@article {pmid42639367,
year = {2026},
author = {Mulaw, G and Kidanemariam, G and Bara, M and Tesfay, T},
title = {Probiotics in Human Health: Current Evidence, Mechanism of Action, and Future Perspectives.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {1721210},
pmid = {42639367},
issn = {1687-918X},
abstract = {Probiotics are widely recognized for their potential to promote human health through diverse mechanisms that influence host physiology and microbial ecology. This review synthesizes current evidence on the biological functions, mechanisms of action, and therapeutic applications of probiotics. A comprehensive narrative literature review was conducted, with 143 records identified, screened, and assessed for eligibility before inclusion in the final analysis. The available evidence indicates that probiotics exert their beneficial effects through modulation of gut microbiota composition, enhancement of intestinal barrier integrity, competitive exclusion of pathogens, production of antimicrobial metabolites, and regulation of innate and adaptive immune responses. Clinical and experimental studies further suggest potential benefits in the prevention or management of antibiotic-associated diarrhea, lactose intolerance, allergic diseases, hypercholesterolemia, colorectal cancer, neurological disorders, and heavy metal toxicity. Despite promising findings, probiotic efficacy remains strain-specific and influenced by host characteristics, dosage, and treatment duration. Challenges related to strain selection, safety assessment, and standardization continue to limit broader clinical application. Overall, this narrative review provides an integrated overview of current knowledge on probiotic functionality, highlights emerging therapeutic opportunities, and identifies key research gaps that should be addressed to support evidence-based probiotic use.},
}

@article {pmid42642057,
year = {2026},
author = {Mairet, F},
title = {Mitochondrial ribosome content as a proxy for respiration.},
journal = {Biology letters},
volume = {22},
number = {8},
pages = {},
doi = {10.1098/rsbl.2026.0144},
pmid = {42642057},
issn = {1744-957X},
mesh = {*Saccharomyces cerevisiae/metabolism/growth & development ; *Mitochondrial Ribosomes/metabolism ; *Oxygen Consumption ; *Oxygen/metabolism ; Mitochondria/metabolism ; Cell Respiration ; *Ribosomes/metabolism ; },
abstract = {Quantifying cellular activities remains a major challenge across fields ranging from microbial ecology to biotechnology and biomedical sciences. Building on the well-established linear relationship between growth rate and ribosome content-the so-called microbial growth law-this study proposes using organelle ribosome content to infer metabolic activity. In exponentially growing yeast (Saccharomyces cerevisiae), including under overflow metabolism conditions, a strong linear correlation was observed between mitochondrial ribosome content and oxygen uptake rate, underscoring the potential of this approach. Additionally, under fully respiratory conditions, cytoplasmic and mitochondrial ribosome fractions were linearly correlated, whereas overflow conditions fell below this linear relationship, providing a means to identify such metabolic states. Although these findings require broader validation across additional species, organelle ribosome quantification may provide a promising proxy for deciphering cellular metabolism.},
}

*Saccharomyces cerevisiae/metabolism/growth & development
*Mitochondrial Ribosomes/metabolism
*Oxygen Consumption
*Oxygen/metabolism
Mitochondria/metabolism
Cell Respiration
*Ribosomes/metabolism

@article {pmid42643400,
year = {2026},
author = {Medaglia-Mata, A and Rojas-Rodríguez, P and Bystrý, V and Guillén-Watson, R and Gómez-Espinoza, O and Núñez-Montero, K},
title = {PUDU (pipeline for universal diversity unveiling): an accessible end-to-end workflow for taxonomic profiling and ecological visualization of environmental microbiomes across amplicon, shotgun, and long-read sequencing.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1909327},
pmid = {42643400},
issn = {2673-7647},
abstract = {BACKGROUND: Environmental microbiome research has advanced through three complementary sequencing modalities, targeted 16S rRNA amplicon sequencing, whole-genome shotgun (WGS) metagenomics, and long-read full-length 16S rRNA profiling, each supported by distinct toolsets with heterogeneous outputs, variable configurations, and different levels of reproducibility documentation. Existing pipelines are typically modality-specific, require substantial configuration expertise, or produce outputs that need further custom scripting before standard ecological analyses can begin. This analytical fragmentation introduces avoidable technical variability and complicates cross-study reproducibility and comparability. PUDU addresses this by integrating all three modalities into a single reproducible workflow with simplified configuration, harmonized outputs across classifiers, and direct compatibility with downstream ecological analysis frameworks.

RESULTS: We present PUDU (Pipeline for Universal Diversity Unveiling), a modular Snakemake workflow that supports amplicon (short-read 16S), shotgun metagenomics (WGS), and long-read 16S analyses from raw reads to standardized outputs for downstream microbial ecology. PUDU performs technology-aware preprocessing and centralized quality control, and integrates established taxonomic approaches, including DADA2 for amplicons, Emu for full-length 16S long reads, and Kraken2/Bracken and Centrifuger for WGS. Across methods, PUDU produces harmonized count and relative-abundance tables at user-defined taxonomic ranks, Krona files, and a standardized Phyloseq-compatible R object to streamline diversity analyses and statistical workflows. PUDU also provides an integrated Shiny interface for metadata-aware alpha/beta diversity, ordination, community composition, and shared-taxa exploration with exportable figures and taxa tables. We demonstrate PUDU on two publicly available environmental datasets spanning rhizosphere WGS and long-read marine sediment 16S, yielding broadly consistent community-level patterns across classifiers (Spearman ρ = 0.936 at phylum level; PERMANOVA R[2] = 0.87-0.95) with peak memory below 45 GB on a standard Linux workstation.

CONCLUSION: PUDU is an end-to-end, reproducible, and extensible framework that enables standardized taxonomic profiling and ecology-oriented analysis across sequencing modalities. By combining harmonized outputs, Phyloseq interoperability, and an integrated visualization layer, PUDU facilitates reproducible, standardized, and comparable environmental microbiome analysis from raw reads to interpretable ecological insights.},
}

@article {pmid42644562,
year = {2026},
author = {Rainey, PB and Timmis, KN and Williams, PA and Karahan, ZC and López-García, P and Chavarria, M and Greening, C and Steward, K and Silva Pereira, C and Giraldo, R and Verstraete, W and Jonjić, S and Ramos, JL and Nunes, O and Ventosa, A and Armstrong, R and Sessitsch, A and Ron, E and Wang, H and Hochberg, ME and Berryhill, B and Levin, BR},
title = {Stop paying predatory publishers of academic journals-A policy proposal to restore scientific integrity and transparency.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70451},
pmid = {42644562},
issn = {1873-3468},
abstract = {Scientific publishing is undergoing a systemic breakdown. Thousands of journals now collect article processing charges (APCs)-increasingly paid from public research funds-while providing minimal editorial oversight. This erodes standards, distorts incentives and threatens public trust in science. APC payments to six major publishers exceeded 8 billion dollars between 2019 and 2023, with almost no transparency over how these fees are set or spent. This cannot continue. We propose that public and institutional funds support journals-whether through APCs, subscriptions or bundled agreements-only where they are accredited against a transparent, enforceable quality standard. Implemented in stages and led by funding bodies and learned societies, such accreditation would narrow the space in which predatory journals operate without resorting to blacklists.},
}

@article {pmid42645451,
year = {2026},
author = {Lee, YC and Cheng, YC and Kung, CM and Huang, CJ},
title = {Modulating Oral Microbiota to Prevent Dental Caries: A Microbial Ecology Approach.},
journal = {Dentistry journal},
volume = {14},
number = {8},
pages = {},
pmid = {42645451},
issn = {2304-6767},
abstract = {Background: Dental caries is a highly prevalent, biofilm-mediated disease characterized by microbial dysbiosis, excessive acid production, and progressive enamel demineralization. Although traditionally managed through restorative treatment, increasing attention has shifted toward preventive strategies focused on modulation of the oral microbiota and maintenance of ecological balance within the oral cavity. Methods: This narrative review summarizes current evidence regarding the ecological and mechanistic basis of dental caries and microbiota-centered prevention strategies. Literature published between January 2000 and March 2026 was retrieved from PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar using keywords related to dental caries, oral microbiota, cariogenic bacteria, biofilms, probiotics, prebiotics, salivary diagnostics, metabolomics, quorum sensing, and artificial intelligence. Results: Current evidence demonstrates that dental caries is driven by ecological shifts favoring acidogenic and aciduric microorganisms within cariogenic biofilms. Emerging preventive approaches include dietary modification, oral hygiene optimization, probiotics, prebiotics, synbiotics, and functional dietary agents aimed at restoring microbial homeostasis and inhibiting cariogenic biofilm maturation. In addition, advances in salivary microbiome profiling, metabolomics, artificial intelligence-assisted predictive modeling, and smart responsive materials have shown promising potential for improving early diagnosis, risk assessment, and personalized prevention strategies. Conclusions: Microbiota-based approaches represent a promising paradigm shift in dental caries prevention by emphasizing ecological modulation rather than pathogen eradication alone. Continued interdisciplinary research integrating microbial ecology, diagnostics, biomaterials, and digital technologies may facilitate the development of personalized and preventive oral healthcare strategies.},
}

@article {pmid42645525,
year = {2026},
author = {Larsen, J and Efthymiou, A and Nicolaisen, MH and Jensen, B and Nybroe, O and Gómez-Muñoz, B},
title = {Penicillium aculeatum pre-activated with cellulose and different phosphorus sources promotes maize growth, nutrition and mycorrhiza formation, and decreases Microdochium bolleyi root infection.},
journal = {Current microbiology},
volume = {83},
number = {10},
pages = {},
pmid = {42645525},
issn = {1432-0991},
mesh = {*Zea mays/microbiology/growth & development ; *Cellulose/metabolism ; *Mycorrhizae/growth & development/physiology ; *Plant Roots/microbiology/growth & development ; *Penicillium/metabolism/physiology ; *Phosphorus/metabolism ; Soil Microbiology ; Soil/chemistry ; *Glomeromycota/growth & development/physiology ; },
abstract = {Microbial plant growth promoters often perform inconsistently under natural soil conditions most likely due to their poor establishment after inoculation. Here, we conducted a growth chamber pot experiment with maize using pre-activated inoculum of the P-solubilizing fungus Penicillium aculeatum to facilitate its establishment in a natural non-sterile agricultural soil. Hence, P. aculeatum was preincubated for one week in soil amended with cellulose as a C source and with different P sources, i.e. sewage sludge ash, Ca3(PO4)2, and no P fertilization as control. Control treatments of C and P sources without P. aculeatum were also included. The pre-activated inocula were mixed into natural agricultural soil (1:40 w/w), maize seeds were sown, and plants were grown for 42 days. Measured variables included shoot and root dry weight, nutrient content, and root colonization by arbuscular mycorrhizal fungi (AMF) and root infection with Microdochium bolleyi. Overall, P. aculeatum inoculation enhanced maize growth, nutrient content and AMF root colonization, while reduced root infection with M. bolleyi, independent of P source used. Both P sources increased maize growth and nutrient content, though sewage sludge ash showed stronger effect than Ca3(PO4)2. None of the P sources affected AMF root colonization, but sewage sludge ash decreased M. bolleyi root infection and increased the population density of P. aculeatum. In conclusion, inoculation with pre-activated P. aculeatum (with cellulose and P sources) enhances maize growth and nutrient uptake, and is associated with increased AMF root colonization and reduced root infection by M. bolleyi.},
}

*Zea mays/microbiology/growth & development
*Cellulose/metabolism
*Mycorrhizae/growth & development/physiology
*Plant Roots/microbiology/growth & development
*Penicillium/metabolism/physiology
*Phosphorus/metabolism
Soil Microbiology
Soil/chemistry
*Glomeromycota/growth & development/physiology

@article {pmid42646070,
year = {2026},
author = {Li, H and Jiao, X and Wang, Y and Sun, N},
title = {Co-Application of Organic and Ca, Mg, Zn Fertilizers Reshapes Depth-Stratified Arbuscular Mycorrhizal Fungal Communities in Orchard Soil.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
pmid = {42646070},
issn = {2309-608X},
support = {KJCX20250926//Beijing Academy of Agricultural and Forestry Sciences/ ; Z191100004019001//Beijing Municipal Science and Technology Commission/ ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are crucial symbiotic microorganisms in terrestrial ecosystems, playing a vital role in maintaining orchard soil health and productivity. However, how organic-and Ca, Mg, Zn fertilizers co-application affect vertical stratification and ecological functions of arbuscular mycorrhizal fungi (AMF) in perennial fruit orchards remains unclear. Based on a five-year in situ peach trial, we established three fertilization regimes: low- (LWF), medium- (MWF), and high-input (HWF) regimes. We systematically analyzed the AMF community structure, diversity, and their correlations with soil physicochemical properties, as well as peach tree physiology, fruit yield, and quality across two soil depths: 0-20 cm (topsoil) and 20-40 cm (subsoil). HWF significantly inhibited AMF root colonization rates and spore density (p < 0.05), while reducing community α-diversity AMF α-diversity (p < 0.05), characterized by the enrichment of genera such as Glomus and a decrease in the relative abundance of Rhizoglomus. Redundancy analysis (RDA) identified available Zn (AZn) and Mg (WMg) as key drivers of this restructuring. Integrating RDA results into depth-specific partial least squares structural equation models (PLS-SEM), we found that subsoil AZn/WMg indirectly boosted yield by reshaping AMF composition (β = 0.34, p = 0.006), mediated via improved canopy status (NDVI, PRI). Total effect analysis confirmed the dominant role of subsoil pathways. These findings challenge the prevailing topsoil-centric view of soil microbial ecology and underscore the importance of considering the full soil profile when evaluating the impacts of agricultural practices on beneficial symbionts. We conclude that sustainable management strategies should account for depth-dependent AMF responses to maintain both productivity and belowground biodiversity across the entire rooting zone.},
}

@article {pmid42646830,
year = {2026},
author = {Liu, J and He, Y and Qiu, K and Zhao, S and Qiu, Z and Gao, S and Nagel, G and Zhu, M},
title = {TrcrtB regulates carotenoid biosynthesis, stress tolerance, conidiation and pathogenicity in the postharvest pink rot fungus, Trichothecium roseum.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-03-26-0608-RE},
pmid = {42646830},
issn = {0191-2917},
abstract = {Trichothecium roseum is a highly destructive postharvest pathogenic fungus that causes pink mold rot in various fruit and leads to significant agricultural and economic losses. Phytoene is crucial for phytopathogens, but the molecular mechanism by which the phytoene synthase gene crtB regulates fungal pathogenicity remains largely unclear. In this study, we evaluated the functions of TrcrtB a phytoene synthase, in T. roseum via in vivo and in vitro assays. Our results showed that knock-out of TrcrtB showed inhibition of production of phytoene and its relevant downstream metabolites, such as lycopene, carotenes and carotenal, resulting in colorless colony and branching at the mycelial edges in the knockout mutant ΔTrcrtB. Compared with the wild type (WT) strain, the colony expansion was significantly reduced 35% at 5 days post-inoculation (dpi), and conidiation was notably decreased to 45%, 36%, and 70% at 3, 5, and 7 dpi in ΔTrcrtB in vitro. Scanning electron microscope observation revealed similar results. Moreover, the ΔTrcrtB showed higher sensitivity to abiotic stresses than WT, as evidenced by inhibition rates of ΔTrcrtB colony expansion up to 71.76% (menadione), 47.73% (Congo red), 23.01% (SDS), and 17.13% (KCl). The pathogenicity of ΔTrcrtB was dramatically impaired by decreasing the rotten area up to 85.26% on apple fruit and 70.30% on pears fruit. These results suggest that TrcrtB and phytoene are critical for development, stress tolerance and pathogenicity of T. roseum. Collectively, our study highlights the roles of TrcrtB and phytoene in the pathogenic fungus T. roseum, providing new insights into the molecular mechanisms of pink rot pathogenesis.},
}

@article {pmid42647083,
year = {2026},
author = {Lv, R and Jiang, Z and Zhong, Y},
title = {The role of gut-lung axis-targeted nursing strategies in immune regulation of COPD.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02947},
pmid = {42647083},
issn = {1588-2640},
abstract = {Chronic obstructive pulmonary disease (COPD) is featured by persistent airflow limitation and chronic inflammation. Considerable evidence highlights the role of the gut-lung axis, suggesting that disruption of gut microbial balance may contribute to aggravated systemic and pulmonary inflammation. This research intended to assess the impacts of a structured gut-lung axis-targeted nursing intervention on immune-inflammatory parameters, gut microbiota, and clinical outcomes in patients with stable COPD. The study involved the randomization of 115 patients to either the intervention or control group in a 1:1 ratio. The intervention group received a 12-week multimodal program, which included personalized high-fiber/probiotic nutrition, customized exercise plans, and stress management techniques. Patients in the control group did not receive the multimodal program and instead received routine care. The findings indicated that the intervention notably lowered serum IL-6, TNF-α, and CRP. Microbiome analysis further revealed that the intervention significantly enhanced α-diversity (Shannon and Chao1), enriched beneficial butyrate-producing genera (Faecalibacterium, Roseburia, and Bifidobacterium), and reduced the relative abundance of potential pathogens (Enterobacteriaceae), indicating a favorable shift in gut microbial ecology. Compared with the control group, the intervention group also experienced fewer moderate-to-severe exacerbations and showed greater sustained improvement in quality of life (SGRQ and CAT scores). In summary, a comprehensive nursing strategy centered on the gut-lung axis can regulate gut microbiota, alleviate systemic inflammation, lead to a reduction in exacerbation frequency and an improvement in the quality of life among patients with stable COPD, thus presenting a promising supplementary strategy to conventional care.},
}

@article {pmid42647465,
year = {2026},
author = {Ali, S and Baig, A and Nagassar, RP and Burke, LP and Fitzpatrick, F and Fitzgerald-Hughes, D},
title = {The Caribbean under the radar? A scoping review of carbapenemase-producing Enterobacterales across the region.},
journal = {PLOS global public health},
volume = {6},
number = {8},
pages = {e0007176},
pmid = {42647465},
issn = {2767-3375},
abstract = {Carbapenemase-producing Enterobacterales (CPE) are a critical antimicrobial resistance (AMR) threat globally. The Caribbean region, despite its high global connectivity, varied healthcare infrastructure and rising antimicrobial use, remains underrepresented in CPE surveillance data. Our study aims to map and characterise the existing literature on CPE in the Caribbean, including bacterial species, carbapenemase types, detection methods, and epidemiological trends. A scoping review was conducted in accordance with PRISMA-ScR guidelines. MEDLINE, EMBASE, Cochrane CENTRAL and Web of Science were searched to 1st July 2025 in addition to grey literature (policy documents, guidelines, websites). Studies were included if they reported carbapenemase production among Enterobacterales from human, animal, or environmental sources in Caribbean nations (defined geophysically). Non-Caribbean studies and non-Enterobacterales organisms were excluded. Fourteen studies published between 2008 and 2024 met inclusion criteria. Reports originated from six countries: Cuba, Puerto Rico, Jamaica, Guadeloupe, the Dominican Republic, and Curaçao. Klebsiella pneumoniae was the most frequently reported species. The most common carbapenemase enzymes were KPC (including KPC-2 and KPC-8), NDM-1, NDM-5 and OXA-48. Co-production of NDM and KPC was documented. Detection was largely hospital-based, though community and environmental isolates were also identified. High levels of AMR were observed, with colistin often the only active agent. Surveillance gaps are evident across many populous Caribbean nations. CPE are established in multiple Caribbean countries, but surveillance remains irregular and limited. Addressing critical gaps in diagnostic capacity, reporting and molecular surveillance is essential to ensure the region's inclusion in the global AMR response.},
}

@article {pmid42649294,
year = {2026},
author = {Sichert, A and Pollak, S and Priest, T and Goyal, A and Miravet-Verde, S and Sunagawa, S and Cordero, OX and Sauer, U},
title = {Synergistic degradation of fucoidans in the ocean.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42649294},
issn = {1476-4687},
abstract = {Fucoidans, a class of complex polysaccharides produced by brown algae and diatoms, contribute to long-term carbon sequestration owing to their resistance to microbial degradation[1,2]. Although individual microorganisms can break down portions of these polysaccharides[3-5], it remains unclear whether complete breakdown is possible in nature and, if so, by what mechanisms. Here we show that fucoidans are degraded through synergistic interactions between specialized bacteria with complementary metabolic functions. Using metabolomic analysis of a reconstructed marine consortium, we uncovered metabolic guilds of bacteria that preferentially degrade either the sulfated fucose backbone or the side branches of rare monomers. This functional division of labour leads to an unexpectedly high number of synergistic interactions between different degraders that enhanced degradation efficiency up to 97.1%. Despite varying fucoidan structures across different types of algae[6], the metabolic functions of degraders remained conserved, enabling quantitative prediction of degradation outcomes based on community and substrate composition. The frequent co-occurrence of functionally complementary fucoidan degraders in ocean metagenomes suggests that synergistic degradation is a globally relevant strategy. Our findings suggest that the environmental turnover of complex biopolymers depends not only on individual metabolic capabilities of degraders but also on ecological interactions shaped by substrate architecture. This work provides a mechanistic framework for understanding carbon cycling in the ocean and for engineering synthetic microbial consortia to degrade recalcitrant polysaccharides.},
}

@article {pmid42650190,
year = {2026},
author = {Godos, J and Caruso, G and Mainas, G and Micek, A and Di Mauro, A and Buccarello, L and Martínez López, NM and Frias-Toral, E and Giampieri, F and Lehoczki, A and Isola, G and Galvano, F and Ungvari, Z and Quiles, JL and Battino, M and Grosso, G},
title = {Oral Microbiota, the Oral-Brain Axis, and Neurodegeneration: Mechanisms and Dietary Modulation.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/antiox15080925},
pmid = {42650190},
issn = {2076-3921},
support = {NA//Italian Ministry of Health/ ; },
abstract = {The oral microbiota represents a complex and dynamic microbial ecosystem that plays a critical role in preserving both oral and systemic homeostasis. Emerging evidence suggests that alterations in oral microbial milieu (dysbiosis) may contribute to the pathogenesis of neurodegenerative disorders, especially Alzheimer's disease (AD), through the oral-brain axis. This review synthesizes current evidence on the pathways linking oral microbiota to cognitive decline, integrating microbial, immunological, and vascular perspectives. Oral pathogens may access the central nervous system via hematogenous dissemination or neural routes, including the trigeminal nerve, while simultaneously promoting systemic inflammation, immune activation, and blood-brain barrier disruption. These processes converge on key neurodegenerative mechanisms, including chronic neuroinflammation, amyloid-β accumulation, and tau pathology. In parallel, alterations in oral microbial composition have been linked to disease severity, supporting a potential role of dysbiosis in both initiation and progression of cognitive impairment. Diet emerges as a critical modifiable determinant of oral microbial ecology. Diets rich in refined sugars may promote dysbiosis and inflammatory signaling, whereas (poly)phenols, probiotics, and prebiotics may support microbial eubiosis and exert neuroprotective effects through modulation of host-microbe interactions. Although current evidence remains largely observational and mechanistic, the diet-oral microbiota-brain axis represents a promising target for preventive and therapeutic strategies aimed at mitigating cognitive decline and promoting healthy aging. Future longitudinal and interventional studies are required to establish causality and translate these insights into clinical practice.},
}

@article {pmid42650527,
year = {2026},
author = {Li, S and Yu, X and Huang, H and Wang, C and Yi, C and Zhang, X and Wen, Y and Xiong, B and Jiang, Q and Yu, K and Ma, Y},
title = {Regulatory Effects of Tannin Supplementation on Microbial Succession and Flavor Formation During Xiaoqu Light-Flavor Baijiu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {16},
pages = {},
doi = {10.3390/foods15162833},
pmid = {42650527},
issn = {2304-8158},
support = {Y2025067//Sichuan University of Science and Engineering/ ; H72313005//Yibin Agricultural Science and Technology Innovation Project/ ; 2022ZDZX0016//Sichuan Province Major Science and Technology Special Project/ ; },
abstract = {Sorghum tannins have been suggested to influence microbial ecology and flavor formation in Xiaoqu light-flavor Baijiu (XLB), but their specific contribution is difficult to distinguish from confounding, cultivar-dependent variations in macromolecular components. To address this limitation, a controlled fermentation system was established using a uniform, low-tannin substrate. Based on preliminary gradient trials, a 1.0% tannin supplementation level was selected, and high-throughput sequencing combined with HS-SPME-GC-MS was employed to investigate tannin-related microbial and volatile changes. Compared with the group without tannin supplementation, 1.0% tannin supplementation altered bacterial and fungal community succession during the fermentation, reducing the relative abundances of Saccharomyces and Weissella, and enriching taxa including Cyberlindnera and Pantoea. The tannin-supplemented group exhibited a more complex and stable microbial co-occurrence network. Furthermore, PICRUSt2 predictions suggested enhanced metabolic potentials primarily related to carbohydrate and amino acid pathways. FUNGuild analysis further suggested that tannin supplementation shifted fungal trophic-mode composition, particularly saprotrophic and saprotroph-containing groups. At the end of fermentation, total volatile compounds increased from 4.208 μg/g to 4.983 μg/g, total esters and acids increased by 27.0% and 112.3%, respectively, whereas total alcohols decreased by 13.3%. Spearman correlation analysis revealed that the enriched non-Saccharomyces fungi and acid-producing bacteria in the tannin-supplemented group were positively associated with the accumulation of acids and esters, whereas the control microbiota was mainly linked to an alcohol-oriented profile. These findings may provide process-level evidence for tannin-related microbial and volatile changes during XLB fermentation.},
}

@article {pmid42650569,
year = {2026},
author = {Hao, M and Liu, J and Kan, C and Zheng, X and Liu, C and Zhang, Y and Shen, L},
title = {Research Progress, Challenges, and Future Trends of Modified Atmosphere Packaging (MAP) Technology for Food and Agricultural Products: A Bibliometric Analysis (2016-2025).},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {16},
pages = {},
doi = {10.3390/foods15162875},
pmid = {42650569},
issn = {2304-8158},
abstract = {Modified atmosphere packaging (MAP) is a preservation and packaging technology used to extend the shelf life of foods and agricultural products, maintain quality stability, and ensure food safety. To systematically review and summarize the current research landscape, technical challenges, and development trends in the MAP field, this study selected 1568 publications related to MAP from the Web of Science Core Collection (WOSCC) database during 2016-2025 and conducted bibliometric and visualization analysis. The results indicate that research activity in the MAP field has remained robust over the past decade, mainly focusing on four research areas: atmosphere regulation and packaging system design; microbial ecology, safety, and spoilage control; physicochemical deterioration and quality regulation; functional packaging materials and integrated preservation technologies. Countries such as China, Italy, and Spain have demonstrated outstanding performance in terms of publication output and academic influence in the MAP field, forming a solid research foundation in the MAP of perishable foods such as fruit and vegetables, meat products, and aquatic products. Research in the MAP field has gradually shifted from the verification of application effects toward system design and mechanistic analysis. Active packaging, intelligent packaging, bio-based materials, natural functional ingredients, volatile organic compounds, microbial community succession, and quality deterioration mechanisms have gradually become research hotspots, indicating a trend toward precision, sustainability, and functionality. These findings may provide references for future research topic selection, innovative packaging system design, and the development of novel food preservation technologies in the MAP field for foods and agricultural products.},
}

@article {pmid42651919,
year = {2026},
author = {Kahraman, O and Wilk, M and Bochynek, M and Bojanowski, K and Quijas, G and Inanc, ZS and Inal, F and Ahmed, I and Lewińska, A and Yilmaz, B},
title = {Effects of Complementary Feed with Postbiotics Derived from Bacillus subtilis on Nutrient Digestibility, Faecal Characteristics, Gut Microbiota, Metabolic and Immune Responses, and Coat Quality in Healthy Senior Dogs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {16},
pages = {},
doi = {10.3390/ani16162515},
pmid = {42651919},
issn = {2076-2615},
abstract = {The aim of this study was to evaluate the effects of a Bacillus subtilis-derived postbiotic on apparent total tract nutrient digestibility, faecal fermentation characteristics, gut microbiota, immune response, blood biochemistry, hematological parameters, serum trace minerals, and coat quality in healthy senior dogs. Twenty-one healthy senior Golden Retriever dogs (9 ± 1.0 years old) were randomly allocated to three dietary treatments for 28 days: a control diet (CON) or the same diet supplemented with 0.3 (POS1) or 0.6 mL/day (POS2) of a Bacillus subtilis-derived postbiotic. Apparent nutrient digestibility, faecal characteristics, blood variables, and coat quality were evaluated, whereas faecal bacterial communities were characterized by 16S rRNA gene amplicon sequencing, followed by taxonomic classification and alpha- and beta-diversity analyses. Postbiotic supplementation significantly improved crude protein and crude fiber digestibility while reducing faecal pH and ammonia concentrations and increasing acetate, propionate, and total short-chain fatty acid concentrations (p < 0.05). Alpha diversity was minimally affected, with a significant difference observed only for amplicon sequence variant (ASV) richness, whereas beta diversity analyses demonstrated significant alterations in overall microbial community composition. Postbiotic supplementation increased the relative abundance of Faecalibacterium, Ligilactobacillus, Bifidobacterium, Prevotella, Turicibacter, and Fusobacterium, while reducing Bacteroides and Achromobacter. Serum IgG concentrations increased, whereas cholesterol and triglyceride concentrations decreased in supplemented dogs (p < 0.05). Coat morphology and gloss also improved, without adverse effects on hematological, biochemical, or serum trace mineral parameters. In conclusion, Bacillus subtilis-derived postbiotic supplementation improved nutrient utilization, beneficially modulated faecal microbial ecology and fermentation, enhanced selected metabolic and immune responses, and improved coat quality, supporting its potential as a functional dietary strategy for promoting gastrointestinal and systemic health in healthy senior dogs.},
}

@article {pmid42652455,
year = {2026},
author = {Antonuccio, GI and López, PJ and Berretta, MF and Sauka, DH},
title = {Genomic Characterization of Aerobically Culturable Gut-Associated Bacteria and Yeasts Isolated from Pooled Larval Midguts of the Lesser Mealworm Alphitobius diaperinus (Coleoptera: Tenebrionidae).},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080800},
pmid = {42652455},
issn = {2075-4450},
support = {INTA 2023-PD-L06-I116//National Agricultural Technology Institute/ ; },
abstract = {Microbial communities associated with insect larvae play key roles in host nutrition, protection against pathogens, immune modulation, and represent a source of biotechnologically relevant traits. In Alphitobius diaperinus, a major poultry pest, the gut microbiota has been mainly studied at the community level, providing limited insight into the potential roles of individual microorganisms. Here, we characterized the aerobically culturable fraction of the larval gut microbiota derived from a single pooled homogenate of fifteen larvae under stable laboratory rearing conditions-an approach that uniquely enables strain-level genomic resolution, functional experimentation, and biotechnological exploitation. Ten bacterial strains and two yeasts were initially isolated; eight bacterial isolates were identical, revealing the most frequently recovered cultivable bacterial morphotype. We provide high-quality draft genomes for five members of the A. diaperinus cultivable gut microbiota-Enterobacter hormaechei subsp. xiangfangensis strain INTA AN1-1, Staphylococcus hominis subsp. novobiosepticus strain INTA AC1-4, Staphylococcus succinus subsp. succinus strain INTA AC1-8, Hyphopichia burtonii strain INTA AB1-1, and Debaryomyces fabryi strain INTA AB1-4-establishing a genome-resolved reference framework validated through a polyphasic approach. Genome-scale annotation enabled us to predict the metabolic potential and hypothesize the functional capabilities among cultivable members, providing a foundation for future studies on this economically relevant pest.},
}

@article {pmid42652525,
year = {2026},
author = {Wu, PR and Shelomi, M},
title = {Effect of Protein Supplementation on the Gut Microbiome of Omnivorous and Herbivorous Goliath Beetles.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080871},
pmid = {42652525},
issn = {2075-4450},
support = {NSTC-114-2311-B-002-017//National Science and Technology Council/ ; 113L7801//Ministry of Education/ ; },
abstract = {Scarab beetles depend on gut microbes for digestive enzymes. Some species' microbiomes show taxonomic conservation regardless of diet, while others have conserved functional profiles. We compared the hindgut microbiomes of two Cetoniinae beetle larvae: the obligately saproxylophagous Mecynorrhinella poggei and the omnivorous/predatory Goliathus goliatus, which requires protein supplementation when reared artificially. Two diets with and without supplementation were used. If diet drives the microbiome, then gut microbes in protein-supplemented hosts should produce fewer lignocellulolytic enzymes and more proteinases regardless of species. If microbiome composition is conserved within a species, then Mecynorrhinella is expected to have more lignocellulolytic microbes while Goliathus should have more proteinolytic microbes regardless of diet. In this study, low-protein diets reduced G. goliatus growth, but gut microbiome composition and predicted function remained largely stable, dominated by Bacteroidales including Dysgonomonas, Proteiniphilum, and Alistipes. Mecynorrhinella's gut microbiome showed some reduced Proteiniphilum and increased Dysgonomonas relative abundance, but otherwise the microbiome composition was statistically stable with no effect of diet on growth or predicted microbiome function. These results highlight that microbiomes of closely related insects can markedly differ even if diet does not and that microbiome functional conservation tied to host physiology may occur even if greater plasticity could theoretically reduce malnutrition.},
}

@article {pmid42652532,
year = {2026},
author = {Gao, X and Li, Q and Yan, F and Su, C and Wang, X and Xu, P and Ren, G and Mao, M},
title = {Parental Broflanilide Exposure Impairs Offspring Fitness and Alters Detoxification Enzymes and Gut Microbiota in Helicoverpa armigera.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080878},
pmid = {42652532},
issn = {2075-4450},
support = {110202401012(LS-02) and 110202401017(LS-07)//Major Special Projects for Green Pest Control/ ; Grant No. ASTIP-TRIC04//Agricultural Science and Technology Innovation Program/ ; },
abstract = {The cotton bollworm Helicoverpa armigera (Hübner, 1808) (Lepidoptera: Noctuidae) is a globally distributed polyphagous pest that damages various crops. Pesticides remain a primary and effective strategy for controlling cotton bollworm populations. This study evaluated the effects of broflanilide on H. armigera by integrating life-table analysis, detoxification enzyme activity assays, and gut microbiome characterization. Broflanilide showed high toxicity against third-instar larvae. Parental LC50 exposure prolonged larval development and reduced larval survival in the F1 generation. In addition, parental exposure to both LC30 and LC50 reduced adult emergence, fecundity and major population growth parameters, especially the intrinsic rate of increase (r) and net reproductive rate (R0), demonstrating a significant transgenerational inhibitory effect. Enzyme assays showed that carboxylesterase (CarE) activity was induced after broflanilide exposure, glutathione S-transferase (GST) activity showed a time-dependent response with the strongest induction generally observed under LC10 treatment, whereas cytochrome P450 monooxygenase (P450) activity was generally inhibited. Gut microbiota analysis showed that LC50 exposure significantly reduced the relative abundance of Enterococcus. Functional prediction further indicated enrichment trends in pathways related to xenobiotic degradation and metabolism. Overall, broflanilide not only exhibited strong lethal activity against H. armigera, but also produced sustained effects on population fitness, detoxification metabolism and gut microbial ecology. These findings provide a theoretical basis for the rational use of broflanilide and improve our understanding of its sublethal physiological and microbial effects on H. armigera.},
}

@article {pmid42652966,
year = {2026},
author = {Martens, A and Schauer, M and Mair, S and Motevalli, M and König, B},
title = {Multidimensional Profiles of Microbial Contamination and Hygiene Risk Across Functional Areas in Family Hotels.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/life16081278},
pmid = {42652966},
issn = {2075-1729},
abstract = {Microbial contamination in hospitality settings remains understudied despite the high density of human contact and diverse operational activities that characterize hotel environments. This study aimed to characterize microbial contamination patterns and environmental hygiene risks across multiple functional areas of family-oriented hotels. A cross-sectional environmental microbiological investigation was conducted in family hotels in Bavaria, Germany. A total of 225 environmental surface samples were collected from guest rooms, child areas, food-related areas, service environments, and water-exposed locations. Bacterial isolates were identified using culture-based microbiology and MALDI-TOF mass spectrometry. Microbial prevalence, contamination severity, microbial richness, and pathogen prevalence were assessed using mixed-effects ordinal logistic regression, generalized additive model (GAM), and integrated hygiene profile, all performed in R (version 4.5.1). Microbial occurrence patterns differed markedly across functional areas. Contamination category distributions differed significantly among areas, with food-related environments showing the strongest enrichment in the highest contamination category (72.7%). Food-related areas showed significantly greater odds of severe contamination than guest rooms (OR = 8.37, 95% CI: 1.89-37.00), child areas (OR = 6.16, 95% CI: 1.20-31.46), and water-exposed environments (OR = 12.34, 95% CI: 2.45-62.10). Microbial richness differed across operational zones (p = 0.048) and was positively associated with contamination severity (β = 0.141, p < 0.001). GAM revealed a significant non-linear richness-contamination relationship (p < 0.001). Integrated hygiene profile consistently identified food-related and service areas as the highest risk environments. Environmental hygiene risks in hospitality settings display functional-area heterogeneity, highlighting the need for targeted, area-specific hygiene management strategies.},
}

@article {pmid42653681,
year = {2026},
author = {Abbas, A and Weiskirchen, R and Bilal, M and Afzal, MK and Malik, A and Akhtar, S and Khan, M and Rashid, I and Khalid, F and Akram, S and Saleem, A and Okoduwa, SIR},
title = {Postbiotics as Next Generation Biotherapeutics Targeting the Gut-Immune-Metabolic Axis: An Integrative Review.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {8},
pages = {},
doi = {10.3390/ph19081184},
pmid = {42653681},
issn = {1424-8247},
abstract = {The gut-immune-metabolic axis has emerged as a central regulator of human health, with growing evidence indicating that microbiota-derived metabolites improve gut microbial ecology, enhance intestinal barrier integrity, reduce systemic inflammation, and maintain metabolic homeostasis. This review synthesizes current mechanistic and clinical evidence on the role of postbiotics in regulating intestinal barrier integrity, immune responses, oxidative stress, and metabolic-endocrine homeostasis. The literature was identified through the PubMed/MEDLINE, Scopus, and Web of Science, integrating evidence from experimental, mechanistic, animal and clinical studies on the therapeutic potential of postbiotics to modulate the gut-immune-metabolic axis. Preclinical studies suggest that postbiotics may enhance epithelial barrier function by improving tight junction integrity through multiple pathways such as PI3K/Akt signaling, stimulating mucin-2 (MUC2) production, and reducing intestinal permeability. They modulate immune responses through interactions with Toll-like receptors, nucleotide-binding oligomerization domain receptors, and G-protein-coupled receptors (GPR41/43), influencing key signaling pathways, including NF-κB and Nrf2, and altering cytokine profiles, such as IL-10, TNF-α, and IFN-γ. Similarly, preclinical investigations have demonstrated that short-chain fatty acids (SCFAs) and other microbial metabolites may improve insulin sensitivity, regulate hepatic gluconeogenesis, stimulate glucagon-like peptide 1 (GLP-1) secretion, and modulate lipid metabolism through the FXR and TGR5 signaling pathways. Emerging human studies suggest potential benefits of postbiotics in regulating gut, immune, and metabolic health; nevertheless, clinical evidence remains limited and is influenced by variability in postbiotic composition, dosage, formulation, and metabolite profiles. Therefore, standardized production approaches and well-designed large-scale randomized clinical trials are required to confirm therapeutic efficacy and establish evidence-based applications of postbiotics.},
}

@article {pmid42654201,
year = {2026},
author = {Yin, J and Wang, Z and Ding, Y},
title = {Dynamic Succession of the Early-Life Gut Microbiota and the Regulatory Role of Human Milk Oligosaccharides.},
journal = {Nutrients},
volume = {18},
number = {16},
pages = {},
doi = {10.3390/nu18162621},
pmid = {42654201},
issn = {2072-6643},
support = {No. 82173503//National Natural Science Foundation of China/ ; No. 2024YFC2707606//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Oligosaccharides/metabolism ; *Milk, Human/chemistry ; *Gastrointestinal Microbiome/physiology ; Infant ; Infant, Newborn ; *Infant Nutritional Physiological Phenomena ; Intestinal Barrier Function ; },
abstract = {Early-life nutrition and the gut microbiota interact to shape host health programming. During early-life development, spanning the neonatal period of initial gut colonization through infancy to toddlerhood, the gut microbiota undergoes dynamic succession driven by feeding patterns, host genetic background, environmental exposures, and other intrinsic and extrinsic factors, among which early feeding practices play a particularly prominent role. Among these factors, human milk oligosaccharides (HMOs), key bioactive components of human milk, contribute to the shaping of infant gut microbial ecology by selectively supporting HMO-utilizing bacteria, influencing microbial metabolism and cross-feeding, and exhibiting structure- and context-dependent effects on pathogen-host interactions, intestinal barrier function, and immune responses. This narrative review summarizes the succession patterns of the gut microbiota in early life and the core regulatory mechanisms by which HMOs shape infant gut microbial ecology, aiming to provide a conceptual basis for understanding the potential long-term health implications of early nutritional interventions.},
}

Humans
*Oligosaccharides/metabolism
*Milk, Human/chemistry
*Gastrointestinal Microbiome/physiology
Infant
Infant, Newborn
*Infant Nutritional Physiological Phenomena
Intestinal Barrier Function

@article {pmid42654221,
year = {2026},
author = {Mu, K and He, M and Liao, R and Shao, C and Xie, P and Xie, J and Liu, Y and Ju, Z and Zhong, K and Yuan, Y and Pang, Y},
title = {Medicinal Plant Polysaccharides as Microbiota-Directed Modulators of Immunosenescence: Structural Determinants, Metabolite Reprogramming, and Host Immune Regulation.},
journal = {Nutrients},
volume = {18},
number = {16},
pages = {},
doi = {10.3390/nu18162641},
pmid = {42654221},
issn = {2072-6643},
support = {zyyzdxk-2023186//State Administration of Traditional Chinese Medicine of the People's Republic of China/ ; Qian Ke He Ji Chu ZD [2026] 141//Guizhou Provincial Science and Technology Department/ ; 2025YJSKYJJ296//Guizhou Provincial Education Department/ ; Guizhongyi TD He Zi [2022]001//Guiyang College of Traditional Chinese Medicine/ ; YCXKYB2025030//Guiyang College of Traditional Chinese Medicine/ ; Qian Ke Xie KJLYRC-2026[041]//Guizhou Provincial Science and Technology Department/ ; //Guizhou "Qian Liu Wei" Daodi Medicinal Materials Advantageous and Characteristic Industrial Cluster Construction Project/ ; },
mesh = {Humans ; *Polysaccharides/pharmacology/chemistry ; *Immunosenescence/drug effects ; *Plants, Medicinal/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects/immunology ; *Microbiota ; Aging/immunology ; },
abstract = {Immunosenescence is a major contributor to age-associated morbidity, yet microbiota-directed strategies capable of restoring immune homeostasis remain insufficiently validated. Medicinal plant polysaccharides (MPPs) are structurally diverse macromolecules that often resist host digestion and undergo microbial transformation in the colon, but their effects cannot be interpreted as those of a homogeneous intervention class. In this structured narrative review, we critically synthesize evidence across structural carbohydrate biology, microbial ecology, metabolite signaling, and immune aging and propose a structure-microbiota-metabolite-immunity framework for evaluating how MPPs may influence immunosenescence. Monosaccharide composition, glycosidic linkages, molecular-weight distribution, branching, uronic acid content, chemical substitutions, and higher-order conformation can shape microbial carbohydrate-active enzyme activity, polysaccharide utilization, and ecological cross-feeding. The resulting changes in short-chain fatty acids, secondary bile acids, tryptophan-derived indoles, and other metabolites may affect epithelial barrier integrity, regulatory T-cell/T helper 17-cell (Treg/Th17) balance, macrophage polarization, nuclear factor-κB (NF-κB) signaling, NLR family pyrin domain-containing 3 (NLRP3) inflammasome activation, and systemic inflammatory tone. However, evidence from in vitro systems and young disease models primarily supports mechanistic plausibility and should not be treated as direct evidence of immunosenescence modification. Translation will require structurally defined preparations, causal validation in aging-relevant models, comparison with established fermentable fibers, identification of responder phenotypes, and adequately powered trials in older adults.},
}

Humans
*Polysaccharides/pharmacology/chemistry
*Immunosenescence/drug effects
*Plants, Medicinal/chemistry
Animals
*Gastrointestinal Microbiome/drug effects/immunology
*Microbiota
Aging/immunology

@article {pmid42631058,
year = {2026},
author = {Medrano, M and Pacheco-Herrero, M and Borges, Z and Laureano, JR and Dominguez-Garcia, J and Gil-Ventura, R and Castro-Tejada, G},
title = {Characterization of the intestinal microbial profile in mild cognitive impairment and Alzheimer's disease.},
journal = {Dementia & neuropsychologia},
volume = {20},
number = {},
pages = {e20250440},
pmid = {42631058},
issn = {1980-5764},
abstract = {UNLABELLED: Alzheimer's disease (AD) and mild cognitive impairment (MCI) are major contributors to dementia, with growing prevalence in Latin America. Evidence suggests that gut microbiota alterations may influence neurodegeneration, but data on Hispanic population are lacking.

OBJECTIVE: Characterize gut microbiota in individuals with AD, MCI, and controls in the Dominican Republic, exploring clinical, demographic, and dietary associations.

METHODS: Prospective-translational study including 88 participants aged ≥60 years. Performed clinical, cognitive, and functional assessments. Stool samples analyzed using 16S rRNA gene sequencing. Bioinformatic processing using Quantitative Insights into Microbial Ecology Version 2 (QIIME2) and R. Alpha and beta diversity, taxonomy, and differential abundance were evaluated. Dietary influences were assessed using PERMANOVA.

RESULTS: No significant differences in alpha diversity (Shannon index 4-5, Simpson index 0.94-0.99, p>0.05) or beta diversity (p>0.05) were observed between groups. Firmicutes (51.9%) and Bacteroidota (34.1%) dominated the microbiota. Higher Desulfobacterota abundance in MCI and AD (0.54 and 0.61%, respectively, vs. 0.34% in controls; p<0.05). The Firmicutes/Bacteroidota ratio was lower in men with MCI (1.09) compared to controls and AD (1.70). MCI and AD were associated with increased levels of the genera Bilophila, Odoribacter, and Parabacteroides (p<0.05) and reduced levels of Mitsuokella and Eubacterium ruminantium. Dietary interactions, e.g., mango, lettuce, and carrot, influenced specific taxa (p<0.05).

CONCLUSION: This study pioneers gut microbiota characterization in AD and MCI in the Dominican Republic, identifying microbial alterations in cognitive impairment and highlighting regional dietary and ethnic factors. Longitudinal and multi-omics studies are warranted to clarify causality and therapeutic potential.},
}

@article {pmid42631186,
year = {2026},
author = {Zdouc, MM and Augustijn, HE and Machushynets, NV and Bayona, LM and Soldatou, S and de Jonge, NF and Casu, S and Jaspars, M and van Wezel, GP and Medema, MH and van der Hooft, JJJ},
title = {FERMO: A Dashboard for Biochemometric Prioritization of Molecular Features from Mass Spectral Data.},
journal = {ACS measurement science au},
volume = {6},
number = {4},
pages = {1011-1022},
pmid = {42631186},
issn = {2694-250X},
abstract = {Many natural products can selectively modulate biological processes, making them prime candidates for drug discovery. However, the complexity of biological samples makes clear attribution of activity to molecules challenging, thereby hampering hypothesis-driven prioritization, with liquid chromatography-tandem mass spectrometry routinely detecting hundreds of molecules per sample. Existing biochemometric tools typically focus on facilitating data-driven exploration to support manual interpretation, rather than more objective, data-driven prioritization and hypothesis generation. Here, we introduce FERMO, a free online dashboard interface for biochemometrics-based prioritization of molecular features and samples. FERMO accepts qualitative and quantitative bioactivity assay data and further integrates group metadata and results from genome mining. FERMO performs automated data processing, organization, and annotation, supporting prioritization with the calculation of custom scores. FERMO supports both exploratory and targeted analysis through efficient interactive visualization, reproducible prioritization, and data filtering. We demonstrate FERMO's utility in benchmarking studies prioritizing bioactive natural products from complex biological matrices. FERMO is freely available at https://fermo.bioinformatics.nl/.},
}

@article {pmid42631634,
year = {2026},
author = {Callejas, C and Bovio-Winkler, P and Etchebehere, C},
title = {Genome-resolved assessment of archaeal diversity in full-scale anaerobic digesters reveals variability in mcrA primer coverage.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag212},
pmid = {42631634},
issn = {1365-2672},
abstract = {AIMS: Methanogenic archaea are key players in anaerobic digestion, driving methane production in biogas reactors. This study aimed to assess the diversity of methanogenic archaea in full-scale anaerobic digesters using genome-resolved metagenomics and to systematically evaluate the taxonomic coverage of commonly used mcrA-targeted qPCR primer sets against this genomic framework.

METHODS AND RESULTS: Methanogenic diversity was assessed using 113 dereplicated archaeal metagenome-assembled genomes (MAGs) recovered from 109 full-scale anaerobic digesters treating diverse substrates. Genome-resolved analyses revealed a diverse archaeal community spanning multiple phyla, dominated by Halobacteriota and Methanobacteriota, with additional representatives from Methanobacteriota_B, Thermoplasmatota, and Thermoproteota. The presence of the mcrA gene was identified in a subset 55 MAGs, which were subsequently used as the genomic framework to evaluate six commonly used mcrA qPCR primer sets in silico. This subset clustered into nine phylogenetic groups and formed the basis for the primer coverage analysis. The evaluation revealed marked differences in taxonomic coverage among primer sets. Most primers preferentially detected Methanobacteriales and Methanosarcinales, while underrepresenting or excluding other methanogenic lineages, including H₂-dependent methylotrophic Methanomassiliicoccaceae.

CONCLUSIONS: Commonly used mcrA primer sets differ substantially in their ability to capture methanogenic diversity, with some showing broad representation of reactor-associated methanogens and others exhibiting strong lineage-specific biases. Genome-resolved metagenomics provides an effective framework for benchmarking primer performance and supports the selection and improvement of molecular tools for more accurate monitoring of anaerobic digestion systems.},
}

@article {pmid42632980,
year = {2026},
author = {Mondal, P and Ganguly, D and Das, B and Sarker, RK and Ghosh, A and Samanta, S and Chakraborty, P and Tribedi, P and Gupta, AD and Trivedi, S and Das, S and Sarkar, S},
title = {Isolation, characterization and identification of antibiotic-resistant biofilm forming bacteria from East Kolkata Wetland, a Ramsar site: an ecological concern.},
journal = {3 Biotech},
volume = {16},
number = {9},
pages = {382},
pmid = {42632980},
issn = {2190-572X},
abstract = {UNLABELLED: The current study holds major socio-economic importance of East Kolkata Wetland (EKW) in India, a Ramsar site, presently under constant threat of anthropogenic wastes that could accelerate antibiotic resistance (AR). The underlying mechanism behind the spread of AR in EKW requires proper investigation. Towards this direction, we focused on the isolation of antibiotic resistant bacteria (ARB) from EKW with adequate characterization by employing biochemical, molecular and antibiotic sensitivity tests. Thus, water samplings were carried out and a total of 32 ARB were isolated from three different study sites at EKW by selective agar plating. The isolates exhibited diverse biochemical properties with multi-antibiotic resistance (MAR) index exceeding 0.2 against 14 antimicrobial agents. MAR is strongly linked with biofilm formation. For comprehensive understanding of MAR among the isolates, their biofilm forming ability was checked. Henceforth, 14 potent biofilm formers were identified by measuring the total biofilm biomass through crystal violet (CV) assay and light microscopy. Furthermore, extracellular polymeric substance (EPS), metabolic activity, auto-aggregation property along with their motility pattern also confirmed their strong biofilm forming ability. Considering their pathogenicity, few exhibited hemolytic activities. Subsequently, these potent biofilm formers were identified by 16S rRNA gene and phylogenetic approach. These biofilm forming ARB in waterbodies of EKW requires vigilant monitoring before it is recycled for household, aquaculture and agricultural activities. Hence this study requires attention from the viewpoint of Sustainable Developmental Goals (SDGs) particularly related to good health (SDG 3) in the context of ensuring clean, sanitary water (SDG 6) and managing life below water (SDG 14).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-05012-6.},
}

@article {pmid42633378,
year = {2026},
author = {Aminullah, N and Danish, F and Zahir, A and Azizi, MN},
title = {Phytogenic as a natural resource for gut health management: a sustainable strategy for modern poultry production.},
journal = {Veterinary and animal science},
volume = {33},
number = {},
pages = {100804},
pmid = {42633378},
issn = {2451-943X},
abstract = {The increasing global demand for poultry products has intensified the need for intervention strategies that enhance productivity while maintaining animal health and food safety. Antimicrobials have historically been used in poultry production to support growth performance and maintain gut health; however, their routine and prolonged use have raised significant concerns regarding antimicrobial resistance, which poses a serious threat to public health. The growing concerns regarding antimicrobial resistance have motivated researchers to seek safer, more sustainable alternatives. This review critically evaluates the mechanisms by which phytogenic feed additives (PFAs) regulate gut health and their potential to support sustainable poultry production as alternatives to conventional antimicrobials. Phytogenic compounds have been shown to enhance intestinal barrier integrity by upregulating tight junction proteins, improve nutrient absorption by stimulating digestive enzyme activity, and promote villus development and mucosal health. Furthermore, these bioactive molecules have demonstrated potential to modulate microbial ecology by favoring beneficial taxa while suppressing pathogenic colonization, thereby improving gut homeostasis and immune competence. These combined effects contribute to improved overall production sustainability. Despite the beneficial effects of PFAs, variation in plant sources, bioactive component concentrations, extraction methods, and dosage leads to inconsistent poultry responses, a limitation that warrants further investigation and standardization. However, advances in formulation technologies and standardization strategies are progressively improving their consistency and practical application. Therefore, PFAs represent a viable nutritional strategy to support gut health and promote more sustainable poultry production with reduced reliance on conventional antimicrobials.},
}

@article {pmid42635434,
year = {2026},
author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0030326},
doi = {10.1128/msystems.00303-26},
pmid = {42635434},
issn = {2379-5077},
abstract = {Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction, and whether it is associated with antibiotic exposure. In two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in certain bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.IMPORTANCEBacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host cell to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death, which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro, whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.},
}

@article {pmid42636907,
year = {2026},
author = {Xiang, S and Tian, Y and Tong, C and Qi, X and Ren, T and Ji, B},
title = {Ionic synergy of Ca[2+], Mg[2+], and Fe[2+] Balances hydrophobicity and microbial ecology in microalgal-bacterial granular sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135700},
doi = {10.1016/j.biortech.2026.135700},
pmid = {42636907},
issn = {1873-2976},
abstract = {Microalgal-bacterial granular sludge (MBGS) faces structural stability challenges that limit its engineering application. To investigate the regulatory mechanisms of divalent metal ions under light-dark cycles, five experimental groups were established: a blank control, Ca[2+] addition, Mg[2+] addition, Fe[2+] addition, and combined ion addition. Results showed that Fe[2+] was crucial for maintaining granule integrity and promoting photosynthetic taxa through regulating hydrophobic carbon group accumulation in extracellular polymeric substances (EPS), though its sole addition caused community specialization and compromised nitrogen/phosphorus removal stability, especially under dark conditions. Ca[2+] enhanced Proteobacteria proliferation and biomass accumulation, improving COD and TN removal, but this effect seemed to be insufficient to counteract granule disintegration caused by iron deficiency. Mg[2+] exhibited limited direct community effects but correlated positively with COD removal and Chl-a/Chl-b ratio. Notably, combined addition achieved balanced EPS hydrophilic-hydrophobic properties, maintained community diversity and functional redundancy, and demonstrated stable pollutant removal through ionic synergy. This study elucidates metal ion regulatory pathways in MBGS, providing theoretical foundations for targeted ion optimization.},
}

@article {pmid42630435,
year = {2026},
author = {Peng, P and Cai, J and Zhang, L and Lu, Y and Kuang, P},
title = {The subgingival microbiome in periodontitis: from ecological dysbiosis and metabolic reprogramming to precision interventions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1906205},
pmid = {42630435},
issn = {1664-302X},
abstract = {Periodontitis is a dysbiosis-driven chronic inflammatory disease characterized by complex interactions among the subgingival microbiome, microbial metabolism, and host immune responses. Accumulating evidence indicates that disease progression is not solely determined by the enrichment of specific periodontal pathogens but is critically associated with ecological disruption and functional reprogramming of the subgingival microbial community. During the transition from periodontal health to disease, microbial metabolism shifts from carbohydrate utilization toward proteolysis and amino acid fermentation, resulting in altered production of short-chain fatty acids, polyamines, volatile sulfur compounds, hydrogen sulfide, and nitric oxide. These metabolic alterations contribute to inflammasome activation, immune dysregulation, osteoclastogenesis, and progressive periodontal tissue destruction. Beyond local pathology, periodontal microorganisms and their metabolites can disseminate through the oral-systemic axis, thereby influencing the pathogenesis of multiple systemic disorders. Recent advances in multi-omics technologies have further revealed that metabolic reprogramming represents a critical mechanistic link connecting ecological dysbiosis with host inflammatory responses. Consequently, therapeutic strategies are evolving from conventional antimicrobial approaches toward precision microbiome-based interventions, including probiotics, postbiotics, bacteriophages, predatory bacteria, metabolic modulation, and oral microbiome transplantation. In this review, we integrate current evidence on microbial ecology, metabolism, and host interactions and propose the Ecological Dysbiosis-Metabolic Reprogramming-Host Crosstalk framework. This framework highlights metabolic reprogramming as the central bridge linking microbial dysbiosis to host inflammatory damage and provides a conceptual basis for the development of precision periodontal medicine.},
}

@article {pmid42630587,
year = {2026},
author = {Boutin, S and Rondeau-Leclaire, J and Roy, A and Laforest-Lapointe, I},
title = {A field-based study of phyllosphere mycobiomes in apple orchards under varying agricultural management strategies.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag203},
pmid = {42630587},
issn = {2730-6151},
abstract = {Microbial communities in the phyllosphere are key players in plant health and disease resistance, yet their response to agricultural management strategies remains poorly understood under field conditions. Here, we compare fungal community composition and diversity across conventional and organic apple orchards using ITS amplicon sequencing. Leaf samples were collected from six sites at three distinct time points during the 2023 growing season (in May, July, and August) corresponding approximately to monthly intervals throughout the summer. Flower samples were collected from the same trees in May. Our analyses reveal that agricultural management strategies are significantly associated with fungal community structure, with effects intensifying from May to July. Both types of management strategies showed enrichment for different genera known to include common apple tree pathogens: Alternaria and Podosphaera were associated with conventional sites, while Didymella and Ramularia were associated with organic sites. Although fungal alpha diversity was higher in May at conventional orchards compared to organic orchards, it declined over time at conventional sites while it remained stable at organic sites. Together, these patterns indicate that distinct management interventions impose contrasting selective pressures on the apple tree phyllosphere mycobiome, thus shaping both broad fungal community composition and the dominance dynamics of key fungal taxa. Our findings underscore the ecological relevance and inherent challenges of field-based microbiome research, and provide insights to inform the development of sustainable orchard management strategies grounded in fungal community dynamics.},
}

@article {pmid42629862,
year = {2026},
author = {Luo, HN and Wu, ZX and Guan, JY},
title = {Frequency locking to environmental forcing suppresses oscillatory extinction in phage-bacteria interactions.},
journal = {Physical review. E},
volume = {114},
number = {1-1},
pages = {014412},
doi = {10.1103/rch2-2hsr},
pmid = {42629862},
issn = {2470-0053},
mesh = {*Bacteriophages/physiology ; *Models, Biological ; *Bacteria/virology/growth & development ; *Extinction, Biological ; *Environment ; },
abstract = {Bacteriophage-bacteria interactions are central to microbial ecology, influencing evolution, biogeochemical cycles, and pathogen behavior. Most theoretical models assume static environments and passive bacterial hosts, neglecting the joint effects of bacterial traits and environmental fluctuations on coexistence dynamics. This limitation hinders the prediction of microbial persistence in dynamic ecosystems such as soils and oceans. Using a minimal ordinary differential equation framework, we demonstrate that environmental fluctuations can suppress destructive oscillations through resonance, promoting coexistence where static models otherwise predict collapse. Counterintuitively, we find that lower bacterial growth rates are helpful in enhancing survival under high infection pressure, elucidating the observed postinfection growth reduction. Our studies highlight bacterial hosts as active builders of ecological dynamics and environmental variation as a potential stabilizing force. Our findings thus bridge a theory-experiment gap and provide a framework for predicting microbial responses to environmental stress, which might have potential implications for phage therapy, microbiome management, and climate-impacted community resilience as well.},
}

*Bacteriophages/physiology
*Models, Biological
*Bacteria/virology/growth & development
*Extinction, Biological
*Environment

@article {pmid42629969,
year = {2026},
author = {Iqbal, MM and Farooq, MA and Lal, R and Abdalla, M and Smith, P},
title = {The Fragile Sink: Reconceptualizing Soil Carbon Stabilization and Its Vulnerability Under Global Change.},
journal = {Global change biology},
volume = {32},
number = {8},
pages = {e71071},
pmid = {42629969},
issn = {1365-2486},
mesh = {*Carbon Sequestration ; *Climate Change ; *Soil/chemistry ; *Carbon/analysis ; *Soil Microbiology ; },
abstract = {Soil carbon sequestration (SCseq) is fundamental to global climate mitigation initiatives; however, growing evidence indicates an expanding disparity between carbon (C) accumulation and its long-term persistence. This article aims to integrate recent advances in microbial ecology, mineral biogeochemistry, and nutrient stoichiometry to examine why increases in soil C (SC) stocks do not necessarily translate into long-term persistence. The article introduces the fragile sink framework, wherein sink durability reflects the balance between internal C throughput and the strength of stabilizing barriers. Global change drivers, including warming, elevated CO2 (eCO2), nutrient enrichment, and anthropogenic disturbance, can accelerate internal C turnover, resulting in soils that are structurally younger, more reactive, and increasingly vulnerable to rapid C loss despite stable or rising stocks. The article shows that destabilization begins at predictable vulnerability frontiers where stoichiometric gating and mineral protection are overridden, while recovery is constrained by kinetic and architectural hysteresis. Thus, it recommends a shift away from stock- and input-centric C farming toward process-centric C defense, emphasizing the protection of slow-cycling, kinetically protected pools under increasing turnover.},
}

*Carbon Sequestration
*Climate Change
*Soil/chemistry
*Carbon/analysis
*Soil Microbiology

@article {pmid42629024,
year = {2026},
author = {Wang, A and Jin, T and Tang, Y and Wang, S and Xia, X},
title = {Obligate anaerobic next-generation probiotics as natural antimicrobials in food systems: mechanisms, applications, and challenges.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 1},
pages = {119776},
doi = {10.1016/j.foodres.2026.119776},
pmid = {42629024},
issn = {1873-7145},
mesh = {*Probiotics ; Humans ; *Food Microbiology ; *Bacteria, Anaerobic/metabolism ; *Anti-Infective Agents ; Anaerobiosis ; *Foodborne Diseases/prevention & control/microbiology ; Biofilms ; },
abstract = {Foodborne pathogens remain a persistent global challenge, threatening food safety and public health. Conventional probiotics have been explored as natural antimicrobials to antagonize foodborne pathogens but still exhibit varied efficacy in pathogen suppression within complex food systems. In recent years, multiple human commensals such as Akkermansia muciniphila, Faecalibacterium prausnitzii, and Anaerobutyricum hallii have emerged as promising next-generation probiotics (NGPs) due to their ecological relevance, metabolic versatility, and capacity to restore host-microbiota homeostasis. This review first summarizes the potential mechanisms by which these anaerobes and their metabolites contribute to pathogen suppression, including metabolite-mediated inhibition, quorum sensing interference, nutrient and adhesion competition, host immune modulation, and biofilm suppression. Special emphasis is placed on the interplay among key NGPs and their synergistic metabolic networks that reshape microbial ecology and enhance colonization resistance. Furthermore, recent advances in incorporating anaerobic probiotics and their postbiotic derivatives into food systems are discussed, noting that such applications remain emerging and currently limited by the challenges of maintaining obligate anaerobes in aerobic matrices. Finally, we highlight current challenges and future opportunities, emphasizing safety assessment and synthetic microbial consortia. Together, this review provides an integrated perspective on obligate anaerobes as potential solutions for improving food safety and human health through NGPs innovation.},
}

*Probiotics
Humans
*Food Microbiology
*Bacteria, Anaerobic/metabolism
*Anti-Infective Agents
Anaerobiosis
*Foodborne Diseases/prevention & control/microbiology
Biofilms

@article {pmid42629157,
year = {2026},
author = {Wilborn, D and Constantinou, A and Franz, A and Schwarzer, R and Menzel, P and Engelhardt, G and Tomova-Simitchieva, T and Amin, R and Zhou, G and Hillmann, K and Kottner, J and Ralle, J and Konietschke, F and Blume-Peytavi, U},
title = {Maternal and Infant Skin Microbiome Synchrony and Divergence: A Longitudinal Study of Skin Microbial Ecology and Early-Life Assembly.},
journal = {Experimental dermatology},
volume = {35},
number = {8},
pages = {e70349},
pmid = {42629157},
issn = {1600-0625},
mesh = {Humans ; Female ; Longitudinal Studies ; Pregnancy ; *Skin Microbiome ; Infant ; *Skin/microbiology ; Infant, Newborn ; Adult ; *Microbiota ; Biodiversity ; },
abstract = {During pregnancy and after childbirth, women's skin undergoes significant changes which may affect the skin's functional and structural characteristics and microbial diversity. Like their mothers, the newborns also experience various skin challenges in the months following birth. Temporal changes in skin microbiome in special groups such as pregnant women and newborns, as well as the interrelation between their skin's microbial diversity, have not been investigated. We followed women from pregnancy through 6 months after delivery, and their infants from 4 weeks to 6 months of age to investigate their skin characteristics and the microbiome, and potential associations. We enrolled 109 pregnant females residing in Berlin, Germany, with 93 mothers-infant pairs completing the study. Microbiome investigations included DNA isolation as single-site sampling using volar forearm skin swabs. Bioinformatic analysis involved OTU clustering at 97% sequence identity, taxonomic assignment using NCBI reference databases, and calculation of biodiversity metrics, including relative abundance of the dominant bacterial phylotypes, bacterial diversity and Shannon diversity index. The maternal skin microbiome showed mild to moderate changes throughout pregnancy and the 6 months postpartum period. In infants, alpha diversity significantly increased (mean species richness from 82.6 at 4 weeks to 116.1 at 6 months), although it did not reach maternal diversity levels (145.4 at 6 months postpartum). Regarding the microbiome consistency of the included women and infants, the within-pair similarity was always significantly higher than between-pair similarity for both time points. Therefore, we conclude that there is likely a relationship between the microbiome of the mother and that of her child.},
}

Humans
Female
Longitudinal Studies
Pregnancy
*Skin Microbiome
Infant
*Skin/microbiology
Infant, Newborn
Adult
*Microbiota
Biodiversity

@article {pmid42623063,
year = {2026},
author = {Sgardioli, BF and Phillips, MC and Miklos, A and Fleiszig-Evans, K and Manson, AL and Scarpa de Mello, S and Shea, T and Urhan, A and Whipple, R and Salamzade, R and Sanders, J and Borges, PAV and Dapkevicius, MdLNE and Earl, AM and Gilmore, MS},
title = {Novelty, diversity, and genetic dark matter in enterococci of invertebrates.},
journal = {mBio},
volume = {},
number = {},
pages = {e0123426},
doi = {10.1128/mbio.01234-26},
pmid = {42623063},
issn = {2150-7511},
abstract = {Enterococci appear to have originated in the guts of early terrestrializing arthropods and invertebrates over 425 million years ago-hosts that are now highly diverse and widespread in nature today. Yet most knowledge of the genus comes from human infection-associated lineages with genomes swollen by the recent accretion of foreign DNA conveyed by mobile elements. Because invertebrates dominate terrestrial animal diversity and biomass, they would be predicted to constitute a major but little-explored reservoir of enterococcal diversity. We therefore systematically examined Enterococcus association and species diversification in invertebrate hosts of the comparatively natural, isolated, but well-characterized environment of the Azorean island of Terceira. Over 100 invertebrate specimens were examined for associated enterococci, which were taxonomically classified by whole-genome sequencing. Supporting the existence of a large pool of uncharacterized enterococci and Enterococcus-adapted genes, 40% (eight of 20) of the Enterococcus species identified were either undescribed, including four candidate new species described here, or very recently discovered. In contrast, control isolates from vertebrates were exclusively of known species typical of sampling elsewhere, discounting geographic isolation as a main driver of the novelty observed. Further, because of the abundance of E. casseliflavus and E. flavescens in this collection, we obtained the resolution necessary to quantify the divergence and decipher the drivers of speciation in the controversial division between these naturally vancomycin-resistant species. These findings provide robust support for the existence of a large pool of new species and unexplored adaptive traits in invertebrate-associated enterococci-diverse environmental survival traits optimized for expression in an enterococcal background, and well positioned for transmission into human-associated enterococcal strains.IMPORTANCEEnterococci are auxotrophic gut-associated bacteria that co-evolved with their terrestrial hosts over many eons. In the last 75 years-the "antibiotic era"-E. faecalis and E. faecium gained genes for antibiotic resistance and enhanced virulence, emerging as leading causes of multidrug-resistant infection. Little is known about the source of those genes or the pathway by which they entered human-associated strains. A recent global survey suggested a potentially large repository of uncharacterized genetic diversity in the enterococci of invertebrates. We directly tested this prospect by examining enterococci of invertebrate hosts in a largely natural and pastoral environment. Our findings provide clear evidence that invertebrates naturally harbor vast unexplored enterococcal diversity. Moreover, associations are likely driven by intrinsic host selection factors rather than geographic isolation. This expands our knowledge of Enterococcus biodiversity, including the identification of four novel species, identifying a vast reservoir of enterococcal genes available to species that colonize and infect humans.},
}

@article {pmid42623751,
year = {2026},
author = {Ranjan, K and Gupta, N and Al-Mustapha, AI and Keenum, I and Shaheryar, M and Bose, D and Sharma, G and Tiwari, A},
title = {Environmental occurrence, ecotoxicity, and management perspectives of β-lactam antibiotics.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120671},
doi = {10.1016/j.ecoenv.2026.120671},
pmid = {42623751},
issn = {1090-2414},
abstract = {β-Lactams are the most widely prescribed antibiotic class globally, comprising penicillins, cephalosporins, carbapenems, and monobactams. Their continual release to the environment raises concerns about both direct ecotoxicity and potential indirect effects on ecosystem function. This review highlights three key findings; 1) environmental concentrations can exceed predicted no-effect concentrations for resistance selection; for example ceftriaxone had been reported 6160 µg/L in wastewater influent and 4150 µg/L in effluent in India, indicating that many β-lactams have removal efficiency below 33%, 2) ecotoxicity data show that cyanobacteria (e.g. Microcystis aeruginosa, EC50 0.0037 mg/L for amoxicillin) are ≥ 1,000-fold more sensitive than macrofauna, and that chronic exposure at ng-µg/L levels may promote selection of antimicrobial resistance and facilitate horizontal gene transfer of these genes and 3). β-lactam resistance genes (blaCTX-M, blaNDM, blaOXA) are ubiquitous in wastewater and manure-amended soils and can persist even after the degradation of the parent compounds. Collectively, these finding indicates that β-lactam antibiotics pose significant risks to aquatic and soil ecosystems by contributing to the proliferation and maintenance of antimicrobial resistance in environmental reservoirs. The widespread environmental occurrence and persistence of β-lactams, along with associated resistance determinants, represent emerging One Health concerns. This narrative review synthesizes current literature on the ecotoxicological effects of β-lactam antibiotics, focusing on their major environmental sources, distribution across environmental matrices, impacts on non-target organisms, and emerging strategies to mitigate their environmental burdens. We further emphasize cross-disciplinary solutions spanning engineering, microbial ecology, policy, identify critical research gaps, and propose pragmatic pathways to reduce environmental selection pressure from β-lactams.},
}

@article {pmid42625292,
year = {2026},
author = {Poppelsdorf, W and de Knijf, A and Melis, B and Rojas-Preciado, N and Yurduseven, R and Deleu, A and Bunkens, K and van Hee, S and Jacquemyn, H and Lievens, B},
title = {Biocontrol potential of Pseudomonas and Pantoea strains against the lettuce root aphid (Pemphigus bursarius L.) in witloof chicory (Cichorium intybus L. var. foliosum).},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71230},
pmid = {42625292},
issn = {1526-4998},
support = {//Agentschap Innoveren en Ondernemen/ ; },
abstract = {BACKGROUND: Although microbial biopesticides are widely applied to manage foliar insect pests, their application against belowground insect pests has received less attention. These pests are generally more challenging to manage due to their concealed soil-dwelling lifestyle and the limited availability of delivery methods. Here, we evaluated the potential of Pseudomonas and Pantoea strains as a biocontrol strategy against the lettuce root aphid (Pemphigus bursarius) in witloof chicory (Cichorium intybus L. var. foliosum) using a realistic delivery approach based on seed inoculation, preceded by a screening via root immersion to identify the most promising strains.

RESULTS: Root immersion of witloof chicory plants in bacterial suspensions significantly decreased aphid survival for 10 out of 19 tested strains, with median lethal times (LT50) ranging from 0.6 to 7.5 days, compared to 10.7 days for the untreated control. When the four best-performing strains, including two Pseudomonas and two Pantoea strains, and a reference strain (Pseudomonas fluorescens PpR24) were applied via seed inoculation, the strains successfully colonized chicory roots at densities exceeding 10[6] colony-forming unit (CFU) g[-1] of root tissue for at least 5 weeks and retained aphicidal activity, albeit with reduced efficacy. In addition, the strains significantly suppressed aphid population development, reducing total aphid population size by up to 82% at 21 days after aphid introduction.

CONCLUSION: In this study, we have identified novel Pseudomonas and Pantoea strains that effectively reduce survival and population development of Pemphigus bursarius on witloof chicory plants, highlighting their potential as a sustainable biocontrol strategy against root aphids. © 2026 Society of Chemical Industry.},
}

@article {pmid42625563,
year = {2026},
author = {Chen, WM and Sun, MY and Ye, JY and Tan, DC and Zhang, ZY and Liu, JJ},
title = {Towards a safer probiotic: clbD deletion attenuates EcN-induced DNA damage responses and epithelial inflammatory transcriptional responses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1812973},
pmid = {42625563},
issn = {2235-2988},
mesh = {*DNA Damage ; *Epithelial Cells/microbiology/immunology ; *Probiotics ; *Escherichia coli/genetics ; *Gene Deletion ; Humans ; Polyketides/toxicity ; Cell Line ; Genomic Islands ; *Escherichia coli Proteins/genetics ; Transcription, Genetic ; Cytokines/metabolism ; Peptides ; },
abstract = {Escherichia coli Nissle 1917 (EcN) is widely used as a probiotic and engineering chassis, but its carriage of the pks genomic island raises safety concerns related to the genotoxin colibactin. Here, we constructed a clbD deletion mutant (EcNΔclbD) and a chromosomally complemented strain (EcNΔclbD::clbD) using a CRISPR/Cas9-based genome-editing strategy. Locus-specific PCR confirmed the expected clbD deletion and restoration patterns. DNA damage responses were evaluated by γH2AX immunofluorescence and alkaline comet assay after bacterial co-culture. Compared with EcN, EcNΔclbD markedly reduced γH2AX positivity and comet-positive cells, whereas clbD complementation restored both phenotypes to levels comparable to EcN. In NCM460 colonic epithelial cells, EcNΔclbD induced lower mRNA expression of pro-inflammatory cytokines and TLR4-MYD88-NFKB1-related transcripts than EcN. Additional CCK-8 and cell-associated bacterial load assays showed no significant differences between EcN- and EcNΔclbD-treated groups, suggesting that the reduced inflammatory transcription was not primarily attributable to altered host cell CCK-8 readout or bacterial exposure. qPCR analysis of neighboring pks genes showed detectable local transcriptional changes after clbD deletion that were restored toward the parental EcN pattern by complementation. Transmission electron microscopy revealed no detectable morphological or ultrastructural disruption after clbD deletion. Exploratory untargeted metabolomics suggested a metabolic shift associated with clbD deletion, while gastrointestinal stress assays revealed condition-dependent fitness effects without a generalized growth defect in LB medium. Together, these findings indicate that clbD deletion attenuates EcN-induced DNA damage responses and epithelial inflammatory transcription in vitro. EcNΔclbD may represent a candidate safety-optimized EcN chassis requiring further validation in additional epithelial models and in vivo systems.},
}

*DNA Damage
*Epithelial Cells/microbiology/immunology
*Probiotics
*Escherichia coli/genetics
*Gene Deletion
Humans
Polyketides/toxicity
Cell Line
Genomic Islands
*Escherichia coli Proteins/genetics
Transcription, Genetic
Cytokines/metabolism
Peptides

@article {pmid42627163,
year = {2026},
author = {Harrison, DJ and Fullmer, MS and Takeuchi, N},
title = {Why are archaea not pathogenic? A hypothesis based on metabolism-habitat covariation.},
journal = {mBio},
volume = {},
number = {},
pages = {e0118526},
doi = {10.1128/mbio.01185-26},
pmid = {42627163},
issn = {2150-7511},
abstract = {Pathogenicity, the ability to cause infectious diseases in multicellular eukaryotes, is widespread among bacteria and eukaryotes but has not been reliably identified in archaea. To explore possible reasons for this disparity, we perform comparative analyses of thousands of bacterial and archaeal isolates. Our results show that isolated bacterial pathogens possess the ability to use organic compounds as sources of energy, electrons, and carbon (chemo-organo-heterotrophy or COH), suggesting that COH is a metabolic prerequisite for pathogenicity. Moreover, we find that isolated archaea capable of COH do not inhabit multicellular eukaryotes and instead predominantly inhabit extreme environments that preclude such eukaryotes. In contrast, all isolated archaea that inhabit multicellular eukaryotes are incapable of COH metabolism. This metabolism-habitat covariation in isolated archaea, together with COH as a potential prerequisite for pathogenicity in bacteria, suggests that the absence of archaeal pathogens may be due to a combination of the two factors: COH-capable archaea lack the environmental opportunity to inhabit multicellular eukaryotes, while non-COH archaea lack the metabolic prerequisite for pathogenicity.IMPORTANCEPathogenicity-the ability to cause infectious disease-is widespread among bacteria and eukaryotes but conspicuously absent from archaea, the third domain of life. To understand why archaea are non-pathogenic, we performed comparative analyses of thousands of bacterial and archaeal isolates. We found that the absence of pathogenic archaea can be explained by a combination of metabolic and environmental factors. Specifically, archaea living within eukaryotic, multicellular hosts lack a metabolic capability correlated with pathogenicity-chemo-organo-heterotrophy-whereas those possessing this metabolism typically live under extreme conditions, such as high temperature, and therefore lack the environmental opportunity to interact with eukaryotic hosts. These findings advance our understanding of microbes by revealing important links between their metabolism, habitats, and pathogenicity.},
}

@article {pmid42627175,
year = {2026},
author = {Post, A and Webb, T and Indugu, N and Smith, BI and Pitta, DW},
title = {Dynamic changes in the hindgut bacterial community of pre-weaning crossbred beef calves in a pasture-based system.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173026},
doi = {10.1128/spectrum.01730-26},
pmid = {42627175},
issn = {2165-0497},
abstract = {The early-life gut microbiome represents a window during which microbial alterations may impact long-term health and productivity. However, most research has focused on confined dairy systems with limited breed variation. To address this gap, we examined bacterial community dynamics in pasture-raised South Poll × Angus and Angus cow-calf pairs (n = 7). Fecal samples were collected from calves at birth and weekly through 8 weeks, with dam's samples collected post-calving. DNA was extracted from fecal samples, and bacterial communities were profiled using the V1-V2 region of the 16S rRNA gene. Alpha diversity increased significantly with age (richness ρ < 0.01, Shannon ρ < 0.01), while beta diversity exhibited strong temporal structuring (weighted R[2] = 0.33, ρ = 0.001; unweighted R[2] = 0.38, ρ = 0.001), as calf communities converged toward adult reference states by 8 weeks. Sex exerted modest but detectable effects on community structure. Taxonomic analyses identified a core microbiome of 25 taxa that accounted for most community structure and defined discrete temporal phases of development. Early fecal samples were dominated by Lactobacillus, Bacteroides, and facultative anaerobes. These taxa declined rapidly with age, coincident with increases in Ruminococcus, Blautia, Dorea, Lachnospiraceae, and Clostridiales (q < 0.05). Calf average daily gain was positively correlated with Streptococcus, Dorea, and Bacillus and negatively correlated with Ruminococcaceae (ρ > 0.3, q < 0.05). These findings demonstrate rapid gut microbiome development in pastured beef calves, similar in pace but distinct in composition from confined dairy systems, underscoring the importance of environment and breed diversity in shaping early-life microbial colonization.IMPORTANCEEarly-life microbial colonization plays a critical role in shaping gastrointestinal physiology and immune-cell maturation, with impacts on long-term productivity in cattle. However, most studies describing microbial succession focused on Holstein calves raised in confinement systems, leaving the microbial ecology of beef calves, particularly crossbreds and those on pasture, poorly characterized. In this study, we longitudinally characterized hindgut microbial development in Angus × South Poll and Angus calves during the first 8 weeks of life. We demonstrate a structured microbial succession driven by a core set of taxa that evolves with age, with continuous dominance of Lactobacillus. These findings establish foundational knowledge of microbiome assembly in a breed of beef calves growing in popularity and highlight microbial taxa and community structures that may relate to breed genetics influencing growth and health. Understanding microbial development in pasture-based beef systems provides an essential framework for designing microbiome-informed management or nutritional interventions aimed at improving productivity and sustainability, particularly in pasture-raised animals.},
}

@article {pmid42629006,
year = {2026},
author = {Asadi, A and Sarand, I and Spuul, P and Fanning, S and Macori, G},
title = {Mapping spoilage microbiota in complex food systems: organisms, mechanisms, and omics-based characterization.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 1},
pages = {119633},
doi = {10.1016/j.foodres.2026.119633},
pmid = {42629006},
issn = {1873-7145},
mesh = {*Food Microbiology/methods ; *Microbiota ; Multiomics ; *Bacteria/classification/genetics ; Food Storage ; Food Loss and Waste ; },
abstract = {Food spoilage is a major cause of food loss, while it remains less understood in complex, multi-component foods than in single-ingredient products. This review reframes spoilage in such foods as a community-driven ecological process, not simply the result of single dominant organisms, and argues that spoilage is best understood through microbial activity rather than microbial presence or relative abundance alone. We develop this framework around three central ideas: (i) ingredient-derived microbiotas interact within a shared matrix, so spoilage depends on microbial succession and competition during storage; (ii) predictions based on individual specific spoilage organisms often perform poorly in heterogeneous mixed foods; and (iii) taxonomic dominance does not necessarily indicate spoilage activity. On this basis, we examine key spoilage-associated groups, including Leuconostoc gelidum, Lactococcus piscium, Latilactobacillus sakei, Latilactobacillus curvatus, Pseudomonas spp., Enterobacteriaceae, yeasts, and moulds, and link them to characteristic metabolites and spoilage patterns under refrigerated and modified-atmosphere storage. We then evaluate analytical approaches, from culture-based methods and MALDI-TOF MS to 16S rRNA and ITS sequencing, shotgun metagenomics, and activity-resolved multi-omics, according to what each can and cannot reveal about viable populations, microbial activity, community succession, and spoilage causation. We also discuss how bioinformatic choices influence interpretation and why gene detection does not necessarily indicate spoilage activity. Finally, we propose an integrated framework for study design and data integration to support more reliable quality control and shelf-life assessment in complex food systems.},
}

*Food Microbiology/methods
*Microbiota
Multiomics
*Bacteria/classification/genetics
Food Storage
Food Loss and Waste

@article {pmid42614744,
year = {2026},
author = {Hu, D and Wang, Z and Xue, Y and Li, X and Li, Y and Liu, S and Gao, L and Liu, H and Yan, H},
title = {Perioperative gut microbial ecology: a new frontier for improving the prognosis of hepatocellular carcinoma surgery.},
journal = {Precision clinical medicine},
volume = {9},
number = {3},
pages = {pbag021},
pmid = {42614744},
issn = {2516-1571},
abstract = {For patients diagnosed with hepatocellular carcinoma (HCC), surgical intervention remains the primary treatment modality. Nonetheless, challenges such as poor postoperative prognosis and the potential for recurrence contribute significantly to patient suffering. During the perioperative period, the stability of the gut microbiota in patients with HCC is significantly disrupted. This disruption can substantially affect the liver microenvironment and ultimately influence postoperative outcomes. Notably, the metabolic reprogramming of the liver induced by gut microbiota dysbiosis, persistent inflammation, and suppressed immune surveillance are key factors in HCC recurrence. Consequently, the gut microbiota has emerged as a critical risk factor in improving perioperative outcomes for patients with HCC. In this review, we summarize the factors contributing to changes in the gut microbiota during the perioperative period in patients with HCC, as well as the potential mechanisms by which gut microbiota dysbiosis affects prognosis. More importantly, we have proposed strategies based on the aforementioned mechanisms affecting prognosis, including restoring the gut microbiota, repairing the gut-liver barrier, providing perioperative relief, and enhancing liver regeneration. Further, this review also outlines potential challenges in clinical applications aimed at improving postoperative outcomes for HCC patients through gut microbiota-based interventions, particularly regarding sampling and patient susceptibility stratification. Collectively, these studies will further advance the development of personalized therapies targeting the microbiome, ultimately improving prognostic strategies for patients undergoing surgical intervention for HCC.},
}

@article {pmid42615635,
year = {2026},
author = {Li, L and Zhang, J and Qu, S and Zhou, Z and Wang, B and Wu, H and Guo, Z and Shi, L and Yin, B and Zhu, X and Wang, Y and Teng, HH},
title = {The iron paradox and particle size sensing: transcriptomic response of Enterococcus faecalis to non-nutritive minerals.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0095426},
doi = {10.1128/aem.00954-26},
pmid = {42615635},
issn = {1098-5336},
abstract = {Minerals are known to influence microbial metabolism as nutrient sources or redox partners, yet whether chemically inert, non-nutritive minerals can regulate microbial physiology, and through what mechanisms, remains poorly understood. Here, we used transcriptomics to investigate the response of Enterococcus faecalis to Al2O3 and SiO2 particles spanning nanoscale to millimeter scale. Mineral exposure triggered extensive transcriptional reprogramming across hundreds of differentially expressed genes. Notably, a massive upregulation of iron acquisition genes (log2FC range from 3.8 to 4.2) concurrent with oxidative stress defenses (catalase, thiol peroxidase, and NADH oxidase) is suggestive of an "iron paradox," which is potentially attributable to mineral-mediated nutrient sequestration and steric hindrance of membrane transporters alongside interfacial reactive oxygen species generation. To adapt, E. faecalis orchestrated a coordinated metabolic shift, repressing serine catabolism (log2FC = -2.7) while investing nitrogen into glutathione biosynthesis (cystathionine synthase genes, log2FC = 3.7). Correlation analysis identified an ompR-sigV axis through which E. faecalis discriminates mineral particle size, with nanoscale particles eliciting stronger transcriptional responses than their larger counterparts. This stress response additionally upregulated virulence-associated genes and antibiotic resistance genes without direct antimicrobial selection pressure. These findings suggest that non-nutritive minerals shape microbial physiology through physical and surface-chemical cues independent of their nutritional value, highlighting the need for further exploration of the non-nutritional functions of minerals in microbial ecology.IMPORTANCEEven in the absence of utilizable nutrients, non-nutritive minerals such as Al2O3 and SiO2 can profoundly influence the transcriptional responses of Enterococcus faecalis. Using transcriptomic sequencing, we show that these inert minerals regulate microbial transcription, enhancing iron acquisition, oxidative stress repair, pathogenicity, and antibiotic resistance. Mineral-mediated transcriptional control is driven primarily by physical contact, surface chemistry, and particle size sensing, rather than conventional metabolic interactions. These findings identify inert minerals as signaling molecules that actively modulate microbial transcription, playing a proactive role in microbial evolution and environmental adaptation. This study redefines inert minerals as active carriers of transcriptional regulation, filling a critical gap in geomicrobiology and providing new insights into microbial environmental responses, biogeochemical cycling, and the mechanisms underlying microbial functional evolution and maintenance.},
}

@article {pmid42617679,
year = {2026},
author = {Zhou, HZ and Sun, ZL and Xiao, YX and Xiao, W and Kang Ma, and Zhou, CH and Ma, YH and He, T},
title = {Litter C/N ratio is associated with POC-to-MAOC transformation potential across forest types in subtropical restoration.},
journal = {Environmental research},
volume = {307},
number = {},
pages = {125520},
doi = {10.1016/j.envres.2026.125520},
pmid = {42617679},
issn = {1096-0953},
abstract = {Forest type is a critical determinant of soil organic carbon (SOC) dynamics during ecological restoration, yet how forest type shapes microbial community assembly and functional gene abundance to govern the partitioning of soil carbon into particulate (POC) and mineral-associated (MAOC) fractions remains poorly resolved. In May 2025, we collected soil samples from 12 plots representing three typical forest types (coniferous, mixed, and broad-leaved forests) in the Lingnan Nature Reserve and applied metagenomic sequencing to characterize soil microbial communities and functional processes. Following over three decades of restoration, SOC in mixed (25 ± 1.5 g/kg) and broad-leaved forest (26 ± 2.1 g/kg) soils increased by ∼18% and 23%, respectively, compared to coniferous forests (21 ± 1.6 g/kg). Litter C/N was lower in mixed and broad-leaved forests, corresponding with their higher SOC. Structural equation modeling further linked litter C/N ratio to POC and MAOC accumulation via microbial biomass carbon (MBC) as a key node, with POC, MAOC, and MBC increasing by 108-134%, 20-22%, and 26-31%, respectively, in mixed and broad-leaved versus coniferous soils. At the community level, variations in forest types selectively enriched Acidobacteriota or Actinomycetota, while co-occurrence network analysis revealed a shift from predominantly negative toward predominantly positive associations among bacterial taxa in broad-leaved and mixed forests, along with enhanced cross-module metabolic flow. Functionally, compared to coniferous forests, mixed and broad-leaved forests exhibited ∼15%/38% and 21%/47% increases in RPKM values of carbon fixation/degradation gene, respectively. GO enrichment analysis further indicated that litter inputs may be converted into stable humus via glycolysis and amino acid synthesis pathways. By integrating community-level microbial ecology, co-occurrence network analysis, and metagenomic functional profiling, this study provides novel mechanistic insight into how forest type shapes soil carbon fraction dynamics during restoration. These findings indicate the gene abundance variation in POC-to-MAOC transformation might be a plausible mechanistic link in the plant-microbe-soil carbon nexus and suggest that promoting broad-leaved or mixed forest restoration may represent a potentially effective strategy for enhancing soil carbon accumulation in subtropical regions.},
}

@article {pmid42618149,
year = {2026},
author = {Mohr, MG and Tanabe, TS and Grosser, M and Dahl, C},
title = {Biochemistry and transcriptional regulation of bacterial sulfur oxidation.},
journal = {Advances in microbial physiology},
volume = {89},
number = {},
pages = {51-154},
doi = {10.1016/bs.ampbs.2026.06.003},
pmid = {42618149},
issn = {2162-5468},
mesh = {Oxidation-Reduction ; *Gene Expression Regulation, Bacterial ; *Sulfur/metabolism ; *Bacteria/metabolism/genetics/enzymology ; Bacterial Proteins/metabolism/genetics ; *Transcription, Genetic ; Oxidoreductases/metabolism/genetics ; Thiosulfates/metabolism ; },
abstract = {Sulfur is one of the most important and versatile elements in biology and forms the basis of energy metabolism in many prokaryotes. Its extensive large-scale redox transformations drive the global biogeochemical sulfur cycle and profoundly influence environmental chemistry. In dissimilatory sulfur oxidizers, the oxidation of reduced sulfur compounds is directly coupled to energy conservation via photosynthetic or respiratory electron transport chains. Sulfur-oxidizing bacteria and archaea are remarkably diverse, reflecting both the wide range of habitats they inhabit and the variety of metabolic pathways through which sulfur compounds are exploited as electron donors. Over the past decades, these pathways have been examined in depth using a spectrum of molecular genetic, biochemical, and omics-based approaches, primarily in model organisms amenable to genetic manipulation. Particular emphasis has been placed on thiosulfate oxidation mediated by the Sox multienzyme system and thiosulfate dehydrogenases, as well as on cytoplasmic sulfane sulfur oxidation involving dissimilatory sulfite reductase and the sulfur-oxidizing heterodisulfide reductase-like sHdr complex. Recent advances have highlighted the central role of specific lipoate-binding proteins that are essential for efficient sHdr-dependent sulfur oxidation. This review provides an overview of current knowledge on prokaryotic sulfur oxidation pathways. In addition, emerging insights into the complex regulatory networks operating in facultative sulfur oxidizers are provided, with particular attention to how these organisms coordinate sulfur metabolism with changing environmental and energetic conditions.},
}

Oxidation-Reduction
*Gene Expression Regulation, Bacterial
*Sulfur/metabolism
*Bacteria/metabolism/genetics/enzymology
Bacterial Proteins/metabolism/genetics
*Transcription, Genetic
Oxidoreductases/metabolism/genetics
Thiosulfates/metabolism

@article {pmid42618789,
year = {2026},
author = {Bartolec, T and Mitosch, K and Potel, C and Corona, F and Yang, ALJ and Karcher, N and Burtscher, ML and Koumoutsi, A and Becher, I and Müller, LS and Bobonis, J and Kumar, M and Galardini, M and Typas, A and Savitski, MM},
title = {Pervasive phosphorylation by phage T7 kinase disarms bacterial defences.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42618789},
issn = {1476-4687},
abstract = {Bacteria and bacteriophages are in a constant arms race to develop defence and anti-defence systems, respectively. Currently known phage-encoded anti-defence systems are specific to the activity of the targeted bacterial defence system. Here we identify a mechanism by which the T7 bacteriophage broadly counteracts bacterial defences using protein phosphorylation. Its kinase (T7K), which has been reported to redirect the function of a few host proteins[1-5], is actually a hyperpromiscuous dual-specificity kinase that phosphorylates nearly all host and phage proteins during infection. The scale of phosphorylation vastly exceeds known phosphosites in Escherichia coli, has no sequence motif specificity and results in a higher proteome-wide phosphorylation density than mammalian cells with around 500 kinases. Stoichiometry analysis of phosphorylation sites revealed strong bias in T7K activity towards nucleic-acid-binding substrates mediated by its C-terminal DNA-binding domain. This highly stoichiometric phosphorylation enables the deactivation of DNA-targeting or DNA-containing bacterial defence systems. We provide mechanistic insights into how T7K weakens DNA-containing Retron-Eco9 through specific phosphorylation events, with single phosphomimetic mutations in key sites of the toxin abolishing defence. Moreover, by screening a large collection of E. coli strains, we provide evidence of broad anti-defence abilities of T7K in nature, as counteracted strains contain diverse bacterial defence systems. T7K homologues are found almost exclusively in phages, with hyperpromiscuous kinase activity probably being enabled by a divergent DFG-like motif in the catalytic centre.},
}

@article {pmid42621978,
year = {2026},
author = {Sanabani, SS},
title = {Regenerative Microbiology: Harnessing Bacterial Antagonism and Spatiotemporal Signaling for Diabetic Wound Repair.},
journal = {Smart medicine},
volume = {5},
number = {4},
pages = {e70044},
pmid = {42621978},
issn = {2751-1871},
abstract = {Chronic diabetic foot ulcers represent a persistent clinical challenge characterized by a "locked" inflammatory phase, biofilm-mediated infection, and impaired tissue regeneration. Because conventional antibiotic and debridement therapies fail to resolve dysbiosis or stimulate healing, microbial antagonism has emerged as a potent biological principle for wound restoration. This narrative review integrates ecological evidence and mechanistic insights from animal models and early human studies to explore how beneficial microorganisms, including probiotics, bacteriophages, and competitive consortia, actively reshape diabetic wound environments. We examined the multifaceted mechanisms of these interactions, ranging from direct pathogen inhibition to host immunomodulation and metabolic signaling via conserved pathways such as the p40/epidermal growth factor receptor (EGFR)/PI3K axis. To address significant translational barriers, we introduce a "Regenerative Microbiology" framework that emphasizes spatiotemporal coordination and precision stratification. By tailoring the use of live biotherapeutics or metabolically independent postbiotics to a patient's vascular and microbial profiles, this approach offers a strategic roadmap for transforming the management of infection-driven tissue damage in chronic diseases.},
}

@article {pmid42622741,
year = {2026},
author = {Okey-Ndeche, NF and Igwe, NH and Adewumi, CN and Ogundolie, FA},
title = {Seasonal shifts in microbial communities and physicochemical quality of a stream from a pristine waterfall in Abuja, Nigeria.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {9},
pages = {},
pmid = {42622741},
issn = {1573-2959},
mesh = {Nigeria ; Seasons ; *Environmental Monitoring ; *Rivers/microbiology/chemistry ; *Water Microbiology ; Bacteria/growth & development ; *Microbiota ; Water Quality ; Fungi/growth & development ; },
abstract = {The effects of seasonal changes on the physicochemical properties and microbial populations of a pristine waterfall stream located near Veritas University, Abuja, Nigeria, were evaluated. Water samples were collected monthly for 12 months during both dry and rainy seasons. Physicochemical parameters such as temperature, pH, conductivity, turbidity, and biochemical oxygen demand (BOD) were done by standard methods. The interaction effect of temperature and pH on the microbial organisms (heterotrophic bacteria, fungi, and yeast) and BOD was modeled using response surface methodology (RSM) based on central composite rotational design (CCRD). Findings indicate that physicochemical parameters such as conductivity (22.82 µS/cm), turbidity (0.96 NTU), and pH (8.23) as well as the number of microbial communities were higher in the rainy season than in the dry season. However, the physicochemical parameters (temperature, pH, conductivity, and turbidity) values are within the acceptable range of values for freshwater systems. The relationships between temperature, pH, and microbial counts were significantly explained through quadratic models (p < 0.05) that show high fitness values (R[2] = 0.7622-0.9728). The significant quadratic effect of temperature on the proliferation of bacteria and fungi and significant influence of pH on yeast and BOD was observed. BOD displayed a model response change from quadratic in the rainy season to linear in the dry season. The research demonstrates that even relatively pristine freshwater ecosystems are vulnerable to seasonal physicochemical variations that influence microbial ecology and probable public health risks. The discoveries in this work therefore, offer a predictive framework that can be adopted for monitoring freshwater ecosystems under increasing anthropogenic and climate-related pressures.},
}

Nigeria
Seasons
*Environmental Monitoring
*Rivers/microbiology/chemistry
*Water Microbiology
Bacteria/growth & development
*Microbiota
Water Quality
Fungi/growth & development

@article {pmid42613647,
year = {2026},
author = {Zarantonello, G and Puente-Sánchez, F and Schmidt, JG and Cuenca, A},
title = {From onset to healing: temporal dynamics of microbial communities pinpoint Midichloria-like organism's key role in the development of the fish skin disease red mark syndrome.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42613647},
issn = {2524-4671},
support = {PhD funding//Danmarks Tekniske Universitet/ ; 101136346//European Union's Horizon Europe Project EUPAHW/ ; 2023-01573//Swedish Research Council for Sustainable Development (FORMAS)/ ; },
abstract = {BACKGROUND: Red mark syndrome (RMS) is an infectious disease affecting rainbow trout (Oncorhynchus mykiss), especially at market size, forcing farmers to downgrade the product with heavy economic repercussions. The causative agent of RMS has not been established according to Koch's postulates, since possible candidates have not been isolated and propagated in vitro. While the 16S rRNA gene of a Midichloria-like organism (MLO) is consistently detected in active skin lesions, the role of other bacteria in the disease has not been excluded. In this work, we provide a temporal perspective to elucidate the relationships between the bacteriome in rainbow trout skin and water, during the development and resolution of clinical disease in naive fish infected by cohabitation with RMS-affected fish in the same tank.

RESULTS: We quantified the MLO by qPCR in skin and, for the first time, in water using environmental DNA, showing that its quantity in both sample types corresponds with disease progression. Using 16S rRNA gene profiling, we provide further evidence that the MLO is likely the primary pathogen triggering RMS, as it was the only significantly enriched taxon in active lesions. Furthermore, the skin microbiome of affected fish reverted to a control-like state during healing. RMS also caused changes in the overall skin microbiome at peak pathology: the relative abundance of "Ca. Branchiomonas" and an unclassified gammaproteobacterium increased in apparently healthy skin areas of RMS-affected fish while remaining low in controls, suggesting they may be opportunistic bacteria implicated in skin dysbiosis.

CONCLUSIONS: Our findings on the temporal dynamics of the skin microbiome during disease progression and recovery strengthen the evidence that Midichloria-like organism is the primary pathogen of RMS. The observed shifts in other bacterial taxa suggest possible secondary roles in disease-associated skin dysbiosis. Finally, detection of MLO in environmental DNA from water provides new insights into RMS transmission and potential monitoring strategies.},
}

@article {pmid42613938,
year = {2026},
author = {Adi, YK and Prakasita, VC and Wahyuni, AETH},
title = {Insights Into Boar Semen Under Tropical Conditions in Smallholder Production Systems: Semen Quality, Potential Microbiota Contamination and Antimicrobial Susceptibility.},
journal = {Reproduction in domestic animals = Zuchthygiene},
volume = {61},
number = {8},
pages = {e70311},
doi = {10.1111/rda.70311},
pmid = {42613938},
issn = {1439-0531},
support = {067/C3/DT.05.00/PL/2025//Directorate of Research and Community Service, Directorate General of Research and Development, Ministry of Higher Education, Science, and Technology, Republic of Indonesia/ ; },
mesh = {Animals ; Male ; *Semen/microbiology ; *Semen Analysis/veterinary ; Bacteria/drug effects/isolation & purification ; *Microbiota ; Indonesia ; Tropical Climate ; Swine ; Microbial Sensitivity Tests/veterinary ; *Sus scrofa/microbiology ; Animal Husbandry ; },
abstract = {This study evaluated boar semen quality, seminal microbiome composition, and antimicrobial susceptibility of bacteria isolated from seminal plasma in a tropical smallholder pig production system in Indonesia. A total of 10 ejaculates were collected from eight sexually mature boars using the gloved-hand technique from two herds located in East Nusa Tenggara (Herd A) and East Java (Herd B). Semen quality was evaluated using conventional methods in Herd A (five ejaculates from three boars) and a mobile semen analysis unit in Herd B (five ejaculates from five boars). Seminal microbiome composition (three ejaculates from three boars in Herd A and five ejaculates from five boars in Herd B) was assessed using next-generation sequencing, and antimicrobial susceptibility of bacterial isolates recovered from seminal plasma (five ejaculates from three boars in Herd A and five ejaculates from five boars in Herd B) was determined using the disk diffusion method. Boar semen quality from Herd A was assessed only for gross motility using subjective observation, yielding a score of 2 out of 3. In Herd B, semen quality was generally high, with a mean ejaculate volume of 232.0 ± 28.6 mL and sperm concentration of 436.9 ± 109.3 × 10[6]/mL. Total and progressive motility were 89.5% ± 6.9% and 84.2% ± 9.5%, respectively, while the proportion of immotile spermatozoa was 10.5% ± 6.9%. Based on 16S rRNA gene sequencing, Chryseobacterium showed the highest relative abundance in semen samples from Herd A, whereas Streptococcus predominated in Herd B. Principal coordinates analysis based on Bray-Curtis dissimilarity demonstrated clear separation of seminal microbiota between herds, with Herd A samples forming a more compact cluster. LEfSe analysis further identified bacterial taxa differentially enriched between herds. Bacterial culture revealed that all semen samples were contaminated with either single or multiple bacterial species, including both Gram-negative and Gram-positive organisms. Escherichia coli and Klebsiella spp. were the most frequently detected isolates. Antimicrobial susceptibility test showed that Herd B exhibited a higher proportion of non-susceptible outcomes (58.3%) compared to Herd A (24.3%). In addition, the proportion of multidrug resistance in Herd A and Herd B were 42.9% and 83.3%, respectively. In conclusion, bacterial contamination in boar semen is unavoidable and may originate from the animal itself or the surrounding environment. Its impact on semen quality may vary depending on the bacterial load and the specific types of microorganisms present. In addition, variations in AMR and seminal microbiota between herds suggest that farm management practices may influence the microbial ecology and resistance patterns in boar semen.},
}

Animals
Male
*Semen/microbiology
*Semen Analysis/veterinary
Bacteria/drug effects/isolation & purification
*Microbiota
Indonesia
Tropical Climate
Swine
Microbial Sensitivity Tests/veterinary
*Sus scrofa/microbiology
Animal Husbandry

@article {pmid42614402,
year = {2026},
author = {Zhang, Q and Cheng, Z and Tang, X and Yan, Y and Xia, Y},
title = {Wastewater treatment plant as a stable contributor affecting coastal ocean water viral communities.},
journal = {mLife},
volume = {},
number = {},
pages = {},
pmid = {42614402},
issn = {2770-100X},
abstract = {Coastal viruses play a vital role in sustaining ecosystem functioning, and yet, the degree to which they are influenced by human activities remains poorly understood. Our study demonstrates that wastewater discharge fundamentally reshapes the coastal ocean virome, overriding its natural seasonal variability and highlighting a profound anthropogenic influence on the distribution, host associations, and ecological roles of viral communities. These findings advance our understanding of viral dynamics in coastal marine systems and establish a critical scientific basis for evaluating how human activities alter marine microbial ecology.},
}

@article {pmid42614511,
year = {2026},
author = {Bartkova, S and Valentino, F and Saraiva, M and Duman, M and Gerilovych, A and Radosavljevic, V and de Marco, A and Saticioglu, IB and Ay, H},
title = {Assessment of water prophylaxis and biosafety in finfish aquaculture - current and emerging technologies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1841960},
pmid = {42614511},
issn = {1664-302X},
abstract = {Effective water quality management is a fundamental component of disease prevention, fish welfare, and sustainable production in finfish aquaculture. As aquaculture continues to expand to meet increasing global food demand, maintaining biosafe aquatic environments has become increasingly challenging due to production intensification, climate change, emerging pathogens, and the spread of antimicrobial resistance. While conventional approaches such as mechanical filtration, biofiltration, ultraviolet disinfection, ozonation, and water exchange remain central to water prophylaxis, increasing attention is being directed toward technologies that support earlier pathogen detection, improved risk assessment, and more targeted intervention strategies. This review examines water prophylaxis and biosafety through an integrated framework that links water quality, microbial ecology, pathogen surveillance, antimicrobial resistance, and preventive interventions. First, the biological and environmental mechanisms through which water quality influences disease susceptibility, microbiome stability, pathogen persistence, and antimicrobial resistance are evaluated. Conventional water-treatment technologies are then assessed alongside emerging approaches, including environmental DNA/environmental RNA monitoring, probiotics, phage therapy, biosensors, smart sensors, microfluidic platforms, and droplet-based molecular diagnostics. Emphasis is placed on their practical applicability, technological readiness, and suitability for different finfish production systems. The review highlights that effective biosafety management depends increasingly on integrating environmental monitoring with molecular diagnostics, risk assessment, and targeted interventions rather than relying solely on water-quality control or reactive disease treatment. Emerging technologies differ substantially in readiness, ranging from established and pilot-stage approaches to experimental technologies that require further validation before routine implementation. To support practical decision-making, the review synthesizes these technologies within an integrated water-prophylaxis and biosafety framework that links monitoring, diagnostics, risk assessment, intervention strategies, and reassessment pathways. Overall, sustainable finfish aquaculture will depend on combining conventional water-treatment infrastructure with advanced surveillance technologies and preventive biological interventions within coordinated biosafety programs. Such integration offers considerable potential to improve fish health, reduce environmental impacts, support responsible antimicrobial use, and enhance the long-term resilience of aquaculture production systems.},
}

@article {pmid42601898,
year = {2026},
author = {Iorizzo, M and Pannella, G and Succi, M and Ganassi, S and Di Criscio, D and Tedino, C and Albanese, G and De Cristofaro, A},
title = {Seasonal dynamics of the gut microbiota in Apis mellifera ligustica: a two-year longitudinal study.},
journal = {Frontiers in insect science},
volume = {6},
number = {},
pages = {1920906},
pmid = {42601898},
issn = {2673-8600},
abstract = {The honey bee gut microbiota plays a crucial role in host nutrition, immunity, and colony health, yet the relative influence of seasonal and colony-specific factors on its long-term dynamics remains incompletely understood. This study investigated temporal variation in the gut bacterial community of three Apis mellifera ligustica colonies maintained in the same apiary and monitored over two consecutive years (2022-2023). Worker bees were sampled during eight seasonal periods, and gut microbiota composition was characterized using 16S rRNA gene amplicon sequencing. Across all sampling periods, the microbiome was consistently dominated by the characteristic honey bee-associated genera Gilliamella, Snodgrassella, Bartonella, Frischella, Commensalibacter, and Lactobacillus, indicating the persistence of a conserved core bacterial community. Seasonal variation was primarily associated with changes in the relative abundance of dominant taxa rather than with major changes in community composition. In particular, Gilliamella apicola and Snodgrassella alvi exhibited complementary seasonal patterns, with Gilliamella reaching its highest abundance during autumn, particularly in autumn 2023, whereas Snodgrassella predominated during spring and winter. Alpha-diversity metrics (Observed OTUs, Chao1, Shannon, and Simpson indices) showed limited seasonal variation, whereas beta-diversity analyses detected significant differences in community composition among seasons. Principal Coordinates Analysis and PERMANOVA identified season as the factor most strongly associated with microbiome variation, while colony identity did not significantly influence bacterial community composition under the standardized experimental conditions adopted in this study. Overall, these findings show that the gut microbiome of A. mellifera ligustica maintains a conserved core bacterial community while exhibiting reproducible seasonal variation in the relative abundance of its dominant members. This study provides a longitudinal baseline for future investigations aimed at understanding the ecological mechanisms underlying seasonal microbiome dynamics and their relationship with honey bee biology and environmental change.},
}

@article {pmid42602598,
year = {2026},
author = {Apajalahti, J and Rinttilä, T},
title = {Strengths and weaknesses in techniques employed to measure the effects of dietary modulation on intestinal microbiota composition and function.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {26},
number = {},
pages = {682-698},
pmid = {42602598},
issn = {2405-6383},
abstract = {In this paper, intestinal microbial habitats in monogastric animals are discussed, with special reference to the intestinal segments of poultry. Physicochemical conditions in different segments vary and determine the selection of microbes that have nutritional and thermodynamic possibilities to thrive in the habitat. Understanding basic microbial ecology is a prerequisite for the knowledge-based development of microbiota modulating feed additives and ingredients. A prevalent research approach involves analysing intestinal parameters and calculating correlations between analytical data, animal health, and performance. However, this method cannot establish causal relationships or capture the dynamics of microbial metabolite production and their uptake by the intestinal brush border. An alternative or complementary approach is to use an ex vivo method, where the fresh, fully functional, authentic microbial community of the target intestinal segment is studied in the laboratory. For this approach to produce unbiased data, extremely careful handling of the oxygen-sensitive bacteria and precise replication of the physicochemical conditions of the target intestinal environment are critical. With such an ex vivo model, the effect of feed additives on the rate of metabolite production by the native microbiota can be accurately evaluated. All research approaches have their pitfalls, the details of which are discussed. Small methodological details can have a major impact on the reliability of the results. The most reliable approaches are unfortunately labour-intensive, and a successful outcome requires the use of multiple approaches in parallel. Although no research approach is perfect, combining multiple methods allows a comprehensive understanding to emerge gradually.},
}

@article {pmid42603915,
year = {2026},
author = {Cherinet, MT and Bereded, NK and Van de Voorde, I},
title = {Traditional Ethiopian fermented condiments: a systematic review of microbial dynamics, nutritional transformations, and future perspectives.},
journal = {Journal of food science and technology},
volume = {63},
number = {9},
pages = {1637-1647},
pmid = {42603915},
issn = {0022-1155},
abstract = {UNLABELLED: Traditional Ethiopian fermented condiments, including Siljo, Datta, Awaze, Helbat, and Azo, are culturally significant and nutritionally valuable. Despite their importance, evidence on their microbial ecology, nutritional transformations, safety, and functional potential remains fragmented and insufficiently characterized. This systematic review, conducted in accordance with PRISMA 2020 guidelines, consolidates current knowledge on the microbial dynamics, nutritional changes, probiotic traits, and food safety of these traditional Ethiopian fermented condiments. A comprehensive literature search was carried out up to December 2025 across PubMed, Scopus, Cochrane Library, Epistemonikos, and Google Scholar. Studies consistently reported that lactic acid bacteria-particularly Lactiplantibacillus plantarum, Pediococcus pentosaceus, and Weissella spp.-dominate spontaneous fermentations, driving acidification to pH values typically between 3.6 and 4.5 and contributing to pathogen suppression. Fermentation also induced product-specific nutritional transformations, including changes in protein content and digestibility, mineral dynamics, and the formation of bioactive compounds. However, outcomes varied considerably depending on substrate composition, microbial consortia, and processing conditions. Data on antinutritional factor reduction (phytates, tannins, and trypsin inhibitors) were absent across all included studies, representing a critical knowledge gap. Despite these promising attributes, research on these condiments is largely limited by reliance on culture-dependent methods, heterogeneous fermentation practices, and inconsistent analytical approaches. The evidence base for some condiments, particularly Azo and Datta, is further constrained by reliance on grey literature and secondary data sources. To fully harness their microbial, nutritional, and commercial potential, future studies should employ integrated research methodologies based on standardized fermentation protocols, metagenomics, metabolomics, and comprehensive nutritional assessments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-026-06764-y.},
}

@article {pmid42603993,
year = {2026},
author = {Elias Masiques, N and De Vrieze, J and Gansemans, Y and Deforce, D and Van Nieuwerburgh, F and De Smet, S and Van Hecke, T},
title = {Pork and salmon diets differentially modulate lipid oxidation along the gastrointestinal tract in rats, with limited effects on gut microbiota.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101517},
pmid = {42603993},
issn = {2665-9271},
abstract = {Red meat consumption has been associated with less favorable health outcomes, whereas fish intake is often considered beneficial. These differences may partly relate to variations in fatty acid composition and heme iron content, which can influence oxidative processes during digestion and thereby affect intestinal and systemic responses. This study investigated the effects of pork- and salmon-based diets, differing primarily in fatty acid profile and heme iron content but matched for macronutrient composition, on oxidative stress, gut microbiota, fermentation metabolites, and inflammation in rats. The pork-based diet supplied 2.3-fold more SFA and 14-fold more heme iron than the salmon-based diet, which in turn provided 14-fold more n-3 PUFA. Consumption of pork significantly increased propanal (+81%), hexanal (17-fold), and 4-hydroxy-2-nonenal (27-fold) in stomach contents, and elevated thiobarbituric acid reactive substances (TBARS, +45%) in plasma. In contrast, salmon consumption raised TBARS in duodenal mucosa (+19%) and C-reactive protein (+30%) in plasma. Only subtle diet-related changes were observed in gut microbiota composition and fermentation metabolites, with no difference in fecal calprotectin. A small number of discriminant taxa were identified, including Clostridioides and Muribaculum in salmon-fed rats and Eubacterium fissicatena, Sellimonas, and Dielma in pork-fed rats, while valerate levels were higher in pork-fed rats. Transcriptomic analysis revealed that no individual genes remained significant after correction for multiple testing. Overall, pork and salmon diets differentially modulated lipid oxidation along the gastrointestinal tract, whereas their effects on gut microbiota were limited.},
}

@article {pmid42608432,
year = {2026},
author = {Feng, X and Xiang-Ling, T and ZhiJie, G},
title = {Functional response of bacterial communities in surface sediments of qingshitan reservoir to anthropogenic disturbance.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42608432},
issn = {2045-2322},
mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Anthropogenic Effects ; Biodiversity ; China ; Ecosystem ; *Microbiota ; },
abstract = {This study investigated the bacterial composition in surface sediments (0-5 cm) of Qingshitan Reservoir to elucidate their ecosystem functions in response to anthropogenic disturbances. Samples were collected in July 2023 from eight ecological points representing varying disturbance levels. High-throughput sequencing revealed significant variations in bacterial community structure. Sediments from the upstream cage aquaculture area (heavily disturbed) exhibited the highest bacterial richness, diversity, and evenness, while midstream and downstream areas (lightly disturbed) showed reduced diversity and uneven community structures. The dominant bacterial phyla included Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota, with the most abundant genera being Lactobacillus, Escherichia-Shigella, Staphylococcus, Corynebacterium, and Brevibacterium.Functional predictions using PICRUSt2 indicated robust metabolic activity across all areas, particularly in amino acid metabolism within the cage aquaculture region. FAPROTAX analysis highlighted enhanced nitrate reduction in disturbed areas, suggesting a potential role in mitigating eutrophication through nitrogen cycling regulation. Additionally, BugBase identified elevated proportions of potentially pathogenic bacteria in upstream cage aquaculture and midstream residential areas, underscoring the need for targeted ecological risk management.These findings provide critical insights into the microbial ecology of Qingshitan Reservoir and its response to anthropogenic pressures, offering a scientific foundation for improving water resource utilization and ecological conservation efforts.},
}

*Geologic Sediments/microbiology
*Bacteria/classification/genetics/isolation & purification
*Anthropogenic Effects
Biodiversity
China
Ecosystem
*Microbiota

@article {pmid42608796,
year = {2026},
author = {Sahingur, SE and Grzech-Leśniak, K and Suslavich, SF and Deeb, JG},
title = {The Oral-Hepatic Axis: Epidemiological and Mechanistic Links Between Periodontal and Liver Diseases.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70159},
pmid = {42608796},
issn = {1600-0765},
abstract = {Chronic liver diseases and periodontitis are prevalent inflammatory disorders that impose substantial global health and economic burdens. Increasing evidence supports an oral-hepatic axis through which periodontal dysbiosis and chronic oral inflammation may influence hepatic homeostasis and disease progression. Epidemiologic studies have linked periodontitis with metabolic dysfunction-associated steatotic liver disease (MASLD), nonalcoholic fatty liver disease (NAFLD), viral hepatitis, cirrhosis, and hepatocellular carcinoma. Although many associations persist after adjustment for shared risk factors, including obesity, diabetes, smoking, nutritional status, and socioeconomic factors, the independent contribution of periodontitis to liver disease remains unclear. Experimental and translational studies indicate that periodontal pathogens and their virulence factors promote systemic inflammation, endotoxemia, microbial translocation, immune dysregulation, and alterations in gut microbial ecology. Nutritional factors may further influence these interactions through their effects on host immunity, inflammation, and microbial communities. Together, these mechanisms converge along the oral-gut-liver axis to activate hepatic inflammatory, oxidative stress and profibrotic pathways that contribute to steatosis, immune activation, and fibrogenesis. Emerging evidence suggests that trained immunity, driven by metabolic and epigenetic reprogramming, may represent an additional mechanism linking periodontitis and liver disease warranting future studies. Preliminary studies indicate that periodontal therapy may reduce systemic inflammatory burden and improve hepatic biomarkers; however, evidence for an effect on liver disease progression or clinical outcomes remains limited. Similarly, hepatic dysfunction may exacerbate immune dysregulation and periodontal breakdown, reinforcing an inflammatory loop. However, overall causal relationships remain to be established. This review summarizes current epidemiological, clinical, and mechanistic evidence linking periodontitis and chronic liver diseases, highlighting the oral-gut-liver axis, shared immunometabolic and nutritional pathways. Understanding these interactions shows the significance of integrated dental-medical care and opens new avenues for prevention and adjunctive therapy to sustain oral and hepatic health.},
}

@article {pmid42609601,
year = {2026},
author = {Park, MR and Bae, M},
title = {Metatranscriptomic characterization of active microbial communities in strawberry hydroponic drainage effluent.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1909518},
pmid = {42609601},
issn = {1664-302X},
abstract = {Hydroponic cultivation systems improve water and nutrient use efficiency; however, little is known about the active microbial communities inhabiting hydroponic drainage effluent. This study employed metatranscriptomic sequencing to characterize active microbial communities present in drainage effluent collected from strawberry cultivation beds within a commercial recirculating hydroponic system. Drainage effluent samples were collected during the spring and winter cultivation periods and subjected to RNA-based metatranscriptomic analysis. Following quality filtering, de novo assembly, and taxonomic classification, bacterial, fungal, and viral-associated transcripts were analyzed to characterize active microbial communities within the drainage environment. Metatranscriptomic sequencing generated 65.2 million and 53.2 million paired-end reads from the spring and winter samples, respectively. Taxonomic classification revealed distinct microbial profiles between the two analyzed drainage samples. Bacterial transcripts represented the dominant classified component in both samples. The spring sample exhibited a relatively diverse bacterial community composed of multiple taxa, whereas the winter sample was strongly dominated by Serratia marcescens and Serratia proteamaculans. Fungal community composition also differed between samples, with a greater representation of yeast-associated fungi in the winter sample. Viral-associated transcripts were detected in both samples and were primarily represented by bacteriophage-related sequences. A large proportion of transcripts remained unclassified, particularly in the spring sample, highlighting the limited representation of hydroponic drainage microorganisms in current reference databases. Although the study was limited to a single commercial production site, the findings should be interpreted as site-specific observations rather than representative characteristics of strawberry hydroponic systems in general. Nevertheless, the study provides an initial metatranscriptomic characterization of active microbial communities inhabiting strawberry hydroponic drainage effluent under commercial cultivation conditions and establishes a baseline dataset for further comparative investigations involving multiple hydroponic production systems. These findings provide baseline information on active microbial and viral assemblages associated with hydroponic drainage effluent and demonstrate the utility of metatranscriptomics for characterizing microbial communities in recirculating cultivation systems.},
}

@article {pmid42612319,
year = {2026},
author = {Zhou, T and Zhang, R and Li, L and Yu, J and Li, H and Liu, H and Zhao, Y and Wang, Y},
title = {Oligomerized flavonoid nanointerfaces regulate gastrointestinal nutrient flux and metabolic inflammation.},
journal = {Biomaterials},
volume = {337},
number = {},
pages = {124554},
doi = {10.1016/j.biomaterials.2026.124554},
pmid = {42612319},
issn = {1878-5905},
abstract = {Oral strategies for obesity and its associated metabolic dysfunction rarely coordinate nutrient digestion, microbial ecology, barrier integrity and low-grade inflammation within the gastrointestinal lumen. Here we report an interface-engineering strategy that converts flavonoid monomers into oligomerized flavonoid-derived polyphenolic nanointerfaces for local gastrointestinal regulation. Five representative flavonoids were oligomerized through an acetaldehyde-mediated reaction and assembled into carrier-free nanoparticles with clustered surface phenolic motifs. Among them, oligomeric EGCG nanoparticles (O-EGCG NPs) showed the strongest interfacial activity, outperforming monomeric EGCG and non-assembled oligomers. Mechanistic analyses showed that O-EGCG NPs non-competitively modulated α-glucosidase, α-amylase, pancreatic lipase and pancreatic cholesterol esterase through enzyme binding and conformational remodeling. After oral administration, the nanoparticles maintained gastrointestinal colloidal stability, prolonged intestinal retention and reduced postprandial carbohydrate and lipid flux in substrate and mixed-meal tolerance tests. Repeated administration in high-fat diet-fed mice attenuated body-weight gain, hepatic lipid accumulation, dyslipidaemia and insulin resistance, accompanied by changes in intestinal barrier status, inflammatory cytokines and gut microbiota composition. These findings establish oligomerized flavonoid nanoparticles as locally acting luminal nanomaterials for regulating nutrient processing and microbiota-associated metabolic inflammation.},
}

@article {pmid42613563,
year = {2026},
author = {G C, B and Wu, C},
title = {A Conditional Plasmid System for Markerless Gene Deletion in Genetically Recalcitrant Fusobacterium nucleatum subsp. animalis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3055},
number = {},
pages = {53-65},
pmid = {42613563},
issn = {1940-6029},
mesh = {*Plasmids/genetics ; *Fusobacterium nucleatum/genetics ; *Gene Deletion ; Bacterial Proteins/genetics ; Carbon-Sulfur Lyases/genetics ; Promoter Regions, Genetic ; Gene Expression Regulation, Bacterial ; Quorum Sensing/genetics ; },
abstract = {Fusobacterium nucleatum subsp. animalis (FNA) plays a prominent role in oral microbial ecology and is increasingly implicated in systemic diseases such as colorectal cancer. However, its genetic intractability has significantly hindered functional studies to understand its pathogenic mechanisms. To address this challenge, we developed a conditional plasmid system that enables efficient, markerless gene deletion in FNA strains. This system features inducible control of plasmid replication via a theophylline-responsive riboswitch regulating repA, and counterselection via the MazF toxin under the control of an anhydrotetracycline-inducible promoter. In this chapter, we provide a detailed, step-by-step protocol for implementing this system using FNA strain 7_1 as a model. We illustrate the procedure by deleting the luxS gene, which encodes S-ribosylhomocysteine lyase-an enzyme involved in AI-2 quorum sensing and biofilm regulation. Our protocol provides a powerful and adaptable tool for advancing genetic studies in this genetically recalcitrant subspecies.},
}

*Plasmids/genetics
*Fusobacterium nucleatum/genetics
*Gene Deletion
Bacterial Proteins/genetics
Carbon-Sulfur Lyases/genetics
Promoter Regions, Genetic
Gene Expression Regulation, Bacterial
Quorum Sensing/genetics

@article {pmid42597253,
year = {2026},
author = {Stefanelli, N},
title = {Gut dysbiosis and vitamin-dependent immune regulation in degenerative musculoskeletal and bone diseases.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1920962},
pmid = {42597253},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology ; Animals ; *Gastrointestinal Microbiome/immunology ; *Bone Diseases/immunology/metabolism ; Vitamin D/metabolism ; *Immunomodulation ; *Vitamins/metabolism ; },
abstract = {Degenerative musculoskeletal and metabolic bone diseases are increasingly recognized as conditions sustained not only by endocrine and mechanical factors, but also by chronic low-grade immune activation and osteo-immune imbalance. This Perspective proposes a mechanistic framework in which gut dysbiosis may contribute to skeletal degeneration through alterations in vitamin-dependent immune regulation, with particular attention to the interaction between vitamin D signaling and microbiota-derived menaquinones. Dysbiosis may impair intestinal barrier integrity and increase exposure to microbial-associated molecular patterns, thereby sustaining innate and adaptive immune activation and promoting a pro-inflammatory cytokine milieu involving IL-6, TNF-α, IL-17, and IL-1β. These pathways may promote osteoclastogenesis and disrupt bone remodeling through the RANKL/RANK/OPG axis. While the immunomodulatory role of vitamin D is well established, microbiota-derived menaquinones may represent a less explored but biologically plausible interface between microbial metabolism, inflammatory signaling, and skeletal homeostasis . However, the extent to which microbiota-derived menaquinones significantly contribute to systemic vitamin K status in humans remains controversial and incompletely characterized. Within this framework, dietary patterns are conceptualized as modulators of microbial ecology and immune activation, while microbiota-modulating strategies may indirectly influence osteo-immune balance through immune-mediated mechanisms. This Perspective integrates microbial, immunological, and vitamin-dependent pathways into an immunology-centered model of skeletal degeneration and highlights the need for studies combining microbiome profiling, immune phenotyping, vitamin-dependent signaling, and bone remodeling outcomes.},
}

Humans
*Dysbiosis/immunology
Animals
*Gastrointestinal Microbiome/immunology
*Bone Diseases/immunology/metabolism
Vitamin D/metabolism
*Immunomodulation
*Vitamins/metabolism

@article {pmid42598118,
year = {2026},
author = {Weinbren, M and Surman-Lee, S},
title = {Sanitation, antibiotics, and the end of the antibiotic era.},
journal = {Public health in practice (Oxford, England)},
volume = {12},
number = {},
pages = {100839},
pmid = {42598118},
issn = {2666-5352},
abstract = {A decade after the publication of the highly influential O'Neill report, Tackling Drug-Resistant Infections Globally, antimicrobial resistance (AMR) continues to accelerate at an unprecedented rate. Despite being a cornerstone of global AMR strategies, antimicrobial stewardship has failed to reverse this trend. This failure reflects a fundamental misunderstanding of AMR as primarily a behavioural or prescribing problem, rather than an environmental one. A major driver of AMR is environmental pollution arising from the large-scale manufacture, release, and accumulation of antimicrobial substances that profoundly disrupt microbial ecosystems. While regulatory attention has focused on antibiotic contamination of local rivers during pharmaceutical manufacturing, this represents only a small fraction of the antibiotics produced and consumed globally. Following administration, and depending on the compound, up to 90% of biologically active antibiotic may be excreted unchanged and subsequently enter healthcare wastewater systems. Healthcare wastewater systems therefore function as a superhighway for the generation, amplification, and transmission of multidrug-resistant organisms-both within healthcare facilities and into surrounding municipal infrastructure. Traditional hospital defences, including Standard Infection Control Precautions, offer limited protection against pathogens originating from wastewater environments. Within these systems, high microbial biomass is continuously exposed to complex mixtures of antimicrobials, disinfectants, and other selective agents, distorting microbial ecology and creating conditions conducive to the selection of AMR. Recognising the healthcare wastewater system as a critical driver of AMR generation and dissemination reframes the problem and opens new opportunities for intervention. Addressing this overlooked reservoir may be essential to containing a global pandemic that, despite decades of effort, shows no sign of slowing.},
}

@article {pmid42600416,
year = {2026},
author = {Lee, H and Haga, S and Roh, S},
title = {Physio-informatics linking rumen biology, systemic metabolism and meat quality in Japanese black cattle.},
journal = {Meat science},
volume = {242},
number = {},
pages = {110130},
doi = {10.1016/j.meatsci.2026.110130},
pmid = {42600416},
issn = {1873-4138},
abstract = {Japanese Black cattle (Wagyu) are raised under a distinctive long-term fattening system designed to enhance intramuscular fat (marbling) and carcass value. Because most metabolizable energy and many metabolic signals in ruminants derive from rumen fermentation products, variation in rumen microbial ecology and fermentation chemistry can extend to systemic metabolism and ultimately influence meat quality traits. Recent work in Japanese Black steers has provided a structured, multi-layered dataset spanning rumen fermentation characteristics, blood metabolites and hormones, liver transcriptome profiles, and rumen microbiome composition and predicted function across fattening stages and metabolic phenotypes. This review integrates these findings with established concepts in ruminant physiology to propose a physio-informatic framework linking rumen microbiota to hepatic metabolic regulation and adipose tissue development via the rumen-liver-adipose axis, with potential relevance to broader meat quality traits. We highlight (i) microbial succession across the three-stage feeding program, (ii) fermentation-derived short-chain fatty acids and their absorption and metabolic fates, and (iii) endocrine and transcriptional regulation of energy partitioning during fattening as an interpretable systems signal rather than a single downstream endpoint. Finally, we discuss potential analytic strategies, including longitudinal modeling, network inference, and machine learning approaches, that may support the future development of predictive biomarkers of carcass traits and intervention strategies potentially applicable to improving marbling consistency and metabolic efficiency.},
}

@article {pmid42600852,
year = {2026},
author = {Pereira, A and Royen, GV and Ganigué, R and Sakarika, M},
title = {Can microbial biomass deliver the techno-functional properties required for more sustainable, animal-free foods? A quantitative synthesis linking microbial biomass type, processing, and techno-functionality.},
journal = {Bioresource technology},
volume = {462},
number = {},
pages = {135609},
doi = {10.1016/j.biortech.2026.135609},
pmid = {42600852},
issn = {1873-2976},
abstract = {The rising population levels and shift to protein-rich diets are increasing the harmful environmental impact of conventional food systems at unprecedented levels. To circumvent the inefficiency of traditional agricultural practices, natural microbial biomass (MB) of fungi, bacteria, yeasts and microalgae, emerges as an alternative source of nutritional protein that can be converted to microbial foods, as it relies on closed-system, climate-independent and efficient production. Although the environmental and nutritional benefits are widely studied, the techno-functional properties (foaming, emulsifying, gelling, oil and water retention properties) of MB and associated ingredients (whole-cell ingredients, cell-disrupted ingredients and protein-enriched extracts) are underexplored. This review compiled the current body of knowledge on MB production processes, including bioproduction, nucleic acid reduction treatments, downstream processing (DSP) to an appealing product, and their described impact on techno-functionality, as well as compared all reported techno-functional properties of MB-based ingredients and food products. MB-based ingredients show promising techno-functional potential, especially in water and oil retention properties, and versatility compared to their plant counterparts. We identified key issues hindering MB commercialization, including the lack of standardized terminology and methodology, limited synergies between upstream and DSP, insufficient diversity in selected microbial strains, ingredient types and final applications, and lack of interdisciplinary research. Strategies to address these challenges include focusing on properties beyond macromolecular composition, using computational approaches for faster screening, and critically evaluating DSP steps. These strategies ensure that the required techno-functional and sensory properties can be achieved without compromising the potential of MB for environmental sustainability and consumer acceptance.},
}

@article {pmid42593109,
year = {2026},
author = {Ge, X and Song, J and Zhang, L and Zhang, C and Yang, Y and Kong, X and Guo, F and Pu, C},
title = {Occupational exposure to Baijiu fermentation environments alters nasal microbiota composition: a comparative analysis of Strong-flavor and Sesame-flavor production systems.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0220225},
doi = {10.1128/spectrum.02202-25},
pmid = {42593109},
issn = {2165-0497},
abstract = {UNLABELLED: Traditional Chinese Baijiu fermentation environments harbor complex microbial consortia critical for product quality, yet their effects on human nasal microbiota remain poorly characterized. This cross-sectional study compared nasal microbiota profiles of Strong-flavor (n = 25) and Sesame-flavor (n = 22) Baijiu workers against non-exposed individuals (n = 30) using 16S rRNA sequencing of environmental samples and nasal swabs. After adjusting for age and working age, no significant differences in Shannon diversity or species richness were observed among the three groups (ANCOVA, P > 0.05). However, community structure differed significantly (PERMANOVA, marginal R[2] = 0.075, P = 0.001), with Strong-flavor workers clustering closer to non-exposed individuals than Sesame-flavor workers. FEAST-based source tracking identified entry-pit fermented grains, Daqu, and air as primary contributors, accounting for 18.63% and 21.39% of nasal microbiota in Strong- and Sesame-flavor workers, respectively. ALDEx2 revealed six genera depleted in both exposed groups (FDR < 0.05): Caproiciproducens, Petrimonas, Proteiniphilum, Sporosarcina, Syntrophomonas, and an uncultured genus. No genera were significantly enriched in either exposed group. These findings indicate occupational exposure to Baijiu fermentation environments reduces the nasal carriage of several anaerobic taxa without altering overall alpha diversity.

IMPORTANCE: This study is the first to systematically compare how two major Baijiu fermentation environments-Strong-flavor and Sesame-flavor-affect the nasal microbiota of workers. By integrating environmental and nasal microbiome data, we show that entry pit grains, Daqu, and air are the main known sources of bacteria found in workers' noses. Occupational exposure in both production systems depletes several anaerobic genera, while overall microbial diversity remains unchanged. These findings connect microbial ecology with occupational health and support practical interventions: improving Daqu storage and ventilation, routine microbial surveillance, and preserving traditional fermentation practices without compromising safety. This work advances our understanding of human environment microbial exchange in traditional food systems with implications for global fermentation industries.},
}

@article {pmid42597171,
year = {2026},
author = {Wang, T and Liang, H and Wu, Y and Zhang, X and Zhang, S and Wei, Z and Li, W and Song, W and Luo, Z and Al-Dalali, S},
title = {Multi-omics profiling of microbial ecology and non-volatile compounds across fermentation stages of spontaneous litchi (Litchi chinensis Sonn.) fermented vinegar-like beverage.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1908193},
pmid = {42597171},
issn = {2296-861X},
abstract = {INTRODUCTION: Litchi fruit vinegar-like beverages (LVBs) are notable processed products derived from litchi fruit, yet few studies have focused on the systematic characterization of microbial and metabolic dynamics during their natural fermentation process.

METHODS: This work employed a comprehensive methodology integrating metagenomics and untargeted metabolomics based on UHPLC-MS/MS (Orbitrap Q Exactive HF-X) to elucidate the dynamic profiles of the microbial community and non-volatile metabolites, as well as their interrelations, across the various spontaneous fermentation stages of LVBs.

RESULTS: Metagenomic analysis indicated reduced microbial diversity and substantial structural changes within the community. Bacteria dominated the fermentation, accounting for 69.16 - 99.04% of the microbial community based on the taxonomically classified reads at the kingdom level. During the preliminary stage, Leuconostoc, Enterobacter, and Klebsiella were the prevalent genera. During the mid-fermentation stage, Komagataeibacter and Lactiplantibacillus emerged as the predominant genera in acid production. In the final stage, the microbial community was dominated primarily by Zymomonas and the Acetobacteriaceae family, including Acetobacter and Komagataeibacter. The non-targeted metabolomics study identified 2,382 metabolites through comprehensive database matching (in-house library, HMDB, KEGG, and metDNA algorithm) and stringent quality filtering (identification score > 0.5 and QC CV < 0.5), which were categorized into 20 distinct groups. Thirty seven metabolites, including amino acids, organic acids, and benzene derivatives, were identified as probable distinct differential metabolites based on a p-value threshold of p < 0.05, VIP > 1.0, and a fold change (FC ≥ 2 or ≤ 0.5) between consecutive fermentation stages in pairwise OPLS-DA of litchi vinegar-like beverage fermentation. Spearman correlation analysis revealed a highly organized ecological interaction network among dominant bacteria, physicochemical parameters, and non-volatile taste metabolites in the LVB fermentation system. Zymomonas mobilis, Acetobacter pasteurianus, Leuconostoc suionicum, and Lactiplantibacillus plantarum facilitated fermentation through metabolic synergy. Meanwhile, stage-specific enrichment of distinct Enterobacteriaceae species (Enterobacter hormaechei, and Enterobacter quasiroggenkampii) reflected species-level niche differentiation and resource competition, rather than a unified family-wide competitive behavior.

DISCUSSION: These findings provide a theoretical framework for engineering synthetic consortia and bioaugmentation approaches, informing the selection of starters and co-cultures to enhance LVB sensory and bioactive properties, alongside facilitating sfruit valorization.},
}

@article {pmid42589999,
year = {2026},
author = {Alghoul, WI and Ashraf, R and Rafiuddin, S and Kharoufeh, AZH and Al-Shammari, WBJ and Abedi, M and Alabid, I and Patni, MM and Yousef, AJ and Hamdy, HA},
title = {The Urogenital Microbiome-Metabolic Interface in Postmenopausal Recurrent Urinary Tract Infection: Estrogen Deficiency, Diabetes, Obesity, and Microbial Reservoirs.},
journal = {Journal of clinical medicine},
volume = {15},
number = {15},
pages = {},
pmid = {42589999},
issn = {2077-0383},
abstract = {Background/Objectives: Recurrent urinary tract infection (rUTI) is common after menopause, but estrogen deficiency alone does not explain variation in recurrence, symptoms, and microbial profiles. This study aimed to synthesize evidence on the interactions among estrogen deficiency, urogenital microbial ecology, diabetes, obesity, microbial reservoirs, and anatomical, neurological, and functional modifiers of postmenopausal rUTI susceptibility. Methods: PubMed and Scopus were searched for original studies published from 1 January 2021 to 15 June 2026. A structured narrative synthesis included 62 original reports comprising clinical interventions, observational cohorts, microbiome and multi-omic studies, and cellular and animal experiments. Evidence was interpreted according to study design, population relevance, and biological directness. Results: Menopause was associated with reduced Lactobacillus dominance, higher vaginal pH, and altered vaginal or urinary communities, although findings were heterogeneous. Vaginal estrogen reduced recurrence and improved the local urogenital environment, but microbiome restoration is not established as its sole mechanism. Gut, rectal, vaginal, urinary, and bladder-wall reservoirs may contribute to persistence or repeated exposure. Diabetes was linked to dysbiosis and impaired urothelial defence, whereas obesity evidence remained less direct. Pelvic organ prolapse with incomplete emptying, elevated postvoid residual urine, age-related detrusor dysfunction, stroke, immobility, functional dependence, incontinence, and catheter exposure may further modify susceptibility. Conclusions: Postmenopausal rUTI is multifactorial. The urogenital microbiome-metabolic interface is a useful integrative framework, but not a validated causal or diagnostic model. Vaginal estrogen, urine culture, metabolic and bladder-function assessment, and antimicrobial stewardship remain the clinical foundation; microbiome-directed strategies require prospective validation.},
}

@article {pmid42593046,
year = {2026},
author = {Barbi, F and Menzel, U and Simone, D and Niskanen, T and Lindahl, BD},
title = {Ectomycorrhizal Cortinariaceae species dominate class II peroxidase gene expression in a boreal forest soil.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71506},
pmid = {42593046},
issn = {1469-8137},
support = {//Sveriges lantbruksuniversitet Uppsala (SLU)/ ; //Stiftelsen skogsvetenskaplig forskning/ ; },
abstract = {Boreal forest ecosystems constitute a large terrestrial reservoir of carbon. In these nitrogen-limited environments, release of nutrients through decomposition of soil organic matter is of fundamental importance. Fungi, particularly saprotrophic Agaricomycetes, are thought to drive this process using lignocellulolytic enzymes to degrade plant litter. However, some ectomycorrhizal fungal lineages have retained ancestral decomposition capabilities, yet evidence of their direct involvement in decomposition under field conditions is scarce. We used metatranscriptomics to examine the involvement of ectomycorrhizal fungi in the production of class II peroxidases in the soil of a Swedish boreal forest. We compared nutrient-poor plots with more fertile ones and related the peroxidase-expressing community to the total and cellulose-degrading fungal communities. We found that overall expression of class II peroxidase genes was upregulated in nutrient-poor soil, with ectomycorrhizal species in the Cortinariaceae family accounting for most of the transcripts. Among cellulose-degrading fungi, there was a shift from saprotrophic Agaricomycetes in nutrient-rich soil to dominance by Ascomycetes under nutrient-poor conditions. Symbiosis may enable ectomycorrhizal fungi to use tree photoassimilates to drive energetically costly oxidation belowground. Ectomycorrhiza-driven oxidation may, thereby, enable trees to indirectly regulate decomposition and nutrient cycling to maintain ecosystem productivity on unfertile soils.},
}

@article {pmid42586669,
year = {2026},
author = {Luo, Z and Fang, Y and Qi, H and Peng, X and Zang, X and Yi, L and Zeng, J and He, L and Zeng, N},
title = {Natural polysaccharides modulate the microbiota-gut-brain axis through multiple targets: A new perspective on the pathogenesis and treatment of depression.},
journal = {Carbohydrate polymers},
volume = {389},
number = {},
pages = {125640},
doi = {10.1016/j.carbpol.2026.125640},
pmid = {42586669},
issn = {1879-1344},
mesh = {Humans ; Animals ; *Polysaccharides/pharmacology/chemistry/therapeutic use ; *Depression/drug therapy/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Brain/drug effects/metabolism ; Blood-Brain Barrier/drug effects/metabolism ; },
abstract = {Depression is increasingly understood as a systemic disorder involving microbiota-gut-brain axis (MGBA) dysfunction rather than only central monoaminergic imbalance. Gut microbial dysbiosis, barrier disruption, immune inflammation, metabolic disturbance, oxidative stress, mitochondrial injury, and impaired neuroplasticity jointly drive depressive pathology. Natural polysaccharides offer a structurally diverse class of MGBA-oriented adjunctive candidates. Their effects are governed not simply by source or total sugar content, but by monosaccharide composition, glycosidic linkages, branching architecture, and molecular-weight distribution. These features determine microbial accessibility, fermentation kinetics, metabolite output, mucus and epithelial interactions, receptor recognition, and possible epithelial uptake, thereby defining distinct routes of MGBA regulation. Through these structure-dependent routes, natural polysaccharides may alleviate depression-related abnormalities by rebuilding gut microbial ecology, reprogramming short-chain fatty acids, tryptophan-derived indoles and bile acid metabolism, restoring intestinal and blood-brain barrier integrity, suppressing neuroimmune activation and oxidative injury, supporting mitochondrial homeostasis and promoting BDNF-TrkB-related neurogenesis and synaptic plasticity. This Review highlights structure-guided MGBA modulation and discusses translational challenges, including activity attribution, quality control, pharmacokinetics, and microbiome-dependent response variability for stratified, mechanism-guided adjunctive use.},
}

Humans
Animals
*Polysaccharides/pharmacology/chemistry/therapeutic use
*Depression/drug therapy/metabolism/microbiology
*Gastrointestinal Microbiome/drug effects
*Brain/drug effects/metabolism
Blood-Brain Barrier/drug effects/metabolism

@article {pmid42587415,
year = {2026},
author = {Peluso, E and van Uden, S and Visentin, S and Petrini, P and Pacheco, DP and Visai, L},
title = {Universal-Bac[3]Gel: A 3D Biofilm-Relevant Matrix That Supports In Vitro Growth and Biofilm Formation of ESKAPE Pathogens.},
journal = {MicrobiologyOpen},
volume = {15},
number = {4},
pages = {e70371},
pmid = {42587415},
issn = {2045-8827},
support = {190135075//HORIZON-EIC-2023-ACCELERATOROPEN-01/ ; //Italian Ministry of University and Research (MUR)/ ; },
mesh = {*Biofilms/growth & development/drug effects ; Humans ; Anti-Bacterial Agents/pharmacology ; Microscopy, Confocal ; Staphylococcus aureus/growth & development/drug effects ; },
abstract = {Human microbiota is increasingly considered to shape health and disease, drawing interest of pharma and biotech industries in advanced models of in vitro human microbiome to streamline drug development. In this context, Universal-Bac[3]Gel represents a new generation of 3D biomaterials designed to mimic the properties of human mucus and biofilm features, including micro-gradients that replicate the heterogeneous environments colonized by microorganisms in the human body. To evaluate the suitability of Universal-Bac[3]Gel for studying clinically relevant species in antimicrobial resistance, the so-called ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) were cultured within this 3D environment. Bacterial growth was monitored at 24- and 48-h post-inoculation via spot plating, while viability, spatial distribution, and organization were assessed by confocal laser scanning microscopy. All ESKAPE strains successfully grew throughout the structure of Universal-Bac[3]Gel. Distinct 3D biofilm architectures were observed across species, ranging from diffuse colonization to compact microcolony formation, in agreement with species-specific biofilm patterns. Ciprofloxacin susceptibility assays revealed reduced susceptibility of bacteria cultured within Universal-Bac[3]Gel compared with their planktonic counterparts, supporting the development of biofilm-associated tolerance phenotypes. Consistent with these findings, crystal violet staining confirmed the accumulation of biofilm-associated biomass within the hydrogel. Notably, the platform's ready-to-use 96-well format allowed direct comparison of these high-priority pathogens under standardized conditions, highlighting species-specific biofilm traits that would be difficult to discern in conventional two-dimensional culture systems. This work highlights the versatility of Universal-Bac[3]Gel as a biofilm-relevant in vitro platform for studying pathogen colonization, biofilm development and antimicrobial susceptibility under controlled conditions.},
}

*Biofilms/growth & development/drug effects
Humans
Anti-Bacterial Agents/pharmacology
Microscopy, Confocal
Staphylococcus aureus/growth & development/drug effects

@article {pmid42588064,
year = {2026},
author = {De Sales-Millan, A and Reyes-Ferreira, P and González-Cervantes, RM and Luna-Álvarez, M and Guillén-López, S and Cobo-Díaz, JF and Ramos, S and Aguirre-Garrido, JF and Velázquez-Aragón, JA},
title = {Clinical Improvement and Taxonomic-Functional Gut Microbiome Remodeling After Six Months of Multi-Strain Synbiotic Supplementation in Mexican Children with Autism Spectrum Disorder.},
journal = {Nutrients},
volume = {18},
number = {15},
pages = {},
pmid = {42588064},
issn = {2072-6643},
support = {E022 Program Recursos Fiscales para la Investigación//Instituto Nacional de Pediatria/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Mexico ; Longitudinal Studies ; *Synbiotics/administration & dosage ; Child ; Feces/microbiology ; Child, Preschool ; Probiotics/administration & dosage ; Dietary Supplements ; Treatment Outcome ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; },
abstract = {Background/Objectives: Gut dysbiosis in children with autism spectrum disorder (ASD) has been associated with alterations in microbial ecology and metabolic function that may contribute to gastrointestinal dysfunction and the severity of clinical manifestations. Synbiotic and probiotic supplementation has emerged as a promising microbiome-targeted strategy for ASD; however, its effects on gut microbiome composition, functional potential, and clinical outcomes remain incompletely understood. We conducted a longitudinal study of Mexican children diagnosed with ASD to analyze changes in the composition, diversity, and functional potential of the gut microbiome during six months of multi-strain synbiotic supplementation. Methods: Stool samples were collected from 25 children with ASD at baseline and after 3 and 6 months of multi-strain synbiotic supplementation. Gut microbiome composition and diversity were analyzed by 16S rRNA gene sequencing, whereas whole metagenome sequencing (WMS) was performed in a subset of samples to evaluate the functional potential of the fecal microbiome. Gastrointestinal symptoms were assessed using the Rome IV criteria, and ASD severity was evaluated with the Childhood Autism Rating Scale (CARS). Results: Twenty-five children with ASD completed the 6 months of synbiotic supplementation. Overall, ASD severity decreased, reflected by a reduction in total CARS score, and improvements in several CARS domains. Gastrointestinal symptoms also decreased significantly. Longitudinal microbiome profiling revealed significant taxonomic and diversity changes over the supplementation period, while WMS identified changes in microbial metabolic potential, including enrichment of tryptophan biosynthesis pathways and reduced L-rhamnose degradation. Conclusions: This exploratory research provides proof-of-concept evidence supporting multi-strain synbiotic supplementation in children with ASD. Larger controlled studies are needed to confirm these findings and clarify their relevance to microbiota-gut-brain axis interactions. The observed concordance between clinical improvements and microbiome remodeling supports further investigation of microbiome-targeted interventions according to ASD severity and duration of supplementation.},
}

Humans
*Autism Spectrum Disorder/microbiology/therapy
Male
*Gastrointestinal Microbiome/genetics
Female
Mexico
Longitudinal Studies
*Synbiotics/administration & dosage
Child
Feces/microbiology
Child, Preschool
Probiotics/administration & dosage
Dietary Supplements
Treatment Outcome
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology

@article {pmid42588172,
year = {2026},
author = {Wu, Y and Zhao, Y and Yao, W and Yang, Y and Bai, H and Bao, S and Li, X and Song, Y},
title = {Gut-Liver Axis Dysfunction in Alcohol-Associated Liver Disease and the Potential Role of Sheep Yogurt: A Scoping Review and Mechanistic Framework.},
journal = {Nutrients},
volume = {18},
number = {15},
pages = {},
pmid = {42588172},
issn = {2072-6643},
support = {2026KJTW0005//Inner Mongolia Autonomous Region's "Tech Breakout" Initiative: "Open Call for Technical Champions"/ ; No.10000-A22103030//2022 Inner Mongolia University "Steed Plan" high-level talent funding/ ; 2022YFD1302202//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Yogurt/microbiology ; *Liver Diseases, Alcoholic/physiopathology/microbiology ; Sheep ; *Liver/physiopathology ; Humans ; Intestinal Barrier Function ; Gastrointestinal Microbiome ; },
abstract = {Background/Objectives: Alcohol-associated liver disease (ALD) is driven by gut-liver axis dysfunction, including intestinal barrier disruption, dysbiosis, microbial translocation, inflammation, metabolic dysfunction, and malnutrition. Fermented dairy foods may modulate several of these domains, yet whether sheep yogurt, as an intact fermented dairy matrix, is relevant in ALD is unknown. This scoping review mapped evidence relevant to sheep yogurt, ALD, and gut-liver axis biology. Methods: A PRISMA-ScR-guided scoping review searched PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar from January 2006 to February 2026. Eligible sources were charted using a prespecified framework classifying evidence as direct, indirect, or mechanistic inference. Mapped domains included ALD pathophysiology; intestinal barrier integrity; bacterial and fungal microbial ecology; bile acid and tryptophan-aryl hydrocarbon receptor signaling; nutritional vulnerability; fermented dairy interventions; and ovine dairy-matrix characteristics. Results: Of 1388 records identified, 121 sources were included after duplication and screening. No eligible study directly tested sheep yogurt or a defined sheep yogurt preparation in ALD-relevant experimental or clinical settings. Indirect evidence supported the relevance of gut-liver axis dysfunction to ALD and indicated that selected fermented dairy products, probiotics, postbiotics, and microbial preparations may influence intestinal permeability, inflammatory signaling, microbial ecology, oxidative stress, and liver-injury outcomes. Compositional data supported sheep yogurt as a distinct food matrix. However, findings from isolated components, probiotic-only interventions, and non-ALD models could not be interpreted as evidence of sheep yogurt efficacy in ALD. Conclusions: The current literature supports a hypothesis-driven research framework rather than any therapeutic claim for sheep yogurt in ALD. Any potential benefit of sheep yogurt in ALD remains hypothetical and cannot support clinical or dietary recommendations until validated experimentally. Future direct, comparator-controlled studies of intact sheep yogurt should assess liver injury, barrier integrity, microbial translocation, relevant metabolites, and nutrition-related outcomes.},
}

Animals
*Yogurt/microbiology
*Liver Diseases, Alcoholic/physiopathology/microbiology
Sheep
*Liver/physiopathology
Humans
Intestinal Barrier Function
Gastrointestinal Microbiome

@article {pmid42589861,
year = {2026},
author = {Butera, A and Maiorani, C and Scribante, A and Rodriguez Y Baena, R and Cucinella, L and Parrotta, GE and Nappi, RE},
title = {Oral Health Across the Menopausal Transition: Biological Pathways, Clinical Implications, and Future Perspectives.},
journal = {Journal of clinical medicine},
volume = {15},
number = {15},
pages = {},
pmid = {42589861},
issn = {2077-0383},
abstract = {Background/Objectives: Menopause is a complex physiological transition characterized by progressive estrogen deficiency and systemic biological changes that can affect multiple organs and tissues, including the oral cavity. Growing evidence suggests that hormonal fluctuations during the menopausal transition may influence periodontal health, salivary function, oral sensory perception, and overall oral health-related quality of life. Objective: This narrative review aims to provide a comprehensive overview of the biological mechanisms and clinical manifestations associated with the relationship between menopause and oral health, with particular attention to periodontal outcomes, salivary changes, oral discomfort, dental status, and the potential role of hormone replacement therapy (HRT). Methods: This narrative review was based on a structured literature search conducted in PubMed/MEDLINE and Scopus to identify studies published between January 2005 and May 2026. Predefined eligibility criteria were applied to identify relevant human studies. The retrieved evidence was synthesized narratively according to major oral health domains and menopausal phenotypes. Results: Fifty studies met the inclusion criteria. Overall, menopause was associated with poorer periodontal parameters, including increased probing depth, clinical attachment loss, and periodontal inflammation. Reduced salivary flow, dry mouth, altered salivary composition, burning symptoms, and taste disturbances were frequently reported in peri- and postmenopausal women. A higher prevalence of caries and tooth loss was also reported, although the contribution of age and other confounding factors varied across studies. New evidence suggests that estrogen deficiency may influence oral health through interconnected pathways involving immune regulation, bone metabolism, salivary gland function, and host-microbiome interactions. Evidence regarding the effects of HRT has been mixed, although several studies have reported improvements in salivary function and periodontal outcomes among treated women. Conclusions: Menopause appears to act as an important systemic modifier of oral health through multifactorial biological mechanisms. Menopause-associated oral manifestations go beyond local tissue changes and reflect broader interactions between hormonal status, inflammation, bone metabolism, and microbial ecology. Increased awareness among dental and medical professionals and a multidisciplinary approach could improve the prevention, diagnosis, and management of oral diseases in postmenopausal women. Further, well-designed longitudinal studies are needed to clarify causal relationships and identify effective therapeutic strategies.},
}

@article {pmid42576889,
year = {2026},
author = {O'Doherty, KC and Beijbom, M and Allen-Vercoe, E and Choudoir, MJ and Silva, DS and Bonilla, C and Debelius, J and Elton, S and Hauptmann, AL and Heyland, A and Morar, N and Skillings, D and Sun, Z and Wolf, PG and Beiko, RG and Ishaq, SL},
title = {Microbiome stewardship: definition and guiding principles for implementation.},
journal = {Sustainable microbiology},
volume = {3},
number = {3},
pages = {qvag028},
pmid = {42576889},
issn = {2755-1970},
abstract = {Microbiomes are essential for ecosystem, plant, animal, and human health. There is accumulating evidence that changes to microbiomes from anthropogenic activities are associated with adverse health outcomes. Despite this evidence and calls for action, almost no oversight mechanisms exist to protect microbiomes or their key functions, in part due to uncertainty about what to protect, and how. We have previously proposed microbiome stewardship as a foundational concept that can act across policy domains to facilitate the ongoing presence of key microbial communities and their functions. The purpose of this article is to provide a working definition of microbiome stewardship and develop guiding principles to support its implementation. The concept of microbiome stewardship is relevant to a wide range of policy domains, such as public health, clinical care, environmental protection, food production, and agriculture. Nonetheless, the implementation of microbiome stewardship will be highly specific, as it needs to be guided by considerations of microbial habitat, objectives of stewardship, and available opportunities for intervention. Accordingly, aligning stewardship responsibility with specific institutions and governance mechanisms will be context-dependent. We conclude with a discussion that situates microbiome stewardship relative to other initiatives.},
}

@article {pmid42576913,
year = {2024},
author = {Peixoto, R and Voolstra, CR and Stein, LY and Hugenholtz, P and Salles, JF and Amin, SA and Häggblom, M and Gregory, A and Makhalanyane, TP and Wang, F and Agbodjato, NA and Wang, Y and Jiao, N and Lennon, JT and Ventosa, A and Bavoil, PM and Miller, V and Gilbert, JA},
title = {Microbial solutions must be deployed against climate catastrophe.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae029},
pmid = {42576913},
issn = {2755-1970},
}

@article {pmid42576914,
year = {2024},
author = {Beattie, GA and Cotrufo, FM and Crowther, TW and Edlund, A and Salles, JF and Gilbert, JA and Jansson, JK and Jensen, PR and Lennon, JT and Makhalanyane, T and Martiny, JBH and Newman, DK and Stevenson, M},
title = {Soil microbial strategies for climate mitigation-report from a climate action workshop in Las Vegas, Nevada, February 2024.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae033},
pmid = {42576914},
issn = {2755-1970},
abstract = {Life on Earth faces an existential crisis due to the enduring repercussions of unsustainable human activities since the beginning of the Industrial Revolution. Among the most pressing issues are greenhouse gas emissions, primarily from fossil fuel combustion, unsustainable agricultural practices, as well as the global erosion of the world's topsoil. While agrochemicals have temporarily increased land productivity, their frequent use has adversely impacted the environment and microbial biodiversity. With half of the global soils already degraded by erosion and a projected 90% at risk by 2050, humanity faces a critical crisis that threatens food production, soil carbon storage, and availability of clean water. In this precarious scenario, microbes and plants may provide promising allies for sustaining life on Earth. Thus, it is crucial for policymakers, scientists, NGOs, and the public to recognize the fundamental importance of the soil microbiome. In February 2024, the workshop "Soil Microbial Strategies for Climate Mitigation" gathered world-leading experts from the most relevant research fields, as well as industry innovators, communicators, artists, and policymakers, to propose soil microbiome-based interventions aimed at enhancing carbon dioxide (CO2) drawdown and mitigating soil erosion. The workshop focused on innovative soil microbial inoculant approaches, examining methodologies for measuring soil carbon, enhancing plant health and soil structure, proposing an action plan, and forming collaborative strategies.},
}

@article {pmid42576937,
year = {2025},
author = {Prescott, SL and Logan, AC and Robinson, JM},
title = {Legalomics: why microbiology matters to the promotion of just societies.},
journal = {Sustainable microbiology},
volume = {2},
number = {4},
pages = {qvaf027},
pmid = {42576937},
issn = {2755-1970},
abstract = {Despite profound socioeconomic and ecological consequences, criminal justice remains an overlooked dimension of sustainability. Sustainable Development Goal (SDG) 16 calls for promoting inclusive societies and ensuring justice for all. Yet the SDG 16 framework largely ignores the biological and structural determinants of behavior related to justice involvement. This perspective article argues that microbial ecology plays a foundational role in cognition and behavior-factors central to justice outcomes. Advances in neuromicrobiology and omics technologies show how microbial disruptions linked to poverty and environmental factors may increase behavioral risks and reinforce inequality. We introduce the legalome concept-the systemic application of microbiome sciences and related omics technologies to forensic and legal psychology. From auto-brewery syndrome to microbial signatures tied to aggression, impulsivity, and neuropsychiatric conditions, evidence is mounting that microbiota-brain interactions have forensic relevance. Yet justice systems often remain rooted in prescientific notions of free will and blame. Carceral institutions often exacerbate dysbiosis through poor nutrition, social isolation, circadian disruptions, acoustic stress, and overall deprivation-further entrenching risk and undermining rehabilitation. We argue that SDG 16 should expand to reflect this evolving science. Integrating microbial ecology into justice reform offers a framework for prevention and healing-bridging sustainability, equity, and dignity.},
}

@article {pmid42577533,
year = {2026},
author = {Dlakić, M and Inskeep, WP},
title = {Improved prediction of microbial optimal growth temperatures with neural networks and protein language models.},
journal = {Frontiers in genetics},
volume = {17},
number = {},
pages = {1874451},
pmid = {42577533},
issn = {1664-8021},
abstract = {INTRODUCTION: Temperature is one of the strongest selective forces that determines the composition of microorganisms in the environment. Structural properties of proteins shape the thermal adaptation of an organism at the macro level, and aggregate protein features can be used for many types of predictions. Because most microorganisms remain uncultured, the inference of physiological traits, such as optimal growth temperature, has become essential for microbial ecology and biotechnology.

METHODS: A large dataset of optimal growth temperatures for microorganisms was compiled from the literature and used to train several machine learning predictors. Our goal was also to test the usefulness of protein language models and to evaluate predictive performance on incomplete genomes.

RESULTS: We confirmed a strong correlation between protein sequence properties and optimal growth temperatures. The analysis showed that calculating better protein sequence features, specifically through protein language models, leads to more accurate predictions.

DISCUSSION: We used state-of-the-art tools and compared our models with several others developed for optimal growth temperature prediction over the past 2 decades. Our models showed excellent ability to generalize across a range of temperatures. We concluded that larger datasets and increased representation of psychrophiles and thermophiles will be needed to continue improving the predictors.},
}

@article {pmid42580912,
year = {2026},
author = {Buret, AG and Allain, T},
title = {The Giardia secretome disrupts gut microbiota biofilms.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.07.011},
pmid = {42580912},
issn = {1471-5007},
abstract = {This review provides a state-of-the-art update on Giardia intestinalis pathogenesis and its immunomodulatory effects during enteric coinfections. We examine mechanisms underlying abnormalities in mucus structure and glycosylation, alongside parasite-induced alterations in host immunity. Recent evidence reveals a protective role for gut microbiota biofilms and demonstrates how the Giardia secretome disrupts these communities. In particular, trophozoite-derived cysteine proteases and extracellular vesicles, along with their small RNA cargo, remodel microbiota biofilms and drive the conversion of commensal bacteria into invasive pathobionts. Collectively, these findings establish Giardia as a central regulator of gut microbial ecology and intestinal barrier function, highlighting its value as a model for developing novel therapeutic strategies against enteric disease.},
}

@article {pmid42585229,
year = {2026},
author = {Fellows Yates, JA and Hübner, A and Borry, M and , and Warinner, C},
title = {De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.},
journal = {PLoS computational biology},
volume = {22},
number = {8},
pages = {e1014591},
doi = {10.1371/journal.pcbi.1014591},
pmid = {42585229},
issn = {1553-7358},
mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome/genetics ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Humans ; },
abstract = {Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both sequencing methods and de novo assembly techniques have not only resulted in a flood of modern metagenomic sequencing data, but they have also allowed palaeogenomicists to retrieve vast amounts of ancient DNA from past microorganisms, including species and strains without modern reference genomes. However, the degraded nature of ancient DNA means that the standard techniques of genome assembly developed for modern DNA are unlikely to perform effectively, unless heavily modified. This hinders the incorporation of ancient data into broader metagenomic studies that would otherwise benefit from having deep time information on the evolution of different microbial species. In this primer and protocol paper, we provide guidance on ways to adapt existing metagenomic de novo assembly processes, including data input, tools, and settings, in order to perform more robustly and effectively on ancient DNA. After assembly, we then further describe how ancient DNA contigs can be identified and validated. The key steps of ancient metagenomic assembly are now integrated in a dedicated ancient DNA mode in the established pipeline nf-core/mag. By introducing support for ancient DNA data in nf-core/mag, we aim to improve the ability of researchers to more regularly integrate de novo assembled ancient microbial data into broader metagenomics studies of microbial ecology and evolution.},
}

*DNA, Ancient/analysis
*Metagenomics/methods
*Metagenome/genetics
*Sequence Analysis, DNA/methods
Computational Biology/methods
Software
Humans

@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.},
}