, neutral soils (pH 6.43-8.87) supported Y-strategists with streamlined genomes and biosynthetic metabolism, promoting microbial necromass accumulation and MAOC stabilization. Distinct functional guilds underpinned the A- and Y-strategies and frequent horizontal gene transfer in acidic soils further reinforced the A-strategy dominance under low pH.

CONCLUSION: Our findings reveal a mechanistic link between microbial life-history strategies and SOC stabilization, demonstrating that pH may shape the balance between A- and Y-strategists and their contrasting carbon pathways. This insight enhances predictive models of SOC dynamics and highlights pH management as a key lever for agroecosystems carbon retention.},
}

@article {pmid42571267,
year = {2026},
author = {Kose, A and Erdemci, L and Yasar, S and Memisoglu, F and Toplu, SA and Eren, C and Yazlak, G and Tanriverdi, ES and Usta, S and Ersoy, Y},
title = {Pandemic-associated shifts in microbial ecology and antimicrobial resistance in a high-volume liver transplant intensive care unit: a 10-year surveillance study.},
journal = {Infection prevention in practice},
volume = {8},
number = {3},
pages = {100564},
pmid = {42571267},
issn = {2590-0889},
abstract = {BACKGROUND: Healthcare-associated infections (HAIs) remain a major source of morbidity in solid organ transplant recipients, particularly in liver transplant (LT) intensive care units (ICUs), where profound immunosuppression and extensive antimicrobial exposure shape local microbial ecology. While reductions in overall infection incidence have been reported in structured surveillance programs, longitudinal changes in pathogen distribution and antimicrobial resistance (AMR) in transplant-specific ICUs remain insufficiently characterized. We aimed to evaluate pandemic-associated shifts in microbial ecology and AMR patterns across a 10-year surveillance period in a high-volume LT ICU.

METHODS: This retrospective analysis was based on prospectively collected surveillance data from adult LT recipients admitted between January 2015 and December 2024. The study period was categorized into prepandemic (2015-2019), pandemic (2020-2021), and postpandemic (2022-2024) phases. All analyses were performed at the HAI-episode level. Isolation density was calculated per 1000 patient-days. Incidence rate ratios were estimated using Poisson regression models with patient-days included as an offset. Period-related differences in AMR were evaluated using logistic regression. A two-sided P value <0.05 was considered statistically significant.

RESULTS: Among 7717 patients corresponding to 48,001 patient-days, 380 clinically significant isolates were analysed. Gram-negative organisms remained predominant throughout the study period, while Gram-positive isolates demonstrated a significant decreasing trend over time. Acinetobacter spp. (31.3%), Klebsiella spp. (25.8%), and Pseudomonas spp. (15.0%) were the leading pathogens. Isolation densities of Acinetobacter spp. and Escherichia coli were significantly higher in the prepandemic period than in the postpandemic period. In contrast, the pandemic and postpandemic phases were associated with significant increases in resistance probabilities among major Gram-negative pathogens. Acinetobacter spp. showed higher resistance to meropenem and amikacin, Klebsiella spp. demonstrated increased aminoglycoside and fluoroquinolone resistance, and Pseudomonas spp. exhibited increased ciprofloxacin resistance in 2020-2024 compared with 2015-2019.

CONCLUSIONS: In this transplant-specific ICU, microbial ecology and resistance trajectories evolved independently of overall infection incidence trends. Pandemic-associated healthcare disruptions were accompanied by organism-specific resistance shifts rather than uniform ecological changes. Continuous surveillance and locally tailored antimicrobial stewardship strategies are essential to preserve therapeutic efficacy and mitigate the growing threat of multi-drug-resistant (MDR) pathogens in transplant ICUs.},
}

@article {pmid42571401,
year = {2026},
author = {Hu, M and Gao, Q and Ren, W and Li, A and Huang, M and Che, L and Chen, D and Wu, A},
title = {Effects of different acidifiers on the growth performance and diarrhea score of weaned piglets under commercial pig farm conditions.},
journal = {Translational animal science},
volume = {10},
number = {},
pages = {txag101},
pmid = {42571401},
issn = {2573-2102},
abstract = {Benzoic acid (BA)-based acidifiers are widely applied in nursery diets; however, formulation can shape their functional outcomes on intake, host robustness, and gut microbial ecology. This study assessed a new-type benzoic acid (NBA) strategy under commercial farm conditions. A total of 210 21-day-old DLY (Duroc × Landrace × Yorkshire) weaned piglets, with equal numbers of males and females and similar body weight (average 6.03 kg ± 0.01 kg), were randomly assigned to 5 groups with 6 replicates per group and 7 piglets per replicate. The control group was fed a basal diet, while the four experimental groups were fed the basal diet supplemented with 0.5% benzoic acid (BA), 0.3% new-type benzoic acid (NBA), 0.25% controlled-release-coated benzoic acid (CBA), or 0.5% compound acidifier (CA) powder, respectively. The trial lasted 42 days. The results showed that compared to the control group, the average daily feed intake (ADFI) from days 15 to 28 was significantly increased (P < 0.05) in the BA, NBA, and CA groups, indicating improved voluntary intake during the mid-nursery period. The diarrhea rate was significantly reduced (P < 0.05) during days 0-14 in the BA, NBA and CBA groups compared to the control group. Compared to the control group, serum total antioxidant capacity (T-AOC) was significantly elevated (P < 0.05) in the BA, CBA, and CA groups, and catalase (CAT) levels increased significantly in the NBA group. White blood cell (WBC), lymphocyte (Lym), and mean corpuscular hemoglobin concentration (MCHC) increased significantly in the BA group compared to the control group, while MCHC levels decreased significantly in the NBA, CBA, and CA groups. Notably, compared with the control group, 0.5% BA, 0.3% NBA, and 0.25% CBA increased the richness and diversity of the intestinal microbiota. Specifically, these treatments promoted the growth of beneficial bacteria such as Lactobacillus while inhibiting the proliferation of Escherichia coli. The results of this study indicate that adding 0.5% BA, 0.3% NBA, and 0.25% CBA all enhance piglets' antioxidant capacity, reduce diarrhea incidence, and enhance gut microbial diversity. Among these, 0.5% BA and 0.25% CBA demonstrated superior efficacy compared to 0.3% NBA, offering potential economic benefits by improving feed efficiency, thereby enhancing overall production performance.},
}

@article {pmid42572451,
year = {2026},
author = {Butterbach-Bahl, K and Philippot, L and Serra, J and Silver, WL and Ogle, S and Abalos, D},
title = {Three Decades of Soil N2O Research-Insights and Gaps.},
journal = {Global change biology},
volume = {32},
number = {8},
pages = {e71038},
doi = {10.1111/gcb.71038},
pmid = {42572451},
issn = {1365-2486},
support = {NNF24SA0091172//the Novo Nordisk Foundation/ ; NNF25SA0112735//Agricultural nitrogen use efficiency platform/ ; },
mesh = {*Nitrous Oxide/analysis ; *Soil Microbiology ; *Greenhouse Gases/analysis ; *Soil/chemistry ; Agriculture ; Greenhouse Effect ; Environmental Monitoring ; },
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas (GHG) whose atmospheric concentration continues to rise, largely driven by nitrogen (N) inputs to agricultural soils. Over the past three decades, research on soil N2O emissions has advanced substantially, yet key uncertainties still constrain mitigation efforts. Here, we synthesize developments in measurement techniques, process understanding, microbial ecology, and modelling from the 1990s to the present, and identify critical gaps for future research. Advances in high-frequency measurements, laser spectroscopy, and isotopic approaches have revealed the importance of temporal "hot moments" and spatial "hotspots," challenging earlier assumptions based on sparse sampling. Concurrently, molecular and multi-omic tools have transformed our understanding of the microbial drivers of N2O production and consumption, highlighting the role of community composition, truncated pathways, and previously overlooked N2O-producing and reducing organisms. Process-based models have evolved from research tools into policy-relevant frameworks underpinning GHG inventories, with emerging integration of data assimilation, ensemble modelling, and artificial intelligence. However, despite these advances, persistent challenges remain in linking scales, reducing uncertainties, and translating mechanistic insights into scalable mitigation strategies. Closing these gaps offers a unique opportunity to translate decades of scientific progress into next-generation mitigation strategies that align agricultural productivity with climate stabilization goals.},
}

*Nitrous Oxide/analysis
*Soil Microbiology
*Greenhouse Gases/analysis
*Soil/chemistry
Agriculture
Greenhouse Effect
Environmental Monitoring

@article {pmid42557861,
year = {2026},
author = {Dai, M and Niu, Z and Lu, Y and Wei, A and Wang, X and Zheng, H and Lai, J and Zong, E and Sun, B and Zheng, J and Xu, Y},
title = {Unveiling the Acidic Backbone of Baijiu: A Comprehensive Review on Composition, Metabolic Pathways, and Quality Implications.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {5},
pages = {e70592},
pmid = {42557861},
issn = {1541-4337},
support = {32572513//National Natural Science Foundation of China/ ; 2023JJ002//Open Foundation of Key Laboratory of Wuliangye-Flavor Liquor Solid-State Fermentation, China National Light Industry/ ; },
mesh = {*Metabolic Networks and Pathways ; *Alcoholic Beverages/analysis/microbiology ; Fermentation ; *Acids/chemistry ; Taste ; Humans ; },
abstract = {Acids constitute fundamental molecular determinants that shape the sensory profile, typicity, and overall quality of Baijiu, a traditional Chinese distilled spirit. In this review, the latest advances in the studies of acidic compounds in Baijiu are systematically summarized within the framework of the "composition-function-microbe interaction" chain, with particular emphasis placed on the relationships among acid metabolism, flavor formation, microbial ecology, and product quality stability. We first catalog the diverse acid profiles in Baijiu, highlighting the four major acids (acetic, lactic, butyric, and caproic acids), and their dynamic evolution during product aging. In addition, the roles of acids in sensory perception, aroma regulation, and quality evaluation are comprehensively discussed, while their potential health-related implications are briefly and critically appraised. Crucially, we elucidate the microbial origins of these acids, detailing key metabolic pathways including glycolysis, amino acid catabolism, and reverse β-oxidation. Current studies have demonstrated that microbial community interactions play critical roles in shaping acid metabolism and acid-ester balance, although the underlying mechanisms remain insufficiently resolved. This review concludes by identifying critical knowledge gaps regarding in situ metabolic flux quantification and predictive modeling of microbial interaction networks governing acid-flavor compound dynamics. Future studies integrating multiomics approaches, ecological modeling, and targeted metabolic regulation are expected to facilitate the transition of Baijiu fermentation from descriptive characterization toward predictive and controllable bioprocesses.},
}

*Metabolic Networks and Pathways
*Alcoholic Beverages/analysis/microbiology
Fermentation
*Acids/chemistry
Taste
Humans

@article {pmid42562513,
year = {2026},
author = {Liu, QJ and Mei, JL and Wen, X and Lu, YH and Zeng, Y and Liu, ZY and Xu, HY and Wang, ST and Jiang, F and Yang, CB and Chi, YL and Xu, ZH},
title = {Cellar age reshapes Huangshui micro-ecosystem and metabolism to drive flavor formation in strong-aroma baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119740},
doi = {10.1016/j.foodres.2026.119740},
pmid = {42562513},
issn = {1873-7145},
mesh = {Fermentation ; Metabolomics ; *Odorants/analysis ; *Taste ; Bacteria/metabolism/genetics ; *Wine/analysis/microbiology ; *Alcoholic Beverages/analysis/microbiology ; Metagenomics ; *Microbiota ; Flavoring Agents ; },
abstract = {Huangshui, a slurry-like liquid exuded during strong-aroma Baijiu fermentation, serves as the core medium for material exchange between pit mud and fermented grains. However, how its micro-ecosystem evolves with cellar age and drives flavor formation remains unclear. Using Huangshui as a dynamic window, this study integrated metagenomics, metabolomics, and flavoromics to compare its temporal dynamics in new and old cellars over a complete fermentation cycle, systematically characterizing how cellar age is associated with the restructuring of the microbial community and metabolic functions of Huangshui, and how these changes are consistent with the flavor profiles observed in the final base liquor. The results showed that Huangshui from old cellars harbored a more diverse and stable microbial community, forming a syntrophic consortium of caproic acid-producing bacteria (Caproicibacterium, Caproiciproducens), syntrophic bacteria (Syntrophomonas), and methanogenic archaea (Methanosarcina), whereas new cellars were dominated by lactic acid bacteria (Acetilactobacillus). Metabolically, the old-cellar community exhibited a clear phase-dependent division. During the acid-producing phase, the TCA cycle, arginine biosynthesis, and pyruvate metabolism were preferentially activated to generate core precursors; during esterification, butanoate metabolism and acyl-CoA supply pathways were enhanced. This orderly shift was associated with higher concentrations of ethyl caproate and ethyl octanoate in old-cellar base liquor. Functional gene analysis revealed coordinated upregulation of chain-elongation, methanogenic, and acetate-activating pathways in old cellars. Network analysis revealed a tightly coupled caproic acid-producing co-occurrence module in old cellars, which was not observed in new ones. Together, these findings suggest that Huangshui may serve as a rapid proxy for assessing both the fermentation status and the maturity level of the cellar. This work identifies potential bioaugmentation targets to accelerate flavor development in new cellars and provides a theoretical basis for the precise micro-ecological management of strong-aroma Baijiu quality.},
}

Fermentation
Metabolomics
*Odorants/analysis
*Taste
Bacteria/metabolism/genetics
*Wine/analysis/microbiology
*Alcoholic Beverages/analysis/microbiology
Metagenomics
*Microbiota
Flavoring Agents

@article {pmid42551103,
year = {2026},
author = {Esener, N and Kırbaş, M and Kal, Y and Aladağ, F},
title = {Microbial signatures of the vaginal microbiome associated with pregnancy outcome in central Anatolian Merino sheep.},
journal = {Theriogenology},
volume = {265},
number = {},
pages = {118119},
doi = {10.1016/j.theriogenology.2026.118119},
pmid = {42551103},
issn = {1879-3231},
abstract = {Reproductive efficiency is a key determinant of sustainability and profitability in sheep farming systems; however, the role of the vaginal microbiome in shaping pregnancy outcomes remains insufficiently understood. This study aimed to characterise the vaginal microbial communities of Central Anatolian Merino sheep using 16S rRNA gene amplicon sequencing and to explore their potential association with reproductive success. Vaginal samples were collected from 20 healthy ewes (10 non-pregnant (G1), that failed to conceive and returned to oestrus and 10 pregnant (G2), conceived at first service) with comparable physiological characteristics before breeding, followed by high-throughput amplicon sequencing to comprehensively profile the bacterial community structure. Comparative analyses were conducted between pregnant and non-pregnant animals to identify microbial patterns linked to pregnancy outcomes. The vaginal microbiome exhibited a diverse yet structured taxonomic composition across both groups, dominated by members of Bacillota (44.8% in G1 and 45.6% in G2), Actinomycetota (12.0% in G1 and 9.3% in G2), Pseudomonadota (6.6% in G1 and 6.2% in G2) and Bacteroidota (5.6% in G1 and 5.9% in G2). Alpha diversity did not differ significantly between groups (Wilcoxon rank-sum test, p > 0.05 across all indices), and beta diversity showed no significant separation (PERMANOVA, R[2] = 0.055, p = 0.38), indicating substantial community overlap. Differential abundance analysis (edgeR) identified 23 taxa that differed between groups (FDR < 0.05), suggesting that reproductive outcomes may be influenced by subtle ecological shifts rather than large-scale microbial restructuring. Collectively, these findings provide novel insights into the vaginal microbial ecology of Central Anatolian Merino sheep and identify candidate microbial signatures that may warrant further investigation as potential correlates of fertility. Given the observational design and limited sample size, these associations should be interpreted as preliminary and hypothesis-generating. By advancing our understanding of host-microbiome interactions within the reproductive tract, this study establishes a foundation for microbiome-informed strategies aimed at improving reproductive performance and supporting sustainable sheep production.},
}

@article {pmid42552662,
year = {2026},
author = {Chen, M and Li, R and Xiang, Y and Ma, X and Yu, X and Zhao, J and Ren, D},
title = {Pasteurized Akkermansia muciniphila AKK PROBIO ameliorates inflammation and metabolic disorder in db/db mice with alterations in gut microbiota and hepatic TLR4/NF-κB and SREBP2/HMGCR signaling.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70969},
pmid = {42552662},
issn = {1097-0010},
support = {//This work was supported by the National Natural Science Foundation of China (Grant No. 32172189), the Natural Science Foundation of Jilin Province (Provincial-Local Joint Fund; Grant No. YDZJ202501ZYTS312), and Jilin Agricultural University (Horizontal Research Project-Safety Evaluation and Metabolic Regulation Function of Akkermansia; Grant No. H20250226)./ ; },
abstract = {BACKGROUND: Diabetes mellitus, especially type 2 diabetes mellitus (T2DM), represents a significant global health challenge. Growing evidence indicates that Akkermansia muciniphila, a promising next-generation beneficial microorganism, could help alleviate metabolic disorders. Nevertheless, its strain-specific effects and associated mechanisms require further investigation. Here, we investigated the potential effects of pasteurized A. muciniphila AKK PROBIO in T2DM using db/db mice.

RESULTS: Our findings show that pasteurized AKK PROBIO supplementation was associated with lower fasting glucose levels, reduced inflammatory markers, and improved cholesterol balance in db/db mice. Pasteurized AKK PROBIO administration was accompanied by changes in gut microbiota composition, including enrichment of bacterial taxa linked to short-chain fatty acid (SCFA) production, and by increased GLP-1 levels and altered serum metabolites, including 9,9'-di-cis-ζ-carotene and l-arginine. These changes were paralleled by reduced hepatic expression of proteins related to the TLR4/MyD88/IKKα/NF-κB and SREBP2/HMGCR signaling pathways.

CONCLUSIONS: Taken together, our findings indicate that pasteurized AKK PROBIO ameliorates metabolic disorder and inflammation in db/db mice, accompanied by changes in gut microbial ecology, serum metabolites, and hepatic inflammatory/lipid metabolic signaling. This study supports pasteurized A. muciniphila AKK PROBIO as a postbiotic for further investigation in metabolic disorders. © 2026 Society of Chemical Industry.},
}

@article {pmid42554875,
year = {2026},
author = {Zhang, H and Zhang, Y and Zhang, C and Yang, Y and Hu, B and He, T and Zhang, J and Song, X and Su, Y},
title = {Microbial architects of cigar fermentation: a critical review of beneficial roles in quality enhancement and detrimental potential for mould spoilage.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42554875},
issn = {1432-072X},
support = {2023530000241002//the Science and Technology Plan Project of the China National Tobacco Corporation, Yunnan Provincial Company/ ; yxyc2023007//General Project of the Science and Technology Program of Yuxi Company, Yunnan Provincial Tobacco Company/ ; },
mesh = {*Fermentation ; *Fungi/metabolism/growth & development ; *Nicotiana/microbiology/metabolism ; *Food Microbiology ; *Bacteria/metabolism/classification/isolation & purification ; },
abstract = {Cigar tobacco fermentation is a microbially driven process that transforms raw tobacco leaves into a product with distinctive sensory attributes, yet the current understanding of the microbial roles in this process remains fragmented between descriptive community surveys and isolated mechanistic studies, with beneficial and detrimental microbial functions rarely integrated into a unified risk-benefit assessment. This review critically examines the microbiology of cigar fermentation through a dual-axis framework organized around beneficial metabolic functions and detrimental spoilage potential, each resolved into microbial identity, biochemical mechanism, and environmental modulation dimensions. We synthesize evidence from culture-dependent and culture-independent studies on microbial community assembly and succession, where Bacillus, Staphylococcus, and Aspergillus emerge as core fermentation genera, and evaluate the complementary three-pathway system - macromolecular enzymatic degradation, targeted biotransformation of tobacco alkaloids and polyphenols, and de novo biosynthesis of aroma-active volatiles - that drives flavor and quality enhancement. We further analyze the contrastive microbial balance governing tobacco-specific nitrosamine (TSNA) formation, where nitrate-reducing bacteria compete with nitrate-assimilating and nitrite-scavenging microorganisms to determine the net TSNA load. In parallel, we critically examine the mould spoilage microbiology of cigar fermentation, identifying the environmental thresholds - humidity above 80% RH, water activity above 0.85, and inadequate aeration - that select for mycotoxigenic Aspergillus and Penicillium species producing aflatoxins and ochratoxin A at levels that persist into the finished product. We survey emerging biotechnological strategies spanning bioaugmentation with defined starter cultures, biostimulation through environmental optimization, and biocontrol of spoilage fungi, and identify five critical research gaps - including the absence of gnotobiotic fermentation models and the predominance of correlative over causal studies - that must be addressed to translate microbial ecology into predictable fermentation biotechnology. By integrating microbial ecology, fermentation biochemistry, spoilage prevention, and applied biotechnology, this review is intended for researchers in tobacco microbiology and fermentation science, as well as cigar manufacturers, quality-control practitioners, and biotechnologists seeking microbiome-based strategies for quality improvement and risk mitigation.},
}

*Fermentation
*Fungi/metabolism/growth & development
*Nicotiana/microbiology/metabolism
*Food Microbiology
*Bacteria/metabolism/classification/isolation & purification

@article {pmid42550534,
year = {2026},
author = {Celik, G and Yanik, E and Inan, N and Yalinay, AM},
title = {Absence of a Consistent Gut or Oral Microbial Signature in Fibromyalgia Under Strictly Controlled Clinical Conditions: A Multi-Compartment 16S rRNA Analysis.},
journal = {Pain physician},
volume = {29},
number = {5},
pages = {E407-E416},
pmid = {42550534},
issn = {2150-1149},
mesh = {Humans ; Female ; *Fibromyalgia/microbiology ; *RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Adult ; *Mouth/microbiology ; Middle Aged ; Prospective Studies ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: Fibromyalgia (FM) has been increasingly studied in the context of gut-brain-immune interactions, and several reports have suggested an association between FM and alterations in gut or oral microbial communities. However, prior studies have often suffered from heterogeneous comorbidities, inconsistent sampling procedures, and limited control for environmental factors, making it unclear whether FM is associated with a reproducible, site-independent microbial signature.

OBJECTIVES: To determine whether women with FM exhibit consistent alterations in gut or oral microbiota when evaluated under strictly standardized physiological, clinical, and environmental conditions.

STUDY DESIGN: A prospective, observational, case-control study.

SETTING: The Department of Pain Medicine and Department of Medical Microbiology at Gazi University, Türkiye.

METHODS: The patient selection comprised 31 women (16 with FM; 15 healthy controls) who met rigorous inclusion and exclusion criteria, minimizing confounding from diet, metabolic disease, medications, hormonal status, and recent infections. No therapeutic intervention was performed; all patients provided paired oral mucosal and fecal samples during the follicular phase of the menstrual cycle. Sequencing of 16S rRNA V3-V4was performed on DNA extracted from all samples. Alpha and beta diversity metrics, taxonomic profiles, and differential abundance analyses (including LEfSe with FDR correction) were compared between groups. The clinical severity of FM was assessed using scores on the visual analog scale (VAS), Widespread Pain Index (WPI), and Symptom Severity Scale (SSS).

RESULTS: No statistically significant differences were observed between FM patients and controls in fecal or oral alpha diversity (Shannon, Simpson, Chao1, Observed OTU indices, all P > 0.05). Beta diversity analyses (Bray-Curtis PERMANOVA) revealed no between-group separation in either compartment (fecal R² = 0.032, P = 0.529; oral R² = 0.032, P = 0.464). Both groups displayed preserved core microbial communities in the gut, dominated by Firmicutes and Bacteroidota and, in the oral cavity, Streptococcus-enriched profiles. Minor genus-level variations were detected, but none remained significant after FDR correction. Cross-site analyses confirmed the expected ecological divergence between oral and fecal habitats but identified no FM-specific microbial pattern. Post hoc sensitivity analysis indicated that the study was powered to detect only moderate effect sizes (R² ≥ 0.11), suggesting that subtle differences might have remained undetected.

LIMITATIONS: A modest sample size, a lack of quantitative dietary assessment, and reliance on 16S rRNA sequencing limited the detection of subtle or functional microbial alterations. Additionally, the cross-sectional design precludes causal inference.

CONCLUSIONS: Under highly controlled sampling and exclusion conditions, FM was not associated with detectable alterations in the diversity or composition of gut or oral microbes. These findings suggest that previously reported dysbiosis may reflect comorbidity-driven or phenotype-specific variation rather than a universal microbial hallmark. Larger, multi-omic and phenotype-stratified studies are needed to clarify functional host-microbiome interactions in FM.},
}

Humans
Female
*Fibromyalgia/microbiology
*RNA, Ribosomal, 16S/genetics
Case-Control Studies
Adult
*Mouth/microbiology
Middle Aged
Prospective Studies
*Microbiota
*Gastrointestinal Microbiome/genetics
Feces/microbiology

@article {pmid42548192,
year = {2026},
author = {Feng, J and Wang, Z and Xu, Y and Peng, J and Xu, C and Xie, Q and Li, Y and Chen, W and Chen, J and Wang, X and Gao, WQ and Li, L and Meng, X},
title = {Intestinal epithelial SETD2 maintains gut microbial homeostasis to attenuate colitis.},
journal = {Clinical and translational medicine},
volume = {16},
number = {8},
pages = {e70754},
pmid = {42548192},
issn = {2001-1326},
support = {2022YFA1302704//National Key R&D Program of China/ ; 2023YFC1404101//National Key R&D Program of China/ ; YG2024ZD11//Interdisciplinary Program of Shanghai Jiao Tong University/ ; 32570684//National Natural Science Foundation of China/ ; 82372604//National Natural Science Foundation of China/ ; U23A20441//National Natural Science Foundation of China/ ; W2431055//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Mice ; *Colitis ; *Histone-Lysine N-Methyltransferase/metabolism/genetics ; *Homeostasis ; *Gastrointestinal Microbiome/physiology/drug effects/genetics ; Mice, Knockout ; *Intestinal Mucosa/metabolism ; Male ; },
abstract = {BACKGROUND: Disruption of host-microbiota homeostasis is a fundamental hallmark of inflammatory bowel disease (IBD) pathogenesis. Host epigenetic modifications and corresponding alterations in gene expression levels can impact the composition of gut microbes. SET domain containing 2 (SETD2) is a critical epigenetic regulator with established tumor-suppressive roles, but its function in intestinal microbial ecology and colitis progression remains unexplored. We aimed to investigate the specific role of SETD2 in maintaining gut microbial homeostasis and modulating colitis progression.

METHODS: RNA sequencing (RNA-seq), assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and cleavage under targets and tagmentation sequencing (CUT&Tag-seq) were conducted on colonic epithelial cells from intestinal epithelial cell-specific SETD2 knockout (Setd2[vil-ko]) mice to identify key mediators contributing to colitis development. Faecal samples underwent 16S rRNA sequencing and non-targeted metabolomics analysis to characterise microbial dysbiosis and metabolic perturbations. Molecular experiments and faecal microbiome transplantation experiment were conducted to explore and validate the role of SETD2 in colitis development.

RESULTS: SETD2 deficiency induced overproduction of Reg3 lectins and disrupted gut microbiota composition. Beneficial commensal bacteria were depleted and dysregulated metabolites were accumulated in Setd2[vil-ko] mice. Supplementation with healthy-like gut microbiota significantly ameliorated the exacerbated colitis induced by SETD2 deficiency.

CONCLUSIONS: Our findings uncover a previously unrecognised role for SETD2 in maintaining microbial homeostasis, offering new mechanistic insights into how epigenetic regulation preserves intestinal homeostasis and suggesting novel therapeutic avenues for IBD.},
}

Animals
Mice
*Colitis
*Histone-Lysine N-Methyltransferase/metabolism/genetics
*Homeostasis
*Gastrointestinal Microbiome/physiology/drug effects/genetics
Mice, Knockout
*Intestinal Mucosa/metabolism
Male

@article {pmid42549413,
year = {2026},
author = {Feng, S and Si, X and Lu, C and Gao, Z and Wang, J and Yang, Q and Lu, S and Su, T and Yang, J and He, X and Wu, L},
title = {Washed microbiota transplantation improves clinical symptoms, gut microbiota, and metabolic profiles in autism spectrum disorder in a twin cohort.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1885281},
pmid = {42549413},
issn = {1664-302X},
abstract = {OBJECTIVE: Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by impaired social communication, repetitive behaviors, and restricted interests. Dysregulation of the microbiota-gut-brain axis is closely associated with the pathogenesis of ASD. Washed microbiota transplantation (WMT) has emerged as a promising intervention for ASD, but existing cohort studies lack genetically identical controls, making it difficult to distinguish intervention-related changes from genetic and environmental confounding factors. This twin-paired controlled study adopted a study design that minimizes the influence of genetics and shared environment, to explore the associations of WMT with clinical symptoms, gut microbiota, and metabolic profiles in children with ASD.

METHODS: Three pairs of age- and environment-matched twins (one ASD-affected, one typically developing sibling) were enrolled. WMT was administered to the ASD participant in each pair. Fecal samples were collected at baseline and post-intervention. Gut microbiota and metabolic profiles were analyzed using metagenomic sequencing and targeted metabolomics, respectively. Clinical outcomes were evaluated using the Childhood Autism Rating Scale (CARS), Autism Behavior Checklist (ABC), Sleep Disturbance Scale for Children (SDSC), and Bristol Stool Form Scale (BSFS). Relevant observations were carried out to explore potential changing trends.

RESULTS: After WMT, CARS, ABC, SDSC, and BSFS exhibited small numerical directional shifts toward healthier values, but none reached statistical significance. Gut microbial structure and function presented a shifting trend toward the profile of their typically developing twin siblings. Abnormal lipid and energy metabolism indicators showed partial ameliorative trends, and the number of differential metabolites between ASD patients and healthy siblings was markedly reduced. Tyrosine and phenylalanine metabolic pathways, together with Segatella, Negativibacillus, and Sangeribacter, may be associated with incomplete phenotypic changes in this cohort.

LIMITATIONS: Although the twin-pair design has high internal validity and can provide strong causal inference evidence for the effect of microbiota transplantation in treating ASD, this study has limitations such as a small sample size, a single-center non-randomized observational design. All findings in this pilot study are merely descriptive trends, and the relevant mechanism analysis only provides correlational clues. A single session of microbiota transplantation failed to fully adjust aromatic amino acid metabolism in ASD children. No definitive causal relationship can be concluded based on the findings of this small-sample pilot study.

CONCLUSION: Under tightly controlled genetic and environmental conditions, gut microbial dysbiosis presents correlational characteristics with ASD-related phenotypes. WMT was associated with consistent remodeling of gut microbial ecology and partial resolution of metabolic dysregulation in ASD children, with multi-omic signatures converging toward healthy twins. Clinical rating scales only displayed non-significant minor numerical shifts, which cannot be interpreted as evidence of clinical symptom improvement. These initial findings provide exploratory mechanistic clues and phenotypic data supporting WMT as a targeted microbiome intervention approach for ASD, and await further validation through large-scale randomized controlled trials.

CLINICAL TRIAL REGISTRATION: Identifier ChiCTR2400091105.},
}

@article {pmid42545919,
year = {2026},
author = {Vielma-Puente, JE and Mosquera-Romero, S},
title = {Green Synthesis of Gold and Silver Nanoparticles Using Plant Extracts, Fungal Filtrates, and Bacterial Cultures.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {233},
pages = {},
doi = {10.3791/70729},
pmid = {42545919},
issn = {1940-087X},
mesh = {*Gold/chemistry/metabolism ; *Metal Nanoparticles/chemistry ; *Silver/chemistry/metabolism ; *Green Chemistry Technology/methods ; *Plant Extracts/chemistry ; Cupriavidus/metabolism/chemistry ; Shewanella/metabolism/chemistry ; Fungi/metabolism/chemistry ; },
abstract = {Green synthesis of metal nanoparticles (NPs) using biological systems provides a sustainable alternative to conventional chemical fabrication methods. This protocol presents reproducible experimental and analytical procedures for the synthesis of gold (Au) and silver (Ag) NPs using bacterial cultures, fungal filtrates, and plant leaf extracts as reducing and stabilizing agents. AgNPs were synthesized using extracts from Psidium guayaquilensis, Acanthophora spicifera, and Earliella sp., exhibiting characteristic ultraviolet-visible (UV-Vis) absorption bands between 405 and 425 nm that confirmed NP formation. A design-of-experiments approach was implemented to evaluate the influence of environmental factors, including oxygen conditions, pH, Au concentration, cell concentration, electron donor type, and temperature, on the synthesis of AuNPs by Shewanella oneidensis and Cupriavidus metallidurans. Under ideal conditions (0.2 mM Au and pH 5), S. oneidensis produced predominantly spherical AuNPs with an average size of 43.6 ± 11.0 nm and a characteristic absorption peak at 520 nm. NP formation and morphology were confirmed using UV-Vis spectroscopy and transmission electron microscopy. This workflow provides a reproducible platform for biogenic NP synthesis and supports applications in biosensing, bioremediation, and antimicrobial technologies.},
}

*Gold/chemistry/metabolism
*Metal Nanoparticles/chemistry
*Silver/chemistry/metabolism
*Green Chemistry Technology/methods
*Plant Extracts/chemistry
Cupriavidus/metabolism/chemistry
Shewanella/metabolism/chemistry
Fungi/metabolism/chemistry

@article {pmid42547937,
year = {2026},
author = {Li, S and Zhang, S and Liu, Y and Liu, Y},
title = {From Mood to Mouth: Unraveling the Impact of Emotional Dysregulation on Periodontitis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70440},
pmid = {42547937},
issn = {1601-0825},
support = {L2510103//Natural Science Foundation of Beijing, China/ ; 82201053//National Natural Science Foundation of China/ ; BJPSTP-2025-29//Beijing Physician Scientist Training Project/ ; JLPYPT2025012//Basic-Clinical Joint Research and Cultivation Platform of Capital Medical University/ ; CXJJ25101//Innovation Foundation of Beijing Stomatological Hospital, Capital Medical University/ ; QML20231506//Beijing Municipal Administration of Hospitals' Youth Programme/ ; YSP202105//Beijing Stomatological Hospital, Capital Medical University Young Scientist Program/ ; CFH20242024-1-2141//Capital's Funds for Health Improvement and Research/ ; 202601AT070266//Yunnan Fundamental Research Projects/ ; },
abstract = {OBJECTIVES: Periodontitis is a chronic infectious disease which is recognized as a major cause of periodontal tissue destruction. Negative emotional states have been associated with periodontitis, although causal inference remains constrained by heterogeneous exposure and outcome measures. This narrative review critically examines the evidence linking emotional dysregulation with periodontitis and summarizes plausible psychoneuroimmunological pathways.

SUBJECTS: This review focuses on the association between psychological stress and periodontitis, including the psychoneuroimmunological pathways mediated by the hypothalamic-pituitary-adrenal axis and sympathetic nervous system. Current experimental models and clinical epidemiological evidence support this psychophysiological interconnection.

RESULTS: Psychological stress may influence periodontal inflammation through HPA axis and SNS/SAM-mediated changes in immune regulation and, potentially, alterations in oral microbial ecology. Converging experimental and clinical evidence supports the biological plausibility of this psychophysiological link, although heterogeneity in exposure assessment, periodontal outcome definitions, and study design limits causal inference.

CONCLUSIONS: Further understanding of stress-periodontitis interactions provides insights into an emerging oral-brain crosstalk mechanism, which may help identify prospective therapeutic targets for interceptive periodontal management.},
}

@article {pmid42544022,
year = {2026},
author = {Doolittle, CJ and Crowther, TW and Delavaux, CS and LaManna, JA},
title = {Environmental stress strengthens plant-mycorrhizal associations: A novel extension of the stress gradient hypothesis.},
journal = {Ecology},
volume = {107},
number = {8},
pages = {e70465},
pmid = {42544022},
issn = {1939-9170},
support = {TMPFP3_209925//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; DEB-2024903//Division of Environmental Biology/ ; DEB-2025755//Division of Environmental Biology/ ; DEB-2310100//Division of Environmental Biology/ ; },
mesh = {*Mycorrhizae/physiology ; *Stress, Physiological ; Oregon ; *Plants/microbiology ; Trees/microbiology/physiology ; },
abstract = {Understanding how environmental stress alters the strength of local interactions is key to explaining diversity in current and future plant communities. Along gradients of increasing environmental stress, traditional theory posits that plants experience stronger facilitative interactions and weaker antagonistic interactions. However, it remains unclear whether this pattern extends to the relative host-specificity of plant-microbe interactions along stress gradients. Understanding these dynamics is particularly important for plant interactions with pathogenic and mycorrhizal fungi, which can drive opposing density-dependent processes that shape plant community compositions. We posit that increases in abiotic environmental stress are associated with stronger associations between plants and mutualists as plants increasingly rely on facilitative resource partnerships to cope with abiotic environmental stressors. We tested this prediction along an abiotic stress gradient in the central Cascade Range of Oregon, USA, using overlapping datasets of large high-resolution forest inventory plots, soil chemistry, and amplicon sequencing. Consistent with our predictions, in low-elevation forest stands with benign abiotic conditions and abundant nutrients, tree composition was more correlated with pathogenic fungal composition than ectomycorrhizal fungal composition. However, in forests at high elevations with limited nutrients and harsher climates, tree community composition was more correlated with ectomycorrhizal fungal composition than pathogenic fungal composition. Additionally, we find that spatial aggregation of ectomycorrhizal fungi increases as abiotic stress increases with elevation and opposing patterns of pathogen and ectomycorrhizal relative abundance in different substrate layers. Together, our findings suggest that facilitative interactions in stressful environments extend to mutualist-plant interactions and such interactions play a key role in shaping forest composition along environmental stress gradients.},
}

*Mycorrhizae/physiology
*Stress, Physiological
Oregon
*Plants/microbiology
Trees/microbiology/physiology

@article {pmid42544462,
year = {2026},
author = {Rizaludin, MS and Dickschat, JS and Raaijmakers, JM and Garbeva, P},
title = {Volatile dialogues between plants and microorganisms.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6np00045b},
pmid = {42544462},
issn = {1460-4752},
abstract = {Covering: up to 2026Volatile organic compounds (VOCs) are key mediators of long-distance communication in biological systems. While their roles in plant-insect interactions are well established, emerging evidence highlights their importance in plant-microbe interactions. In this highlight, we discuss the biosynthesis and ecological functions of plant VOCs (pVOCs) and their impact on microbiome assembly and function. We examine how constitutive and stress-induced pVOCs shape microbial community composition and how microbial VOCs (mVOCs) influence plant growth and defense by modulating hormonal and metabolic pathways. We further address the bidirectional nature of volatile-mediated interactions and the challenges associated with studying complex VOC blends in natural environments. Understanding these dynamic volatile dialogues provides new opportunities for microbiome engineering and sustainable crop production.},
}

@article {pmid42545019,
year = {2026},
author = {Kulosa, M and Belisário-Ferrari, MR and Semmler, F and Büttner, M and Duck, C and Namazi, Z and Jehmlich, N and von Bergen, M and Bonitz, T and Kaysser, L},
title = {Establishment of an in vitro aerobic bacterial community as a model of the human lung microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0049126},
doi = {10.1128/msystems.00491-26},
pmid = {42545019},
issn = {2379-5077},
abstract = {The human lung microbiome is increasingly recognized as a key player in drug metabolism, yet it remains largely understudied. To replicate this complex physiological environment in a controlled setting, we developed a simplified artificial lung microbiome model composed of four representative bacterial species: Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei. We successfully established a stable 10-day co-culture at 34°C using brain heart infusion medium, as validated by quantitative PCR, viability PCR, and conventional microbiological methodologies. Integrated bioinformatic analyses revealed a variety of potential microbe-microbe interactions, which were supported by metaproteomic analysis using mass spectrometry. Our model provides a foundation for in-depth studies, such as, for example, the effects of pulmonary drugs on the lung microbiome, and how, in turn, the microbiome may influence therapeutic outcomes.IMPORTANCEOnce thought to be sterile, the lung microbiome is now understood to host a dynamic microbiome capable of influencing respiratory health and disease. Understanding interactions among the microbes within this community is essential, as these relationships may drive disease progression or foster resilience in both acute and chronic inflammatory conditions. We developed a reproducible lung microbiome model comprising Pseudomonas koreensis, Rothia aeria, Streptococcus downei, and Neisseria cinerea. Simplified models enable controlled studies to dissect specific microbial interactions, laying the foundation for insights into lung microbial ecology. In the future, more complex models will enhance our understanding of microbial roles in disease outcomes, with our platform serving as a basis for testing therapeutic strategies.},
}

@article {pmid42545497,
year = {2026},
author = {Hossen, S and Groß, C and Roy, F and Kellner, H and Noll, M and Borken, W},
title = {Chronic Nitrogen Deposition Alters Diazotrophic Community Composition, Reduces Biological Nitrogen Fixation, and Restructures Fungal-Diazotroph CO-Occurrence Networks in Deadwood.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42545497},
issn = {1432-184X},
mesh = {*Nitrogen Fixation ; *Nitrogen/metabolism/analysis ; *Fungi/metabolism/genetics/classification ; *Trees/microbiology/metabolism ; *Wood/microbiology/metabolism ; Soil Microbiology ; Oxidoreductases/genetics ; Bacteria/metabolism/genetics/classification/isolation & purification ; },
abstract = {Biological nitrogen fixation (BNF) by diazotrophs contributes to increasing nitrogen (N) availability in nutrient-poor deadwood during the decomposition process. However, chronically elevated atmospheric N deposition may increase N availability, thereby reshaping diazotrophic community and suppressing BNF. We simulated high N deposition by repeatedly applying ammonium-nitrate solution to deadwood of 13 tree species over 9 years (N addition) and compared diazotrophic community composition and BNF rates with untreated controls. Deadwood N concentrations increased over time in both control and N addition, with N addition resulting in higher N concentrations at the final sampling, although significant treatment effects were detected only in Tilia and Pinus. Chronic high-N addition was associated with reduced BNF activity, with significant suppression primarily observed in coniferous deadwood, while responses among broadleaved species were weak, variable, or absent. The N addition altered diazotroph richness and community composition by increasing the abundance of Bradyrhizobium and by reducing Methylocapsa across all tree species. Under N addition, BNF correlated positively with nifH gene copy numbers in broadleaved deadwood but negatively in coniferous deadwood. Co-occurrence networks were more interconnected and modular under N addition, with diazotrophs (e.g., Azospirillum) central in broadleaved deadwood and fungi (e.g., Meliniomyces, Athelia) central in coniferous deadwood. Tree clade (coniferous vs. broadleaved) strongly shaped richness and community response, with broadleaved and coniferous species showing distinct patterns.Overall, the largely robust diversity and community composition of diazotrophs and BNF activity under high N addition suggest that moderately increasing N deposition has little influence on fungal deadwood decomposition and the function of deadwood as a carbon pool in forest ecosystems.},
}

*Nitrogen Fixation
*Nitrogen/metabolism/analysis
*Fungi/metabolism/genetics/classification
*Trees/microbiology/metabolism
*Wood/microbiology/metabolism
Soil Microbiology
Oxidoreductases/genetics
Bacteria/metabolism/genetics/classification/isolation & purification

@article {pmid42545607,
year = {2026},
author = {Li, R and Yuan, B and Yi, X and Yin, E and Huang, B and Min, Q and Zhou, J and Lv, M and Zhang, B and Zhao, N},
title = {Dietary Bacillus sp. ‌Modulates Multi-tissue Metabolism Through Gut Microbiota Remodeling in High-fat Fed Larimichthys crocea.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42545607},
issn = {1867-1314},
support = {ZJW-2023-01//the Fund of Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang)/ ; 2023A1515010576//the Guangdong Basic and Applied Basic Research Foundation/ ; 2025TQ09A155//Guangdong High-Level Talent Special Support Program-Young Top-Notch Talent in Science and Technology Innovation/ ; },
abstract = {High-fat diets (HFDs) are widely utilized in aquaculture and result in multiple health and welfare problems in aquatic animals, yet the systemic impacts on host metabolism and gut microbial ecology of HFDs remain insufficiently understood let alone the exact solutions. Here, we investigated the effects of Bacillus thuringiensis Sd_h10 (abbreviated as h10) supplementation on gut microbiota composition, metabolic homeostasis and growth performance in juvenile Larimichthys crocea fed with a high-fat diet. Our results showed that high-fat diet with h10 partially altered intestinal microbial community composition, enhanced the complexity of microbial co-occurrence and was associated with tissue-specific alterations in lipid distribution. Specifically, h10 promoted the deposition of polyunsaturated fatty acid (PUFA) and glucose utilization in intestinal and muscle tissues, while concurrently alleviating hepatic lipid accumulation. Moreover, the expression of genes associated with lipid metabolism, carbohydrate utilization and protein turnover was differentially regulated in the intestine, liver, and muscle, indicating coordinated metabolic adjustments across tissues. Fish in the HFD + h10 exhibited significantly higher relative weight gain and length gain than those in other treatments (P < 0.05). This enhanced growth performance was accompanied by upregulation of growth-promoting genes (gh1, igf1, and myod) and suppression of the growth-inhibitory gene (mstnb) in multiple tissues. Furthermore, partial least squares path modeling (PLS-PM) revealed significant structured associations linking gut microbiota composition, tissue-specific metabolic phenotypes, and growth performance. Collectively, our findings indicated that h10 supplementation may modulate gut microbiota and be associated with multi-tissue metabolic coordination under high-fat dietary conditions. This study provides new insights into the potential role of microbiota-associated metabolic regulation in supporting growth performance in marine aquaculture species.},
}

@article {pmid42535857,
year = {2026},
author = {Szafrański, SP and Joshi, AA and Steglich, M and Yang, I and Qu, T and Behrens, W and Muthukumarasamy, U and Melidis, D and Schaefer-Dreyer, P and Grischke, J and Hegermann, J and Nejdl, W and Häussler, S and Stiesch, M},
title = {High-resolution taxonomic profiling and metatranscriptomics identify microbial, biochemical, host, and ecological factors in peri-implant disease.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0075425},
doi = {10.1128/msystems.00754-25},
pmid = {42535857},
issn = {2379-5077},
abstract = {UNLABELLED: Biofilm-associated diseases like peri-implant mucositis (PIM) and peri-implantitis (PI) are significant clinical challenges affecting millions of dental implant patients globally. Although studies have described the role of microbial, host, or environmental factors in disease development, their complex interplay, particularly during dysbiosis, remains poorly understood. This cross-sectional study characterized the microbiome composition and metatranscriptomes of 125 peri-implant biofilms from 48 individuals, uncovering molecular signatures linked to peri-implant health (PIH), PIM, and PI. Distinct variations were observed in biofilm amount, microbial composition and activity, phage populations, and host response. Biofilms were categorized into four community types (CTs) based on the bacterial transcriptional activity: one linked to PIH, one to PI, and two to PIM. PIH and PIM were primarily characterized by aerotolerant taxa with increased anabolic processes, while PI was dominated by obligate anaerobes with complex biofilm morphology. PIM samples, relative to PIH, were characterized by biofilm expansion with minimal functional changes, except for the Neisseria-rich PIM subtype showing higher pyruvate and lipoic acid metabolism. The phagome mirrored the bacterial compositional variations across disease states. Furthermore, human transcriptome responses varied, indicating increased keratinization in PIH, enhanced expression of ribosome components in PIM, and inflammatory signaling and hypoxia in PI. Additionally, we identified complex species-enzyme, phage-bacterium, and host-microbe associations within the peri-implant ecosystem. Our integrative multi-omics approach provides a comprehensive view of microbial, biochemical, host, and ecological factors associated with dysbiosis, offering novel insights into peri-implant disease dynamics.

IMPORTANCE: Peri-implant mucositis and peri-implantitis are highly prevalent inflammatory conditions that compromise the long-term survival and success of dental implants, yet their underlying biological mechanisms are largely unresolved. The full-length 16S rRNA gene amplicon sequencing (full-16S) allows for high-resolution taxonomic profiling of peri-implant biofilms, thereby advancing our understanding of microbial composition across health and peri-implant diseases. The integration of metatranscriptomics, furthermore, captures actively transcribed genes within the biofilm and offers direct insights into microbial community functions and the broader molecular context of peri-implant dysbiosis. DNA- and RNA-derived abundances were strongly correlated, with only a few microbial classes showing moderate diagnosis-related differences after DNA-based normalization of transcriptional activity. In this study, we integrated full-16S with metatranscriptomic profiling to simultaneously assess microbial taxonomy, functional activity, phage dynamics, and host gene expression in peri-implant biofilms. Importantly, we provide a systems-level view and report previously undescribed associations between different molecular signatures in the peri-implant ecosystem.},
}

@article {pmid42537292,
year = {2026},
author = {Han, S and Mo, Q and Wen, X and Wang, X and Wang, X and Yu, Y and Yang, Y and Yang, C and Cai, Z and Zhou, J},
title = {AI-2 type quorum-sensing signal enhances mercury resistance and adsorption in thermotolerant Bacillus subtilis.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143148},
doi = {10.1016/j.jhazmat.2026.143148},
pmid = {42537292},
issn = {1873-3336},
abstract = {Heavy metal contamination in coastal sediments threatens marine microbes and ecological health. Elucidating microbial community synergistic resistance mechanisms is essential for developing novel bioremediation strategies. Microorganisms are known to regulate population-level adaptation to environmental stress through quorum-sensing signals, yet the role of autoinducer-2 (AI-2) in mercury (Hg) resistance and immobilization remains poorly understood. Here, we isolated a thermotolerant Bacillus subtilis strain from coastal sediments and demonstrated that Hg stress selectively activated luxS-associated AI-2 production. AI-2 addition enhanced bacterial survival under combined Hg and heat stress by reducing intracellular reactive oxygen species, increasing antioxidant enzyme activities, promoting biofilm formation, and strengthening Hg adsorption. Sediment microcosm validation further showed that the B. subtilis + AI-2 treatment reduced soluble Hg by 29.6% after 24 h and increased the biomass-associated Hg fraction. These results reveal an AI-2-associated microbial strategy that links intracellular detoxification with extracellular Hg immobilization. While further genetic validation is needed to establish its causal role, this mechanism provides mechanistic insight for microbiome-assisted mercury remediation in thermally dynamic coastal sediments.},
}

@article {pmid42538384,
year = {2026},
author = {Chang, M and Wang, Y and Ha, J and Neale, ZR and Ajami, NJ and Diggs, LP and Nalin, AP and Ma, Y and Dong, S and Hoballah, YM and Day, A and Jeong, SD and Wu, A and Schrank, BR and Edwards, JL and Wang, T and Wang, X and Chang, YT and Tang, C and Lim, AJ and Torres, MN and Deng, W and Peitsch, T and Dufilho, MJ and Goswami, S and Jiang, D and Koong, AC and Sharma, P and Wargo, JA and Jiang, W and Kim, BYS},
title = {A transferable gut microbiota-bile acid pathway programs nanomedicine pharmacokinetics and therapeutic response.},
journal = {Nature materials},
volume = {},
number = {},
pages = {},
pmid = {42538384},
issn = {1476-4660},
abstract = {The clinical efficacy of nanomedicines is often limited by hepatic sequestration, yet the endogenous programs determining this clearance state remain incompletely understood. Here we identify the gut microbiota as a regulator of nanomedicine biodistribution through bile-acid-associated programming of Kupffer cell phagocytic state. Using germ-free mice, microbial perturbation, faecal microbiota transplantation and multiomic profiling, we show that metronidazole remodels the gut microbial ecology and reprograms Kupffer cells into a reduced-uptake state, thereby suppressing hepatic clearance and enhancing the tumour accumulation of nanomedicines across multiple formulations and tumour models. Single-cell RNA sequencing reveals a shift in Kupffer cell populations from phagocytic to quiescent states, whereas metabolomic profiling identifies microbiota-dependent reductions in bile acid availability. Gut-bacteria-derived bile acids induce Kupffer cell phagocytosis, and faecal transfer transmits the low-clearance phenotype, defining a transferable gut microbiota-bile acid-Kupffer cell pathway affecting nanomedicine clearance.},
}

@article {pmid42539514,
year = {2026},
author = {Li, Y and Zhu, J and Huang, M and Liu, X and Wang, L},
title = {Microbiota-innate immune crosstalk drives atherosclerosis: mechanisms, disease progression, and emerging therapeutic strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1900899},
pmid = {42539514},
issn = {1664-3224},
mesh = {Humans ; *Atherosclerosis/immunology/metabolism/therapy/microbiology/etiology ; *Immunity, Innate ; Animals ; Disease Progression ; *Gastrointestinal Microbiome/immunology ; Signal Transduction ; },
abstract = {Atherosclerosis (AS) is a complex cardiovascular disease driven by the interplay of dysregulated lipid metabolism, chronic inflammation, and immune dysfunction. Increasing evidence has revealed that the gut microbiota not only regulates host metabolic homeostasis but also actively contributes to the initiation and progression of AS through intricate interactions with the innate immune system. Microbial-derived signaling molecules, including lipopolysaccharides, outer membrane vesicles, extracellular nucleic acids, and TMAO, can activate Toll-like receptors, the NLRP3 inflammasome, and nucleic acid-sensing pathways, thereby promoting inflammatory cytokine production, endothelial dysfunction, and foam cell formation. In contrast, beneficial microbial metabolites such as short-chain fatty acids, bile acids, and tryptophan-derived metabolites exert immunomodulatory and vasculoprotective effects through signaling pathways involving FFAR2/3, the AhR, the FXR, and TGR5. Conversely, the innate immune system shapes microbial composition and function through barrier defense, phagocytic clearance, and antimicrobial factor production, establishing a dynamic and reciprocal microbiota-immune interaction network. This review systematically summarizes alterations in microbial ecology and innate immune homeostasis associated with atherosclerosis, elucidates the key molecular mechanisms underlying microbiota-innate immune crosstalk, and examines its dynamic involvement across four critical stages of disease evolution: endothelial dysfunction, foam cell formation, plaque progression, and plaque destabilization and rupture. In addition, emerging therapeutic approaches, including microbiota remodeling, modulation of microbial metabolic pathways, and precision microbiome-based interventions, are comprehensively discussed. The microbiota-innate immune axis provides a novel conceptual framework for understanding atherosclerosis pathogenesis and represents a promising target for future disease prevention, risk stratification, and precision therapeutics.},
}

Humans
*Atherosclerosis/immunology/metabolism/therapy/microbiology/etiology
*Immunity, Innate
Animals
Disease Progression
*Gastrointestinal Microbiome/immunology
Signal Transduction

@article {pmid42541272,
year = {2026},
author = {Duru, VC and Mustafa, BE and Beveridge, I and Gauci, C and Elati, K and Ghafar, A and Nijhof, AM and Jabbar, A},
title = {First in vitro feeding of the Australian marsupial tick, Ixodes hirsti Hassall, 1931, with preliminary microbiome profiling and observations on the nymphal morphology.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {10},
number = {},
pages = {100413},
pmid = {42541272},
issn = {2667-114X},
abstract = {Artificial tick feeding systems (ATFS) provide a valuable alternative to animal-based models for studying tick biology. Ixodes hirsti, an Australian tick species that parasitises marsupials, remains understudied due to challenges in laboratory maintenance. Here, we report the first successful in vitro feeding of I. hirsti larvae, provide preliminary microbiome profiles of unfed larvae and larvae recovered after artificial feeding and present the first molecularly confirmed morphological description of the nymphal stage. Field-collected engorged females of I. hirsti were allowed to oviposit under laboratory conditions. Hatched larvae were artificially fed on blood using silicone membranes supplemented with kangaroo hair and/or kangaroo hair extract. Microbiomes were characterised by 16S rRNA amplicon sequencing, while scanning electron microscopy (SEM) and sequencing of 16S rRNA and cox1 genes were used for morphological and molecular characterisation of nymphs. Membranes treated with hair extract alone yielded the highest attachment rate (71%), whereas kangaroo hair-treated membranes produced superior feeding performance, with shorter time to engorgement (9.26 ± 1.00 days) and a higher engorgement weight (0.91 ± 0.01 mg). Exploratory microbiome profiling showed that fed larval pools had numerically lower microbial richness and evenness than unfed larval pools, although these differences were not significant. A total of 80 microbial taxa were shared between groups, whereas seven and 17 taxa were unique to fed and unfed larvae, respectively. Stenotrophomonas was more abundant in fed larval pools, while Coxiella-like and Rickettsia-like endosymbionts were detected in both fed and unfed larvae. These findings demonstrate that ATFS can be adapted for wildlife-associated ticks with specialised host preferences and provide a practical framework for investigating the biology and microbial ecology of ticks.},
}

@article {pmid42542067,
year = {2026},
author = {Mandal, A and Ghosh, A and Bhadury, P},
title = {Decoding the spatio-temporal dynamics within the benthic foraminiferal community structure from the northeast coastal Bay of Bengal.},
journal = {Marine environmental research},
volume = {221},
number = {},
pages = {108266},
doi = {10.1016/j.marenvres.2026.108266},
pmid = {42542067},
issn = {1879-0291},
abstract = {Benthic foraminiferal assemblages are widely used as bioproxy for coastal environment monitoring. The present study investigated seasonal variation in benthic foraminiferal assemblages and their co-occurrence patterns in response to freshwater influx and nutrient dynamics along the northeast coast of the Bay of Bengal. Over a one-year period (2021-2022), benthic foraminiferal communities, sediment total organic carbon and dissolved nutrient concentrations in surface and porewater were analyzed from intertidal zones spanning Junput and Tajpur. The benthic foraminiferal abundance varied seasonally, with Junput showing increased abundance during the post-monsoon, followed by a decline in the pre-monsoon. In Tajpur, the benthic foraminiferal abundance decreased from post-monsoon 2021 to pre-monsoon 2021, then increased in monsoon 2021 samples. The benthic foraminiferal assemblages were dominated by Asterorotalia pulchella, Ammonia sp.1, and Ammonia sp.2. Notably, Asterorotalia pulchella showed a significant positive correlation with monsoonal rainfall and sediment total organic carbon, suggesting its potential as bioproxy for monsoon-influenced environments. Network analysis revealed the negative association between Asterorotalia pulchella and members of Ammonia spp., while Asterorotalia pulchella positively co-occurred with Trochammina inflata and Quinqueloculina seminula during the monsoon. Pearson correlation and multivariate analyses revealed that surface and porewater concentrations of dissolved nitrate and ammonia, along with precipitation, were key environmental variables associated with the spatio-temporal dynamics and co-occurrence patterns within the foraminiferal communities. These findings highlight the responses of benthic foraminifera to episodic nutrient enrichment and freshwater input and underscore their utility in ecological monitoring and paleoenvironmental reconstructions across tropical estuarine systems.},
}

@article {pmid42543866,
year = {2026},
author = {Turky, M and Cooper, PR and Dummer, PMH},
title = {Precision Endodontics-Advancing Towards Omics-Guided Personalisation: A Narrative Review.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70247},
pmid = {42543866},
issn = {1365-2591},
abstract = {AIM: To critically evaluate the emerging contribution of genomics, transcriptomics, proteomics, metabolomics and microbiomics to the development of precision endodontics, and to examine the opportunities and translational challenges associated with integrating omics technologies into clinical endodontic practice.

METHODOLOGY: This narrative review synthesises recent literature across the biomedical and dental sciences, encompassing endodontic research and the principles of translational precision medicine and dentistry to assess the potential applications of omics technologies in endodontics, focusing on how these innovative approaches can inform clinical practice.

RESULTS: Emerging evidence suggests that omics technologies may enhance understanding of the biological mechanisms underlying pulpal and periapical diseases and support the identification of candidate biomarkers relevant to diagnosis, prognosis, treatment selection and outcome monitoring. Genomic and transcriptomic studies have identified molecular signatures associated with host susceptibility, inflammatory responses and tissue repair processes. Proteomic and metabolomic investigations have revealed biomarkers and metabolic pathways that may improve disease characterisation and provide insight into pulpal vitality and periapical healing. Microbiomic analyses have expanded understanding of the complex microbial ecology of endodontic infections and may contribute to the development of more targeted disinfection strategies. Furthermore, integrating multi-omics platforms and data with artificial intelligence (AI) could yield sophisticated predictive models to support personalised decision-making, thereby advancing individualised patient care. However, despite these advances, the current evidence remains largely exploratory. Many reported biomarkers and molecular signatures have not undergone robust validation, and significant challenges persist regarding standardisation, reproducibility, data integration, cost-effectiveness and clinical implementation.

CONCLUSION: The concept of precision endodontics represents a potential evolution from conventional 'one-size-fits-all' approaches to more tailored interventions guided by extensive omics data. The synergistic integration of omics and AI may provide a roadmap for developing the next generation of biologically individualised endodontic therapies. However, translating omics-driven approaches into clinically applicable diagnostic and therapeutic tools remains at an early stage. Future progress will depend on rigorous validation studies, interdisciplinary collaboration and the development of practical translational frameworks. While the combined application of omics technologies and AI has considerable potential, substantial evidence gaps must be addressed before precision endodontics can be routinely implemented in clinical practice.},
}

@article {pmid42529392,
year = {2026},
author = {Cambara, JCO and Cuber, P and Khattak, F and Lebre, PH and Galgano, S and Houdijk, J and Smallman, D and Estridge, P and Allen, MJ and Short, F and Sutcliffe, M and Mkrtchyan, HV},
title = {Long-reads metagenomics reveals the effects of dulse supplementation on the poultry caecal bacteriome and its associated genetic repertoire.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1868730},
pmid = {42529392},
issn = {1664-302X},
abstract = {INTRODUCTION: Dulse (Palmaria palmata) is a macroalgal feed ingredient rich in polysaccharides and bioactive compounds that offers a sustainable strategy to enhance animal health and productivity through modulation of gut microbiota. However, the impact of dulse supplementation on the taxonomic composition and genetic repertoire of the broiler chicken caecal microbiota remains poorly characterised.

METHODS: We applied long-read shotgun metagenomic sequencing on 18 caecal samples collected from 27-day-old male Ross 308 broilers following a 7-day feeding trial with three dietary treatments - a reference diet, a soyabean meal-supplemented diet, and a diet supplemented with 30% dulse - to investigate the effects of dulse inclusion on microbial community composition, genetic diversity, and antimicrobial resistance (AMR) and virulence determinants.

RESULTS: Across all dietary treatments, the Clostridia class predominated (71%), whereas primary fermenters (L. phocaeense), lactic acid bacteria (L. salivarius), and hydrogenotrophic cross-feeders (B. hydrogenotrophica) were enriched in the reference diet, dulse-supplemented and soyabean meal-supplemented groups, respectively (KW p < 0.05), contributing to potential improvements in caecal function, immune resilience, and nutrient utilisation while reducing pathogen load. The overall resistome profiles were comparable across dietary treatments and were dominated by genes conferring resistance to tetracyclines, lincosamides, and aminoglycosides. In contrast, the virulome displayed diet-associated shifts: Enterobacteriaceae were enriched in the dulse and reference diets relative to the soyabean meal diet, with an expanded functional repertoire of virulence-associated genes, particularly those involved in adhesion, iron acquisition, and secretion systems. Multidrug resistance genes, virulence determinants, and Col/IncF-type plasmid replicons were associated with E. coli reads, highlighting its potential resistance and virulence arsenal within the caecal microbiota.

DISCUSSION: Our findings suggest that the benefits of dulse extend beyond its nutritional value, residing in its ability to foster ecosystem resilience; by promoting a diverse, niche-stabilised microbiota, dulse minimises the risk of opportunistic pathogen proliferation, supporting its use as a sustainable, functional feed ingredient.},
}

@article {pmid42530560,
year = {2026},
author = {Boath, JM and Nardella, LL and Puschhof, J},
title = {Windows of Opportunity for Genotoxic E. coli in Colorectal Cancer Initiation.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag192},
pmid = {42530560},
issn = {1365-2672},
abstract = {Polyketide synthase-positive Escherichia coli (pks+ E. coli) has attracted significant attention following the discovery that its genotoxic metabolite, colibactin, imprints distinct mutational signatures in intestinal epithelial cells that are detectable in ∼12% of colorectal cancer (CRC) cases. Although these signatures are present in established tumors, growing evidence suggests that colibactin acts early in tumorigenesis, positioning pks+ E. coli as a potential contributor to CRC initiation. Mechanistic studies show that colibactin genotoxicity is highly context dependent and requires direct epithelial contact-a condition that is typically restricted in the healthy adult intestine. Here, we propose that colibactin mutagenesis occurs during discrete temporal windows when host barriers and microbial ecology transiently permit pks+ E. coli-epithelial interactions. These windows may arise during inflammatory disease states or early-life gut development, two contexts that share disrupted epithelial defenses, expansion of facultative anaerobes, and dynamic oxygen gradients. Defining such permissive states will be essential for establishing causal links between pks+ E. coli exposure and CRC initiation and may reveal opportunities for prevention by targeting microbial colonization during critical periods of susceptibility.},
}

@article {pmid42534899,
year = {2026},
author = {Guitart-Matas, J and Bravo, M and Tort-Miró, C and Giler-Baquerizo, N and Fraile, L and Caldas-Ramayo, Y and Ballester, M and Migura-Garcia, L},
title = {Dynamics of archaeal diversity and functionality in the piglet gut microbiome under common antimicrobial treatments.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1833734},
pmid = {42534899},
issn = {2235-2988},
mesh = {Animals ; *Archaea/classification/genetics/drug effects ; Swine ; Metagenomics ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Metagenome ; Weaning ; *Biodiversity ; *Anti-Infective Agents/administration & dosage/pharmacology ; Gene Expression Profiling ; Phylogeny ; Diarrhea/drug therapy/veterinary ; Anti-Bacterial Agents ; },
abstract = {INTRODUCTION: The gut microbiota comprises a diverse and dynamic community of microorganisms that collectively enhance host metabolism, physiology, and overall functionality. In this context, the swine archaeome remains largely underexplored despite growing evidence that archaea may greatly influence host health. Advances in high-throughput approaches provide new opportunities to reveal the dynamics and composition of archaea. Herein, we uncover the taxonomic and functional landscape of the piglet archaeome during the weaning transition under multiple experimental conditions, integrating shotgun metagenomic and metatranscriptomic analyses to elucidate its contribution to gut microbial ecology.

METHODS: The seven experimental conditions included four antibiotic treatments for post-weaning diarrhoea (trimethoprim/sulfamethoxazole, colistin, gentamicin, amoxicillin), an oral vaccine, acidifiers in drinking water, and a no-intervention group. A total of 280 faecal samples were collected longitudinally one day before weaning (ST1), three days (ST2), two weeks (ST3), and four weeks (ST4) after the start of the treatment. Treatment was initiated eleven days after arrival at the experimental farm following the onset of clinical signs. Shotgun metagenomics was used to assess archaeal taxonomic diversity and recover archaeal metagenome-assembled genomes (aMAGs), while metatranscriptomics was integrated to assess differentially expressed genes at ST1, ST2, and ST4.

RESULTS: The results revealed archaea as the second most abundant microorganism, exhibiting a longitudinal increase in diversity over the experimental time. The most predominant genus was Methanobrevibacter, including Methanobrevibacter smithii. Eleven high-quality aMAGs were recovered, belonging to the Methanobacteriota and Thermoplasmatota phyla. Genome-inferred functional analyses revealed that the predominant metabolic processes included the biosynthesis of nucleic acids, amino acids, organic anions, and vitamins. Additional functional traits suggested potential roles in the degradation of sugars, amino acids, and antibiotics were also observed. Moreover, significant differences were detected on the archaeal metatranscriptome between the experimental groups treated with antibiotics and the rest of the groups, underscoring their response to changes in microbial interactions, substrate availability and, in some cases, direct effect of the antimicrobials on metabolic pathways.

DISCUSSION: Altogether, this study highlights the biological significance of archaeal dynamics during initial life stages and demonstrates how combining metagenomics and metatranscriptomics uncovers their functional potential and the pathways actively expressed in the piglets' gut.},
}

Animals
*Archaea/classification/genetics/drug effects
Swine
Metagenomics
*Gastrointestinal Microbiome/drug effects
Feces/microbiology
Metagenome
Weaning
*Biodiversity
*Anti-Infective Agents/administration & dosage/pharmacology
Gene Expression Profiling
Phylogeny
Diarrhea/drug therapy/veterinary
Anti-Bacterial Agents

@article {pmid42526436,
year = {2026},
author = {Fang, Q and Schneider, KM},
title = {Bile acids in cancer: From metabolism to immunomodulation.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2026.07.003},
pmid = {42526436},
issn = {1097-4180},
abstract = {Bile acids have emerged as compartmentalized immunometabolic signals that link host metabolism, microbial ecology, and tumor immunity. Altered bile acid profiles are common across malignancies and are associated with tumor progression, immune tone, and responsiveness to immunotherapy. Bile acids shape the gut microbiota, and in turn, microbial enzymes diversify the bile acid pool, generating distinct bile acid species that can remodel the tumor immune landscape. Depending on species identity, concentration, and context, bile acids can support immune surveillance or enforce immune escape by reshaping antigen priming, lymphocyte fitness, myeloid suppression, and immune cell trafficking. Here, we synthesize emerging concepts defining a microbiome-bile acid-immune axis in cancer and highlight therapeutic opportunities to harness bile acid signaling as next-generation strategies in oncology.},
}

@article {pmid42528698,
year = {2026},
author = {Selim, S and Adhikary, K and Sarkar, R and Ganguly, K and Misra, A and Kashmiry, AA and Alshareef, SA and Alkhatib, SN and Hagagy, N and Maiti, R},
title = {Ecological and functional roles of plant microbiomes in environmental detoxification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1883316},
pmid = {42528698},
issn = {1664-302X},
abstract = {Plant-associated microbiomes play a crucial role in environmental detoxification by influencing the degradation, immobilization, and resistance to toxins in polluted settings. The ecological and functional activity of endogenous microbial communities, such as rhizobacteria and endophytic microorganisms, is not well studied when examining contaminants and their environments, despite the fact that plant-mediated bioremediation has garnered a lot of research attention. The majority of previously published research focuses on a single biodegradation route or solitary plant-microbe interactions. Our knowledge of how the microbiome's composition, functional diversity, and ecological stability of microbial communities work together to produce detoxifying results in practical applications is currently lacking. To advance understanding of how plant microbiomes cooperatively mediate environmental detoxification through metabolic interactions, adaptive responses, and host-microbiome communication, this review integrates insights from microbial ecology and functional microbiology. Its primary objective is to synthesize current knowledge on key microbial functions, including metal sequestration, xenobiotic degradation, redox regulation, and modulation of plant responses to biotic stress, while linking these functions to ecological processes such as host specificity, niche specialization, and community assembly. A distinctive aspect of this review is its ecosystem-level perspective, which shifts the focus from individual microbial taxa to the functional resilience of microbial communities in determining detoxification efficiency. The information provided in this review has a scope to provide framework to develop ecologically-sustaining, microbiome-based strategies for the detoxification of the environment and for conducting future bioremediation research.},
}

@article {pmid42528744,
year = {2026},
author = {Wayah, SB and Arakawa, K and Philip, K},
title = {Bacteriocins from Limosilactobacillus and Ligilactobacillus: ecological logic, mechanistic diversity, and translational potential in the post-Lactobacillus taxonomy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1875597},
pmid = {42528744},
issn = {1664-302X},
abstract = {Bacteriocins are ribosomally synthesized antimicrobial peptides that contribute to microbial competition, niche establishment, and community structure. The 2020 taxonomic reorganization of the former broad Lactobacillus genus provides a useful framework for reinterpreting bacteriocin diversity in lineage-specific ecological contexts. This review focuses on bacteriocins produced by species now assigned to Limosilactobacillus and Ligilactobacillus, two host- and food-associated genera that include several reported bacteriocin producers. These genera were selected because they contain bacteriocins with diverse structural features, including cyclic peptides, class IIa and IIb peptides, class IId peptides, defensin-like peptides, and larger proteinaceous bacteriocins, and because many producer strains originate from competitive ecological niches such as the gastrointestinal tract, oral cavity, vagina, milk, poultry, livestock, and fermented foods. We synthesize evidence on bacteriocin biosynthetic gene clusters, molecular diversity, antimicrobial mechanisms, ecological functions, physicochemical stability, and translational potential. This review also distinguishes bacteriocin-specific evidence from effects attributable to bacteriocin-producing strains, particularly for immunomodulation, co-aggregation, pathogen exclusion, and microbiota modulation. Finally, we address how comparative genomics, structured genome mining and artificial intelligence-aided prediction can speed bacteriocin discovery, emphasizing the necessity of experimental validation, standardized activity assays, safety evaluation and scalable production. This study gives a systematic framework to understand the bacteriocins of Limosilactobacillus and Ligilactobacillus in the post-Lactobacillus era by integrating taxonomy, ecology, mechanism and translational evidence.},
}

@article {pmid42528952,
year = {2026},
author = {Liu, X and Cheng, W and Li, C and Dessie, W and Qi, C and Ayaz, M and Xu, X},
title = {Integrated metagenomic and metabolomic insights into microbial metabolic reprogramming in the rhizosphere of the invasive plant Praxelis clematidea under low-temperature stress.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852122},
pmid = {42528952},
issn = {1664-302X},
abstract = {A primary factor preventing the spread of the invasive plant Praxelis clematidea to higher latitudes and altitudes is the low-temperature stress induced by global climate change. The present study investigated the impact of low-temperature stress on the rhizosphere soil micro-ecosystem of P. clematidea, with the aim of examining its adaptive micro-ecological mechanisms via a comprehensive multi-omics approach. The rhizosphere soils of plants were compared under low-temperature (LT, 5 °C) or normal-temperature (HT, 25 °C) treatments. Using soil physicochemical analysis, enzyme activity assay, metagenomics, and non-targeted metabolomics, we observed that LT stress did not significantly alter microbial alpha diversity but strongly shifted the community structure. This change enriched cold-tolerant bacterial taxa, including Nocardiopsis, Sphingobium and Azoarcus. The LT stress was associated with altered carbon and nitrogen cycling, as indicated by increased soil urease activity but decreased alkaline phosphatase and catalase activities. The nitrate-N and ammonium-N levels increased, but total nitrogen, total organic carbon, and organic matter were reduced. Additionally, metagenomic study revealed overexpression of major microbial carbon metabolism genes (e.g., TCA cycle and glycolysis) and downregulation of nitrogen assimilation genes (e.g., glnA and NasA). Furthermore, metabolomics indicated a rise in carbohydrates and vitamins, along with a notable accumulation of stress-resistant secondary metabolites such as phenolic acids, flavonoids, and terpenes in the rhizosphere soils under LT stress. Correlation analysis indicated strong positive associations between the enriched cold-tolerant genera and these stress-resistant metabolites (e.g., costunolide and choline sulfate). Functional enrichment analysis suggested a metabolic reprogramming signature coupled with low-temperature treatment. Finally, this integrated multi-omics study reveals that P. clematidea is associated with an altered rhizosphere microbiome, differential functional gene abundance, and reorganized metabolic networks under low-temperature conditions. These findings offer a vital micro-ecological elucidation for P. clematidea effective colonization and propagation in novel, colder habitats.},
}

@article {pmid42519700,
year = {2026},
author = {Pellegrinetti, TA and Molligan, J and Mendes, LW and Pedrinho, A and Pérez-López, E},
title = {Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1884628},
pmid = {42519700},
issn = {1664-302X},
}

@article {pmid42520245,
year = {2026},
author = {Lingappa, UF and Borrego, SD and Sindermann, ES and Edwards, JL and Chiang, LTE and Chastain, JL and Perrino, C and Craig, RJ and Nicora, CD and Purvine, SO and Merchant, SS},
title = {Field strains of the unicellular alga Chlamydomonas reinhardtii exhibit multicellular characteristics that shape their interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag202},
pmid = {42520245},
issn = {1751-7370},
abstract = {Chlamydomonas reinhardtii is a unicellular green alga long studied as a biological model system but rarely considered from the perspective of its own ecology, thus epitomizing the disconnection between reductionist biology in the laboratory and life in nature. Here we present insights into its ecology understood from field strains. We examined bacterial communities that coenriched with C. reinhardtii from the field, revealing specific associations. We then compared the biology of C. reinhardtii field strains to laboratory strains, illuminating strain level heterogeneity and adaptations to life in the field vs. laboratory. Field strains exhibited more robust photosynthesis, higher abundances of pherophorin proteins, a propensity for pallmeloid formation, and high cell wall permeability. Finally, we phenotyped cocultures of C. reinhardtii with a coenriched bacterial partner, demonstrating how differences between field and laboratory strains manifest in biotic interactions. Although the organisms in question are classically understood as unicellular, our observations of field strains highlighted their participation in multicellular units, challenging the utility of unicellular frameworks in extending our knowledge of model organism biology in the laboratory towards understanding microbial ecology.},
}

@article {pmid42522045,
year = {2026},
author = {Duan, L and Liang, L and Liu, W and Huang, Y and Xu, X and Liang, W and Pang, J and Wu, C},
title = {Polygonatum polysaccharides: structure-dependent gut microbiota modulation, SCFA-mediated mechanisms, and systematic health effects regulation.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70950},
pmid = {42522045},
issn = {1097-0010},
support = {KFB23129A//Science and Technology Innovation Special Fund Project of Fujian Agriculture and Forestry University/ ; },
abstract = {Dietary polysaccharide-gut microbiota interactions form a critical foundation of precision nutrition by shaping microbial ecology, metabolic outputs, and host systemic health. Polygonatum sibiricum is a traditional medicinal and edible plant rich in Polygonatum polysaccharides (PPs), which exhibit antioxidant, anti-inflammatory, and immunomodulatory activities. Despite increasing evidence for these bioactivities, the mechanistic relationships linking PPs structural characteristics with specific gut microbiota responses, defined metabolic outputs, and downstream host signaling pathways remain poorly integrated. Recent studies indicate that PPs can modulate gut microbiota composition and function by selectively enriching beneficial bacteria and enhancing short-chain fatty acid (SCFA) production. These microbial metabolites act as key signaling mediators regulating host immunity and metabolic homeostasis through G protein-coupled receptors and related pathways. However, the influence of PPs molecular weight, monosaccharide composition, branching architecture, and glycosidic linkages on microbial selectivity and metabolic specificity has not been systematically elucidated, limiting the rational design of PP-based interventions. To address these gaps, this review proposes a four-level regulatory framework, 'PPs structure-microbiota targets-SCFA pathways-host health,' which integrates PP structural features with microbiota modulation, SCFA-mediated signaling, and health outcomes, providing a theoretical basis for the precise development of PP-based functional foods and therapeutic agents. © 2026 Society of Chemical Industry.},
}

@article {pmid42524220,
year = {2026},
author = {Crous, PW and Akram, W and Albuquerque, GMR and Alfenas, AC and Alfenas, RF and Altés, A and Alvarado, P and Amirmijani, AR and Arumugam, E and Asif, M and Bandini, D and Barreto, GG and Barreto, RW and Batista, VEC and Bezerra, JDP and Bilański, P and Bizio, E and Castañeda-Ruiz, RF and Chaves, J and Condé, TO and Costa, MM and Custódio, FA and Courty, PE and Czachura, P and Damm, U and Darmostuk, V and Dearnaley, J and De la Peña-Lastra, S and Delgado, G and de Silva, NI and Dovana, F and Drummond-Herdman, A and Eberhardt, U and Esteve-Raventós, F and Ferisin, G and Ferreira, RJ and Ferro, LO and Firmino, AL and Flakus, A and Fournier, J and Gardiennet, A and Gerbeau-Pissot, P and Ghobad-Nejhad, M and Gruhn, G and Guard, FE and Harms, K and Heilmann-Clausen, J and Hongsanan, S and Hülsewig, T and Inokuti, EM and Jankowiak, R and Kaliyaperumal, M and Kehlet, T and Lacerda, SR and Larsson, E and Leão, AF and Lebel, T and Lima, AA and López-Villalba, Á and Maciá-Vicente, JG and Mateos, A and Mejía, LC and Mendes, DR and Möller, L and Mombert, A and Monteiro, MBN and Moreno, G and Nagy, L and Niskanen, T and Nogueira, PTS and Oliveira, JA and Oliveira, PHF and Ortiz, DA and Pancorbo, F and Paz, A and Pazmiño, DA and Pereira, OL and Piątek, M and Plata, O and Pordel, A and Raaijmakers, JM and Ralaiveloarisoa, AB and Ramos, DO and Ravikumar, S and Rigueiro-Rodríguez, A and Rivas-Torres, GF and Rodrigues, JG and Rodriguez-Flakus, P and Romero, M and Saba, M and Sánchez, A and Sánchez-Dueñas, G and Santana, JS and Serrano, M and Silva, JAS and Stępniewska, H and Stryjak-Bogacka, M and Tennakoon, DS and van 't Hof, P and van Vuuren, NI and Varga, T and Vauras, J and Vieira, BS and Visagie, CM and Wipf, D and Woods, R and Groenewald, JZ},
title = {Fungal Planet description sheets: 1868-1920.},
journal = {Persoonia},
volume = {56},
number = {},
pages = {1-173},
pmid = {42524220},
issn = {0031-5850},
abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Marasmius ballator on leaf litter in subtropical rainforest, Marasmius carbinensis on litter and twigs of Hyptis suaveolens, Marasmius clocca on leaf litter of regenerating subtropical rainforest. Bolivia, Aggregatorygma saraanense on trunk of Trichilia inaequilatera. Brazil, Arthropolymorpha endophytica (incl. Arthropolymorpha gen. nov.), from healthy roots of Coffea arabica, Didymella digitariae on Digitaria insularis, Geastrum baseiae on soil, Magnibotryascoma souzamottae as endophyte from cladodes of Tacinga inamoena, Neoleptosporella agapanthi from stalks of Agapanthus praecox, Penicillifer endoradicis as endophyte from roots of Musa acuminata, Sirastachys cavernicola from leaf litter, Toxicocladosporium atratum as root endophyte of Cattleya locatellii. China, Fasciatispora citri on dead twig of Citrus maxima. Denmark, Inocybe leucantheana on wet ground with Alnus, Betula and Picea. Ecuador (Galapagos Islands), Fusarium cristobalense on Scalesia gordilloi, Fusarium scalesiae on Scalesia pedunculata. Finland, Inocybe ranaria on mull soil, near Betula pendula and Abies sp. France, Bullatosporium pinophilum on the bark of Pinus nigra subsp. nigra, Dialonectria eutypellicola on Eutypella prunastri, on branches of Prunus spinosa, Mycobernardia involucriformis on dead Bambusa sp., Pseudocosmospora perforaticola on dead stromata of Hypoxylon perforatum on Fraxinus, Stylonectria colleeniae on Trimmatostroma scutellare, with Lophium mytillinum, on dead branch of Larix decidua. French Guiana, Neocosmospora duolechatii on dead bark of Bauhinia sp. Germany, Inocybe giovannii on soil under Abies alba, Fagus sylvatica and Picea abies, Triseptosporium fallopiae (incl. Triseptosporium gen. nov.) on Fallopia japonica. India, Phylloporia bharatavarsa on living tree of Phyllanthus emblica. Iran, Fusarium phoenicis on roots of Phoenix dactylifera. Italy, Inosperma confusum on soil under Quercus ilex and Pinus halepensis, Inosperma subinodorum on calcareous soil in Picea abies forest. Madagascar, Oudemansiella viscida on dead wood or branches. Netherlands, Colletotrichum urticicola from leaf spots on Urtica dioica. Pakistan, Agrocybe punjabensis on soil on fallen remains of Saccharum officinarum. Panama, Ijuhya panamaensis and Sarcopodium panamaense on twig litter of angiosperm. Poland, Cytospora tatrensis from dead stems of Pinus mugo, Myxotrichum flavum on resin of Picea abies, Symphoricola tarnoviensis (incl. Symphoricola gen. nov.) from sooty mould community on Symphoricarpos albus. Portugal, Hypoxylon azoricum on fallen branch of Laurus azorica, Tuber honstrassii in clayey and calcareous soil under Quercus rotundifolia and Arbutus unedo. South Africa, Paraphaeosphaeria andropogonicola on leaves of Andropogon eucomus, Talaromyces armstrongii from soil. Spain, Geoglossum martinae on soil under Quercus ilex and Cistus ladanifer, Inocybe percastanea on sandy, acidic soils under Cistus ladanifer and Pinus pinaster, Lamproderma stephensonii on twigs of Pinus sylvestris, Ramariopsis alboviolacea on soil under Prunus lusitanica subsp. lusitanica, Russula olivaceopinetorum on acidic sandy soil among Pinus sylvestris needles, Scolecobasidium endophyticum from root-associated soil collected in a grassland, Tuber danielis in acidic soil beneath Cistus ladanifer, Quercus ilex, and Genista scorpius. Sweden, Inocybe adusticans on soil, in snow bed area with Salix herbacea and Bistorta vivipara, Inosperma friesii on soil in mixed deciduous forest. Switzerland, Stylonectria stoeckliana on Cytospora sp. on twigs of Salix sp. Thailand, Neoleptosporella camporesiana on dead branch of unidentified plant. Uganda, Bjerkandera ugandensis on a rotting log. UK (Scotland), Narcissea scotica on decaying dung of Lagopus scotica. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Akram W, Albuquerque GMR, Alfenas AC, Alfenas RF, Altés A, Alvarado P, Amirmijani AR, Arumugam E, Asif M, Bandini D, Barreto GG, Barreto RW, Batista VEC, Bezerra JDP, Bilański P, Bizio E, Castañeda-Ruiz RF, Chaves J, Condé TO, Costa MM, Custódio FA, Courty P-E, Czachura P, Damm U, Darmostuk V, Dearnaley J, De la Peña-Lastra S, Delgado G, de Silva NI, Dovana F, Drummond-Herdman A, Eberhardt U, Esteve-Raventós F, Ferisin G, Ferreira RJ, Ferro LO, Firmino AL, Flakus A, Fournier J, Gardiennet A, Gerbeau-Pissot P, Ghobad-Nejhad M, Gruhn G, Guard FE, Harms K, Heilmann-Clausen J, Hongsanan S, Hülsewig T, Inokuti EM, Jankowiak R, Kaliyaperumal M, Kehlet T, Lacerda SR, Larsson E, Leão AF, Lebel T, Lima AA, López-Villalba Á, Maciá-Vicente JG, Mateos A, Mejía LC, Mendes DR, Möller L, Mombert A, Monteiro MBN, Moreno G, Nagy L, Niskanen T, Nogueira PTS, Oliveira JA, Oliveira PHF, Ortiz DA, Pancorbo F, Paz A, Pazmiño DA, Pereira OL, Piątek M, Plata O, Pordel A, Raaijmakers JM, Ralaiveloarisoa AB, Ramos DO, Ravikumar S, Rigueiro-Rodríguez A, Rivas-Torres GF, Rodrigues JG, Rodriguez-Flakus P, Romero M, Saba M, Sánchez A, Sánchez-Dueñas G, Santana JS, Serrano M, Silva JAS, Stępniewska H, Stryjak-Bogacka M, Tennakoon DS, van 't Hof P, van Vuuren NI, Varga T, Vauras J, Vieira BS, Visagie CM, Wipf D, Woods R, Groenewald JZ (2026). Fungal Planet description sheets: 1868-1920. Persoonia 56: 1-173. doi: 10.3114/persoonia.2026.56.01.},
}

@article {pmid42525349,
year = {2026},
author = {Dos Reis, JBA},
title = {Functional diversity and ecological consequences of endophytic Bacillus-plant interactions.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42525349},
issn = {1874-9356},
abstract = {The genus Bacillus, particularly endophytic species, has been widely studied as a source of plant growth-promoting bacteria in agricultural systems. These microorganisms contribute to plant performance through nutrient acquisition, phytohormone production, pathogen suppression, microbiome modulation, and enhanced tolerance to biotic and abiotic stresses. However, their ecological roles, functional plasticity, and genomic diversity remain poorly integrated into conceptual frameworks that extend beyond crop-based applications. Functional plasticity is reflected in their ability to colonize diverse plant hosts and tissues and to promote similar plant responses through distinct molecular mechanisms. Likewise, genomic diversity is evidenced by variation in accessory genomes, biosynthetic gene clusters, and regulatory networks that shape ecological functions and metabolite production. This review examines endophytic Bacillus as a model for understanding how metabolically versatile and genomically plastic bacteria establish functional, but context-dependent, associations with plants. Drawing on evidence from functional genomics, pangenomics, metabolomics, and microbial ecology, we discuss mechanisms associated with plant growth promotion and emphasize their dependence on host identity, environmental conditions, and microbial interactions. We address functional convergence arising from distinct genetic and metabolic routes, the contribution of accessory genomes and regulatory variation, and the ecological consequences of microbial inoculation in resident plant-associated microbiomes. We also highlight the limitations of in vitro screening approaches and the need for experimental validation across multiple biological scales to establish robust genotype-phenotype relationships. Finally, we extend the discussion beyond agricultural systems to consider the use of endophytic Bacillus in wild plant systems and ecological restoration, emphasizing the importance of evaluating both functional outcomes and ecological impacts.},
}

@article {pmid42518164,
year = {2026},
author = {Sattar, Z and Asili, J},
title = {Probiotics and Plant Extracts in the Gut-Brain Axis: Mechanisms, Interactions, and Clinical Perspectives.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42518164},
issn = {1867-1314},
abstract = {Growing evidence highlights the microbiota-Gut-Brain Axis (MGBA) as a critical pathway linking diet to neurological health. This review synthesizes current evidence on the complementary, additive, and potentially synergistic interactions between probiotics and plant-derived phytochemicals within the MGBA. While the individual benefits of these dietary components are well established, their combined synbiotic application offers expanded mechanistic breadth through coordinated modulation of microbial ecology, epithelial barrier integrity, immune inflammatory signaling, and neurochemical pathways. Probiotics and phytochemicals interact bidirectionally via microbial biotransformation, enhancing short-chain fatty acid production, reducing endotoxin translocation, and attenuating systemic and neuroinflammation. These effects are further linked to indirect modulation of neurotransmitter systems and neurotrophic signaling relevant to mood regulation, cognitive function, and neurodegenerative processes. Evidence from preclinical and emerging clinical studies supports the relevance of these mechanisms in conditions such as Alzheimer's disease, Parkinson's disease, mood disorders, and Autism Spectrum Disorder, although human data remain limited. Overall, this narrative review proposes a mechanistic framework describing how probiotics and plant-derived phytochemicals may interact through complementary microbial, immune, and neurochemical pathways within the Microbiota-Gut-Brain Axis. It also highlights current knowledge gaps and emphasizes the need for well-designed clinical studies to validate their combined therapeutic potential.},
}

@article {pmid42519323,
year = {2026},
author = {Chen, W and Sun, Y and Meng, CF and Wu, ST and Jiang, XY and Meng, XM and Wang, QF},
title = {Aging-driven metabolic abnormalities remodel intercellular communication through the gut-liver-heart axis and may promote coronary artery disease: the key role of bile acid metabolism.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1870980},
pmid = {42519323},
issn = {1664-3224},
mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Coronary Artery Disease/metabolism/etiology/immunology ; Animals ; *Aging/metabolism/immunology ; *Liver/metabolism/immunology ; *Cell Communication ; Gastrointestinal Microbiome ; Signal Transduction ; Receptor, Farnesoid X-Activated ; Cellular Senescence ; },
abstract = {Coronary artery disease (CAD) remains the leading cause of cardiovascular mortality worldwide and shows a strong age-dependence that classical risk-factor models do not fully explain. A growing body of work indicates that aging is closely associated with CAD and, in preclinical models, can promote it through immunometabolic remodeling of the gut-liver-heart axis, in which bile acid metabolism is proposed to act as a central molecular link. Here we integrate cellular, molecular, and clinical evidence to outline how aging perturbs this axis and sustains chronic vascular inflammation. At the cellular level, senescent cells in the intestinal, hepatic, and vascular compartments generate the senescence-associated secretory phenotype (SASP) - a process linked to cGAS-STING and NLRP3 inflammasome activation, mitochondrial dysfunction, and decline of the NAD[+]-SIRT3 axis - and help establish the systemic state of inflammaging. In the gut, age-related dysbiosis lowers bile salt hydrolase and 7α-dehydroxylase activities, contracts the secondary bile acid pool, weakens epithelial barrier integrity, and triggers metabolic endotoxemia that maintains LPS-TLR4-NF-κB signaling. In the liver, Kupffer cell M1 polarization, attenuated farnesoid X receptor (FXR) signaling, and altered exosomal cargo amplify systemic inflammatory output. Reduced FXR and Takeda G-protein-coupled receptor 5 (TGR5) signaling weakens the endogenous restraint of macrophage activation, vascular smooth muscle cell phenotypic switching, and cardiomyocyte metabolic protection. The downstream result is endothelial dysfunction, foam cell formation, plaque instability, and adverse cardiac remodeling. We then appraise emerging immune-metabolic interventions - microbiota remodeling, FXR/TGR5 agonists, senolytic therapies, metformin, and integrated biomarker frameworks for early risk stratification - while noting that most are currently supported only by preclinical or early-phase human data. By placing bile acid signaling at the interface of innate immunity, microbial ecology, and metabolic homeostasis, this review offers an immunological framework for aging-associated CAD and identifies candidate immune-metabolic targets for prevention and therapy in older adults.},
}

Humans
*Bile Acids and Salts/metabolism
*Coronary Artery Disease/metabolism/etiology/immunology
Animals
*Aging/metabolism/immunology
*Liver/metabolism/immunology
*Cell Communication
Gastrointestinal Microbiome
Signal Transduction
Receptor, Farnesoid X-Activated
Cellular Senescence

@article {pmid42519405,
year = {2026},
author = {Van Holm, W and Marynissen, J and Van Campenhout, L and Minnebo, Y and Mermans, F and Lauwens, K and Teughels, K and Saghi, M and Zayed, N and Boon, N and Teughels, W},
title = {Oral colonization of probiotics: one size fits all?.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100642},
pmid = {42519405},
issn = {2666-5174},
abstract = {The clinical application of probiotics for oral health is increasing, yet their colonization dynamics remain poorly understood. This study investigated whether administration timing, strain origin, and host-specific factors influence oral persistence. Two Limosilactobacillus reuteri strains (oral vs. non-oral isolate) were evaluated in two in vivo studies. In the first, participants consumed probiotics either during the day or before bedtime; in the second, daily administration continued for 28 days, followed by a 7-day washout. Probiotic abundance was qPCR quantified and oral microbiomes were sequenced. Additionally, a retrospective analysis of periodontitis patients receiving probiotics was performed. Bedtime administration significantly prolonged probiotic detectability compared to daytime intake. Both strains were largely transient, disappearing within days post-administration, though the oral isolate showed enhanced adhesion. Notably, a subset of participants retained the probiotic for up to a week, suggesting interindividual variability and potential biomarkers of colonization. Periodontitis patients who had higher concentrations of probiotics also displayed more improvement in pocket probing depth of deep pockets. These findings highlight the need to consider timing, strain selection, and host factors in probiotic-based oral health interventions.},
}

@article {pmid42276550,
year = {2026},
author = {Gronniger, JL and Larin-Henriquez, D and Bernardin, JR and Shoemaker, LG and Bittleston, LS},
title = {Environmental complexity shapes maintenance of bacterial diversity through context-dependent interactions among niche axes.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42276550},
issn = {1751-7370},
support = {DEB 2236782//National Science Foundation CAREER award/ ; 00001638//Simons Foundation Early Career Investigator Award in Aquatic Microbial Ecology and Evolution/ ; OIA 2019528//NSF/ ; DEB 2441720//NSF/ ; },
abstract = {Microbial communities are often more species-rich than predicted from classical ecological models. The high levels of coexistence observed in nature are typically attributed to forces that modulate niche availability and stabilize communities. Specific drivers of niche partitioning are often tested in isolation, and the interactive effects of niche variation across resources, space, and time have not been tested together experimentally to determine how they affect community responses. Here, we used 26 bacterial strains previously isolated from carnivorous pitcher plant (Sarracenia purpurea) aquatic pools to construct and expose species-rich synthetic communities to four factors that alter environmental complexity in a fully factorial design, creating combinations of resource complexity, spatial niche structure, and temporal fluctuations. Across treatments, increased niche complexity generally, but not always, promoted the long-term retention of more species, with a saturating effect at the highest levels of complexity. Resource complexity emerged as a primary driver of diversity, with its effects also depending on other niche axes. Interactions among factors frequently deviated from additive expectations, with both synergistic and antagonistic effects observed depending on the combination of conditions. Together, these results show that environmental complexity shapes bacterial diversity through context-dependent, nonlinear interactions among niche dimensions, highlighting that the relationship between niche dimensionality and diversity is contingent on how environmental factors combine.},
}

@article {pmid42505138,
year = {2026},
author = {Chaput, G and Deen, EA and Pham, EQ and Crystal, S and Matayoshi, A and Andeer, P and Northen, TR and Eisen, JA and Stachowicz, JJ and Sogin, EM},
title = {Microbiota assembly in Zostera marina during early host development across controlled growth experiments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0072226},
doi = {10.1128/msystems.00722-26},
pmid = {42505138},
issn = {2379-5077},
abstract = {Seagrass restoration practices are evolving to leverage microbiome applications, similar to agricultural systems that have demonstrated how targeted microbial communities enhance crop resilience in challenging environments. While adult seagrass microbiome research has expanded significantly, research on the seed microbiome remains critically understudied. This gap is important given that seeds represent a large portion of restoration efforts. Advancing seed microbiome research requires standardized experimental systems for controlled plant-microbe interaction studies, which are currently lacking in seagrass research. Here, we tested fabricated ecosystem devices (EcoFAB 2.0) as a standardized system for growing Zostera marina (eelgrass) seedlings, enabling a controlled study of aquatic plant-microbe interactions. Using these chambers, we addressed three key questions: (i) can we reliably grow eelgrass in a controlled laboratory setting, (ii) can we manipulate eelgrass microbiota assembly and its long-term trajectory, and (iii) can we detect shifts in the microbiota during plant development (host filtering)? Host morphology measurements and 16S rRNA gene amplicon sequencing were used to track microbiota assembly across three early developmental stages of the host. Because plants were grown in a sterile environment, surface sterilization of seeds (bleach and ethanol) removed epiphytes without disturbing the shared endophytic community, yet microbiota composition remained divergent at Stage 6 (143 differentially abundant ASVs), indicating that seed coat epiphytes make a lasting and distinct contribution to assembly trajectory. We also identified 26 stage-specific indicator ASVs across eelgrass development, suggesting stage-specific microbial associations during seedling establishment. This work demonstrates the potential for targeted manipulation of the microbiome in seagrass for restoration efforts.IMPORTANCEUsing the Fabricated Ecosystem 2.0 (EcoFAB 2.0), we were able to successfully control the microbial environment of eelgrass, Zostera marina, resulting in the reduction of epiphytes and maintaining low microbial diversity across plants without compromising the morphology and growth of seedlings. Our findings advance the marine plant model system, Z. marina, by identifying taxonomic indicators across life stages. This work lays the foundation for a targeted understanding and application of microbiomes for seagrass restoration, bridging the critical knowledge gap between agricultural seed microbiome success and marine restoration applications.},
}

@article {pmid42505610,
year = {2026},
author = {Bariz, K and Saoudi, B and Lahcene, S and Moualek, I and Sebbane, H and Rekbi, F and Belkhalfa, H and Derguini, A and Ibrahim, NA and Alsalamah, SAA and Aleissa, MS and Basher, NS and Trabelsi, L and Houali, K},
title = {Antibiofilm Activity of Three Essential Oils Against ESBL-Producing Klebsiella pneumoniae: An In Vitro and In Silico Investigation of Putative Molecular Targets.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {42505610},
issn = {2079-6382},
support = {IMSIU-DDRSP2601//This work was supported and funded by the Deanship of Scientific Research at Imam Moham-mad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Biofilm formation is a major contributor to antibiotic resistance in Klebsiella pneumoniae, posing a serious challenge to current therapeutic strategies. Thus, this study aims to evaluate the antibiofilm activity of three essential oils Thymus hirtus Willd. Ssp. algeriensis Boiss, Syzygiuma romaticum, and Eucalyptus globulus against four clinical isolates of ESBL-producing K. pneumoniae, along with the reference strain K. pneumoniae ATCC 700603. The antibiofilm activity of essential oils was assessed with crystal violet assay using MICs ranging from 3.38 ± 0.2 to 27.1 ± 0.56 mg/mL, 2 ± 0.19 to 32 ± 0.55 mg/mL, and 13.78 ± 0.62 to 110.25 ± 3.37 mg/mL, for TEO, SEO and EEO, respectively. In vitro tests showed that S. aromaticum EO and T. algeriensis EO exhibited the best anti-adhesive activity with a percentage of up to 75.39%, while no difference was observed between the EO in their eradication activity. Microscopic observations confirmed the disorganization of the biofilm after treatment with T. algeriensis. The molecular docking analysis of the three EOs main compounds with MrkH, SdiA and MrkD revealed that SdiA was the most favorable target, with p-cymene (-7.7 kcal/mol), α-pinene (-7.5 kcal/mol), and eucalyptol (-7.1 kcal/mol) showing the strongest binding affinities. Thymol and p-cymene showed also a favorable affinity with MrkD. Overall, p-cymene and α-pinene demonstrated the most favorable binding profiles, whereas linalool exhibited the weakest predicted interactions. These results highlight the promising potential of these EOs, as multi-target antibiofilm agents against MDR- K. pneumoniae biofilms.},
}

@article {pmid42505979,
year = {2026},
author = {Liu, S and Wu, Y and Lv, Y and Shao, M and Lv, D and Li, Q and Shang, Q},
title = {Fermentation of Structurally Defined Alginate Oligosaccharides by the Human Gut Microbiota Enriched in Bifidobacterium, Bacteroides, Faecalibacterium, or Blautia.},
journal = {Marine drugs},
volume = {24},
number = {7},
pages = {},
pmid = {42505979},
issn = {1660-3397},
support = {32471335//National Natural Science Foundation of China/ ; 2024CXPT048//Key R&D Program of Shandong Province/ ; },
mesh = {Humans ; *Alginates/chemistry/metabolism ; *Oligosaccharides/chemistry/metabolism ; Fermentation ; Prebiotics ; Bacteroides/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Fatty Acids, Volatile/metabolism ; Faecalibacterium/metabolism ; Bifidobacterium/metabolism ; },
abstract = {Alginate oligosaccharides (AOS) are attractive candidates for prebiotic development, yet how oligosaccharide structure and baseline microbial community composition interact to shape fermentation remains an open question. In this study, we stratified fecal microbiota from healthy donors into operational genus-predominance groups (Bifidobacterium, Bacteroides, Faecalibacterium, or Blautia) and selected representative samples for in vitro fermentation of six structurally distinct AOS preparations (SAOS-1, SAOS-2, OAOS, UAOS, SMOS, and SGOS). Substrate consumption, short-chain fatty acid (SCFA) production, and shifts in microbial community structure were profiled. The six preparations differed in structural type, number-average molecular weight, and average degree of polymerization. Among them, SAOS-1 exhibited the most consistent utilization across all four groups and yielded the highest total SCFA production. SAOS-1 fermentation also attenuated inter-group community divergence and enriched several beneficial or functionally relevant taxa, including Bacteroides and Faecalibacterium. Interestingly, the magnitude and direction of microbial responses remained enterotype-dependent, with the Bacteroides-predominant group assembling the most complex fermentative consortium. These findings demonstrate that AOS structure and baseline microbial ecology jointly dictate fermentation outcomes, positioning SAOS-1 as a strong candidate for precision prebiotic development. This structure-community interaction paradigm provides a rational basis for the targeted deployment of marine oligosaccharides in personalized gut health strategies.},
}

Humans
*Alginates/chemistry/metabolism
*Oligosaccharides/chemistry/metabolism
Fermentation
Prebiotics
Bacteroides/metabolism
Feces/microbiology
*Gastrointestinal Microbiome/physiology
Fatty Acids, Volatile/metabolism
Faecalibacterium/metabolism
Bifidobacterium/metabolism

@article {pmid42507180,
year = {2026},
author = {Hayat, M and Parveen, R and Nawaz, MS and Rao, MA and Waqar, A and Naqvi, RZ and Anwar, MA and Zahir, ZA and Qasim, M and Dogar, MA and Sandino, TS and Singh, BK and Imran, A},
title = {Plant growth-promoting rhizobacteria (PGPR) producing ACC deaminase and exopolysaccharides enhance salt tolerance in wheat.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42507180},
issn = {1573-0972},
mesh = {*Triticum/microbiology/growth & development/physiology ; *Carbon-Carbon Lyases/metabolism/biosynthesis ; *Salt Tolerance ; Rhizosphere ; Soil Microbiology ; *Polysaccharides, Bacterial/metabolism/biosynthesis ; Seedlings/growth & development/microbiology ; Salinity ; Plant Roots/microbiology/growth & development ; Bacillus/metabolism ; Plant Development ; Pseudomonas/metabolism/enzymology ; *Bacteria/metabolism/enzymology/genetics ; Sodium Chloride ; Biomass ; },
abstract = {Soil salinity severely impairs crop growth and yield by inducing ion toxicity, osmotic stress, and disrupting plant nutrient uptake. This pervasive stressor poses a major threat to global cereal production and food security, especially the wheat crop. Plant growth-promoting rhizobacteria (PGPR) capable of producing 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) and exopolysaccharides (EPS) offer a promising biological strategy to enhance plant tolerance under saline conditions. This study evaluated the combined application of halotolerant ACCD- and EPS-producing bacterial strains to mitigate salt stress (150 mM NaCl) in wheat. Eight strains were selected based on functional traits: ACCD producers (sz18 Brevibacterium frigoritolerans, sz30 Bacillus spizizienii, sz35 Pseudomonas glycinis, sz80 Pseudomonas grimontii) and EPS producers (EP5 Bacillus tequilensis, EP8 Bacillus spizizienii, EP29 Pseudomonas koreensis, EP35 Bacillus subtilis). All strains successfully colonized the wheat rhizosphere. Co-inoculation of ACCD and EPS-producing bacteria significantly enhanced seedling performance under salinity, increasing fresh biomass and root and shoot length by approximately 30% compared with uninoculated controls. Gene expression analysis further demonstrated that inoculated plants exhibited substantial upregulation of key salt-responsive genes: rbcS (~ 3-fold), rbcL (~ 6-fold), cAPX (~ 6-fold), and DREB2 (~ 2-fold). These transcriptional changes indicate improved photosynthetic capacity, antioxidant defense, and stress-responsive regulation in treated plants. Overall, the findings highlight the synergistic potential of ACCD- and EPS-producing PGPR in alleviating salinity stress in wheat. If validated under field conditions, this microbial consortium could serve as an effective, sustainable approach to improve wheat resilience and productivity in salt-affected soils.},
}

*Triticum/microbiology/growth & development/physiology
*Carbon-Carbon Lyases/metabolism/biosynthesis
*Salt Tolerance
Rhizosphere
Soil Microbiology
*Polysaccharides, Bacterial/metabolism/biosynthesis
Seedlings/growth & development/microbiology
Salinity
Plant Roots/microbiology/growth & development
Bacillus/metabolism
Plant Development
Pseudomonas/metabolism/enzymology
*Bacteria/metabolism/enzymology/genetics
Sodium Chloride
Biomass

@article {pmid42508699,
year = {2026},
author = {Chopra, C and Kukkar, D and Kaur, H and Samudrala, R},
title = {QIIME2-based pooled re-analysis of 16s rRNA sequences reveals gut microbiota dysbiosis in diabetic nephropathy mouse models.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108732},
doi = {10.1016/j.micpath.2026.108732},
pmid = {42508699},
issn = {1096-1208},
abstract = {Diabetic nephropathy (DN) is a progressive microvascular and renal disease that develops due to chronic suffering from diabetes. Growing research evidences have suggested the role of gut microbiota dysbiosis advancement of DN. In this regard, our study analyses publicly available 16S rRNA sequencing datasets from murine models (38 DN, 37 healthy controls (HCs), and 33 diabetic mellitus (DM) samples) using the quantitative insights into microbial ecology 2 (QIIME2) pipeline to explore gut microbial alterations associated with disease progression. This study provides a focused re-analysis of publicly available 16S rRNA datasets from DN mouse models, complementing previous broader DM microbiome studies. Following quality filtration, trimmomatic, and DADA2 assisted denoising, taxonomic classification was performed using the SILVA database, and alpha diversity was assessed through shannon, faith's PD, pielou's evenness, and observed feature indices. Firmicutes and Bacteroidota were found to be the dominant group, with minor contributions from Proteobacteria and Actinobacteriota. Controls showed the higher abundance of Faecalibacterium, Roseburia, and Blautia, whereas Escherichia-Shigella and Alistipes were elevated in DN groups. Alpha diversity analysis revealed insignificant differences in richness or evenness between DN and control samples, suggesting that disease-associated microbial variations are primarily driven by specific taxonomic shifts rather than overall diversity. These findings highlight the potential involvement of gut dysbiosis in DN pathophysiology and support the therapeutic relevance of targeting the gut-kidney axis.},
}

@article {pmid42509522,
year = {2026},
author = {Chen, PY and Hsu, TW and Chiang, TY and Huang, CL},
title = {Comparative analysis of root microbiomes in four Swertia species from Taiwan.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {42509522},
issn = {1618-0860},
support = {NSTC 103-2621-B-006-002-//National Science and Technology Council/ ; },
abstract = {Swertia (Gentianaceae) comprises four species endemic to Taiwan that possess significant medicinal potential. While root microbiomes are known to promote plant adaptation, the microbial ecology of Taiwanese Swertia remains largely unexplored. We investigated the rhizosphere and root endosphere microbiomes of these species using 16S rRNA gene sequencing and predictive functional profiling, integrated with host phylogenetic data. Our results revealed that rhizosphere bacterial communities were significantly more diverse than those in the root endosphere. PERMANOVA indicated that host species and plant compartment significantly influenced bacterial communities, but the high residual variance suggests that much of the community variation remains unexplained by the variables measured in this study. Phylogenetic analysis indicated that the root endosphere is more strongly influenced by host phylogeny, with closely related species harboring more similar communities. Functional profiling further demonstrated that the rhizosphere is predicted to be enriched in pathways related to nitrogen fixation and organic matter degradation, whereas the endosphere harbors bacterial taxa potentially associated with pathogen suppression. These findings underscore the multifaceted roles of the root microbiome in supporting the development, stress adaptation, and ecosystem sustainability of Swertia species in Taiwan's unique altitudinal gradients.},
}

@article {pmid42510761,
year = {2026},
author = {Tian, M and Liang, Y and Lu, J and Shi, W and Zhao, Y and Gan, W and Jia, S and Xiao, C and Zhao, T and Zhang, H},
title = {Global Genomic Analysis of Bovine-Associated Klebsiella pneumoniae Reveals Genetic Diversity and Resistance-Virulence Profiles.},
journal = {Biology},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/biology15141215},
pmid = {42510761},
issn = {2079-7737},
support = {BT-2025-TCYC-0066//Xinjiang Uyghur Autonomous Region "Tianchi Talent" Youth Doctoral Talent Program/ ; RCZK202578//Shihezi University/ ; 2024AB034//Science and Technology Development Project of Xinjiang Production and Construction Program/ ; 2025YD013//Central Government-Guided Local Science and Technology Development Project/ ; 2025AB083, 2024AB034 and 2024AB035//Scientific and Technological Tackling Plan for Key Fields of Xinjiang Production and Construction/ ; },
abstract = {Bovine-associated Klebsiella pneumoniae is an important bacterial species linking animal health, microbial ecology, and One Health-oriented antimicrobial resistance research. In this study, we performed a global genomic analysis of 1291 publicly available bovine-associated K. pneumoniae genomes collected from 18 countries between 2005 and 2024 using data retrieved from NCBI. MLST, core-genome phylogenetic analysis, pangenome analysis, CARD, VFDB, and PlasmidFinder were used to characterize sequence types, genomic diversity, antimicrobial resistance-associated genes, virulence-associated genes, and plasmid replicons. A total of 256 sequence types were identified, among which ST107 was the most common. Core-genome phylogenetic analysis revealed multiple genomic lineages, while pangenome analysis identified 46,325 gene clusters, including 1967 core genes and 40,595 cloud genes, indicating an open pangenome structure and substantial accessory gene diversity. Virulence-associated genes were unevenly distributed, with yagZ/ecpA being the most frequently detected determinant. In total, 138 antimicrobial resistance-associated genes or potential resistance determinants were detected across 16 antimicrobial categories, including clinically important β-lactamase- and carbapenemase-associated genes. IncF-family plasmid replicons, particularly IncFIB(K)_1_Kpn3, were frequently detected, suggesting widespread plasmid replicon-associated genomic backgrounds; however, physical co-localization between resistance genes and specific plasmid backbones could not be confirmed. Overall, this study reveals the genetic diversity, resistance-associated gene reservoir potential, heterogeneity of virulence-associated genes, and plasmid replicon backgrounds of bovine-associated K. pneumoniae. Importantly, the genome-predicted AMR potential identified in this study should not be interpreted as confirmed phenotypic resistance without further experimental validation. These findings provide genomic insights for risk surveillance, candidate control-target screening, and microbiota-oriented intervention research.},
}

@article {pmid42511090,
year = {2026},
author = {Liu, C and Chen, X and Fu, C and Ouyang, K and Qu, M and Qiu, Q},
title = {Dietary 4-Hydroxy-2,5-Dimethyl-3(2H)-Furanone Supplementation in Hu Sheep: Implications on Fecal and Rumen Microbiota.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {14},
pages = {},
doi = {10.3390/ani16142212},
pmid = {42511090},
issn = {2076-2615},
support = {32260861//National Natural Science Foundation of China/ ; 20243BCE51165//Major Discipline Academic and Technical Leaders Training Program of Jiangxi Province/ ; },
abstract = {This study aimed to investigate the effects of dietary 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) supplementation on ruminal and fecal microbial diversity, community composition, and predicted functional pathways. A total of 24 four-month-old female Hu sheep with similar body weights (20.6 ± 0.5 kg) were randomly allocated to two groups, with six replicates per group and two sheep per replicate. One group was fed a basal diet (CON), and the other received the same basal diet supplemented with 100 mg/kg HDMF. The results showed that ruminal microbial alpha diversity did not differ between the CON and HDMF groups (p > 0.05), whereas fecal microbial richness and evenness were higher in the CON group than in the HDMF group (p < 0.05). Beta diversity of ruminal microbiota did not differ between groups (R = 0.0667, p = 0.217), whereas fecal microbiota exhibited significant differences (R = 0.7333, p = 0.002). Dietary HDMF supplementation increased the relative abundances of Lachnospiraceae and Oribacterium in the rumen, elevated Spirochaetota and Lachnospiraceae AC2044 group in feces, and concurrently decreased Desulfobacterota and Alistipes in feces. Correspondingly, PICRUSt2-based functional prediction indicated putative associations between HDMF-induced microbial shifts and altered functional pathways, including increased relative abundances of amino acids biosynthesis and ABC transporter pathways, concomitant with decreased relative abundances of glycolysis/gluconeogenesis and pyruvate metabolism pathways in feces. These results suggest that dietary HDMF supplementation was associated with more pronounced alterations in fecal microbiota than in ruminal microbiota. This study provides a preliminary microbial ecology perspective on gastrointestinal microbiota in response to dietary HDMF supplementation in ruminants.},
}

@article {pmid42511801,
year = {2026},
author = {Cheng, A and Ee, KP},
title = {Deciphering Stress Resilience in Black Pepper (Piper nigrum L.): From Current Advances to Emerging Opportunities.},
journal = {International journal of molecular sciences},
volume = {27},
number = {14},
pages = {},
pmid = {42511801},
issn = {1422-0067},
support = {FRGS/1/2024/STG01/UM/02/1//Ministry of Higher Education/ ; },
abstract = {Black pepper (Piper nigrum Linn.), one of the world's most economically important spice crops, is increasingly challenged by climate-related stresses, emerging pests and diseases, and declining soil health, all of which threaten its productivity and sustainability. While previous reviews have predominantly focused on black pepper genomic resources, breeding strategies, and disease management, the integration of multi-omics technologies, microbiome science, and artificial intelligence (AI) to enhance its stress resilience has received comparatively limited attention. This review synthesizes recent advances in the molecular mechanisms underlying black pepper responses to biotic and abiotic stresses, with emphasis on omics approaches (such as genomics and transcriptomics), as well as the roles of beneficial microbial communities in enhancing stress tolerance, nutrient acquisition, and disease suppression. We further discuss emerging microbiome-assisted strategies, including the development of beneficial microbial consortia and targeted manipulation of microbial functions, for enhancing black pepper resilience under changing environmental conditions. In addition, we explore how AI-driven analytical approaches can integrate complex multi-omics and microbiome datasets to unravel the complex molecular networks governing black pepper-microbe interactions under stress conditions and accelerate precision breeding. By integrating genomics, microbial ecology, and AI, this review presents a systems-level framework for understanding and improving stress resilience in black pepper. This interdisciplinary perspective highlights new opportunities to accelerate the development of climate-resilient cultivars and advance sustainable black pepper production.},
}

@article {pmid42512165,
year = {2026},
author = {Pereira, CV and Garcia, NG and Fonseca, DC and Machado, PG and Rezende, MF and Alcântara, SFM and Andrade, EF and Pereira, LJ},
title = {Smoking and Depth-Related Anaerobic Bacteria in Endodontic-Periodontal Lesions: A Pilot Study.},
journal = {International journal of environmental research and public health},
volume = {23},
number = {7},
pages = {},
pmid = {42512165},
issn = {1660-4601},
support = {309610/2023-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-01552-21//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
abstract = {Endodontic-periodontal lesions are complex conditions in which endodontic infection and periodontal breakdown coexist and may create anaerobic microbial niches along the root surface. Although smoking is a well-established modifier of periodontal disease progression and subgingival microbial ecology, its influence on the depth-related distribution of anaerobic periodontal bacteria in teeth affected by endodontic-periodontal lesions remains incompletely understood. This cross-sectional study investigated the distribution patterns and co-occurrence of selected anaerobic periodontal bacteria in smokers and non-smokers with endodontic-periodontal lesions, considering periodontal pocket depth and anatomical site. Subgingival samples were collected from periodontal pockets of different probing depths (3-4 mm, 5-6 mm, and ≥7 mm), as well as from healthy gingival sulci and oral mucosa, in 26 patients with endodontic-periodontal lesions. The presence of Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia, Prevotella nigrescens, and Aggregatibacter actinomycetemcomitans was assessed. Detection was performed using polymerase chain reaction (PCR). Qualitative detection frequencies and microbial co-occurrence patterns were compared between smokers and non-smokers across sites and pocket depths. Non-smokers showed higher detection of Tannerella forsythia in pockets ≥ 7 mm (p < 0.05). Overall microbial co-occurrence was lower in smokers in deeper periodontal pockets, whereas detection patterns in healthy gingival sulci and oral mucosa were broadly comparable between groups. Our findings suggest that smoking may be associated with an attenuated depth-related detection pattern and reduced co-occurrence of selected anaerobic periodontal bacteria in endodontic-periodontal lesions.},
}

@article {pmid42513562,
year = {2026},
author = {Hau, HM and Jahn, N and Karitnig, R and Hasenhütl, SM and Sucher, R and Stiegler, P and Laudi, S},
title = {Microbiome-Targeted Modulation in Renal Transplantation.},
journal = {Journal of clinical medicine},
volume = {15},
number = {14},
pages = {},
doi = {10.3390/jcm15145648},
pmid = {42513562},
issn = {2077-0383},
abstract = {The gut microbiome has emerged as a critical determinant of health and disease across virtually all organ systems. In the context of chronic kidney disease (CKD) and renal transplantation, mounting evidence reveals a complex bidirectional relationship between the intestinal microbiota and kidney function-commonly referred to as the gut-kidney axis. Patients with CKD harbor a profoundly altered gut microbial ecosystem characterized by reduced diversity, depletion of beneficial commensal organisms, and expansion of pathobiont taxa capable of generating uremic toxins and pro-inflammatory mediators. These perturbations are further compounded by the uremic milieu itself, dietary restrictions, frequent antibiotic exposure, and the use of immunosuppressive agents following transplantation. The gut-liver-kidney axis adds an additional layer of complexity, linking hepatic metabolism, bile acid signaling, endotoxemia, and systemic immune activation to the progression of renal disease. Gut-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, trimethylamine N-oxide (TMAO), and tryptophan-derived uremic solutes such as indoxyl sulfate and p-cresyl sulfate-serve as molecular mediators of inter-organ crosstalk and have been identified as both biomarkers and therapeutic targets. A growing body of literature supports the diagnostic and prognostic utility of microbiome composition and its metabolic signatures in patients with CKD and those undergoing renal replacement therapy. Therapeutic strategies aimed at restoring microbial homeostasis-encompassing dietary interventions, prebiotics, probiotics, synbiotics, fecal microbiota transplantation (FMT), bile acid-based therapies, and novel pharmacological approaches-hold considerable promise for improving outcomes in CKD and transplant recipients. Importantly, the bidirectional relationship between immunosuppressive drugs and the gut microbiota has emerged as a clinically significant determinant of both microbial ecology and drug pharmacokinetics: each major immunosuppressive agent class-corticosteroids, calcineurin inhibitors, mycophenolate mofetil, and mTOR inhibitors-induces characteristic dysbiotic patterns, while in turn, the microbiota modulates drug bioavailability through enzymatic biotransformation (notably bacterial beta-glucuronidase activity affecting mycophenolic acid enterohepatic recirculation) and modulation of host drug-metabolizing enzymes. This narrative review provides a comprehensive overview of the current understanding of microbiome dysbiosis in the setting of renal disease and transplantation, examines the mechanistic underpinnings of the gut-liver-kidney axis, details the multifaceted impact of dysbiosis on transplant outcomes-including allograft function and rejection, infection, post-transplant diabetes, and cardiovascular complications-and critically appraises the translational potential of microbiome-targeted interventions. We conclude by highlighting ongoing challenges and future directions toward personalized, microbiome-informed clinical care.},
}

@article {pmid42513909,
year = {2026},
author = {Luo, D and Ponsero, AJ and Wright, K and Baker, DJ and Telatin, A and Townsley, C and Giotis, ES},
title = {Microbiome Stability in Wild and Rehabilitated Insectivorous Bats Revealed by Shotgun Metagenomics.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071403},
pmid = {42513909},
issn = {2076-2607},
support = {MR/Z506242/1/MRC_/Medical Research Council/United Kingdom ; RGS\R2\242527//Royal Society/ ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG2260/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Wildlife rehabilitation can alter host-associated microbial communities, yet the effects of temporary managed care on the gut microbiome of insectivorous bats remain poorly understood. We used shotgun metagenomic sequencing to investigate gut microbiome composition in wild and rehabilitated bats from Yorkshire, United Kingdom. A total of 25 faecal metagenomes were analysed from four bat species (Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula, and Nyctalus leisleri), including wild baseline individuals and bats undergoing temporary managed care for 1-49 days. Microbial community structure clustered primarily according to host species and roost location, with no significant separation associated with rehabilitation status. Among bats in managed care, bacterial alpha diversity did not differ significantly with time in care (H = 2.30, p = 0.32). Archaeal communities displayed markedly lower interindividual variation than bacterial communities (coefficient of variation: 12.2% vs. 41.8%), indicating a highly conserved archaeal microbiome across hosts. Rehabilitated bats exhibited modest compositional shifts in bacterial communities, including increased relative abundances of Yersiniaceae and Lactobacillaceae and reduced abundances of environmentally associated taxa such as Pseudomonadaceae and Erwiniaceae. These changes may reflect controlled dietary provision and reduced environmental exposure during care. Overall, no marked rehabilitation-associated differences in gut microbiome diversity or community structure were detected under the current sampling design. These findings are consistent with microbiome stability during temporary managed care, although longitudinal studies are required to confirm microbiome dynamics within individual bats. Nonetheless, this study provides an initial baseline for future microbiome-informed wildlife rehabilitation studies.},
}

@article {pmid42514002,
year = {2026},
author = {Semenzato, G and Barberini, S and Menicucci, F and Atzori, G and Brunetti, C and Marino, G and Palchetti, V and Fani, R and Centritto, M and Emiliani, G},
title = {Plant-Endophyte Cross-Talk in Origanum heracleoticum L. In Vitro Axenic Culture: Endosphere-Driven Bacterial Interactions and Plant Metabolic Responses.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071497},
pmid = {42514002},
issn = {2076-2607},
abstract = {Origanum L. (Lamiaceae) is a commercially important medicinal and aromatic plant genus worldwide. Endophytic bacterial communities are recognized for promoting plant growth and physiology, although their interactions with host metabolism remain insufficiently understood. In this work, an in vitro model of axenic Origanum heracleoticum plants was established to investigate the relationship between endophytic bacteria and their tissue of origin. Specifically, we evaluated the adaptation of two strains, Bacillus sp. OHL2 and Pseudomonas sp. OHS18, and the potential role of Bacillus sp. OHL2 in modulating plant physiology and secondary metabolism. Bacterial inoculation and re-isolation highlighted niche-specific adaptation and possible co-evolution within the host, suggesting an active role of the plant in regulating bacterial colonization within the endosphere. Inoculation with Bacillus sp. OHL2 significantly enhanced photosynthetic rate, leaf area, dry weight, and chlorophyll content. No substantial overall changes in secondary metabolism were detected. Rosmarinic acid was the predominant phenolic, while monoterpenes dominated, with carvacrol dominant. A significant tissue-by-inoculation interaction was observed for α-humulene, which decreased in leaves of inoculated plants. Overall, the in vitro system provides a valuable platform to study plant-endophyte interactions and bacterial mechanisms underlying the stimulation of plant growth and metabolic responses.},
}

@article {pmid42514056,
year = {2026},
author = {Di Gregorio, F and Polizzi, A and Marmo, GM and Angjelova, A and Jovanova, E and Campagna, R and Mascitti, M and Isola, G},
title = {Revisiting the Oral-Gut Axis: Microbial Symbiosis, Dysbiosis, and Bidirectional Links Between Periodontitis and Inflammatory Bowel Disease.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071551},
pmid = {42514056},
issn = {2076-2607},
support = {PNRR-POC-2023-12 377 354//Ministero della Salute/ ; },
abstract = {BACKGROUND: Recent scientific evidence indicates that the oral-gut axis represents a critical interface in host-microbiota interactions, carrying profound implications for both periodontal and gastrointestinal diseases. This scoping review aims to evaluate the reciprocal influence between periodontitis and inflammatory bowel disease (IBD). Specifically, the underlying mechanisms of microbial translocation, immune interaction, and metabolite-mediated signaling linking the oral microbiota to gut microbial ecology are critically evaluated.

METHODS: Studies were selected from the PubMed, Web of Science, and Scopus databases up to May 2026. Eligible criteria included in vivo studies written in English and conducted within the last 10 years, whereas human studies involving participants under 18 years of age were excluded. The included studies analyze the effects of oral and gut dysbiosis on the opposing district. Through the database search, 2094 records were identified, and 34 articles were selected based on the eligibility criteria.

RESULTS: The included studies demonstrate the interconnection between the oral and gut microbiota. The included studies reveal that predominant oral taxa, specifically Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans, alter intestinal microbial composition. In particular, P. gingivalis colonizes the gut, exacerbating both oral and intestinal inflammation by stimulating pro-inflammatory cytokine expression via Th17 cell activation. Finally, salivary microbial composition appears to be associated with the presence and status of IBD.

CONCLUSIONS: Understanding these interconnected microbial ecosystems provides valuable insights that may support the future development of integrated diagnostic and therapeutic strategies for patients suffering from periodontitis and IBD. Further large-scale studies with longer follow-up periods are required to standardize potential salivary markers and multidisciplinary therapeutic protocols for the management of periodontitis and IBD.},
}

@article {pmid42514091,
year = {2026},
author = {Valiakhmetov, EE and Frolov, M and Sukhanov, AY and Miftakhov, AK and Validov, SZ},
title = {Strain-Specific Loci in Bacterial Genomes: Whole-Genome Discovery, Genomic Context, and Application for Multi-Strain qPCR Monitoring.},
journal = {Microorganisms},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/microorganisms14071587},
pmid = {42514091},
issn = {2076-2607},
support = {FMEG-2027-0007//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Monitoring individual strains in complex microbial communities remains a fundamental challenge in microbial ecology and biotechnology. Here, we present an integrated pipeline for identifying and validating strain-specific loci (SSL) in four biotechnologically relevant plant growth promoting strains from three genera (Stenotrophomonas, Bacillus, and Pseudomonas). The pipeline applies a two-round specificity-filtering strategy combining whole-genome comparison and high-sensitivity BLASTn validation of revealed strain-specific loci (SSL) against the NCBI nucleotide database. SSL count decreased with increasing Average nucleotide identity (ANIb) of the strains used for the analysis, ranging from one locus in B. halotolerans (ANIb = 98.91%) to 15 loci in S. rhizophila (ANIb = 86.49%). All 25 SSL were universally AT-rich, mainly accessory-genome-associated, with flanking regions enriched in genes of unknown function (34.6%) and mobile genetic elements (19.2%). TaqMan qPCR assays targeting SSL demonstrated high specificity-no target sequences were detected across ten geographically distinct soil samples, nor in a native rhizosphere metagenome-and sensitivity, with limits of detection of 0.01-0.1 pg of genomic DNA. Spike-in experiments in soil yielded method detection limits (MDL) of 850-15,000 CFU/g. All four strains were detected in the wheat rhizosphere seven days after consortium application in a field experiment, validating the pipeline for multi-strain field monitoring.},
}

@article {pmid42514156,
year = {2026},
author = {Schulze-Makuch, D and Bartholomäus, A and Arens, FL and Mangelsdorf, K and Wagner, D},
title = {Small-Scale Mineral and Microbial Heterogeneities near a Fumarole at the Furnas Hydrothermal Zone on the Azores.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {7},
pages = {},
pmid = {42514156},
issn = {2075-1729},
abstract = {The Azores are characterized by intense volcanic activity, creating unique environments such as fumarole sites, where geothermal gases and high temperatures drive distinct chemical and biological processes. To investigate small-scale heterogeneity within such a site, six visually distinct samples were collected within a 30 cm radius at an active fumarole on São Miguel Island. The samples were analyzed for elemental and mineralogical composition, bacterial lipid biomarkers (PLFAs), and microbial community structure using a novel DNA separation technique to specifically target the living microbiome. Despite mineralogical similarities across all samples-predominantly composed of alunite, alkali-feldspar, and quartz-significant microbial heterogeneity was observed. Both PLFA and bacterial iDNA analyses revealed distinct microbial communities associated with specific conditions indicated by the specific colors: red and brown samples were dominated by Proteobacteria and Actinobacteriota, yellow and green by Thermoplasmatota and Actinobacteriota, and white and gray by Crenarchaeota. Interestingly, the gray samples exhibited a broader microbial composition, sharing some taxa with all other samples. These striking color variations are likely driven by differences in both specific mineral composition and microbial pigmentation, reflecting localized biogeochemical processes. Our findings demonstrate that extreme microbial heterogeneity can occur over remarkably small spatial scales within fumarolic systems, underscoring the complex interplay between chemical and biological factors in these dynamic volcanic habitats.},
}

@article {pmid42514643,
year = {2026},
author = {Nassar, N and Tharwat, M and Tayel, A and Tariq, M and Khan, YM and Alshanbari, FA and Khan, IM},
title = {From Gut to Gain: The Microbiome's Contribution to Broiler Health and Productivity.},
journal = {Veterinary sciences},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vetsci13070633},
pmid = {42514643},
issn = {2306-7381},
support = {QU-APC-2026//Qassim University/ ; },
abstract = {The gut microbiome plays a central role in regulating nutrient utilization, immune function, and disease resistance, thereby directly influencing growth performance and feed efficiency. Existing microbiome modulation strategies, including probiotics, prebiotics, dietary interventions, and antibiotic alternatives, are critically evaluated. Despite their reported benefits, the effectiveness of these approaches often remains inconsistent across production systems. Evidence suggests that this variability is largely driven by complex interactions among microbial communities, host factors, and environmental and management conditions, which are frequently overlooked in conventional intervention-based approaches. To address this gap, this review proposes an integrated microbiome-host-environment framework that links microbial ecology with host physiology and production conditions. The framework provides a systems-level perspective for understanding the factors governing microbiome stability and production responses, offering a basis for more targeted and reliable microbiome management strategies. Finally, current challenges and future research priorities are discussed, including the integration of multi-omics technologies, precision nutrition, and data-driven approaches to support next-generation poultry production systems. By emphasizing the interconnected nature of microbiome regulation, this review contributes a conceptual foundation for improving broiler productivity and sustainability through more consistent and effective microbiome optimization.},
}

@article {pmid42514673,
year = {2026},
author = {Zhou, G and Liu, Y and Pu, X and Ning, Q and Guo, X and Wang, L and Zhong, Y and Wang, G and Guo, X and Wang, M},
title = {Conjoint Analysis of Sheep Microbiome, Metabolome, and Transcriptome Revealed the Effect Mechanisms of Feeding with Broccoli Extract.},
journal = {Veterinary sciences},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/vetsci13070663},
pmid = {42514673},
issn = {2306-7381},
support = {BSGJSYS202603//Key Laboratory of Livestock and Forage Resources Utilization around the Tarim Basin, Ministry of Agriculture and Rural Affairs-Provincial-Ministerial Co-construction Project/ ; },
abstract = {Alterations in microbiota, transcript and metabolites are critical to intestinal homeostasis and host health. This study used a combination of 16s rRNA, transcriptome sequencing and liquid chromatography-mass spectrometry to investigate intestinal microbiota, genes and metabolic profiles in the ileum of Hu sheep fed broccoli extract. Here, we randomly allocated 14 Hu sheep to two diets: a basal diet without any supplementation (NC) and a basal diet supplemented with 200 mg/kg broccoli tail (BT). After 60 days of treatment, blood and jejunal samples were collected for serum biochemical indicators and multi-omics analysis. In this study, the extract of broccoli tails had a significant effect on the serum biochemical indicators, including white blood cells, red blood cells, mean corpuscular volume, mean corpuscular hemoglobin concentration, mean platelet volume, triglycerides and total protein in Hu sheep (p < 0.05). Transcriptomic analysis showed that the 672 differentially expressed genes between the NC and BT groups were primarily enriched in linoleic acid metabolism, steroid hormone biosynthesis, and cholesterol metabolism. Metabolomics analysis using Kyoto Encyclopedia of Genes and Genomes enrichment showed that the 41 differentially abundant metabolites were mainly enriched in bile secretion, vitamin B6 metabolism, and the mTOR signaling pathway. 16S rRNA sequencing results indicated that the extract of broccoli tails increased the relative abundance of Peptostreptococcaceae and decreased the relative abundance of Lachnospiraceae, Lachnospirales, and Bacteroidaceae. Integrated transcriptome, metabolome, and microbiome analysis showed that the gut microbiota and host transcriptomic changes may participate in systemic metabolic regulation by modulating amino acid metabolism, lipid signal transduction, nucleotide metabolism, and vitamin B6-related metabolic pathways. These findings demonstrate that the extract of broccoli tails modulates intestinal gene expression, systemic metabolism, and gut microbial ecology in Hu sheep, providing new insights into the utilization of agricultural byproducts as a functional feed supplement for ruminants.},
}

@article {pmid42515062,
year = {2026},
author = {Hussien, RHM and Kortsinoglou, AM and Wood, MJ and Kouvelis, VN and Mellikeche, W and Touray, M and Tembeni, B and Alzain, M and Alotaibi, F and Sobhy, IS and Saud, Z and Loveridge, EJ and Eastwood, DC and Butt, TM},
title = {Endophytic Entomopathogenic Fungi Shape Herbivore Behavior and Plant-Insect Interactions: Implications for Biological Control.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/pathogens15070735},
pmid = {42515062},
issn = {2076-0817},
support = {UKRI239//UK Research and Innovation/ ; EP/X525637/1//Engineering and Physical Sciences Research Council/ ; 2019-2022//Ministry of Higher Education and Scientific Research/ ; NA//Saudi Arabia Cultural Bureau in London/ ; },
abstract = {Entomopathogenic fungi (EPF) are well established as biological control agents, but their emerging role as endophytes reveals a broader and more powerful function in crop protection. By colonizing plant tissues, endophytic entomopathogenic fungi (EEPF) create a dynamic tripartite interaction between plants, fungi, and herbivores, enabling systemic, plant-mediated pest suppression. This review synthesizes current knowledge on the behavioral and ecological responses of herbivorous arthropods to EEPF-colonized plants, with an emphasis on the mechanisms and implications for integrated pest management (IPM). Growing evidence indicates that EEPF consistently modify herbivore behavior and performance across diverse crops and insect taxa. Colonization frequently alters feeding, host selection, and oviposition, often deterring pests, although mediated responses may vary among fungal species, host plants, insect taxa, and environmental conditions. These responses are driven by EEPF-induced changes in plant chemistry, including shifts in volatile organic compounds (VOCs) and defensive metabolites. In parallel, EEPF impair insect fitness by delaying development, reducing survival, and lowering fecundity, thereby suppressing pest populations. These plant-mediated and behavioral changes extend to multitrophic interactions, potentially affecting associations with natural enemies and the transmission efficiency of some insect vectors of plant viruses. Despite rapid progress, critical gaps remain in resolving the mechanistic basis of these interactions and their stability under field conditions. Advancing the application of EEPF will require integrated approaches combining microbial ecology, chemical ecology, and insect behavioral biology. Harnessing these interactions offers a compelling pathway to reduce reliance on synthetic pesticides while enhancing the resilience and sustainability of agricultural systems.},
}

@article {pmid42515698,
year = {2026},
author = {Garcia, J and Olo-Fontinha, E and Silva, J and Dias-Costa, R and Alves, MJ and Gouvinhas, I},
title = {Mushroom-Derived Phenolic Compounds as Emerging Prebiotic-like Modulators of Gut Microbiota, Intestinal Health, and Metabolism.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {7},
pages = {},
doi = {10.3390/ph19071014},
pmid = {42515698},
issn = {1424-8247},
support = {2024.04884.RESTART//Fundação para a Ciência e Tecnologia/ ; UID/04033/2025//Fundação para a Ciência e Tecnologia/ ; UID/00772/2025//Fundação para a Ciência e Tecnologia/ ; 2024.06281.BDANA//Fundação para a Ciência e Tecnologia/ ; 01/C05-i02/2022//RE-C05-i02 - Missão Interface/ ; },
abstract = {Background/Objectives: Mushroom-derived phenolic compounds are gaining attention as bioactive molecules with potential roles in gut microbiota modulation, intestinal health, and metabolic regulation. Although mushroom polysaccharides are well established as fermentable substrates, the contribution of fungal phenolics to microbiota-host interactions remains less defined. This review aimed to critically analyse the evidence supporting mushroom-derived phenolic compounds as emerging prebiotic-like modulators of gut microbiota, intestinal function, and host metabolism. Methods: A narrative critical review was conducted using scientific literature retrieved from PubMed, Scopus, Web of Science, and Google Scholar. Studies addressing phenolic profiling in edible and medicinal mushrooms, gastrointestinal digestion, colonic fermentation, microbial biotransformation, gut microbiota modulation, intestinal barrier function, inflammation, and metabolic outcomes were considered. Particular attention was given to chromatographic and mass spectrometry-based studies, in vitro digestion/fermentation models, mechanistic studies, animal experiments, clinical trials, systematic reviews, and meta-analyses. Results: Current evidence shows that mushrooms contain diverse phenolic compounds, mainly phenolic acids such as gallic, protocatechuic, caffeic, p-coumaric, ferulic, vanillic, syringic, and cinnamic acids. Due to limited small intestine absorption, a substantial fraction of these compounds may reach the colon, where they undergo microbial biotransformation into smaller phenolic metabolites. These metabolites may influence microbial ecology, support beneficial taxa, modulate short-chain fatty acid production indirectly, attenuate oxidative stress and inflammatory signaling, and contribute to intestinal barrier integrity. However, most evidence derives from in vitro and preclinical studies, while human data remain limited and are mainly based on whole-mushroom interventions. Conclusions: Mushroom-derived phenolic compounds are promising prebiotic-like modulators within the microbiota-metabolite-host axis. Nevertheless, their specific contribution cannot yet be quantitatively distinguished from that of other mushroom constituents, particularly β-glucans, chitin, and other fungal polysaccharides, because most available evidence derives from whole-mushroom matrices, crude extracts, or polysaccharide-rich preparations rather than isolated phenolic fractions. Future studies should compare whole mushroom preparations, polysaccharide-rich fractions, and standardized phenolic-rich extracts, integrating metabolomics, microbiome profiling, and well-designed clinical trials to clarify the relative mechanistic and therapeutic relevance of mushroom phenolics. Future studies should use standardized phenolic-rich extracts, metabolomics, microbiome analysis, and well-designed clinical trials to clarify their mechanistic relevance, clinical significance, and translational potential.},
}

@article {pmid42517205,
year = {2026},
author = {Xiao, W and Zhou, X and Cheng, L and Bodelier, PLE and Wang, G and Yang, Z and Zhou, J},
title = {Microbial Functional Gene Abundance-Integrated Modeling of Global Methane Sinks in Upland Soils Under Future Climate Change.},
journal = {Global change biology},
volume = {32},
number = {7},
pages = {e71026},
pmid = {42517205},
issn = {1365-2486},
support = {32171635//National Natural Science Foundation of China/ ; },
abstract = {Methanotrophs are key microbial regulators of soil methane (CH4) sinks, but the global impact of their functional gene abundance on CH4 oxidation remains unquantified. This gap limits the integration of key functional genes abundance parameters (e.g., pmoA) into soil CH4 sink model. We integrated meta-analysis, machine learning, and process-based modeling to assess the relationship between pmoA gene abundance and soil CH4 uptake. Our developed Functional Gene Abundance-Based Methanotrophy Model (FGA-MeMo) incorporates pmoA as a proxy for CH4 oxidation capacity, significantly improving model simulations. FGA-MeMo estimates global upland soil CH4 uptake at 45.74 ± 0.26 Tg year[-1], which is 56%-58% higher than MeMo model. Under SSP5-8.5 scenario, this increases to 64.68 ± 0.35 Tg year[-1] by 2100, with mid- and high-latitude regions showing enhanced CH4 oxidation due to greater pmoA abundance. These findings highlight the importance of integrating microbial functional genes into Earth system models for improved CH4 cycle predictions.},
}

@article {pmid42517643,
year = {2026},
author = {Ochsner, N and San Román, M and Jiménez-Fernández, A and Bonhoeffer, S and Pascual-Garcia, A},
title = {misosoup: a metabolic modeling tool for identifying minimal microbial communities, facilitates the exploration of microbial ecology and biotechnological applications.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0068826},
doi = {10.1128/msystems.00688-26},
pmid = {42517643},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial survival and function often depend on metabolic interactions within communities. Therefore, a central question in disentangling microbial organization is determining which minimal groups of strains are able to thrive in a given medium-referred to as "minimal communities." Answering this question is essential for understanding microbial distribution, enhancing laboratory cultivation, and designing synthetic communities (SynComs). Here, we introduce misosoup, a Python package for identifying minimal communities (minimal supplying community search). Through genome-scale constraint-based metabolic modeling, misosoup enables the systematic identification of communities that support microbial growth in environments where individual strains fail to survive alone. We validate misosoup against experimentally verified minimal communities, demonstrating its ability to predict known cooperative interactions, cocultures, and consortia with biotechnological potential. We further illustrate the use of misosoup to investigate broad microbial ecology questions by applying it to a set of 60 marine microbes, finding pervasive cross-feeding-driven niche expansion, and showing how the detailed outputs provided by misosoup facilitate research on hot topics such as the identification of functional groups. In summary, misosoup provides a powerful tool for microbial ecology and community design, with potential applications in both research and biotechnological innovation.

IMPORTANCE: Microbes often rely on each other to survive, especially in environments where they cannot live alone. Understanding which small groups of microbes can thrive together-called minimal communities-is key to improving laboratory research, designing synthetic ecosystems, and exploring how microbes spread in nature. To support this, we developed misosoup, a Python tool that identifies these communities using advanced metabolic modeling. misosoup helps scientists discover how microbes cooperate by sharing nutrients, a process known as metabolic cross-feeding. When tested on sets of species from different origins, the tool showed that species could thrive in more environments when part of a group. This finding highlights the importance of cooperation in microbial life. misosoup not only predicts these interactions but also provides detailed insights that can guide ecological studies and biotechnological innovation. By revealing how microbes support each other, misosoup contributes to a deeper understanding of life's interconnectedness and offers tools for solving real-world challenges.},
}

@article {pmid42496113,
year = {2026},
author = {Piperni, E and Blanco-Míguez, A and Mengoni, C and Piccinno, G and Punčochář, M and Ren, J and Segata, N and Asnicar, F and Poole, AC},
title = {Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0076326},
doi = {10.1128/spectrum.00763-26},
pmid = {42496113},
issn = {2165-0497},
abstract = {Resistant starch (RS) can confer benefits for the gut microbiome and host cardiometabolic health. However, different types of resistant starch can differentially affect gut microbiome composition and functional capacity, especially given interindividual variability in responses, thus limiting the application of resistant starch in dietary strategies. We used shotgun metagenomics to perform a secondary analysis of samples collected during a previously reported randomized clinical trial to determine the effects of dietary supplementation with two types of resistant starch (RS2 and RS4) and a digestible starch (control) on the gut microbiome. Both resistant starch types induced distinct but transient alterations in the gut microbial community. RS2 enriched the keystone degrader, Ruminococcus bromii, and Blautia glucerasea, whereas RS4 favored Parabacteroides distasonis and known but uncharacterized microbial species such as a Lachnospiraceae bacterium. Moreover, we detected strain-level differences in the response of Bifidobacterium adolescentis to resistant starch. Microbial functional profiling revealed an enhanced capacity for complex carbohydrate utilization following resistant starch intake, including increased abundance of specific α-amylases, glycoside hydrolases, starch utilization systems, and other currently uncharacterized genes. Identifying the bacterial strains and genes that respond to different RS types will help to more accurately predict who will benefit from a given RS type. Our findings demonstrate that RS2 and RS4 differentially shape microbial ecology and metabolic capacity and provide a foundation for microbiome-informed personalization of resistant starch-based dietary interventions.IMPORTANCEDietary intake influences human health by modulating metabolism, partly by shaping the microbiota inhabiting the gut. Resistant starch (RS), a dietary fiber, is associated with metabolic improvements. While previous research has explored how RS alters the gut microbiome, RS comprises five types with differing physical and chemical characteristics, and the distinct impacts of each type on the microbiome and host health have not been fully characterized, particularly using high-resolution approaches such as shotgun metagenomics. In this secondary analysis of samples from a longitudinal crossover intervention study, we link dietary supplementation with RS2 and RS4 with distinct and transient changes in the composition and functional potential of the human gut microbiome. Specifically, we identify species that increase in abundance with each RS type, accompanied by increases in genes and pathways involved in complex carbohydrate utilization. The findings support the development of precision nutrition strategies utilizing RS supplementation to improve metabolic health.This study is registered with ClinicalTrials.gov as NCT05743790.},
}

@article {pmid42498510,
year = {2026},
author = {Li, Z and Yang, Q and Lv, L and Shang, Y and Sun, X and Dong, M and Xiao, Q and Huang, F and Cai, M and Zhang, J and Yu, Z and Zheng, L},
title = {Synergistic role of egg-associated bacteria in promoting egg hatching of black soldier fly (Hermetia illucens L.).},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70327},
pmid = {42498510},
issn = {1744-7917},
support = {2025BBB013//Key Research and Development Project of Hubei Provincial Department of Science and Technology/ ; 32172783//National Natural Science Foundation of China/ ; },
abstract = {The black soldier fly (Hermetia illucens L.) is a critical species for organic waste bioconversion, yet the microbial ecology regulating its embryonic development remains obscure. This study investigated the diversity, temporal dynamics, and functional role of the egg-associated microbiota in black soldier fly hatching. Surface sterilization experiments revealed that the presence of surface microbes significantly facilitates hatching, as sterilization reduced hatching rates from 77.06% to 33.72%. Notably, this reduction was substantially reversed by re-inoculation with native egg-derived bacteria. High-throughput 16S rRNA gene sequencing demonstrated dynamic temporal shifts within the bacterial community during the 72 h incubation period, which was consistently dominated by the phyla Proteobacteria and Firmicutes. Functional prediction via PICRUSt indicated that the abundance of genes encoding chorion-degrading enzymes, including chitinases and proteases, fluctuated synchronously with critical hatching stages. Furthermore, culture-dependent screening identified Bacillus and Staphylococcus as key hatching promoters. Co-inoculation of these two strains resulted in synergistic improvements in hatching success compared to single-strain treatments. These findings suggest that specific members of the egg-associated microbiota function cooperatively to assist hatching, likely through enzymatic modification of the chorion. This study provides new insights into early-stage insect-microbe interactions and offers a potential microbial management strategy for optimizing black soldier fly mass rearing.},
}

@article {pmid42499706,
year = {2026},
author = {Chen, XP and Xu, JQ and Zhang, NN and Huang, Q and Zhu, TH and He, C},
title = {Gut microbiota-derived metabolites and EVs-mediated signaling in type 2 diabetes mellitus.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1862369},
pmid = {42499706},
issn = {2296-634X},
abstract = {Type 2 diabetes mellitus is characterized by systemic insulin resistance, chronic low-grade inflammation, and progressive metabolic dysfunction. Increasing evidence identifies the gut microbiota as a central regulator of host immunometabolism through a diet-microbiota-host axis. Gut microbiota-derived metabolites, including short-chain fatty acids, bile acids, branched-chain amino acids, and trimethylamine N-oxide, integrate endocrine signaling, intracellular metabolic pathways, and inflammatory responses across intestinal and systemic compartments, thereby shaping glucose homeostasis and metabolic balance. Diet acts as an upstream determinant by modulating microbial composition and metabolic activity. Beyond soluble metabolites, extracellular vesicles have emerged as an additional mode of intercellular communication. Vesicles derived from diet or microbiota carry bioactive cargos such as proteins, lipids, and small RNAs, enabling the transfer of functional signals that may influence both microbial ecology and host immunometabolic processes. This review summarizes metabolite-dependent and vesicle-mediated signaling pathways and highlights how these interconnected mechanisms position the gut microbiota as a signaling hub linking dietary inputs to host cellular regulation. This framework provides a conceptual basis for microbiota-targeted strategies in the prevention and treatment of type 2 diabetes.},
}

@article {pmid42501131,
year = {2026},
author = {Nithyapriya, S and Sundaram, L and Eswaran, SUD and Perveen, K and Alshaikh, NA and Sayyed, RZ and Mastinu, A},
title = {Retraction Note: Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
doi = {10.1007/s00248-026-02838-8},
pmid = {42501131},
issn = {1432-184X},
}

@article {pmid42502862,
year = {2026},
author = {Xu, Y and Ji, L and Liu, T and Qian, L and Zhou, H and Zhuang, C and Chen, H and Zhou, X and Zhao, L and Zhou, X},
title = {Volatile aroma profiles and associated microbiota of Yunnan Shiping sour-pulp-fermented stinky tofu.},
journal = {Food chemistry: X},
volume = {38},
number = {},
pages = {104217},
pmid = {42502862},
issn = {2590-1575},
abstract = {Yunnan Shiping stinky tofu is a traditional sour-pulp-fermented soybean product with distinctive volatile aroma characteristics. In this study, headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS), relative odor activity value (ROAV) analysis, and 16S rRNA/ITS amplicon sequencing were used to characterize volatile organic compounds (VOCs) and associated microbial communities in samples collected from four local production facilities. A total of 418 VOCs were detected, and ROAV analysis indicated that sulfur-containing compounds, heterocyclic compounds, furanone derivatives, terpenoid-derived odorants, and unsaturated aldehydes contributed substantially to the volatile aroma profile. The bacterial communities were mainly composed of Proteobacteria, Bacteroidota, and Firmicutes, whereas the fungal communities were dominated by Ascomycota and Basidiomycota. Correlation analysis suggested potential associations between selected bacterial or fungal genera and aroma-active compounds; however, these associations should be interpreted as hypothesis-generating rather than causal evidence. These findings provide a descriptive basis for understanding the volatile aroma characteristics and microbial ecology of Yunnan Shiping sour-pulp-fermented stinky tofu and may guide future targeted isolation, safety assessment, and validation of aroma-associated microorganisms.},
}

@article {pmid42503325,
year = {2026},
author = {Zhang, X and Li, J and An, Y and Zheng, J and Xu, G and Wang, J and Chen, L and Lu, Y},
title = {Vitamin B12-mediated microglial immunometabolic reprogramming: A novel mechanistic insight into diabetes-associated cognitive impairment.},
journal = {Progress in neuro-psychopharmacology & biological psychiatry},
volume = {},
number = {},
pages = {111861},
doi = {10.1016/j.pnpbp.2026.111861},
pmid = {42503325},
issn = {1878-4216},
abstract = {Diabetes-associated cognitive impairment (DCI) is an increasingly recognized neurological complication of type 2 diabetes mellitus characterized by chronic neuroinflammation and microglial immunometabolic dysregulation. Vitamin B12 (VB12) deficiency, which is highly prevalent in patients with diabetes, has been strongly associated with cognitive decline, hippocampal atrophy, and white matter injury. Emerging evidence suggests that VB12 plays a critical role in maintaining one‑carbon metabolism, mitochondrial function, and redox homeostasis. Mechanistically, VB12 deficiency promotes homocysteine accumulation, disrupts the S-adenosylmethionine/S-adenosylhomocysteine balance, impairs mitochondrial oxidative phosphorylation, and enhances oxidative stress, thereby driving pro-inflammatory microglial activation and sustained neuroinflammation. In addition, gut microbiota dysbiosis, particularly reduced abundance of Akkermansia muciniphila and other VB12-producing bacteria, may further impair VB12 bioavailability and aggravate neuroinflammation through the gut-brain axis. This review summarizes current evidence linking VB12 deficiency to microglial immunometabolic remodeling in DCI and discusses the therapeutic potential of targeting VB12 metabolism and gut microbial ecology for preventing diabetes-related cognitive decline.},
}

@article {pmid42504676,
year = {2026},
author = {Okechukwu, VO and Njobeh, PB and Okonkwo, JO},
title = {Photocatalytic and Biotechnological Strategies for Remediation of Persistent Organic Pollutants: Mechanisms, Toxicity, and Antimicrobial Perspectives.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.70172},
pmid = {42504676},
issn = {1522-7278},
support = {PSTD250327306922//National Research Foundation (NRF) of South Africa/ ; },
abstract = {Persistent organic pollutants (POPs) pose significant ecological and human health risks due to their persistence, bioaccumulation, toxicity, and global distribution. Conventional remediation methods are often inadequate for achieving complete mineralization, demonstrating the need for advanced and substantial approaches. Recent studies have explored photocatalytic and biotechnological methods as promising alternatives; however, critical gaps remain regarding the toxicity of transformation products, implications for antimicrobial resistance (AMR), and the scalability of hybrid systems. This review assesses photocatalytic and biotechnological strategies for POP remediation, focusing on their mechanisms, performance, and environmental impacts. Photocatalysis enables the rapid degradation of recalcitrant compounds with reported removal efficiencies often exceeding 70%-95% under optimized conditions for pollutants. In contrast, biotechnological approaches facilitate selective and complete mineralization through microbial and enzymatic processes but are influenced by environmental conditions and pollutant bioavailability. Hybrid photocatalytic-biological systems demonstrate enhanced efficiency by coupling oxidative pretreatment with biodegradation, although their performance may vary depending on system integration and operational conditions. This review focuses on the formation and fate of intermediate by-products, their potential toxicity, and the influence of remediation processes on microbial communities and AMR dynamics. Unlike previous studies, this work integrates material science, environmental toxicology, and microbial ecology while emphasizing emerging tools such as omics technologies, synthetic biology, and digital optimization to advance risk-informed and sustainable remediation strategies.},
}

@article {pmid42504986,
year = {2026},
author = {Han, JJ and Guzman, AR and Zhou, A and Zhang, H and Gupte, R and Jung, H and Delgado, K and Skariah, S and Sultan, A and Jayaraman, A and de Figueiredo, P and Han, A},
title = {Polychip-A High-Throughput Droplet Microfluidics Platform for Interrogating Microbial Interactions.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e23854},
doi = {10.1002/advs.202523854},
pmid = {42504986},
issn = {2198-3844},
support = {/NH/NIH HHS/United States ; 1R01AI168685-01A1//National Institute of Allergy and Infectious Diseases/ ; R01AI141607-01A1//National Institute of Allergy and Infectious Diseases/ ; R21AI139738-01A1//National Institute of Allergy and Infectious Diseases/ ; M2404535//Texas A&M University Advancing Discovery to Market/ ; NPRP9-001-2-001//Qatar National Research Foundation/ ; W911NF1920013,HR00112320006//Defense Advanced Research Projects Agency (DARPA)/ ; },
abstract = {Microbial interactions are fundamental to ecology, health, and disease, yet high-throughput tools to study these complex relationships remain scarce. We introduce Polychip, a fully integrated, high-throughput droplet microfluidics platform that revolutionizes microbial interaction screening. By seamlessly combining six microfluidic operations onto a single chip, Polychip achieves 99.7% efficiency and accelerates screening by 11-14 times compared to traditional high-throughput liquid handling robotic methods, with minimal human input. Using the Polychip, we screened 2.24 × 10[6] soil-extracted microorganisms against the multidrug-resistant (MDR) pathogen Pseudomonas aeruginosa. This process recovered 1.96 × 10[4] hit droplets with an antimicrobial activity confirmation accuracy of 48%. Three environmental isolates (Stenotrophomonas sp.) exhibiting high potency and broad-spectrum antimicrobial activity were identified through this screen. Supernatants from these three environmental isolates suppressed growth of both gram-negative MDR pathogen Acinetobacter baumannii and gram-positive methicillin-resistant Staphylococcus aureus (MRSA). Through whole-genome sequencing, metabolic pathway analysis, and mass spectrometry, we identified the secreted compound as enterochelin. This demonstrates Polychip's unprecedented single-cell resolution and high throughput screening capability in rapidly discovering antimicrobial activities, opening new frontiers in combating resistant microbial pathogens, as well as more broadly advancing microbial ecology research.},
}

@article {pmid42493633,
year = {2026},
author = {Rock, R and Zhang, S and Noecker, C and Turnbaugh, PJ},
title = {Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42493633},
issn = {1740-1534},
abstract = {Despite a tremendous body of literature on environmental Actinomycetota, their role in the human gut remains poorly understood. In this Review, we highlight the representative species Eggerthella lenta, which has emerged as a major player in the gut microbiota and is increasingly amenable to mechanistic dissection. We discuss the unique metabolic niche of this asaccharolytic obligate anaerobe, including growth on amino acids and short-chain fatty acids, versatile anaerobic respiratory capacity, and the extensive biotransformation of endogenous, diet-derived and pharmaceutical small molecules. E. lenta is associated with a wide range of chronic diseases in humans and sufficient to exacerbate disease in preclinical models, prompting a renewed consideration of the pathogenic potential of this common member of the gut microbiota. Further mechanistic dissection coupled with the development of microbiome-editing tools is essential to understand E. lenta and its multifaceted contributions to gut microbial ecology and host pathophysiology.},
}

@article {pmid42494685,
year = {2026},
author = {Li, D and Kyawt, Y and Wang, Q and Gao, J and Wang, R and Wang, M and Duan, C and Lv, D and Zhu, W and Wanapat, M and Cheng, Y},
title = {High-dose phytosterols supplementation improves lactation performance, modulates rumen microbiota, and reduces methane emission intensity in mid-lactation Holstein dairy cows.},
journal = {Veterinary world},
volume = {19},
number = {6},
pages = {2339-2357},
pmid = {42494685},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Enteric methane emission from dairy cows contributes substantially to greenhouse gas production and represents an inefficient loss of dietary energy. Phytosterols are plant-derived bioactive compounds with lipid-modulating and rumen fermentation-regulating properties; however, their effects on methane emission intensity and rumen microbial ecology in lactating dairy cows remain insufficiently explored. This study evaluated the effects of dietary phytosterols supplementation on lactation performance, nutrient digestibility, serum biochemical parameters, rumen fermentation characteristics, methane emission intensity, and rumen microbial composition in mid-lactation Holstein dairy cows.

MATERIALS AND METHODS: Thirty-four multiparous Holstein dairy cows with similar days in milk and milk yield were randomly assigned to either a control (CON) group or a phytosterols (PHY) group receiving 15 g/d of a commercial phytosterols product containing 5% active phytosterols. The experimental period lasted 50 days, including 7 days of adaptation and 43 days of data collection. Feed intake and milk yield were recorded daily. Milk composition, apparent nutrient digestibility, serum biochemical indices, rumen fermentation parameters, methane emission intensity, quantitative polymerase chain reaction, and 16S rRNA gene sequencing were analyzed. Methane and carbon dioxide emissions were measured using an automated head-chamber system.

RESULTS: Dietary phytosterols supplementation significantly improved milk yield, milk fat percentage, milk protein percentage, energy-corrected milk, and 3.5% fat-corrected milk compared with the CON group (p < 0.05). Apparent digestibility of organic matter, crude protein, neutral detergent fiber, and ether extract was also significantly enhanced. Serum glucose and blood urea nitrogen concentrations increased, whereas total cholesterol and low-density lipoprotein cholesterol concentrations decreased in the PHY group. Phytosterols supplementation significantly reduced methane emission intensity per kilogram of energy-corrected milk. Ruminal acetate proportion and acetate-to-propionate ratio decreased, whereas microbial crude protein and branched-chain volatile fatty acids increased. In addition, phytosterols altered rumen microbial composition by increasing the abundance of beneficial bacterial genera, including Succinivibrionaceae UCG-001 and Prevotella, while reducing methanogenic archaea, particularly Methanobacteriota and Methanimicrococcus.

CONCLUSION: High-dose phytosterols supplementation improved lactation performance, enhanced nutrient utilization, modulated rumen microbial communities, and reduced methane emission intensity in mid-lactation dairy cows. These findings indicate that phytosterols may serve as a promising natural feed additive for improving dairy production efficiency while supporting methane mitigation strategies in sustainable dairy farming.},
}

@article {pmid42491472,
year = {2026},
author = {Lusi, EA and Rifici, C},
title = {Nickel-resistant gut microbiota: a missing link between environmental exposure and metabolic disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852314},
pmid = {42491472},
issn = {1664-302X},
abstract = {Environmental factors are emerging as important modulators of the gut microbiome, with significant implications for metabolic health. Among these, nickel-a ubiquitous dietary metal traditionally regarded as an allergen-is gaining recognition as a systemic immune-metabolic modulator. Chronic nickel exposure has been linked to overweight and metabolic alterations, particularly in nickel-allergic individuals, suggesting that environmental nickel may represent an underrecognized contributor to metabolic dysfunction in susceptible populations. Recent studies have identified nickel-resistant bacteria within the gut microbiota of affected individuals, providing a biologically plausible framework linking environmental metal exposure to microbial ecology. These microorganisms contribute to nickel detoxification and may influence host physiology through interactions with microbial metabolism, energy balance, and immune signaling. Under conditions of chronic exposure, ecological selection of nickel-resistant communities may contribute to dysbiosis and altered host-microbiome interactions. By integrating clinical observations with emerging microbiological evidence, this Perspective explores the hypothesis that nickel-resistant gut microbiota may represent candidate mediators at the intersection of environmental exposure, immunity, and metabolism. Understanding how dietary metals shape microbial ecosystems may provide new insights into metabolic disease and highlights metal-microbiota interactions as a promising area for future investigation.},
}

@article {pmid42492502,
year = {2026},
author = {Majamäki, R and Wasiljeff, J and Purkamo, L and Hultman, J and Kohl, L and Asmala, E and Yli-Hemminki, P and Jørgensen, KS and Muurinen, J and Virtasalo, JJ},
title = {Different Ferromanganese Concretion Morphologies Host Distinct Microbial Communities and Metal Accumulation Patterns in the Baltic Sea.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70390},
pmid = {42492502},
issn = {1462-2920},
support = {332249//Research Council of Finland/ ; 20240020//Foundation for Research of Natural Resources in Finland/ ; },
mesh = {*Bacteria/metabolism/classification/isolation & purification/genetics ; *Seawater/microbiology/chemistry ; Finland ; *Manganese/metabolism ; *Iron/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Microbiota ; *Metals/metabolism ; Gammaproteobacteria/metabolism ; *Ferric Compounds/metabolism ; },
abstract = {Ferromanganese (Fe-Mn) concretions are porous accumulations of iron and manganese (hydr)oxides. While recent studies suggest that microbes contribute to metal accumulation in Baltic Sea concretions, the detailed composition of microbial communities and their impact on metal enrichment across different concretion morphotypes remain unexplored. We investigated how microbes influence the accumulation and release of trace metals and rare-earth elements in Fe-Mn concretions from the Gulf of Finland through 15-week microcosm incubation experiments with biotic and abiotic treatments, focusing on three main concretion morphotypes: crust, discoidal, and spheroidal. Elemental analysis showed that microbes enhanced metal incorporation in discoidal and spheroidal morphotypes. Characterisation of microbial composition revealed that all three morphologies host distinct communities. Discoidal and spheroidal morphotypes had a higher relative abundance of Gammaproteobacteria and sulfate-reducing bacteria, and a lower abundance of Entotheonellaeota, compared to crusts. In all morphotypes, the bacterial phylum Pseudomonadota dominated, with several genera of Fe- and Mn-oxidisers and reducers. Fe-Mn concretions also host communities involved in methane oxidation and nitrogen cycling, consistent with decreased methane and increased nitrous oxide, nitrite, and nitrate concentrations in the microcosms. Our findings underscore that distinct microbial communities are associated with different concretion morphotypes, potentially influencing nutrient and metal cycling on the seafloor.},
}

*Bacteria/metabolism/classification/isolation & purification/genetics
*Seawater/microbiology/chemistry
Finland
*Manganese/metabolism
*Iron/metabolism
*Geologic Sediments/microbiology/chemistry
*Microbiota
*Metals/metabolism
Gammaproteobacteria/metabolism
*Ferric Compounds/metabolism

@article {pmid42489313,
year = {2026},
author = {Kim, SY and Kim, Y and Kim, DJ and Chang, HS},
title = {Long-read rRNA operon sequencing reveals bacterial community divergence between traditional and industrial soybean fermentations.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag064},
pmid = {42489313},
issn = {1472-765X},
abstract = {Traditional and industrial soybean fermentations harbor distinct microbial communities that influence product quality and safety. In this study, long-read rRNA operon sequencing was applied to investigate the bacterial communities of traditional and commercial doenjang and cheonggukjang. The 16S-23S rRNA operon (∼4.2 kb) was amplified and sequenced using the Oxford Nanopore MinION platform to obtain high-resolution taxonomic profiles. Traditional doenjang and cheonggukjang exhibited greater microbial diversity than commercial products, as revealed by alpha and beta diversity analyses. Bacillus species, particularly B. velezensis and B. subtilis, were dominant across all samples, while Loigolactobacillus coryniformis, Caldifermentibacillus hisashii, and Tetragenococcus halophilus were more abundant in traditionally fermented samples. These genera are associated with proteolysis, amino acid metabolism, and flavor compound formation during fermentation. Overall, these findings provide insights into the microbial ecology of fermented soybean foods and suggest that non-starter lactic acid bacteria and thermophilic species may contribute to the unique sensory characteristics of traditionally fermented doenjang.},
}

@article {pmid42490025,
year = {2026},
author = {Pereira, D and Moreira, FC and da Silva, VCS and de Souza Avelar, D and Ramos, SAA and da Silva, JMC and da Silva Mourão, RM and da Silva, RF and Guimarães, KSP and Pinto, JBA and da Conceição, M and Barra, WF and Demachki, S and Casseb, SM and Burbano, RMR and de Assumpção, PP},
title = {Comprehensive analysis of the gastric metatranscriptome reveals specific viral signatures associated with gastric cancer.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42490025},
issn = {1618-1905},
abstract = {Gastric cancer (GC) remains highly lethal, and although gastric microbiome dysbiosis has been linked to carcinogenesis, the viral component is still poorly explored. Here, we used metatranscriptomics to characterize the gastric virome and evaluate its association with GC and clinicopathological features. We analyzed 238 gastric tissues (214 GC and 24 non-tumors, NT) with clinicopathological data. Viral classification was performed using Kraken2 with the RVDB database. Virome diversity, composition, and clustering were assessed using phyloseq-based analyses, Jensen-Shannon divergence with PAM clustering, and ordination methods. Differential abundance and diversity were evaluated using LEfSe and statistical tests, and viral gene expression was investigated for clinical relevant viruses. We identified 106 viral genera, predominantly bacteriophages and dsDNA viruses, with distinct GC- and NT-associated viral signatures. Clustering revealed three viral community types (GT-1, GT-2, GT-3) that significantly separated GC and NT samples and showed reduced alpha diversity in GC-associated clusters. GT-1 was dominated by Lymphocryptovirus, GT-2 by Gorganvirus, and GT-3 (NT) exhibited the highest diversity. GC tissues were enriched in oncologically relevant viruses, including Lymphocryptovirus (EBV), Cytomegalovirus, and Alphapapillomavirus, whereas several bacteriophages predominated in NT. Virome composition was significantly associated with Lauren histological subtype, but not with clinical stage, tumor location, or neoadjuvant therapy. EBV-high tumors displayed a predominantly latent transcriptional program, with strong expression of ncRNAs (RPMS1, EBERs) and low lytic activity. These findings highlight major virome restructuring in GC and support a potential role of the gastric virome in tumor-associated microbial ecology, warranting further mechanistic and clinical investigation.},
}

@article {pmid42490939,
year = {2026},
author = {Xie, Q and Yang, Y and Lin, J and Ye, Y and Lin, J and Wu, M and Guo, Z and Shen, A and Zeng, W and Peng, J},
title = {Gut microbiota-derived butyrate contributes to baicalin-induced attenuation of hypertensive vascular remodeling via adventitial immunity.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1835174},
pmid = {42490939},
issn = {1663-9812},
abstract = {BACKGROUND: Baicalin shows potent vasculoprotective effects against hypertension despite poor oral bioavailability. We investigated whether gut microbiota modulation contributes to the systemic vasculoprotective effects of orally administered baicalin.

METHODS: We utilized an Angiotensin II-induced hypertensive mouse model, employing broad-spectrum antibiotics, 16S rRNA sequencing, metabolomics, and in vitro co-culture assays to map the gut-immune-vascular axis.

RESULTS: Oral Baicalin significantly attenuated Ang II-induced blood pressure elevation and improved the intestinal barrier integrity. Antibiotic-induced microbiota depletion substantially weakened these protective effects, supporting a major microbiota contribution under the present experimental conditions. Baicalin reshaped the gut microbial community, enriched SCFA-supporting taxa, and restored a putative butyrate-associated microbial signature, enriching Akkermansia and Lactobacillus accompanied by increased cecal butyrate levels. Exogenous sodium butyrate recapitulated several major protective features of Baicalin treatment, including expansion of Foxp3+ regulatory T cells in mesenteric lymph nodes. These immune changes were accompanied by increased Foxp3+ regulatory immune-cell accumulation in the aortic adventitia. In vitro, butyrate-licensed Tregs suppressed Ang II-induced vascular smooth muscle cell (VSMC) proliferative responses, at least partly through IL-10-mediated inhibition of MAPK/ERK signalling.

CONCLUSION: Baicalin alleviates Ang II-associated vascular remodelling, at least in part, by reprogramming gut microbial ecology, increasing luminal butyrate availability, promoting regulatory immune responses, and suppressing VSMC proliferative signalling.},
}

@article {pmid42479765,
year = {2026},
author = {Fant, L and Macocco, I and Grilli, J},
title = {Eco-evolutionary dynamics lead to functionally robust and redundant communities.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014437},
doi = {10.1371/journal.pcbi.1014437},
pmid = {42479765},
issn = {1553-7358},
abstract = {Microbial communities are taxonomically diverse and variable: species presence and abundances widely fluctuate over time, space, and even across biological replicates under controlled experimental conditions. However, environmental conditions exert strong selection on the traits of community members and their functions. Similar environmental conditions are expected to produce functionally similar communities. This environmental selection, combined with taxonomic variability, leads to the influential concept of functional redundancy - the idea that many species can perform the same function, allowing communities with different species compositions to maintain identical functional profiles. Despite the centrality of functional redundancy in microbial ecology, we lack a theoretical understanding of its origin. Here we study the eco-evolutionary dynamics of communities interacting through competition and cross-feeding. We show that eco-evolutionary trajectories rapidly converge to a "functional attractor" - a functional composition uniquely determined by environmental conditions. Taxonomic composition follows non-reproducible dynamics while being constrained by the conservation of functional composition. Our framework provides a theoretical foundation for understanding functional robustness and redundancy in microbial communities.},
}