@article {pmid41754095,
year = {2026},
author = {Mafe, AN and Büsselberg, D},
title = {The Diet-Microbiota-Polyamine Axis in Intestinal Aging: Microbial Pathways, Functional Foods, and Physiological Implications.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754095},
issn = {2072-6643},
support = {NPRP 14S0311-210033//Qatar National Research Fund/ ; },
abstract = {Intestinal aging is characterized by a gradual decline in epithelial renewal capacity, barrier function, immune balance, and metabolic regulation, often accompanied by shifts in gut microbial composition. Polyamines, including putrescine, spermidine, and spermine, are vital microbial-host metabolites that support intestinal cell growth, autophagy, immune modulation, and mucosal repair. With advancing age, both host-derived and microbiota-mediated polyamine production declines, contributing to intestinal dysfunction and heightened vulnerability to inflammation and age-related disorders. This review explores the diet-microbiota-polyamine axis as a key biological framework influencing intestinal aging. It aims to integrate evidence on how dietary components and functional foods shape gut microbial ecology and, in turn, regulate microbial polyamine biosynthetic pathways that impact intestinal health. The review highlights major microbial contributors to polyamine metabolism, particularly lactic acid bacteria, and outlines mechanistic pathways linking polyamines to epithelial regeneration, inflammatory control, and gut barrier maintenance. It further discusses how age-associated dysbiosis disrupts these interactions and evaluates nutritional and microbial-based strategies such as fermented foods, prebiotics, and probiotics that may enhance polyamine availability and restore gut homeostasis. From the standpoint of food microbiology and human physiology, this synthesis underscores the translational potential of targeting microbial polyamine production through diet-based interventions. This article presents a narrative review synthesizing experimental, animal, and emerging human evidence on microbial and dietary polyamines in intestinal aging. In conclusion, modulating the diet-microbiota-polyamine axis represents a promising strategy to promote healthy intestinal aging, meriting deeper mechanistic exploration and validation through clinical studies.},
}

@article {pmid41753780,
year = {2026},
author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Dass, SC},
title = {Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753780},
issn = {2076-2607},
support = {2020-67017-30776//USDA-NIFA/ ; },
abstract = {Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage-bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction-modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria-phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms.},
}

@article {pmid41753774,
year = {2026},
author = {Dobrzyński, J and Naziębło, A and Kulkova, I and Szpytma, M and Antosik, A and Sitarek-Andrzejczyk, M and Wróbel, B},
title = {Paenibacillus-Pseudomonas Consortium Improves Barley Performance with Minimal Impact on Native Rhizobacterial Community.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
pmid = {41753774},
issn = {2076-2607},
abstract = {The intensive use of mineral nitrogen fertilizers in cereal production contributes to environmental degradation, highlighting the need for more sustainable crop management strategies. Plant growth-promoting bacteria (PGPB) offer a promising alternative; however, their effects on native rhizosphere communities remain underexplored, particularly in barley. This study evaluates the impact of a bacterial consortium composed of Paenibacillus sp. Z15 and Pseudomonas sp. KR227 on barley growth, yield, and rhizosphere bacteria under field conditions in temperate climate (2025). Plant biometric traits, photosynthetic pigment content, and soil properties were measured, and rhizobacterial communities were analyzed using 16S rRNA gene (V3-V4) sequencing. The PGPB consortium significantly increased early root biomass (120%), shoot height (7.8%), and grain yield (15.5%), while no significant effects were observed on soil chemistry or photosynthetic pigments. Sequencing revealed no major changes in alpha or beta diversity; however, transient shifts in the relative abundance of specific taxa were detected relatively shortly after inoculation and mostly disappeared by harvest. These findings indicate that the Paenibacillus-Pseudomonas consortium can enhance barley performance without disrupting native rhizobacterial communities. Overall, the results support the potential of PGPB as a sustainable agronomic tool and provide new insights into PGPB-microbiome interactions in barley under field conditions.},
}

@article {pmid41753768,
year = {2026},
author = {Frantz, CM and Crump, BC and Carpenter, S and Firth, E and Orellana, MV and Light, B and Junge, K},
title = {Microbial Ecology of Rotten Sea Ice: Implications for Arctic Carbon Cycling with Global Warming.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020482},
pmid = {41753768},
issn = {2076-2607},
support = {1656026//USA National Science Foundation/ ; PLR-1304228//USA National Science Foundation/ ; },
abstract = {"Rotten" sea ice, ice in an advanced stage of melt, represents an important but understudied habitat in the rapidly changing Arctic. As Arctic warming accelerates, this late-season ice type will become more prevalent, yet little is known about its microbial inhabitants or their roles in Arctic marine biogeochemical cycles. We examined microbial communities (prokaryote and algal abundance, 16S and 18S rRNA gene and transcript sequencing) and biogeochemical properties of rotten sea ice and earlier-season ice near Utqiaġvik, Alaska, USA. Rotten ice was comparatively warm, isothermal, and largely drained of brine, with extensive, interconnected pore networks linked to melt ponds above and seawater below. Unlike earlier-season ice, fluids saturating rotten ice were vertically homogeneous in pH, dissolved inorganic carbon, prokaryote and phytoplankton abundance, and microbial community composition. However, particulate carbon and nitrogen exhibited strong vertical gradients, with the highest concentrations near the surface. Microbial communities in rotten ice were significantly different from those in earlier-season ice and varied between individual floes. These findings indicate that rotten ice constitutes a distinct microbial habitat and may serve as an important source of nutrient-rich particulate matter in the future Arctic Ocean during the summer melt season.},
}

@article {pmid41753753,
year = {2026},
author = {Lerner, A and Lieber, AD and Nelson-Dooley, C and Leu, A and Perro, M and Koch, G and Benzvi, C and Smith, J},
title = {Genetically Modified Microorganisms: Risks and Regulatory Considerations for Human and Environmental Health.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020467},
pmid = {41753753},
issn = {2076-2607},
abstract = {Advances in affordable genetic engineering have accelerated the creation and large-scale environmental release of genetically modified microorganisms (GMMs). While beneficial applications exist, GMMs may present unique, long-term risks to human and environmental health. Unlike static chemicals, GMMs are biologically active, self-replicating entities capable of rapid mutation and global dispersal. Current regulatory frameworks place responsibility on each country to regulate GMMs, without a clear, coordinated international policy. This review details critical risk scenarios, including horizontal gene transfer to native species and the possible disruption of vital human microbiomes (gut, oral, and infant), which could increase resistance to degradation, promote traits that expand a microbe's range of hosts or ecological niches, and enhance the production of novel metabolites with unexpected biological activity. In soil, GMMs may support the emergence of "super bugs" or destabilize carbon sequestration cycles, potentially impacting climate resilience. Engineered microbial enzymes in the food supply may also act as environmental drivers of autoimmunity. Given the limited understanding of microbial ecology, we propose a decision-based biosafety workflow emphasizing pre-release risk assessment and continuous post-release monitoring. We urge national and international regulators to adopt the precautionary principle to better protect human health and the environment from the potential negative outcomes of GMMs.},
}

@article {pmid41753641,
year = {2026},
author = {Pérez-García, LA and Sáenz-Mata, J and Fortis-Hernandez, M and Preciado-Rangel, P},
title = {Plant Growth-Promoting Rhizobacteria as a Strategy to Enhance Enzymatic and Metabolic Tolerance of Cucumis sativus L. Under Salinity Stress.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020351},
pmid = {41753641},
issn = {2076-2607},
abstract = {Cucumis sativus L., a salt-sensitive horticultural crop, is severely affected by soil salinity, which disrupts photosynthetic efficiency and metabolic homeostasis. This study quantified the effects of Plant Growth-Promoting Rhizobacteria (PGPR)-Pseudomonas paralactis, Bacillus cereus, Sinorhizobium meliloti, and Acinetobacter radioresistens-on key enzymatic indicators of cucumber seedlings exposed to 0, 50, 100, and 150 mM NaCl. PGPR inoculation significantly enhanced bacterial stress-mitigation and hormonal pathways, with ACC-deaminase activity increasing by up to 78.8% (A. radioresistens, 150 mM NaCl) and nitrilase activity by 50.5% (S. meliloti, 50 mM NaCl). Auxin-related pathways were strongly induced, as reflected by increases of up to 51.1% in the IAM pathway (P. paralactis) and 42.9% in the IPA pathway (A. radioresistens). In plant tissues, key metabolic enzymes exhibited high stability under salinity, with ProDH and NDPK activities increasing by up to 4.5% and 2.35%, respectively, while RuBisCO activity remained unaffected across treatments. These results demonstrate that PGPR function as effective bioestimulants by coordinating hormonal regulation and metabolic resilience, providing a sustainable biotechnological strategy to enhance cucumber tolerance to salinity stress.},
}

@article {pmid41751059,
year = {2026},
author = {Tapingkae, W and Srinual, O and Srinual, P and Khamtavee, P and Pintalerd, N and Chaiyaso, T and Yachai, M and Tapingkae, T and Kanmanee, C},
title = {Dietary Coffee Silverskin Supplementation: Effect on Growth Performance, Carcass Traits, and Gastrointestinal Health of Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/ani16040598},
pmid = {41751059},
issn = {2076-2615},
support = {FF66/045//Fundamental Fund 2023, Chiang Mai University/ ; },
abstract = {Coffee silverskin (CSS) remains a neglected poultry additive; investigating its bioactive potential is essential for optimizing agricultural productivity and enhancing food security via advanced nutrition. This study analyzed how dietary CSS supplementation influences broiler growth, slaughter characteristics, meat quality, cecal microbial ecology, and intestinal histomorphology. A total of 400 one-day-old male Ross 308 broilers were randomly assigned to four dietary treatments with 10 replicates of 10 birds each. Experimental treatments consisted of a negative control (NC, basal diet) and CSS-supplemented groups (0.5, 1.0, and 2.0 g/kg, designated CSS0.5, CSS1.0, and CSS2.0, respectively). All data were subjected to one-way ANOVA using the procedure of SPSS 23.0. Coffee silverskin supplementation, specifically at 1.0-2.0 g/kg, optimized broiler growth performance, significantly elevating body weight and average daily gain (p < 0.05). While carcass yield improved in a dose-dependent manner, fundamental meat quality-pH and shear force-remained stable. Crucially, CSS inclusion reconfigured cecal ecology, selectively suppressing Escherichia coli and Salmonella sp. while enhancing Lactobacillus populations (p < 0.001). This microbial shift mirrored histological gains, notably enhanced villus height and villus height-to-crypt ratios (p < 0.05). These findings demonstrate that CSS, particularly at 1.0-2.0 g/kg, enhances broiler performance, carcass quality and gut health.},
}

@article {pmid41750824,
year = {2026},
author = {Oh, SC and Lee, SJ and Ding, K and Shen, J and Huang, C and Kang, SN and Reaney, MJT and Kim, YJ and Shim, YY},
title = {Kimchi Fermentation-Driven Detoxification of Flaxseed: Impact on Physicochemical Quality and Antioxidant Potential.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/foods15040632},
pmid = {41750824},
issn = {2304-8158},
support = {RS-2023-00263064//Ministry of Science and ICT/ ; },
abstract = {Flaxseed (Linum usitatissimum L.) is a rich source of α-linolenic acid (ALA) and lignans but contains toxic cyanogenic glycosides (CGs) that limit its application in foods. This study investigated the efficacy of a specialized Lactobacillaceae consortium in detoxifying flaxseed and the subsequent effects of adding this cyanogenic glycoside-depleted flaxseed (CGDF) to a kimchi matrix. Ground flaxseed and CGDF were added to the kimchi seasoning mixture at concentrations of 0.5%, 1.0%, and 2.0% (w/w) and fermented at 4 °C for 8 weeks. Analytical results confirmed that the fermentation process reduced linustatin and neolinustatin to undetectable levels (<500 mg/kg) and reduced total hydrogen cyanide (HCN) to below the Japanese regulatory limit of 10 mg/kg established under the Food Sanitation Act. During fermentation, CGDF-supplemented groups exhibited a delayed decrease in pH and higher retention of free sugars and vitamin C compared to the control and raw flaxseed groups. Notably, the 2.0% CGDF group maintained high oxidative stability of ALA, which we attribute to a putative antioxidant protection mechanism driven by the bioconversion of lignan glycosides into bioactive aglycones. These findings suggest that incorporating biologically detoxified flaxseed into kimchi creates a functional food system that ensures safety while enhancing nutritional stability. Overall, this work provides foundational evidence for developing safe, nutritionally enhanced functional foods within the One Health framework, integrating food safety, microbial ecology, and improved bioactive compound availability.},
}

@article {pmid41750446,
year = {2026},
author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Ferrante, M and Agodi, A},
title = {The Wastewater Resistome: A Shotgun Metagenomics Analysis of Urban Treatment Plants in Sicily.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/antibiotics15020148},
pmid = {41750446},
issn = {2079-6382},
support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) in wastewater represents a valuable reservoir of information for wastewater-based epidemiology (WBE) and a major environmental and public health concern, as wastewater treatment plants (WWTPs) are recognized hotspots for the accumulation and dissemination of antimicrobial resistance genes (ARGs). Within the One Health framework, and to better understand the contribution to AMR spread and the potential of metagenomic surveillance, this study aimed to characterize the taxonomic, functional, and resistome profiles of three WWTPs in Sicily, specifically those located in Catania, Giarre, and Syracuse. Methods: Sixty-nine composite influent samples were collected between February 2022 and December 2023. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq platform. Bioinformatic analyses were conducted to assess microbial community composition, functional pathways, and ARG prevalence across sites. Results: Dominant genera included Aliarcobacter, Bacteroides, and Acinetobacter. Site-specific taxonomic variations reflected differences in local microbial ecology. Functional profiling revealed enrichment in membrane-associated, ribosomal, and energy metabolism pathways, consistent with the expected functional redundancy of wastewater microbiomes. Resistome analysis detected a diverse and ubiquitous array of ARGs, dominated by β-lactam and macrolide resistance genes, followed by aminoglycoside, sulphonamide, and tetracycline classes. Conclusions: These findings highlight urban wastewater as a relevant reservoir and dissemination route for AMR and support the integration of metagenomic approaches into wastewater surveillance programs. By providing region-specific, integrated taxonomic, functional, and resistome data from Sicilian WWTPs, this study contributes to the growing body of evidence supporting WBE as a valuable tool for AMR monitoring and One Health-oriented risk assessment.},
}

@article {pmid41749772,
year = {2026},
author = {Shang, J and Dong, C and Zhou, Q and Chai, J and Wei, Y},
title = {The Bacteriophage VMY 22 Has Enhanced the Stability of Its Functional Proteins via Adaptive Evolution in a Temperature-Varying Environment.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/bioengineering13020233},
pmid = {41749772},
issn = {2306-5354},
abstract = {Temperature fluctuations strongly affect microbial viability, often inducing adaptive responses. In this study, we employed the psychrophilic bacterium Bacillus mycoides 41-22 and its associated phage VMY22, originally isolated from the Mingyong Glacier, to investigate phage adaptability under varied temperature conditions. Through selective enrichment at 4 °C, 15 °C, 28 °C, and 32 °C, we observed clear differences in phage infectivity, as assessed by plaque assays, along with genomic mutations and protein structural changes. Notably, mutations predominantly occurred in functional genes (ATPase, endolysin), while the examined structural loci remained conserved. Homology modeling revealed distinct adaptations in protein tertiary structures corresponding to environmental temperatures, suggesting that phage evolution mainly affects post-adsorption processes. Our findings elucidate a novel mechanism of temperature-driven functional protein evolution among cold-adapted bacteriophages (phage) and providing insights into their potential applications in microbial ecology and biotechnology.},
}

@article {pmid41748761,
year = {2026},
author = {de Lima, LVA and da Silva, MF and de Oliveira, LM and de Assis, MCT and Carvalho, ICO and Fuzinatto, IM and Semprebon, SC and de Oliveira Nocetti, RV and Lazarin-Bidoia, D and Nakamura, CV and Felicidade, I and Lepri, SR and Favaron, PO and Dealis, ML and Cabeça, LF and Filho, GA and Mantovani, MS},
title = {PEGylated liposomal fluopsin C triggers cuproptosis and ferroptosis pathways and suppresses 3D tumor spheroid growth in NCI-H460 cells.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
pmid = {41748761},
issn = {1432-0738},
}

@article {pmid41747730,
year = {2026},
author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C},
title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.01.021},
pmid = {41747730},
issn = {1097-4172},
abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.},
}

@article {pmid41746386,
year = {2026},
author = {Wang, Z and Wang, Q and Liu, Y and Du, W and Hong, L and Zhou, D and Asiegbu, FO and Wu, P and Ma, X and Wang, K},
title = {Soil Nutrient Availability By Beneficial Bacteria of Forest Trees: From Mechanisms To Applications.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02728-z},
pmid = {41746386},
issn = {1432-184X},
abstract = {As global environmental challenges intensify, enhancing forest health and soil quality has emerged as a crucial area of research. Understanding and application of beneficial bacteria in forestry industry is urgently needed as an environmentally friendly and sustainable approach. Although thousands of patents have been registered for microbial application in agriculture and forestry, the mechanisms and application of beneficial bacteria on the soil nutrient availability have not been well summarized. This review investigated the role of beneficial bacteria in tree growth, particularly their contributions to soil nutrient availability in forest trees. We summarized that beneficial bacteria significantly enhance the availability of essential elements such as nitrogen, phosphorus, potassium, and iron by promoting nutrient cycling and transformation within the soil. This process supports tree growth and improves soil quality. Additionally, beneficial bacteria facilitate plant growth by synthesizing plant hormones and inducing resistance to biotic and abiotic stresses. This review concludes by discussing practical implications of beneficial bacterial colonization and application for enhancing soil nutrient levels, along with potential future research directions. We have enriched the theoretical framework of forest-associated bacteria and provided a scientific basis that can inform forest management and ecological restoration.},
}

@article {pmid41745260,
year = {2026},
author = {Christinaki, AC and Floudas, D and Myridakis, AI and Gonou-Zagou, Z and Kouvelis, VN},
title = {Cladobotryum rhodochroum sp. nov. (Hypocreales, Ascomycota): A New Fungicolous Species Revealed by Morphology, Phylogeny, and Comparative Genomics.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {2},
pages = {},
pmid = {41745260},
issn = {2309-608X},
support = {19620//Hellenic Foundation for Research and Innovation/ ; },
abstract = {Species of the ascomycetous genus Cladobotryum (Hypocreales, Hypocreaceae) are ecologically and economically important mycoparasites that cause cobweb disease in cultivated and wild mushrooms. Despite their significance as fungal pathogens and producers of bioactive metabolites, the taxonomy of Cladobotryum remains unresolved due to extensive morphological plasticity, complex teleomorph-anamorph connections, and the presence of cryptic species. This study employs an integrative approach combining micro- and macromorphological characterization, multi-locus phylogeny (ITS, rpb2, and tef-1a), and comparative genomics to clarify the taxonomic position of the Greek isolate Cladobotryum sp. ATHUM 6904, previously designated as an unclassified red-pigmented (URP) strain. Phylogenetic analyses demonstrated that URP strains form a distinct, well-supported clade closely related to C. tenue and C. rubrobrunnescens, yet genetically and morphologically distinct from both. Comparative genomic analyses of isolate ATHUM 6904 and the ex-type strains of C. tenue and C. rubrobrunnescens revealed pronounced divergence in transposable element content, mitochondrial genome architecture, gene order, orthologous gene composition, secondary metabolite biosynthetic potential, and overall genomic distance. Micro- and macromorphological comparisons further supported the differentiation of isolate ATHUM 6904 from both reference species. Based on the combined molecular, morphological, and genomic evidence, the Greek isolate ATHUM 6904 is described as a novel species, Cladobotryum rhodochroum sp. nov.},
}

@article {pmid41744634,
year = {2026},
author = {Pérez, E and Sanjuán, E and Jůzl, M and Raposo, A and Saraiva, A and Jaber, JR and Carrascosa, C},
title = {Active Antimicrobial Packaging Systems: Mechanisms of Microbial Control and Applications in Food Preservation.},
journal = {Biology},
volume = {15},
number = {4},
pages = {},
pmid = {41744634},
issn = {2079-7737},
abstract = {Microbial spoilage and foodborne pathogens remain central challenges in food safety, driven by the metabolic resilience and ecological adaptability of bacteria, yeasts, and molds across diverse food matrices. Active antimicrobial packaging has emerged as a biologically informed strategy that directly targets microbial physiology through controlled release or contact-mediated mechanisms. These systems employ natural antimicrobials, bacteriocins, essential oils, and metal nanoparticles to disrupt cell membranes, inhibit enzymatic pathways, generate reactive oxygen species, or interfere with quorum sensing, resulting in substantial reductions in microorganisms such as Listeria monocytogenes, Salmonella spp., E. coli O157:H7, Pseudomonas spp., Brochothrix thermosphacta, and spoilage fungi. In real food environments, these interventions achieve multi-log reductions and attenuate microbial metabolism, though efficacy varies with pH, water activity, fat content, and storage temperature. Oxygen scavengers further reshape microbial ecology by suppressing aerobic spoilage organisms while inadvertently favoring anaerobic competitors. Despite promising outcomes, concerns regarding nanoparticle migration, microbial resistance potential, and matrix-dependent performance highlight the need for deeper microbiological validation. Future progress will require integrative research linking microbial ecology, packaging material science, and mechanistic toxicology. By aligning with microbial behavior at the cellular and ecosystem levels, active antimicrobial packaging represents a powerful, biologically grounded approach to mitigating foodborne risks.},
}

@article {pmid41744504,
year = {2026},
author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T},
title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0137325},
doi = {10.1128/msystems.01373-25},
pmid = {41744504},
issn = {2379-5077},
abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.

IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.},
}

@article {pmid41743866,
year = {2025},
author = {Tarigan, MB and Saragih, RM and Tarigan, KA and Ginting, F},
title = {Antimicrobial resistance and empirical antibiotic use in diabetic foot infections: A retrospective study from Indonesia.},
journal = {Narra J},
volume = {5},
number = {3},
pages = {e2895},
pmid = {41743866},
issn = {2807-2618},
abstract = {Diabetic foot infection (DFI) represents a major complication of diabetes mellitus with significant morbidity, frequently leading to amputation if not optimally managed. The aim of this study was to analyze clinical, microbiological, and antibiotic susceptibility data from patients with type 2 diabetes who presented with foot infections in Indonesia. The retrospective study, conducted at St. Elisabeth Hospital in North Sumatra, Indonesia, predominantly comprised male farmers with a mean diabetes duration of 8.6 years, most of whom exhibited advanced ulcer severity (64.5% at Wagner grade III). Surgical debridement was performed in 79.0% cases, and amputation in 21.0% of cases. Laboratory investigations revealed poor glycemic control (mean HbA1c 10.12%) and biochemical markers indicative of systemic inflammation and renal impairment. Microbial cultures identified a predominance of Gram-negative bacteria (58.1%), primarily Klebsiella pneumoniae, Proteus mirabilis, and Escherichia coli, whereas Gram-positive isolates (41.9%) were dominated by Staphylococcus aureus, including methicillin-resistant strains. Empirical outpatient and inpatient antibiotic regimens commonly included amoxicillin, ciprofloxacin, metronidazole, and ceftriaxone; however, in vitro susceptibility testing demonstrated limited efficacy of β-lactams such as ampicillin and amoxicillin (<10% sensitivity). In contrast, linezolid, amikacin, vancomycin, carbapenems, and fosfomycin exhibited superior activity against the isolated pathogens. These findings emphasize the critical need for empirical antibiotic guidelines tailored to local microbial ecology and resistance profiles, integrated with early surgical management, stringent glycemic control, and multidisciplinary care. This comprehensive approach is essential to reduce the risk of amputation and improve clinical outcomes in tropical, resource-limited settings.},
}

@article {pmid41743643,
year = {2026},
author = {Markfeld, M and Talpaz, I and Biton, B and Maheriniaina Randriamoria, T and Soarimalala, V and Goodman, SM and Nunn, CL and Titcomb, G and Pilosof, S},
title = {Host traits and environmental factors shape infection heterogeneity in wild rat-protozoa networks.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag026},
pmid = {41743643},
issn = {2730-6151},
abstract = {The occurrence of microbes in animal hosts is highly heterogeneous, shaped by interactions among host traits, environmental context, and microbial diversity. Understanding this heterogeneity is particularly critical for endoparasite infections, where some hosts harbor diverse, high-burden assemblages that elevate disease spread and spillover risk. Yet the mechanisms underlying such heterogeneity remain poorly understood in wild systems, especially at the individual-host level. We addressed this challenge by studying protozoan infections in introduced black rats (Rattus rattus) across environmental gradients in Madagascar. Using network-based stochastic block modeling, we identified three infection profiles capturing meaningful variation in protozoan richness and composition, providing a structured framework for understanding heterogeneity. To uncover the predictors of these profiles, we trained machine-learning models incorporating host traits with environmental variables. Our models consistently outperformed no-skill baselines, with host traits contributing [Formula: see text]40% more to predictions than environmental factors. Body mass and gut microbiome composition emerged as the strongest host predictors, while rat and other non-native species densities were the most influential environmental predictors. These results show that infection heterogeneity arises from the interplay of intrinsic host traits and extrinsic environmental conditions. Our approach illustrates how combining network analysis with predictive modeling can (i) uncover latent heterogeneity in host-microbe associations, (ii) identify the relative contribution of the factors driving this heterogeneity, and (iii) predict host infection profiles. Our framework advances microbial ecology by linking host traits, microbial communities, and environmental context, while also informing disease ecology at human-animal interfaces where zoonotic pathogens circulate.},
}

@article {pmid41743513,
year = {2025},
author = {Hylling, O and Forero-Junco, LM and Ellegaard-Jensen, L and Dedon, PC and Cui, L and Nielsen, TK and Hansen, M and Neve, H and Johansen, A and Kot, W},
title = {Novel Modification Sites of dPreQ0 in Aminobacter niigataensis Phage Erebus Provide New Insights into the Role of 7-Deazaguanine Modifications in Bacteriophages.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {6},
number = {4},
pages = {250-258},
pmid = {41743513},
issn = {2641-6549},
abstract = {BACKGROUND: Bacteriophages protect themselves against host-encoded defense systems through DNA modifications. This study introduces Erebus, a newly identified phage infecting Aminobacter niigataensis, a bacterium capable of mineralizing 2,6-dichlorobenzamide- a common pesticide metabolite. The use of such bacterial degraders has been proposed for the bioremediation of contaminated groundwater. However, the presence of bacteriophages targeting these degraders poses a potential challenge to the success of such strategies.

MATERIALS AND METHODS: The Erebus phage was isolated and subjected to whole-genome sequencing. Phylogenetic analysis was performed to determine its taxonomic placement and genomic synteny. DNA modifications were identified using a combination of liquid chromatography-mass spectrometry (LC-MS) and Oxford Nanopore Technologies sequencing. Transmission electron microscopy was used to determine the phage morphology.

RESULTS: Phylogenetic analysis revealed that Erebus belongs to an unclassified genus, showing high synteny with Rhizobium phages of the Kleczkowskaviridae family. The phage possesses a double-stranded DNA genome of 52,229 base pairs, which includes a functional 7-deazaguanine DNA-modification system. Nanopore sequencing and LC-MS analysis confirmed the presence of PreQ0 modifications at novel GG and AG motifs, conferring resistance against multiple restriction endonucleases.

CONCLUSIONS: This is the first report of a phage infecting the genus Aminobacter, highlighting the potential impact of bacteriophages on microbial biodegradation strategies. The findings underscore the importance of considering phage-host interactions when deploying bacterial degraders for environmental remediation.},
}

@article {pmid41743133,
year = {2026},
author = {Zhang, W and Jiang, H and Zhu, Q and Shi, Z and Chen, W and Xu, X and Peng, F and Chi, Y},
title = {Microbial diversity and water quality changes in mangrove sediments in Quanzhou Bay.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1743704},
pmid = {41743133},
issn = {1664-302X},
abstract = {This study investigated the diversity, composition, and environmental drivers of bacterial communities in the mangrove sediments of Quanzhou Bay, a subtropical estuary under anthropogenic pressure. Using high-throughput sequencing of the 16S rRNA gene, we analyzed samples from four sites (Fengze-FZ, Jinjiang-JJ, Luojiang-LJ, and Shishi-SS) representing a gradient of terrestrial influence and environmental conditions. The bacterial communities were predominantly composed of Pseudomonadota and Chloroflexi, a pattern consistent with global mangrove ecosystems but with distinct local structuring. Beta-diversity analyses (NMDS/PCA) revealed a significant spatial divergence, with the FZ site forming a distinct cluster separate from JJ, LJ, and SS, correlating with its unique environmental profile. Redundancy analysis (RDA) identified dissolved oxygen (LDO) and salinity as the key environmental factors shaping community structure. Functional prediction indicated a conserved potential for core metabolic processes (e.g., amino acid biosynthesis, bacterial chemotaxis) across sites, suggesting functional redundancy, while differences in the relative abundance of these pathways pointed to adaptive metabolic adjustments along the environmental gradient. Our findings demonstrate that the sedimentary microbial community structure in Quanzhou Bay is primarily shaped by localized environmental heterogeneity, providing critical insights into the microbial ecology of mangroves in urbanized coasts and a baseline for assessing ecosystem health and biogeochemical functioning under anthropogenic influence.},
}

@article {pmid41740962,
year = {2026},
author = {Scheuerl, T and Rivett, DW},
title = {A Concept Using α-Niche Evolution Within Bacterial Communities to Direct β-Niche Evolution of Focal Species.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70255},
doi = {10.1111/1462-2920.70255},
pmid = {41740962},
issn = {1462-2920},
support = {316807//UIBK/ ; 325779//Tyrolian Science Foundation/ ; 101067338//MSCA Postdoctoral Fellowship/ ; EP/X024830/1//EPSRC Postdoc Fellowship/ ; ISS-2021-109666//Vertex Pharmaceuticals Research/ ; },
abstract = {The process of bacterial adaptation has a profound impact on human wellbeing and health, but our toolkit to modify evolution is limited. Here, we present a concept of how steering adaptation can be achieved by integration of bacterial evolution and microbial ecology. The fundamental question is how specific species bloom after community perturbation and subsequently evolve. We consider two kinds of traits-α-niche traits involved in partitioning resources (e.g., broadened resource consumption) and β-niche traits driven by changes in the abiotic environment (e.g., pH adaptation or resistance after antibiotic treatment). We suggest that the evolution of the second trait can be directed indirectly via the evolution of the first trait, exploiting specific interspecies interactions. Thus, understanding how these traits interact in co-evolving communities may offer unprecedented opportunities to deflect trait evolution. Summarising current knowledge, emphasising open questions and highlighting conceptual ideas, we hope to stimulate new studies that are needed to move this field forward.},
}

@article {pmid41739277,
year = {2026},
author = {Silva, MLOM and Martins, AKS and Sandes, SHC and Alvim, LB and Nunes, ÁC and Camargo, ILBC and Tinoco, HP and Nicoli, JR and Martins, FS},
title = {Isolation and evaluation of antagonistic activity against pathogenic bacteria by Lactobacillus and Enterococcus spp. from the saliva of Speothos venaticus and Chrysocyon brachyurus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {41739277},
issn = {1678-4405},
abstract = {UNLABELLED: Saliva plays a crucial role in oral defense across mammals by combining host-derived antimicrobial factors with antagonistic indigenous microbiota. Understanding the composition of the oral lactic microbiota in wild canids may provide valuable insights into microbial ecology and animal health. In this study, Lactobacillus and Enterococcus spp. isolated from the saliva of South American bush dogs (Speothos venaticus) and maned wolves (Chrysocyon brachyurus) were enumerated, identified, and evaluated for their antagonistic activity against pathogenic bacteria. For bacterial isolation, MRS agar and BHI agar supplemented with sodium azide (BHI-SA) were used for Lactobacillus and Enterococcus, respectively. Identification of the bacterial isolates was performed using PCR-ARDRA and multiplex PCR. Antagonistic activity was assessed using a double-layer agar diffusion assay, which detects diffusible inhibitory effects without identifying the compounds involved. A total of 23 bacterial isolates were obtained from BHI-SA and 24 from MRS for bush dogs, while 15 were recovered from BHI-SA and 23 from MRS for maned wolves. Salivary bacterial counts ranged from 4.0 to 5.0 log10 CFU/mL. In bush dogs, Enterococcus faecalis and Enterococcus faecium were identified, while E. faecalis and Enterococcus hirae were found in maned wolves. Limosilactobacillus reuteri, Lactiplantibacillus paraplantarum, Lactiplantibacillus plantarum and Lactobacillus johnsonii were isolated from bush dogs, while Ligilactobacillus salivarius and Latilactobacillus curvatus were identified in maned wolves. Antagonistic activity against indicator pathogens was more frequent among Lactobacillus isolates. These results suggest that the antibacterial properties observed in the saliva of these wild canids may be partly attributed to indigenous Lactobacillus and Enterococcus species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-026-01877-0.},
}

@article {pmid41739174,
year = {2026},
author = {Sánchez-Astráin, B and Borrego-Ramos, M and Viso, R and de la Hoz, CF and Blanco, S and Juanes, JA},
title = {Unravelling Diatom-Microbiome Dynamics in the Red Alga Gelidium Corneum (Florideophyceae, Rhodophyta).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02723-4},
pmid = {41739174},
issn = {1432-184X},
}

@article {pmid41738851,
year = {2025},
author = {Kim, M and Hakeem, WGA and Rothrock, MJ},
title = {Key Farm-to-Fork Factors Influencing E. coli Levels in Pastured Poultry Production.},
journal = {Avian diseases},
volume = {69},
number = {4},
pages = {395-406},
doi = {10.1637/aviandiseases-D-25-00033},
pmid = {41738851},
issn = {1938-4351},
mesh = {Animals ; *Escherichia coli/isolation & purification/physiology ; *Animal Husbandry/methods ; *Chickens ; Feces/microbiology ; *Escherichia coli Infections/veterinary/microbiology/epidemiology ; Soil Microbiology ; *Poultry Diseases/microbiology/epidemiology ; Farms ; Southeastern United States ; },
abstract = {Pastured poultry farms offer a unique model for investigating microbial ecology in less controlled environments, presenting challenges and opportunities for food safety management. This study aims to identify the key factors that influence Escherichia coli levels with two complementary modeling approaches: a linear mixed-effect model (LMM) and a random forest (RF) model. Data were collected from 11 pastured poultry farms in the southeastern United States from 2014 to 2017. Five sample types were analyzed: soil (n = 812), feces (n = 817), ceca (n = 206), postprocessing whole carcass rinse (WCR-P; n = 235), and final product whole carcass rinse (WCR-F; n = 230). Two different sets of predictor variables were used separately: 1) 32 farming practices and 26 physicochemical properties and 2) 80 meteorological factors. The model performance was compared with the randomized mean squared error (RMSE) with a test dataset. LMM was not used for meteorological factors because of the multicollinearity. Significant differences (α = 0.05) in E. coli levels were observed between all sample types, with feces samples showing the highest level. Compared to LMMs, RF models generally showed higher predictive accuracy (lower RMSE) on the test dataset. For soil samples, higher pH and sodium levels were linked to higher E. coli levels. The same trend with pH was observed in fecal samples. WCR-P samples showed that the organic acid treatment in the rinse water led to lower E. coli levels than other treatments. In WCR-F samples, longer storage time led to lower E. coli levels. Meteorological factors showed a weaker relationship with E. coli levels compared to farming practices and physicochemical properties, but in soil samples, mild and stable temperature played an important role in E. coli survival. This study can help stakeholders develop data-driven management strategies targeting key factors to aid in the reduction of food safety and animal health risk.},
}

Animals
*Escherichia coli/isolation & purification/physiology
*Animal Husbandry/methods
*Chickens
Feces/microbiology
*Escherichia coli Infections/veterinary/microbiology/epidemiology
Soil Microbiology
*Poultry Diseases/microbiology/epidemiology
Farms
Southeastern United States

@article {pmid41736367,
year = {2026},
author = {Keum, HL and Sul, WJ and Kim, S and Chung, IY and Koh, A and Kim, HS},
title = {Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.71150/jm.2511012},
pmid = {41736367},
issn = {1976-3794},
abstract = {Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.},
}

@article {pmid41735517,
year = {2026},
author = {Piaszczyk, W and Lasota, J and Foremnik, K and Błońska, E},
title = {Tree species determine soil microbial diversity: variation in fungal and bacterial communities in temperate forests.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41297-6},
pmid = {41735517},
issn = {2045-2322},
support = {2022/06/X/NZ9/00006//Narodowe Centrum Nauki/ ; },
abstract = {This study investigates the influence of three deciduous tree species: small-leaved linden (Tilia cordata), common beech (Fagus sylvatica), and sessile oak (Quercus petraea) on soil microbial diversity in temperate forest ecosystems. Conducted on loess soils in southern Poland, the research clarifies species-specific effects on soil microbiota and chemical properties, providing insights into tree-microbe-soil interactions in forest environments. Soil samples were collected from monospecific stands and analysed using next-generation sequencing (NGS). Fungal and bacterial DNA was extracted, and libraries targeting the ITS1 (fungi) and 16 S rRNA V3-V4 (bacteria) regions were sequenced using the Illumina MiSeq platform. Microbial communities were evaluated in relation to soil pH, nutrient content, and exchangeable cations. Linden soils had the highest pH (5.1-7.0) and calcium content (18.9 cmol(+)·kg[-1]), while beech soils were the most acidic (pH 3.8-5.7) with the lowest calcium (8.0 cmol(+)·kg[-1]). Fungal communities were dominated by Basidiomycota, Ascomycota, and Mortierellomycota, with varying proportions across species. Bacterial diversity was highest in linden and oak stands. Dominant bacterial phyla included Actinobacteriota, Proteobacteria, and Acidobacteriota. Each tree species hosted a distinct microbial community, reflecting its impact on soil properties and microbial structure. Tree species significantly shape soil microbial diversity and chemistry. Incorporating microbial data into forest management may enhance soil function, biodiversity conservation, and ecosystem resilience. Broader spatial sampling is recommended to generalize findings.},
}

@article {pmid41734518,
year = {2026},
author = {Dhillon, A and Yadav, P and Gupta, S and Singh, SV and Sohal, JS and Rawat, KD},
title = {Microbiome alterations and host-pathogen interactions in paratuberculosis: A one health perspective.},
journal = {Veterinary microbiology},
volume = {315},
number = {},
pages = {110940},
doi = {10.1016/j.vetmic.2026.110940},
pmid = {41734518},
issn = {1873-2542},
abstract = {Paratuberculosis is a chronic ruminal-enteric infection caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has significant economic, trade, and public health implications. In addition to evading host immunity, MAP modulates the gut microbiome, resulting in dysbiosis that exacerbates disease progression. A conceptual framework is proposed in which Johne's disease (JD) can serve as the paradigm of chronic infection, based on dysbiosis in microbial imbalance, immune escape, and pathogen survival in a self-sustaining loop, as in human tuberculosis and Crohn's disease. This review evaluates the evidence on MAP-induced microbiome alterations and their impact on host-pathogen relations, immune responses, and metabolic processes in cattle, sheep, goats, and other ruminants. JD-associated dysbiosis is characterized by reduced microbial diversity, depletion of butyrate-producing taxa (e.g., Ruminococcaceae and Lachnospiraceae), enrichment of pro-inflammatory Enterobacteriaceae, and disruption of short-chain fatty acid (SCFA) metabolic pathways. Recent studies suggest that such alterations in microbes can be the initial signs of diagnosis and pre-treatment components, such as probiotics, prebiotics, dietary modifications, and microbiome-based vaccinations. This summary bridges the research on the veterinary and human microbiome, revealing that MAP-Microbiome interactions reflect immunological evasion and microbial persistence schemes observed with other intracellular pathogens. Evidence across species and disciplines highlights the interdependence between host microbiome stability, pathogen persistence, and disease progression. However, variances between studies show the need to adopt standardized methodologies, longitudinal studies, and multi-omics designs to establish whether dysbiosis precedes or follows MAP infection. The review is the first to combine molecular, immunological, and microbiome-level data into the One Health concept of MAP persistence. Moreover, this review takes a One Health approach where the investigation of MAP-induced dysbiosis offers an understanding of chronic inflammation, microbial ecology, and persistence strategies applicable to veterinary as well as human health. This way, we can emphasize the diagnostic, therapeutic, and translational opportunities of microbiome-based interventions in JD using a One Health model that connects ruminant disease to human inflammatory bowel diseases, including Crohn's disease.},
}

@article {pmid41733768,
year = {2026},
author = {Zhou, S and Yao, Y and Yuan, R and Chu, W},
title = {Comparative Microbiome Analysis of Rhodiola fastigiata Rhizosphere Versus Bulk Soil in Xizang with Targeted Isolation of Rhizosphere-Derived Functional Strains.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41733768},
issn = {1559-0305},
support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Rhodiola fastigiata, a critically endangered medicinal plant of the Qinghai-Xizang Plateau, faces severe threats from habitat degradation. This study aimed to support its microbial-assisted conservation by characterizing the rhizosphere microbiome and isolating functional plant growth-promoting (PGP) bacteria. Using high-throughput sequencing of the 16S rRNA gene and ITS region, we found the rhizosphere community to be distinct and enriched in key taxa (e.g., Sphingomonas, Mortierella). Metabolic predictions suggested upregulated stress-adaptive pathways. Crucially, from 126 isolates, we obtained four Bacillus strains that concurrently produce protease, amylase, and cellulase and solubilize phosphate-quantifying a multifunctional PGP profile critical for nutrient-poor soils. These culturable, spore-forming strains provide direct resources for developing synthetic inoculants. Our work bridges microbial ecology with applied biotechnology, delivering both a foundational microbial map and candidate strains to enable the cultivation and conservation of this endangered species in extreme environments.},
}

@article {pmid41733363,
year = {2026},
author = {Ziegert, ZA and Troester, A and Frebault, J and Goffredo, P and Gaertner, WB and Jahansouz, C and Staley, C},
title = {SparCC co-occurrence networking reveals intracommunity dynamics of the microbiome following colorectal surgery.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0397325},
doi = {10.1128/spectrum.03973-25},
pmid = {41733363},
issn = {2165-0497},
abstract = {The intestinal microbiota plays a critical role in post-surgical wound healing following bowel resection; however, perioperative, prophylactic antibiotic administration may deleteriously affect it. We previously used 16S rRNA amplicon sequencing of stool samples to assess perioperative and longitudinal changes in the microbiome through 6 months in patients undergoing (i) colonoscopy after mechanical bowel prep (MBP) alone, (ii) non-resectional colorectal surgery after MBP with oral antibiotics and prophylactic intravenous antibiotics no longer than 24 h post-operative (surgical bowel prep [SBP]), and (iii) resectional colorectal surgery with SBP. Our objective in this study was to investigate the translational utility of SparCC co-occurrence networking to uncover biologically relevant patterns. Network topological parameters and hub species were calculated using NetCoMi, and permutational statistical tests were used to compare parameters. Network similarity among cohorts and time points generally matched changes in beta diversity, except in the resectional cohort, where all networks could not be differentiated statistically. Similarity in centrality measures among hub species was frequently significantly less similar than expected by chance and corresponded to an increased edge density and modularity, suggesting the latter parameters may reflect re-stabilization of the microbiome following surgery. We further noted the infrequently reported genera Enterocloster and Ruthenibacter were hub species during time points associated with surgical recovery, suggesting potentially novel roles for these genera in wound healing. Streptococcus, frequently implicated in surgical site infections at our center, was also frequently positively associated with Blautia throughout all networks, suggesting an increasing abundance of commensal bacteria serves as a prophylactic strategy.IMPORTANCEThis study employs the emerging approach of co-occurrence networking to assess ecological dynamics in the microbiome following colonoscopy and colorectal surgery. We expand upon applications of this approach to determine hub species and investigate clinically translational interpretations of network topological parameters in the context of recovery across three different trajectories of perturbation. Our results provide a context in which to interpret these network parameters biologically and represent a foundational step in beginning to quantitatively leverage network-based approaches to study microbial ecology. Furthermore, we identify network hub taxa that may play previously unexplored roles in wound healing.},
}

@article {pmid41733159,
year = {2026},
author = {Diab, E and Du, C and Tigani, W and Elsayed, SS and van Wezel, GP},
title = {Plant Coumarins Modulate Natural Product Biosynthesis in a Streptomyces Root Endophyte.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c01626},
pmid = {41733159},
issn = {1520-6025},
abstract = {The plant microbiome plays a central role in regulating plant health and resilience, providing eco-friendly alternatives to agrochemicals. Plant-associated Streptomyces species are prolific producers of structurally diverse natural products with a demonstrated role in promoting plant growth. Coumarins are prevalent plant metabolites that shape the root microbiome, but their impact on microbial natural product biosynthesis is poorly understood. Here, we demonstrate that the coumarins scopoletin and its glucoside scopolin remodel specialized metabolism in the Arabidopsis root endophyte Streptomyces sp. ATMOS53. Multiomics analyses revealed that the coumarins activate the biosynthesis of the pyrrolizidine alkaloids bohemamines and alter the balance in anthracycline biosynthesis, with reduced production of late-stage anthracycline congeners and accumulation of shunt metabolites earlier in the pathway. These metabolic shifts resulted in a marked reduction of the antimicrobial activity of ATMOS53 against plant-associated Bacillus and Paenibacillus species. Notably, coumarin-mediated repression of anthracycline production was also observed in the established producers Streptomyces peucetius and Streptomyces galilaeus, indicating that the regulatory effect on anthracycline biosynthesis is conserved in streptomycetes. Our findings highlight coumarins as modulators of specialized metabolism of Streptomyces and show the significance of plant-derived chemicals for the control of the biosynthetic capacity of plant-associated microbes.},
}

@article {pmid41732360,
year = {2026},
author = {Yash, and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P},
title = {Dataset on ecological health and microbial communities of coastal aquaculture ponds from surrounding region of Sundarban mangroves.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112542},
pmid = {41732360},
issn = {2352-3409},
abstract = {Integrated Mangrove Aquaculture (IMA) and Sustainable Aquaculture in Mangrove Ecosystem Fisheries (SAIME) are key activities undertaken across coastal regions globally to meet growing demand for brackish-water aquaculture products through sustainable practices. An in-depth biomonitoring study was conducted to map the ecological health of IMA and non-IMA aquaculture ponds in the surrounding region of the Indian Sundarbans mangroves located along the northeast coast of Bay of Bengal. Surface water samples were collected from six aquaculture ponds, four IMA (IMA_C1, IMA_C3, IMA_DB1, and IMA_DB4) and two non-IMA (C6_NM and DB5_NM) in the month of October 2022, for characterizing niche-specific biological communities using the environmental DNA (eDNA) approach. During sampling, in-situ environmental parameters were recorded. Mangrove litter-derived phenolics (tannic and gallic acids) and dissolved nutrients were estimated using a UV-Vis spectrophotometer, while dissolved organic carbon (DOC) was measured with the elemental analyzer. Metal and metalloid concentrations were determined by inductively coupled plasma mass spectrometry approach (ICP-MS). IMA ponds showed ideal conditions for shrimp aquaculture, with pH ranging from 7.913 to 8.633 and dissolved oxygen (DO) between 5.32 and 6.03 mg/L, indicating no hypoxic conditions despite higher concentrations of phenolics. High-throughput sequencing (HTS) based on Oxford Nanopore Technologies (ONT) sequencing chemistry was undertaken on the MinION platform, revealing the predominance of Proteobacteria among prokaryotes and Bacillariophyta as well as Chlorophyta among eukaryotes from extracted eDNA in each studied pond. Additionally, members of the family Cyprinidae were also detected, reflecting the biodiversity of fish population in these ponds. Functional gene profiling indicated signatures associated with nitrogen, phosphorus, sulphur, potassium and iron acquisition and metabolism, along with pathways related to aromatic compound degradation. Overall, dissolved nutrients, dissolved organic carbon (DOC), metal and metalloid ion concentrations as well as structure and functional profiles of biological communities provide a comprehensive basis for evaluating the ecological health of aquaculture ponds. This study generates important baseline information for long-term monitoring and represents the first eDNA-based high-throughput sequencing assessment of IMA and non-IMA aquaculture ponds from surface water in close proximity to the Sundarbans mangrove.},
}

@article {pmid41729252,
year = {2026},
author = {Li, Y and Chen, D and Liu, X and Li, Y and Chen, F},
title = {Zooplankton-associated Bacterial Communities are Dominated by Host-Specific Rather than Environmentally Random Taxa.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02702-9},
pmid = {41729252},
issn = {1432-184X},
}

@article {pmid41725809,
year = {2026},
author = {Zenati, K and Braun, SD and Belhadi, D and Moawad, AA and Müller, E and Diezel, C and Brandt, C and Mostefaoui, R and Monecke, S and Zaidi, FZ and Belmahdi, M and Touati, A and Ehricht, R},
title = {The oral cavity as a reservoir for resistance- and hypervirulence-associated genes of Klebsiella pneumoniae in hospitalized patients.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1751947},
pmid = {41725809},
issn = {1664-302X},
abstract = {INTRODUCTION: This study investigated the epidemiology and distribution of carbapenem resistance and virulence genes in Klebsiella pneumoniae strains isolated from the oral cavity of hospitalized patients, highlighting their role as reservoirs in non-epidemic contexts.

METHODS: Carbapenem-resistant Klebsiella spp. were isolated from the oral cavity of 180 hospitalized patients in medical wards at two hospitals in Bejaia, Algeria. Screening for carbapenem resistance was performed on oral mucosa and saliva using Carba-MTL broth. Antibiotic susceptibility was assessed with the Vitek2 system and interpreted according to EUCAST guidelines. Whole genome sequencing (WGS) was carried out using Oxford Nanopore Technologies, with ABRicate used for resistance/virulence gene detection and Kleborate for hypervirulence assessment. Whole-genome sequences were further examined to identify single-nucleotide polymorphisms (SNPs) and to reconstruct a SNP-based phylogenetic tree in order to assess the genetic relatedness among the isolates.

RESULTS: Twenty Klebsiella strains were identified as K. pneumoniae. Among these, 85% were carbapenem-resistant, carrying OXA-48 (80%) or NDM-5 (5%), and all harbored blaCTX-M-15. WGS of the 20 K. pneumoniae strains revealed a broad resistome, including β-lactamases (CTX-M-15, CMY-4, OXA-1, TEM-1), sulfonamide (sul1, sul2), aminoglycoside (aac(3)-IIa, aadA2, aph(3')-VI, armA, strA, strB), trimethoprim (dfrA12, dfrA5, dfrA14), and tetracycline (tetA). Quinolone resistance was linked to QRDR mutations (gyrA S83I, parC S80I) and plasmid-mediated genes (qnrS1, qnrB10, qnrS10, aac(6')-Ib-cr). Five distinct sequence types (STs) were identified, including high-risk clones ST13 and ST48. Virulence profiling revealed yersiniabactin (85%), frequently linked to ICEKp elements (ICEKp4, ICEKp10), and colibactin (40%) among OXA-48 isolates. Notably, a single K. pneumoniae isolate harboring NDM-5 (K21) carried both hypervirulence markers (ybt9/ICEKp3, iuc1, rmp1/kpvp-1) and carbapenem resistance, documenting, for the first time in Algeria, the convergence of these traits in oral isolates. ICEKp was identified as the key vehicle for dissemination of yersiniabactin and colibactin, and a novel association between ICEKp and kpvp-1 was observed. Capsular typing showed predominance of K57-O1/O2v2 among OXA-48 producers and K27/O4 among NDM-5 strains.

CONCLUSION: This study provides the first evidence in Algeria of OXA-48- and NDM-5-producing K. pneumoniae in the oral cavity of hospitalized patients. The coexistence of carbapenem resistance and hypervirulence underscores the oral cavity as a critical reservoir, potentially fueling nosocomial infections and the dissemination of high-risk clones within hospitals and the wider community.},
}

@article {pmid41720792,
year = {2026},
author = {Mohammadzadeh, R and Mahnert, A and Zurabishvili, T and Wink, L and Kumpitsch, C and Habisch, H and Sprengel, J and Filek, K and Mertelj, P and Pernitsch, D and Hingerl, K and Durdevic, M and Gorkiewicz, G and Diener, C and Loy, A and Kolb, D and Trautwein, C and Madl, T and Moissl-Eichinger, C},
title = {Cross-domain metabolic interactions link Methanobrevibacter smithii to colorectal cancer microbial ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69711-7},
pmid = {41720792},
issn = {2041-1723},
support = {10.55776/P32697//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776/CoE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776/CoE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
abstract = {The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea, an evolutionarily distinct group of microbes, in human disease remains elusive. By analyzing 19 independent clinical studies, we demonstrate that associations between Archaea and human diseases are widespread yet highly heterogeneous, with a pronounced and consistent enrichment of Methanobrevibacter smithii in colorectal cancer (CRC) patients. Metabolic modelling and in vitro co-culture identified distinct mutualistic interactions of M. smithii with CRC-causing bacteria such as Fusobacterium nucleatum, including metabolic enhancement. Metabolomics further reveal archaeal-derived compounds with tumor-modulating properties. Together, our results provide mechanistic insights into how the human gut archaeome may participate in CRC-associated microbial networks through metabolic cooperation with bacteria.},
}

@article {pmid41720095,
year = {2026},
author = {Wang, T and George, AB and Maslov, S},
title = {Higher-order interactions in auxotroph communities enhance their resilience to resource fluctuations.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101491},
doi = {10.1016/j.cels.2025.101491},
pmid = {41720095},
issn = {2405-4720},
abstract = {Auxotrophs are prevalent in microbial communities, enhancing their diversity and stability-a counterintuitive effect considering their dependence on essential resources from other species. To address the ecological roles of auxotrophs, our study introduced a consumer-resource model (CRM) to capture the complex higher-order interactions within these communities. We also developed an intuitive graphical and algebraic framework, which assesses the feasibility of auxotroph communities and their stability under resource fluctuations and biological invasions. Validated against experimental data from synthetic E. coli auxotroph communities, the model accurately predicted outcomes of community assembly. Our findings highlight the critical role of higher-order interactions and resource dependencies in maintaining the diversity and stability of microbial ecosystems dominated by auxotrophs. A record of this paper's transparent peer review process is included in the supplemental information.},
}

@article {pmid41716220,
year = {2026},
author = {Gomes-Neto, JC and Crook, A and Hestrin, R and Li, G and Liew, CS and Rosa, G and Singh, KD and Tuggle, CK and Summers, KL and Valdes, C and Fahlgren, N and Clarke, J},
title = {Challenges and opportunities: computational biology and the future of agriculture.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag003},
pmid = {41716220},
issn = {2635-0041},
abstract = {MOTIVATION: The world of agriculture is rapidly changing with advances in artificial intelligence and demands for greater feed and food security considering environmental and sustainability challenges. The 30th Conference on Intelligent Systems in Molecular Biology (ISMB) held in July 2022 featured an invited session on the role of computational biology in Digital and Precision Agriculture. This session featured presentations by experts from various subdisciplines on novel research discoveries and a panel discussion on Digital Agriculture at Scale. Topics discussed during the session included genetics, epigenetics, and genomics of agriculturally relevant species; foodborne pathogen genomics and epidemiology; plant and animal phenomics; AI/machine learning; image analysis; remote sensing; educational innovations; discoveries resulting from public-private partnerships; data sharing and findable, accessible, interoperable, and reproducible (FAIR) data standards; biotechnology; and soil microbial ecology and biogeochemistry.

RESULTS: We present several of the current and future challenges and opportunities for computational biology in agriculture including why these challenges are important to address, what barriers exist, and what skills and competencies are required to be successful as a computational biologist in agriculture. We intend this summary to engage the computational biology community and attract them to the opportunities available for interesting and impactful work toward ensuring sustainable food security.},
}

@article {pmid41715924,
year = {2026},
author = {Marín, MDC and Konno, M and Rozenberg, A and Béjà, O and Inoue, K},
title = {Novel light-driven schizorhodopsins from Antarctic patescibacteria and cyanobacteria.},
journal = {Biophysical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bpj.2026.02.022},
pmid = {41715924},
issn = {1542-0086},
abstract = {Microbial rhodopsins represent a diverse superfamily of light-sensitive proteins composed of seven transmembrane helices with expanding phylogenetic diversity driven by advances in metagenomics. Among these, schizorhodopsins constitute a divergent family originally identified as inward proton pumps from Promethearchaeota (Asgard archaea). Here, we report that in addition to archaeal schizorhodopsins, many members of the family originate from bacteria and detail a comprehensive biophysical characterization of two schizorhodopsins from uncultured Antarctic bacteria: paSzR from Minisyncoccota (Patescibacteria) and psSzR from a Pseudanabaenacea cyanobacterium. Both proteins function as light-driven inward proton pumps, as confirmed through pH measurements in Escherichia coli cells. Laser-flash photolysis experiments identified multiple photointermediates (K, L, and M) characteristic of microbial rhodopsin photocycles, though with slower turnover rates compared to archaeal schizorhodopsins. Site-directed mutagenesis of conserved residues in the third and sixth transmembrane helices demonstrates differential structural requirements between paSzR and psSzR. Our phylogenetic reconstruction reveals that most bacterial schizorhodopsins cluster in a single lineage distinct from archaeal variants. These findings expand our understanding of microbial rhodopsin diversity and provide crucial insights into alternative molecular mechanisms for light-driven proton translocation, with implications for microbial ecology in extreme environments.},
}

@article {pmid41715245,
year = {2026},
author = {Luna, N and Hernández, C and Ramírez, AL and Urbano, P and Barragán, K and Ariza, C and Muñoz, M and Patiño, LH and Ramírez, JD},
title = {Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {22},
pmid = {41715245},
issn = {2524-4671},
abstract = {BACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due to its hematophagous feeding behaviour and ecological adaptability, both of which enhance its potential for cross-species pathogen transmission. Despite its well-established relevance to public health, the microbial communities associated with D. rotundus remain poorly characterised. This study aimed at investigating the composition, diversity, and interactions of prokaryotic, eukaryotic, and viral communities, alongside feeding sources, using high-throughput sequencing in 27 D. rotundus individuals from a rural area in Casanare, eastern Colombia.

RESULTS: We analysed a total of 81 samples (blood, faeces, and oral swabs) using long-read amplicon sequencing of the 16S- and 18S-rRNA genes and viral metagenomics via Oxford Nanopore Technologies. The microbial profiles revealed highly diverse assemblages, encompassing a wide range of bacterial, fungal, eukaryotic parasites, and viral taxa, with significant variation in community structure and diversity metrics across the three sample types collected from each bat. Taxa of public health concern were detected, including Enterococcus faecalis, Mycoplasma spp. Acanthamoeba spp. and viruses from the families Coronaviridae, Retroviridae, and Circoviridae. Correlation analyses suggested potential intra- and inter-domain interactions and co-occurrence dynamics among these microbes. Additionally, feeding source profiling, based on vertebrate assignments from faeces and swab samples, indicated evidence of livestock consumption, suggesting possible transmission pathways between bats and domestic animals.

CONCLUSIONS: The detection of multiple co-occurring pathogens across distinct sample types, coupled with their association with feeding sources, highlights the role of D. rotundus as a functionally specialised reservoir capable of harbouring and potentially disseminating zoonotic microbes. This study provides new insights into the cross-domain microbial ecology of hematophagous bats and underscores the need to integrate microbial community profiling with host behavioural data to enhance surveillance and mitigation strategies for zoonotic disease transmission.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00504-x.},
}

@article {pmid41714654,
year = {2026},
author = {Rabaey, JS and Lewis, ASL and Attermeyer, K and Aurich, P and Bansal, S and Bartosiewicz, M and Bertolet, BL and Bussmann, I and Cadieux, SB and Calamita, E and Capelli, C and Carey, CC and Cillero, C and Clayer, F and D'Ambrosio, SL and Davidson, TA and Deemer, BR and Denfeld, BA and Eckert, W and Esposito, C and Ford, P and Gorsky, A and Griffiths, NA and Grossart, HF and Hamilton, DP and Holgerson, MA and Huser, BJ and Iwata, T and Jansen, J and Jones, SE and Juutinen, S and Kortelainen, P and Koschorreck, M and Kragh, T and Laas, A and Larmola, T and Läubli, S and Laurion, I and Lehmann, MF and Liu, L and Martikainen, PJ and Matoušů, A and McCord, SA and Montes-Pérez, JJ and Nizzoli, D and Ordóñez, C and Peacock, M and Pilla, RM and Prėskienis, V and Pu, J and Riis, T and Saarela, T and Santoso, AB and Schubert, CJ and Sepulveda-Jauregui, A and Sherman, BS and Sø, JS and Stenehjem, KJ and Strock, KED and Tsuchiya, K and Wendt-Potthoff, K and Weyhenmeyer, GA and Znachor, P and Zopfi, J},
title = {Depth-resolved carbon dioxide and methane concentrations in 522 lakes, ponds, and reservoirs worldwide.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06751-0},
pmid = {41714654},
issn = {2052-4463},
abstract = {Lakes, ponds, and reservoirs (hereafter: "lakes") are important sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Emissions of CO2 and CH4 from lakes are regulated in part by in-lake processes, including the production and storage of gases in the lower parts of the water column (bottom waters). However, while substantial efforts have been made to improve estimates of greenhouse gas emissions from lakes, limited data on gas concentrations along depth profiles have prevented the incorporation of bottom-water processes in global emission estimates. Here, we present GHG-depths: the largest existing dataset of depth-profile CO2 and CH4 measurements worldwide, including 522 lakes across 38 countries and all seven continents. These data include contributions from 45 research teams and 56 published studies, totaling 2558 discrete sampling events. As global change continues to alter biogeochemical cycling in lakes, these data can help improve mechanistic models to better predict greenhouse gas production and emission from lakes worldwide.},
}

@article {pmid41714186,
year = {2026},
author = {Wang, B and Gao, P and Zhang, P and Zheng, Y and Liu, X and Ling, N and Shan, J and Yao, R and Zhao, S and Zhang, Z and Zhu, G and Jung, MY and Zou, J and Yan, X and Lee, S and Hazard, C and Nicol, GW and Zhou, J and Yang, Y and Zhu, Y and Stahl, DA and Wagner, M and Gao, Y and Jiang, J and Qin, W},
title = {Elevated Temperature Simulating Heatwaves Restructures Active Nitrifying Communities and Associated Viruses in Tidal Flats and Agricultural Soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag037},
pmid = {41714186},
issn = {1751-7370},
abstract = {Global heatwave intensification under climate change will impact the nitrogen cycle, yet its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus-host interaction strategies in a land-use-dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.},
}

@article {pmid41713418,
year = {2026},
author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD},
title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.01.007},
pmid = {41713418},
issn = {1097-4172},
abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.},
}

@article {pmid41713400,
year = {2026},
author = {Wang, XW and Wang, T and Liu, YY},
title = {Artificial intelligence for microbiology and microbiome research.},
journal = {Cell systems},
volume = {17},
number = {2},
pages = {101531},
doi = {10.1016/j.cels.2026.101531},
pmid = {41713400},
issn = {2405-4720},
mesh = {*Artificial Intelligence/trends ; *Microbiota/physiology ; Humans ; Machine Learning ; *Microbiology/trends ; },
abstract = {Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine-learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We first introduce foundational AI techniques and offer guidance on choosing between traditional machine-learning and sophisticated deep-learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas from taxonomic profiling, functional annotation and prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, and clinical microbiology to prevention and therapeutics. Finally, we discuss challenges in this field and highlight some recent breakthroughs. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.},
}

*Artificial Intelligence/trends
*Microbiota/physiology
Humans
Machine Learning
*Microbiology/trends

@article {pmid41708342,
year = {2026},
author = {Alfahl, Z and Lynch, R and O'Dwyer, C and Kelly, JP},
title = {Medical versus science students: Knowledge, perceptions and learning of core pharmacology concepts.},
journal = {British journal of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bcp.70498},
pmid = {41708342},
issn = {1365-2125},
abstract = {AIMS: Pharmacology is a core discipline underpinning both medical and biomedical science education, essential for understanding drug action, safety and therapeutic efficacy. This study compared pharmacology knowledge, perceptions and learning experiences between second-year medical and science students to evaluate how effectively each curriculum supports acquisition of internationally defined core pharmacology concepts.

METHODS: A mixed-methods design was employed, involving pre- and post-module surveys and curriculum mapping against the global pharmacology core concept framework. Quantitative data were analysed using chi-squared tests, while qualitative responses were evaluated thematically. Participants included students enrolled in MD214 Introduction to Pharmacology (medical) and PM208 Fundamental Concepts in Pharmacology (science) at the University of Galway.

RESULTS: Medical students demonstrated stronger baseline and post-module understanding of pharmacokinetic and pharmacodynamic principles, particularly in applied pharmacokinetics such as drug-drug interactions and variability in drug response. Science students showed significant improvement over time, reflecting effective conceptual learning. Both cohorts reported positive perceptions of module relevance and teaching effectiveness (mean scores 7.7-8.9/10) and moderate to high confidence in mastering core concepts. YouTube and textbooks were the most common supplementary resources. Curriculum mapping showed alignment with 23 of 24 core concepts in the medical module and 20 in the science module.

CONCLUSIONS: Medical students exhibited greater initial competence and perceived relevance, whereas science students benefited substantially from targeted instruction. Findings highlight the value of concept-based, contextually integrated pharmacology teaching and support continued curriculum development guided by international core concept frameworks.},
}

@article {pmid41705859,
year = {2026},
author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM},
title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0134625},
doi = {10.1128/mra.01346-25},
pmid = {41705859},
issn = {2576-098X},
abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.},
}

@article {pmid41705204,
year = {2026},
author = {Verbunt, J and Mennens, L and Jocken, J and Blaak, EE and Savelkoul, P and Stassen, FRM},
title = {From food to vesicle: nutritional influences on gut microbial inflammatory signaling.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1756462},
pmid = {41705204},
issn = {2296-861X},
abstract = {Diet is a pivotal determinant of gut microbial ecology, giving not only rise to specific bacterial compositionality but also its functional output. Studying functional readouts-such as microbial metabolite production-could provide a more accurate and mechanistically informative measure of intervention outcome than traditional compositional profiling alone. Bacterial membrane vesicles (bMVs) are gaining attention as mediators of microbial metabolism and output. These nanoparticles are selectively released as carriers of bioactive proteins, lipids, nucleic acids, and metabolites reflective of the activity of the parent bacteria. Importantly, bMVs are rigid, can efficiently be isolated from feces, and are able to stably transport their cargo to interact with the host. In interacting with immune cells or pathogen recognition receptors, they can potentiate inflammatory responses. Given their extensive, multifaceted involvement in inter-Kingdom communication, bMVs represent an important biomarker for evaluating dietary modulation of gut microbial function. We propose that characterization of gut-derived bMVs offers a highly sensitive, mechanistically grounded approach to titrating impact of dietary interventions. By capturing shifts in microbial metabolic activity and inflammatory potential, bMV-based assessments could complement or surpass traditional measures of microbiome compositional change. Integrating bMV profiling into dietary intervention studies may therefore provide new insight into the functional consequences of diet-microbiome interactions and help refine strategies aimed at reducing inflammation and promoting host health.},
}

@article {pmid41704769,
year = {2026},
author = {Yinhang, W and Xueli, J and Zheng, W and Xiaojian, Y and Shu, X and Qingjie, Z and Ying, L and Shuwen, H},
title = {Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114664},
pmid = {41704769},
issn = {2589-0042},
abstract = {The gut microbiota is a key hallmark of colorectal cancer (CRC), yet gut fungi remain understudied. We characterized the gut fungal landscape and its associations with bacteria, metabolites, and trace elements in CRC using fecal samples from healthy controls (n = 401), colorectal polyp patients (n = 162), and CRC patients (n = 253). Fungal annotation was performed using genomic data from NCBI (PRJNA833221) as reference. Fungal diversity increased in CRC patients, with seven genera showing differential abundance. Rhizopus was specifically enriched in CRC, while Sporisorium, etc. enriched in polyps. Ablation study identified an optimal 31-microbial-marker panel (28 bacteria and three fungi) that effectively distinguished intestinal disease groups (AUC = 0.89). Structural equation modeling revealed three fungal markers-Penicillium citrinum, Penicillium sp. PG10607D, and Rhizopus stolonifera-that influence bacterial-metabolite-trace element networks. This study delineates the gut fungal atlas in CRC and reveals complex cross-kingdom interactions, offering new insights into CRC pathogenesis.},
}

@article {pmid41703880,
year = {2026},
author = {Mipun, P and Sarma, P and Dey, G and Terangpi, L and Hajong, B and Chakraborty, D and Kshetriya, D and Mandal, SM and Dinata, R and Baindara, P},
title = {Ethnic fermentation secrets of Northeast India and emerging functional food insights.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118431},
doi = {10.1016/j.foodres.2026.118431},
pmid = {41703880},
issn = {1873-7145},
mesh = {India ; *Fermentation ; *Fermented Foods/microbiology ; Humans ; *Functional Food/microbiology ; *Food Microbiology ; *Ethnicity ; Probiotics ; },
abstract = {Northeast India is home to an incredible variety of ethnic fermented foods, shaped over centuries by cultural wisdom and adaptation to the local environment. From bamboo shoots, soybeans, and rice to fish, dairy, vegetables, and traditional beverages, these foods are deeply woven into daily life and are rich in beneficial microorganisms with probiotic potential. Understanding the microbial ecology, biochemical transformations, and functional metabolites of Northeast India's traditional fermented foods provides a scientific basis for improving safety, identifying bioactive ingredients, and guiding the development of next-generation fermented products. This review brings together insights from ethnomicrobiological surveys and culture-based studies to explore the microbes, fermentation pathways, and biochemical changes that give these foods their distinctive qualities, as well as their nutritional benefits and safety considerations. We highlight lesser-known products, examine toxin-producing pathogens, and profile antimicrobial peptides (AMPs), uncovering varying levels of pathogen risk across products. Additionally, fermentation space analysis reveals exciting opportunities to create new foods by creatively combining local ingredients. Finally, we look at how modern tools, including artificial intelligence (AI) and machine learning (ML), can help scale up production, standardize quality, and ensure safety. Overall, by blending traditional knowledge with modern biotechnology and AI, these unique fermentation foods could find their place globally while preserving their cultural roots.},
}

India
*Fermentation
*Fermented Foods/microbiology
Humans
*Functional Food/microbiology
*Food Microbiology
*Ethnicity
Probiotics

@article {pmid41568973,
year = {2026},
author = {Downing, BE and Gupta, D and Shalvarjian, KE and Nayak, DD},
title = {Genus-specific remodeling of carbon and energy metabolism facilitates acetoclastic methanogenesis in Methanosarcina spp. and Methanothrix spp.},
journal = {Journal of bacteriology},
volume = {208},
number = {2},
pages = {e0044825},
doi = {10.1128/jb.00448-25},
pmid = {41568973},
issn = {1098-5530},
support = {F32GM150233/NH/NIH HHS/United States ; Packard Fellowship in Science and Engineering//David and Lucile Packard Foundation/ ; S589706//U.S. Department of Energy/ ; Sloan Research Fellowship//Alfred P. Sloan Foundation/ ; Early Career Investigator in Marine Microbial Ecology and Evolution//Simons Foundation/ ; Beckman Young investigator Award//Arnold and Mabel Beckman Foundation/ ; Searle Scholars Award//Kinship Foundation/ ; 202299857//National Science Foundation Graduate Research Fellowship Program/ ; },
mesh = {*Methane/metabolism/biosynthesis ; *Methanosarcina/metabolism/genetics ; *Energy Metabolism ; Acetates/metabolism ; *Carbon/metabolism ; Archaeal Proteins/metabolism/genetics ; Gene Expression Regulation, Archaeal ; Acetyl Coenzyme A/metabolism ; },
abstract = {UNLABELLED: Methanogenic archaea (methanogens) are microorganisms that obligately produce methane as a byproduct of their energy metabolism. While most methanogens grow on CO2+H2, isolates of the genera Methanosarcina and Methanothrix can use acetate as the sole substrate for methanogenesis. Methanogenic growth on acetate, i.e., acetoclastic methanogenesis, is hypothesized to require two distinct genetic modules: one for the activation of acetate to acetyl-CoA and another for producing a chemiosmotic gradient using electrons derived from ferredoxin. In Methanosarcina spp., the activation of acetate to acetyl-CoA is mediated by acetate kinase (Ack) and phosphotransacetylase (Pta), whereas Methanothrix spp. encode AMP-forming acetyl-CoA synthetases (Acs). The Rhodobacter nitrogen fixation complex (Rnf) or energy-converting hydrogenase (Ech) is critical for energy conservation in Methanosarcina spp. during growth on acetate, and a F420:methanophenazine oxidoreductase-like complex (Fpo') likely plays an analogous role in Methanothrix spp. Here, we tested the proposed modularity of these pathways to facilitate acetoclastic methanogenesis. First, we surveyed over 100 genomes within the class Methanosarcinia to show that the genomic potential for acetoclastic methanogenesis is widespread. We then used the genetically tractable strain, Methanosarcina acetivorans, to build all modular combinations that might support acetoclastic methanogenesis. Our results indicate that Acs, while functional, cannot replace Ack+Pta to rescue acetate growth in M. acetivorans. Similarly, the Fpo' bioenergetic complex cannot replace Rnf. As such, our work suggests that, in addition to horizontal gene transfer of core catabolic modules, acetoclastic metabolism in methanogens requires changes to core energy metabolism too.

IMPORTANCE: A large fraction of biogenic methane is derived from acetate, yet acetoclastic methanogens, i.e., methanogens that grow on acetate, remain poorly characterized due to their slow growth. Two groups of methanogens, Methanosarcina spp. and Methanothrix spp., perform acetoclastic methanogenesis using distinct sets of genes for acetate activation and energy conservation. It is widely hypothesized that these genetic modules from Methanosarcina spp. and Methanothrix spp. are functionally analogous and would thus be interchangeable. To test this hypothesis, we engineered different combinations of modules for acetoclastic growth in Methanosarcina acetivorans. Our results challenge this hypothesized paradigm of modularity, and we posit that other changes to the carbon and electron transfer pathways are crucial for the emergence of acetoclastic methanogenesis.},
}

*Methane/metabolism/biosynthesis
*Methanosarcina/metabolism/genetics
*Energy Metabolism
Acetates/metabolism
*Carbon/metabolism
Archaeal Proteins/metabolism/genetics
Gene Expression Regulation, Archaeal
Acetyl Coenzyme A/metabolism

@article {pmid41703847,
year = {2026},
author = {Gil, MI and Tudela, JA and Illán, G and Hernández, N and Andújar, S and Sabater, D and Allende, A and Truchado, P},
title = {Industrial-scale application of bacteriophages on baby spinach: One-year study of Listeria control, quality and microbial community shifts.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118384},
doi = {10.1016/j.foodres.2026.118384},
pmid = {41703847},
issn = {1873-7145},
mesh = {*Spinacia oleracea/microbiology ; *Bacteriophages ; *Food Microbiology/methods ; *Listeria/virology ; Listeria monocytogenes/virology ; Microbiota ; *Food Preservation/methods ; Food Handling/methods ; Food Contamination/prevention & control ; },
abstract = {Bacteriophages have emerged as promising biocontrol agents against pathogenic bacteria due to their strong antimicrobial activity and host specificity. In this study, we evaluated a previously validated industrial bacteriophage cocktail (PhageGuard Listex™) for its performance on baby spinach, focusing on product quality and microbial community dynamics. Twenty industrial trials conducted over one year compared non-treated and phage-treated baby spinach samples after processing (day 0) and after 10 days of storage under commercial (3 d at 4 °C followed by 7 d at 7 °C) and abusive (continuous 10 °C) temperature conditions. Phage stability was confirmed in the application solution and persistence on the product surface after storage. Although Listeria monocytogenes was not detected in any sample (0/600), the proportion of samples positive for Listeria spp. was significantly lower in the phage-treated group (6%) than in the non-treated group (12%). The preventive phage application did not affect headspace gas composition, sensory attributes, or objective color parameters. Quality deterioration was observed only at 10 °C, regardless of phage treatment. Despite the reduction in Listeria spp. prevalence, microbial diversity and community structure were unaffected by phage application, consistent with the low relative abundance of Listeria spp. in the microbiota and the narrow host range of the phage cocktail; storage conditions, particularly temperature, were the most influential factor affecting bacterial taxonomic composition. The relative abundance of Pseudomonas and Flavobacterium increased during storage, while Bacillus and Exiguobacterium decreased. These findings support the feasibility of using this bacteriophage-based treatment as a preventive intervention that does not affect product quality and preserves the natural microbial ecology of baby spinach during storage.},
}

*Spinacia oleracea/microbiology
*Bacteriophages
*Food Microbiology/methods
*Listeria/virology
Listeria monocytogenes/virology
Microbiota
*Food Preservation/methods
Food Handling/methods
Food Contamination/prevention & control

@article {pmid41703844,
year = {2026},
author = {Fang, X and Pu, Q and Qu, A and Wang, C and Shen, T and Wu, S and Li, M and Sui, M and Ji, Z and Huang, Y},
title = {Mechanisms of phenolic conversion in anaerobic fermentation of tea leaves revealed by integrating microbiome and metabolome analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118381},
doi = {10.1016/j.foodres.2026.118381},
pmid = {41703844},
issn = {1873-7145},
mesh = {*Fermentation ; *Phenols/metabolism/analysis ; *Plant Leaves/microbiology/metabolism/chemistry ; *Microbiota ; *Tea/microbiology/chemistry/metabolism ; *Metabolome ; Anaerobiosis ; Metabolomics/methods ; Bacteria/metabolism ; *Camellia sinensis/microbiology ; Flavonoids/metabolism ; },
abstract = {To systematically investigate the phenolic transformation mechanisms during tea anaerobic fermentation, the changes in phenolics and microbial communities of pickled teas under varying extrusion degrees were analyzed by combining metabolomics and microbiomics. The changes in 118 differential phenolics (p < 0.05, variable importance in projection >1.0, and fold change >1.2 or < 1/1.2) revealed that anaerobic fermentation drives the bioconversion of bound phenolics into free phenolics and their derivatives in tea leaves. Additionally, the potential metabolic pathways of tea phenolics in anaerobic fermentation were comprehensively proposed, mainly including hydrolysis of polymerized/galloylated catechins, hydrolysis of flavonoid glycosides, and hydrolysis of galloylated phenolics to release gallic acid and its further derivatization. The degree of extrusion significantly influenced microbial community succession: high-extrusion enriched Enterobacter, Cladosporium, Setophoma, and Vishniacozyma, enhancing the hydrolysis of flavonoid glycosides and depsides, while light-extrusion promoted Candida, Cyberlindnera, Lactobacillus, and Pantoea, favoring the accumulation of free phenolics and their derivatives. These findings establish a mechanistic link between microbial ecology and phenolic biotransformation, providing a foundation for precision fermentation in tea processing.},
}

*Fermentation
*Phenols/metabolism/analysis
*Plant Leaves/microbiology/metabolism/chemistry
*Microbiota
*Tea/microbiology/chemistry/metabolism
*Metabolome
Anaerobiosis
Metabolomics/methods
Bacteria/metabolism
*Camellia sinensis/microbiology
Flavonoids/metabolism

@article {pmid41700860,
year = {2026},
author = {Machushynets, NV and Elsayed, SS and Du, C and Lysenko, V and de la Cruz, M and Sanchez, P and Genilloud, O and Martin, NI and Liles, MR and van Wezel, GP},
title = {Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associated Paenibacillus species.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149625},
doi = {10.1128/msystems.01496-25},
pmid = {41700860},
issn = {2379-5077},
abstract = {The growing threat of antimicrobial resistance necessitates the discovery of novel antibiotics with activity against drug-resistant pathogens. Members of the genus Paenibacillus are a rich source of nonribosomal peptides (NRPs), including well-known antibiotics such as polymyxins, paenibacterin, and tridecaptins. Here, we use a targeted mass spectrometry query language (MassQL)-based approach to identify the NRPs produced by a collection of 227 taxonomically diverse plant-associated Paenibacillus strains, providing detailed insights into their NRP-producing potential. Using MassQL to zoom in specifically on NRPs containing basic amino acids, we discovered a novel family of bacitracins, which we designated paenitracins. The paenitracins are the first bacitracin-type peptides reported in Paenibacillus and are distinguished from canonical bacitracins by three previously unseen amino acid substitutions. The paenitracins exhibit potent activity against gram-positive pathogens, including vancomycin-resistant Enterococcus faecium E155. Our work provides a novel metabolomics-guided and genomics-guided workflow for the discovery of bioactive NRPs as a strategy to prioritize natural product chemical space and accelerate antibiotic discovery.IMPORTANCEMembers of the genus Paenibacillus play an important role in soil ecology, producing a range of important nonribosomal peptides (NRPs). A collection of plant-associated Paenibacillus spp. were analyzed for their phylogenetic and metabolic diversity. We developed a novel discovery pipeline that combines feature-based molecular networking with mass spectrometry query language queries to systematically prioritize bioactive NRPs containing basic amino acids. Thus, we provide a comprehensive genus-wide inventory of NRPs produced by Paenibacillus spp. We thereby identified the paenitracins, a new sub-family of bacitracins active against multidrug-resistant gram-positive pathogens. Our pipeline enables the discovery of novel peptidic natural products to accelerate the prioritization of chemical space for antibiotics.},
}

@article {pmid41700805,
year = {2026},
author = {Zhou, S and Bai, X and Xue, B and Chu, W},
title = {A Vaginal Microbiota-Ovary Axis in Chemotherapy-Accelerated Ovarian Aging: Single-Cell Insights into Cellular Dysregulation.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioag042},
pmid = {41700805},
issn = {1529-7268},
abstract = {BACKGROUND: Chemotherapy-induced premature ovarian failure (POF) represents a major challenge to female reproductive health, yet the potential regulatory role of vaginal microbiota in this process remains largely unexplored.

RESULTS: Using a well-established model of chemotherapy-induced ovarian aging, we observed significant disruptions in vaginal microbial ecology characterized by depletion of Lactobacillus species and concomitant enrichment of pathogenic bacteria. Microbiota transplantation effectively reversed these dysbiosis patterns and restored ovarian function. Single-cell transcriptomic analysis revealed that microbial intervention promoted the recovery of granulosa and luteal cell populations while simultaneously suppressing inflammatory activation in ovarian stromal cells, demonstrating the vaginal microbiota's capacity to maintain follicular integrity. Further mechanistic insights showed that microbiota transplantation upregulated key antioxidant defense systems and ribosomal protein networks within ovarian cells, suggesting coordinated actions to mitigate oxidative stress and enhance cellular repair capacity, although the specific microbial metabolites mediating these effects require further elucidation.

CONCLUSIONS: Our findings establish for the first time the existence of a functional vaginal microbiota-ovary axis and delineate its critical role in protecting against chemotherapy-induced ovarian damage. This work not only advances our fundamental understanding of microbial-endocrine crosstalk but also identifies concrete microbial targets for developing innovative strategies to preserve fertility in cancer patients.},
}

@article {pmid41697449,
year = {2026},
author = {Zavřel, T and Pohland, AC and Pfennig, T and Matuszyńska, AB and Tóth, SZ and Bernát, G and Červený, J},
title = {Correction to: Estimating the redox state of the plastoquinone pool in algae and cyanobacteria via OJIP fluorescence: perspectives and limitations.},
journal = {Photosynthesis research},
volume = {164},
number = {2},
pages = {14},
doi = {10.1007/s11120-026-01203-7},
pmid = {41697449},
issn = {1573-5079},
}

@article {pmid41697388,
year = {2026},
author = {Ding, Z and Guo, Y and Guo, L and Ren, B and Yang, J and Li, J and Bai, L},
title = {Reintroduction of Grassland Plant Species Shapes Soil Bacterial Ecological Groups and Contributes Differently To Bacterial Diversity.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02718-1},
pmid = {41697388},
issn = {1432-184X},
support = {LJKMZ20221053//Foundation of Liaoning Province Education Administration/ ; X2021012//Shenyang Agricultural University/ ; },
}

@article {pmid41696024,
year = {2026},
author = {Pendleton, A and Schmidt, ML},
title = {Interpreting UniFrac with absolute abundance: a conceptual and practical guide.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf250},
pmid = {41696024},
issn = {2730-6151},
abstract = {[Formula: see text]-diversity is central to microbial ecology, yet commonly used metrics overlook changes in microbial load (or "absolute abundance"), limiting their ability to detect ecologically meaningful shifts. Popular for incorporating phylogenetic relationships, UniFrac distances currently default to relative abundance and therefore omit important variation in microbial abundances. As quantifying absolute abundance becomes more accessible, integrating this information into [Formula: see text]-diversity analyses is essential. Here, we introduce "Absolute UniFrac" ([Formula: see text]), a variant of Weighted UniFrac that incorporates absolute abundances. Using simulations and a reanalysis of four 16S rRNA metabarcoding datasets (from a nuclear reactor cooling tank, the mouse gut, a freshwater lake, and the peanut rhizospere), we demonstrate that Absolute UniFrac captures microbial load, composition, and phylogenetic relationships. While this can improve statistical power to detect ecological shifts, we also find Absolute Unifrac can be strongly correlated to differences in cell abundances alone. To balance these effects, we also incorporate absolute abundance into the generalized extension ([Formula: see text]) that has a tunable, continuous ecological parameter ([Formula: see text]) that modulates the relative contribution of rare versus abundant lineages to [Formula: see text]-diversity calculations. Finally, we benchmark GU[A] and show that although computationally slower than conventional alternatives, GU[A] is comparably sensitive to noise in load estimates compared to conventional alternatives like Bray-Curtis dissimilarities, particularly at lower [Formula: see text]. By coupling phylogeny, composition, and microbial load, Absolute Unifrac integrates three dimensions of ecological change, better equipping microbial ecologists to quantitatively compare microbial communities.},
}

@article {pmid41695957,
year = {2026},
author = {Dobrzyński, J and Gradowski, M and Radkowski, A and Bujak, H},
title = {Chloroflexota in agricultural soils: current knowledge and future research directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705889},
pmid = {41695957},
issn = {1664-302X},
abstract = {The review organizes current knowledge on the biofunctions, life-history strategies, and environmental responses of Chloroflexota in agricultural soils. Members of this phylum play key roles in carbon, nitrogen, and phosphorus cycling through a high degree of metabolic versatility, including photosynthesis, redox reactions, and the degradation of complex organic compounds such as cellulose and lignin. Chloroflexota contribute to major soil processes, including nitrification, denitrification, and nitrogen fixation. In agricultural soils, the predominant classes are Anaerolineae and Ktedonobacteria, each exhibiting distinct ecological strategies. Anaerolineae members, such as Leptolinea, Bellilinea, and Anaerolinea, are often associated with nutrient-enriched conditions, suggesting copiotrophic or competitor- and ruderal-like traits. In contrast, Ktedonobacteria show negative responses to increased soil carbon and nitrogen, suggesting that its members are oligotrophic. Despite these trends, responses to soil organic carbon, nitrogen, phosphorus, and pH vary substantially across studies, likely due to functional heterogeneity within the phylum and insufficient taxonomic resolution in metataxonomic datasets. Emerging evidence from metagenome-assembled genomes (MAGs) reveals that Chloroflexota harbor genes involved in carbon fixation, nitrogen transformations, and phosphorus solubilization, highlighting their previously underestimated ecological significance. However, most Chloroflexota remain uncultured, and available genomic data are still limited. Future research integrating high-resolution taxonomic profiling, metagenomics, and cultivation-based approaches is needed to clarify the ecological roles and life-history strategies of Chloroflexota members. Such advances may ultimately establish this phylum as an important microbial indicator of soil fertility and environmental change in agricultural soils.},
}

@article {pmid41695945,
year = {2026},
author = {Kothe, CI and Mak, T and Julienne, A and Okazaki, K and Jahn, LJ and Evans, JD},
title = {Miso without kōji: nesashi miso ecology driven by spontaneous fermentation with Mucor plumbeus.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1759987},
pmid = {41695945},
issn = {1664-302X},
abstract = {Nesashi miso is a rare, traditionally fermented soybean paste from Japan, and unlike most misos is produced through spontaneous fermentation without the use of a kōji starter. Here we analyzed a nesashi miso alongside two other misos from the same producer (rice and black soybean) as well as a hatchō miso from another producer which, like the nesashi, is based only on soybeans. Shotgun metagenomics confirmed that while Aspergillus oryzae dominated the three kōji-based misos, nesashi miso lacked this starter culture, and revealed that it was instead dominated by other filamentous fungi, mainly Mucor spp. and Penicillium spp., and contained typical yeast and bacterial genera found in traditional misos such as Zygosaccharomyces and Tetragenococcus. Principal component analysis (PCA) of 65 publicly available metagenomes showed that the nesashi miso sample clustered with other spontaneous solid-state fermentations like Chinese qu rather than with traditional kōji-based misos. To further characterize this unique fermentation, we isolated the Mucor sp. from nesashi miso, and sequenced it using long-read genomic sequencing. Pangenomic analysis confirmed its identity as M. plumbeus, and revealed close relationships between food- and environment-derived strains, suggesting that some Mucor species may already be naturally equipped to grow, establish and function in food fermentation niches. The nesashi strain specifically shared a large core genome with M. racemosus C, a strain patented for use in food, suggesting the former's potential for use in and potentially even adaptation to food environments. Functional annotation highlighted unique genes in the food strain group associated with amino acid metabolism, which may contribute to flavor formation. Together, these findings bridge traditional fermentation practices with meta/genomic insights, highlighting the built fermentation environment as a reservoir of potential starter cultures and the genus Mucor as a worthy candidate for future food fermentation research and innovation.},
}

@article {pmid41695141,
year = {2025},
author = {Uh, YR and Park, SN and Song, MJ},
title = {Characterization of the gut micro biota in Koreans and investigation of its association with probiotic consumption: implications for microbial ecology and host health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745533},
pmid = {41695141},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut micro biota is reportedly closely related to human health, and its composition and diversity are determined by a variety of factors, including age, diet, and probiotic intake. Although many studies on the gut micro biota have been conducted, most have focused on Western populations or have been limited by small sample sizes, making it difficult to understand micro biota differences across populations and lifestyles. In this study, we analyzed a large Korean cohort of 3,450 individuals, focusing on gut micro biome differences according to age and host-related markers, as well as the impact of probiotic supplementation.

METHODS: Fecal samples from 3,450 Koreans were analyzed using 16S rRNA gene sequencing (V3-V4 region). Bioinformatics and taxonomic analyses were performed to compare microbial composition and diversity according to age and probiotic intake.

RESULTS: The data revealed a significant increase in microbial diversity with age and distinct shifts in taxonomic composition between younger and older participants. In addition, probiotic intake did not alter overall community diversity but increased the detection of probiotics, suggesting that they serve as moderators rather than direct drivers of diversity.

CONCLUSION: These findings emphasize the importance of population-specific micro biome research and suggest that diverse host-related and lifestyle factors jointly contribute to shaping gut microbial ecology in Koreans. Probiotic supplementation primarily increased the detection of specific lactic acid bacteria and bifidobacterial species without substantially altering overall alpha diversity, consistent with a modulatory role on targeted taxa rather than broad community restructuring. Together, these results provide a useful framework for future studies linking probiotic-responsive microbial features to human health outcomes and for developing precision nutrition and probiotic strategies in Korean and similar populations.},
}

@article {pmid41695122,
year = {2026},
author = {Yash, and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P},
title = {Genomic insights into Brevibacterium sediminis strain IMA_C3 isolated from an integrated mangrove aquaculture pond.},
journal = {Access microbiology},
volume = {8},
number = {2},
pages = {},
pmid = {41695122},
issn = {2516-8290},
abstract = {Brevibacterium sediminis strain IMA_C3, a Gram-positive bacterium, was isolated from an integrated mangrove aquaculture pond near the Sundarbans mangrove. The bacterium was isolated from mangrove leaf litter and grown on Luria-Bertani medium at a salinity of 20. Phylogenetic analysis based on 16S rRNA sequencing showed a 99.67% identity with Brevibacterium linens AE038-8 from the International Nucleotide Sequence Database Collaboration DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was carried out using long-read sequencing on the Oxford Nanopore MinION platform, with genome annotation performed against the NCBI Reference Sequence Database and The Genome Taxonomy Database databases. The genome is ~4.1 Mb in size, with a G+C content of 64.59 mol%. Functional analysis of the genome revealed genes related to complex carbon utilization, nitrogen and phosphate metabolism and metal transport. Additionally, the genome encodes secondary metabolites, including ε-poly-l-lysine, ectoine, terpene and phenazine, which could have potential applications in controlling viral infections in indigenous shrimp populations within integrated mangrove aquaculture systems.},
}

@article {pmid41695029,
year = {2026},
author = {Qin, H and Zhang, L and Rao, Z and Wei, X and Táncsics, A and Sheng, R and Liu, Y and Chen, A and Fang, C and Huang, F and Long, P and Zhu, B},
title = {Decoding endophytic microbiome dynamics: engineering antagonistic synthetic consortia for targeted fusarium suppression in monoculture regimes.},
journal = {Horticulture research},
volume = {13},
number = {2},
pages = {uhaf286},
pmid = {41695029},
issn = {2662-6810},
abstract = {Biological control leveraging endophytic microbes represents a promising eco-friendly strategy to mitigate soil-borne diseases, yet the efficacy and mechanistic underpinnings of synthetic microbial communities (SynComs) derived from plant endophytes remain poorly understood. This study employed a holistic approach-integrating field sampling, microbial profiling, and functional validation-to investigate the dynamics of edible lily (Lilium) microbiomes under continuous cropping and develop targeted SynComs against Fusarium oxysporum. Metacommunity analysis revealed that prolonged monoculture co-enriched both potentially beneficial taxa (e.g. Pseudomonas, Bacillus) and pathogenic Fusarium, reflecting a dynamic equilibrium where naturally recruited antagonists were insufficient to prevent pathogen dominance, while increasing the complexity of endophytic co-occurrence networks. Keystone bacterial lineages, including Burkholderiaceae and Pseudomonas, emerged as critical stabilizers of the endosphere microbiome. Notably, 50% of endogenous bacterial taxa exhibited rhizospheric origins, contrasting with fungal communities where <10% derived from soil-a finding underscoring host-specific filtering mechanisms. Through systematic isolation and combinatorial testing, we engineered SynComs combining core antagonistic strains (Rhizobium, Methylobacterium, Talaromyces) with auxiliary microbes. Fungal-integrated SynComs outperformed bacteria-only consortia in plant growth promotion and pathogen suppression. By bridging fundamental microbial ecology with translational agriculture, our findings establish SynComs as scalable tools for sustainable soil health management, reducing reliance on synthetic fungicides while addressing the yield-limiting challenges in continuous cropping systems.},
}

@article {pmid41694331,
year = {2026},
author = {Mourot, R and Lebert, S and Martinez-Rabert, E and Barani, A and Grégori, G and Nunige, S and Dufour, A and Guasco, S and Larose, C and Bradley, JA},
title = {SIESTA Project: Svalbard summer 2025 expedition report.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {23},
pmid = {41694331},
issn = {2732-5121},
abstract = {Microbial dormancy plays an important role in the persistence, dispersal, and functioning of microbial communities in moderate to extreme environments. The activity or inactivity of microbial communities also has implications for rates of biogeochemical transformations and thus elemental stocks and redox conditions. Microbial communities inhabiting glacier surface environments encounter harsh and variable environmental conditions including nutrient limitation, low temperatures, and light availability across various micro-habitats including cryoconite and the bare ice surface. The metabolic states of cells within these microhabitats and in relation to their environment is fundamental to the functioning of the ecosystem and has implications for ecosystem resilience, responses to environmental change, and biogeochemical cycling. This report describes an expedition to Brøggerhalvøya, north-west Svalbard, carried out in July 2025, within the framework of the ERC SIESTA project. A major objective of the project is to resolve microbial activity and dormancy on an individual cell basis, to characterise the adaptive and functional traits of active and dormant fractions of the native glacier microbial population, and to link microbial metabolic states to broader ecological and biogeochemical dynamics. Here we report the site characteristics, the samples collected, the analyses undertaken, and the future analyses planned. Two small valley glaciers near to Ny-Ålesund were selected for investigation during this summer campaign: Midtre Lovénbreen and Austre Brøggerbreen. The data collected in the field, combined with subsequent laboratory analyses, will provide insights into the spectrum of dormancy and activity in situ among glacier microbial communities, and the taxa and functions associated with active and inactive fractions of the communities. These findings will contribute to a deeper understanding of the impacts and role of both short- and long-term microbial dormancy in glacial environments.},
}

@article {pmid41692701,
year = {2026},
author = {Keneally, C and Gaget, V and Chilton, D and Dornan, TN and Hensel, J and Keneally, AE and Kidd, SP and Brookes, JD},
title = {Extreme Salinity Change Governs Microbial Community Assembly and Interactions.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70301},
doi = {10.1111/1758-2229.70301},
pmid = {41692701},
issn = {1758-2229},
support = {2024316//Medical Research Future Fund/ ; },
mesh = {*Salinity ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; *Archaea/genetics/classification/metabolism/isolation & purification ; South Australia ; Ecosystem ; Seawater/microbiology/chemistry ; Wetlands ; Sulfur/metabolism ; },
abstract = {Coastal wetlands are highly vulnerable to climate-driven salinisation, which reshapes critical microbial processes underpinning nutrient cycling and energy flow. We examined how sediment microbial communities vary with salinity across the Coorong Lagoon (South Australia), spanning estuarine (0-40 g L[-1]), intermediate (40-100 g L[-1]) and hypersaline (100-150 g L[-1]) waters. Salinity was found to be the dominant driver of sediment microbial community composition, diversity and assembly. High salinity favoured specialists and homogenous community structures, with generalist bacteria persisting across intermediate salinities and supporting ecosystem resilience. Sulfur and carbon cycling is likely dependent on salinity, as bacterial sulfur-oxidisers were abundant estuarine specialists, whereas methane producers (Archaeal methanogens) and sulfate-reducers were enriched at high salinity. Deterministic microbial community assembly (homogeneous selection) was dominant, increasing at extreme salinity, which acted as a strong environmental filter. Community complexity increased at both high and low salinity ranges, with intermediate salinity exhibiting less complexity, suggesting community reorganisation under osmotic stress. The varied roles of specialists and generalists at different salinities support ecosystem function, where increased heterogeneity and specialisation in hypersaline conditions suggest vulnerability of the community to disturbance. These findings provide insight into how microbially underpinned ecosystems may respond to future climate-driven salinisation, important for making predictions and informing mitigation strategies.},
}

*Salinity
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
*Geologic Sediments/microbiology/chemistry
*Archaea/genetics/classification/metabolism/isolation & purification
South Australia
Ecosystem
Seawater/microbiology/chemistry
Wetlands
Sulfur/metabolism

@article {pmid41691943,
year = {2026},
author = {Huang, J and Tan, Z and Sun, R and Dai, Z and He, L and Li, C},
title = {Vertical and spatial variations of microbial communities in sediment cores from the mangrove of Gaoqiao National Nature Reserve.},
journal = {Marine pollution bulletin},
volume = {226},
number = {},
pages = {119416},
doi = {10.1016/j.marpolbul.2026.119416},
pmid = {41691943},
issn = {1879-3363},
abstract = {Sediment microbial communities act as key regulators of mangrove ecosystem functions. However, systematic studies on the spatial distribution characteristics, potential functions, and environmental driving mechanisms of microbial communities within sediment cores in mangrove ecosystems remain scarce. In this study, fifteen sediment cores were obtained from the mangrove within the Gaoqiao National Nature Reserve. The microbial community composition within the sediment cores was investigated using 16S rRNA high-throughput sequencing. Significant differences in microbial community structure were observed among the three designated zones (Nearshore, Mangrove, and Offshore) and across different sediment depths ranging from 0 to 80 cm. The dominant bacterial phyla identified comprised Pseudomonadota, Actinomycetota, and Chloroflexota, along with the archaeal phylum Thermoplasmatota. Their distributions demonstrated clear biogeographic and vertical stratification patterns. Functional prediction revealed that microbial communities extensively involved in carbon, nitrogen, and sulfur cycles exhibited higher richness, as these communities demonstrated stronger expression of metabolic functional genes. Furthermore, the abundance of metabolic functional genes was found to be higher in the mid-depth sediments at depths of 30 to 45 cm. Redundancy analysis (RDA) and variation partitioning analysis (VPA)demonstrated that sediment pH, electrical conductivity (EC), and total organic carbon (TOC) content were identified as the primary environmental factors governing the succession of both microbial community structure and function. This study advances our understanding of mangrove sediment microbial ecology and provides a scientific basis for targeted conservation and restoration of the Gaoqiao mangrove ecosystem.},
}

@article {pmid41691853,
year = {2026},
author = {Wei, Y and Chen, Y and Lv, S and Ou, D and Tao, Y and Zhou, Y and Yang, J and Song, X},
title = {Persistence of the coccidiostat robenidine in soil and its impacts on the soil microbiome and enzyme functions.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119858},
doi = {10.1016/j.ecoenv.2026.119858},
pmid = {41691853},
issn = {1090-2414},
abstract = {Robenidine is a synthetic coccidiostat that is excreted from animals in its prototype form, leading to soil contamination. Despite its widespread use, comprehensive environmental risk assessments remain limited. Consequently, we initially constructed a manure-soil microcosm and investigated the degradation pattern of robenidine using a highly efficient HPLC-dSPE method. The degradation half-lives of robenidine in soil were 14.74 days at 0.8 mg/kg and 21.26 days at 8 mg/kg. Exposure to 8 mg/kg of robenidine significantly altered the soil microbial community, leading to a 140.0 % increase in the abundance of Proteobacteria. However, the Shannon index indicated that soil microbial diversity decreased by 32.4 % from 1 d to 60 d. Compared to the control check group, 8 mg/kg of robenidine significantly increased the abundance of harmful bacteria (e.g., unclassified_Intrasporangiaceae increased by 33.5 %) in the soil at 60 d, while simultaneously reducing the populations of beneficial bacteria such as Bacillaceae (decreased by 23.8 %), Pseudograilibacillus (decreased by 39.6 %), and Massilia (decreased by 31.7 %). Network correlation and FAPROTAX analyses indicated that long-term exposure to robenidine inhibited chitinolysis and aromatic compound degradation pathways. Furthermore, low-dose robenidine increased the activities of dehydrogenase, acid phosphatase, and β-glucosidase by 34.0 %, 24.7 %, and 21.6 % at 1 d, respectively, while these enzymes returned to control levels over time. These findings provide critical insights into the biological and metabolic impacts of robenidine exposure on soil microbial communities, which is crucial for clarifying the ecological concerns associated with robenidine.},
}

@article {pmid41691349,
year = {2026},
author = {Fan, S and Liu, H and Yan, Y and Xu, M and Wan, X and Hao, Y and Gong, C and Wang, C and Zhang, Y and Liu, D and Zheng, J and Chen, J},
title = {Metatranscriptomic analyses of gut bacterial and viral communities in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) under distinct environments.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00528-x},
pmid = {41691349},
issn = {2524-4671},
}

@article {pmid41690572,
year = {2026},
author = {Koffel, T and Grimaud, G and Litchman, E and Klausmeier, CA},
title = {Metabolically structured population models: a unifying framework for microbial ecology and evolution.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {112410},
doi = {10.1016/j.jtbi.2026.112410},
pmid = {41690572},
issn = {1095-8541},
abstract = {Cells grow by acquiring external resources and transforming them internally, forming new cells as they divide. Metabolic networks focus on the flow of such resources within the cell as they undergo series of biochemical reactions. How population growth emerges from these complex dynamical networks remains unclear. Modeling the emergence of population growth, a central ecological concept, is thus essential to understand the forces shaping microbial communities. Here we present a novel theoretical framework that builds on structured population theory to model the growth of cell populations whose intracellular dynamics are driven by arbitrarily complex metabolic networks. Population growth is driven by limitation regimes, which capture how reaction-level limitations combine in the network to determine growth rate. Resource availability changes trigger switches between limitation regimes, capturing resource interaction and colimitation. We also discovered alternative metabolic states, where different regimes are reached depending on initial metabolite concentrations. We first use a minimal metabolic network of limitation by two essential resources to illustrate our framework, then apply it to E. coli's glycolysis pathway to showcase its capabilities on a more realistic, albeit still simplistic, network. By integrating metabolic networks into ecological theories, our work provides a mechanistic foundation for understanding the structure and evolution of microbial communities.},
}

@article {pmid41646430,
year = {2026},
author = {Thompson, AW and Lamberson, K and Sutherland, KR},
title = {Coexisting salps exhibit distinct feeding selectivity on microorganisms in the North Pacific Subtropical Gyre.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {41646430},
issn = {2693-5015},
abstract = {Mortality mechanisms play an important role in how oceanic microorganisms contribute to global biogeochemical cycles. Salps are widespread pelagic tunicates known to remove phytoplankton from coastal and high-latitude waters, but their interaction with microorganisms in the vast tropical and subtropical gyres is not well quantified. Using quantitative measurements of six major marine microorganisms in the guts of six distinct but co-occurring salp species from the North Pacific Subtropical Gyre, we examined the impact and dynamics of salp feeding on marine microorganisms in a vast open ocean region. All salps preferentially removed prey greater than 1 μm in diameter, including marine Synechococcus, diatoms, Crocosphaera, and Chrysochromulina, while the smaller Prochlorococcus and SAR11 were not a major source of prey biomass. We also found that salp feeding varied between salp taxa with some salp guts dominated by both Crocosphaera and Chrysochromulina while others were dominated by Crocosphaera alone. Together, these results suggest that salp impacts are not uniform across taxa and their patterns of selective feeding among marine microbes requires consideration of species-specific feeding strategies and environmental context. Further, this work suggests that the mortality pressure of salp feeding on marine microorganisms may shape microbial community structure and that this pressure varies with the diversity and dynamics of macrozooplankton predators.},
}

@article {pmid41690245,
year = {2026},
author = {Hu, J and Zhou, Y and Ishii, S and Ahmed, W and Sadowsky, MJ and Xia, X and Du, Z and Cytryn, E and Mwakalapa, EB and Rivera, WL and Zhou, Y and Rensing, C and Zhang, Q},
title = {Sources, contamination pathways, and monitoring of pathogens in urban estuaries.},
journal = {Marine pollution bulletin},
volume = {226},
number = {},
pages = {119415},
doi = {10.1016/j.marpolbul.2026.119415},
pmid = {41690245},
issn = {1879-3363},
abstract = {Urban estuaries are critical ecological and socio-economic interfaces but are increasingly impacted by microbial pathogen contamination driven by anthropogenic activities such as wastewater discharge, stormwater runoff, agriculture, and wildlife inputs. Despite extensive documentation of estuarine pathogens, effective risk assessment and management remain constrained by key knowledge gaps related to source apportionment, environmental fate, and monitoring relevance. This review synthesizes current understanding of pathogen sources and transmission pathways in urban estuaries and critically examines the physicochemical, hydrodynamic, and sediment-mediated processes that regulate pathogen persistence, redistribution, and exposure risk. We identify three interconnected challenges: (i) limited resolution in differentiating human and non-human contamination sources due to overlapping microbial signatures; (ii) inadequate incorporation of estuarine hydrodynamics and sediment reservoirs into fate-and-transport frameworks; and (iii) misalignment between conventional monitoring indicators and actual pathogen and antimicrobial resistance risks. Emerging approaches, including microbial source tracking, sequencing-based surveillance, biosensors, and hybrid predictive modelling, are evaluated for their capacity to support risk-relevant decision-making. Framed within a One Health perspective, this review integrates microbial ecology, environmental processes, and surveillance technologies to support evidence-based management and sustainable mitigation of pathogen risks in urban estuaries.},
}

@article {pmid41689629,
year = {2026},
author = {Mohammadzadeh, MH and Asadollahpour, M and Sharbatdar, HR and Darbouy, MS and Fekrirad, Z},
title = {Voices of Eukaryotic Microbes: Chemical Communication Via Quorum Sensing.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02716-3},
pmid = {41689629},
issn = {1432-184X},
abstract = {Quorum sensing (QS) is a cell-cell communication mechanism mediated by secreted hormone-like signaling molecules that operates in both Gram-positive and Gram-negative bacteria, driving coordinated alterations in gene expression once a critical cell density is reached. In these prokaryotic systems, bacteria produce, release, detect, and respond to small autoinducers, such as acyl-homoserine lactones in Gram-negative bacteria, oligopeptides in Gram-positive bacteria, and the universal autoinducer-2, to regulate community behaviors including biofilm formation, virulence factor production, and stress adaptation. The concept of QS in eukaryotic microbes emerged decades ago, and later investigations confirmed that unicellular fungi and protozoa similarly measure population density to regulate collective activities. In Saccharomyces cerevisiae, aromatic alcohols (2-phenylethanol, tryptophol, tyrosol) serve as QS signals to control filamentous growth, biofilm assembly, and environmental stress responses. Candida albicans employs farnesol to suppress hyphal development while utilizing tyrosol to accelerate germ tube emergence and biofilm maturation. African trypanosomes, including Trypanosoma brucei and related species, generate oligopeptides via secreted peptidases that accumulate as stumpy induction factors (SIFs), triggering a density-dependent shift from proliferative slender forms to transmission-competent stumpy forms essential for tsetse fly infection. QS-based mechanisms influence virulence factors in fungal and protozoan pathogens, affecting their ability to colonize hosts. Exploring QS in eukaryotic organisms opens new possibilities for antifungal treatments and parasite management. By interfering with QS signaling, researchers can disrupt fungal biofilm formation and regulate protozoan development, paving the way for innovative disease control methods.},
}

@article {pmid41687498,
year = {2026},
author = {Liao, B and Wang, Q and Zhang, T and Lu, X and Fang, N},
title = {Optimizing carbon source strategy for denitrification using food waste fermentation liquid: Synergistic mechanisms of butyrate and sucrose.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128950},
doi = {10.1016/j.jenvman.2026.128950},
pmid = {41687498},
issn = {1095-8630},
abstract = {Food waste fermentation liquid, rich in volatile fatty acids (VFAs) and carbohydrates, serves as a sustainable electron donor for biological nitrogen removal. However, the compositional fluctuation of fermentation liquid often leads to unstable denitrification, and the mechanistic influence of mixed VFA-saccharide interactions on microbial ecology remains poorly understood. In this study, four carbon-source systems-three simulating typical mixed fermentation products (acetate + sucrose, propionate + sucrose, butyrate + sucrose) and one single-carbon control (acetate alone)-were systematically evaluated in sequencing batch reactors (SBRs). Results indicated that the butyrate-sucrose system (A3) exhibited superior performance, achieving a nitrate removal efficiency of 98.5%, which was 13.5% and 8.2% higher than that of the acetate-sucrose (A1) and propionate-sucrose (A2) systems, respectively. Furthermore, A3 maintained the lowest nitrite accumulation (<0.5 mg/L). Mechanistically, A3 facilitated the selective enrichment of functional genera Ferruginibacter and Terrimonas. PICRUSt2 functional predictions revealed that this specific combination significantly enhanced KEGG pathways related to membrane transport (ABC transporters) and energy metabolism, suggesting a synergistic effect that accelerates electron transfer and metabolic turnover. This study demonstrates that regulating acidogenic fermentation towards a butyrate-dominant composition is a promising strategy to maximize the utility of food waste as a carbon source, ensuring robust nitrogen removal in wastewater treatment.},
}

@article {pmid41687164,
year = {2026},
author = {Kim, D and Yun, N and Du, H and Li, C and Preheim, S and Rossi, R},
title = {Enabling microbial electrolysis cell scale-up via electrochemistry-, hydrodynamic-, and microbial ecology-informed framework.},
journal = {Water research},
volume = {294},
number = {},
pages = {125503},
doi = {10.1016/j.watres.2026.125503},
pmid = {41687164},
issn = {1879-2448},
abstract = {Microbial electrolysis cells (MECs) can produce green hydrogen while removing organic contaminants from liquid waste streams by leveraging the metabolic activity of electroactive microorganisms. Despite their potential in a sustainable, circular economy, large-scale MECs that can treat relevant volumes of wastewater have failed to deliver performance proportional to their lab-scale counterparts. The reason behind this lower performance at scale remains unclear. In this study, we developed a combined electrochemistry-, hydrodynamic-, and microbial ecology-informed framework to analyze and optimize MEC performance during scale-up, enabling accurate quantification of major limitations and the identification of strategies to overcome them, ultimately facilitating equivalent performance at scale. Applying this framework to the scale-up of a zero-gap MEC from 9 cm[2] electrode area to 100 cm[2] electrode area, resulted in similar maximum current densities in a 100 cm[2] MEC (21.7 ± 1.1 A/m[2]) compared to a 9 cm[2] system (25.1 ± 2.7 A/m[2]), as well as equivalent hydrogen production rates of 69.3 L/L-d (100 cm[2]) and 67.7 ± 2.4 L/L-d (9 cm[2]). COMSOL flow dynamics simulations were used to scale up the reactor configuration without negatively affecting electrolyte velocity and distribution in the cell, minimizing the increase in internal resistances during scale-up (11.7 ± 0.5 mΩm[2] at 9 cm[2]; 19.7 ± 1.3 mΩm[2] at 100 cm[2]). Microbial community structures were assessed at both scales using high-throughput sequencing, highlighting the differences of populations across electrode dimensions and operational parameters. The framework presented here accelerates the development of effective strategies toward the scale-up of MECs by furthering the understanding of how electrochemical, hydrodynamic, and microbial ecology parameters change as the reactor dimension is increased. Ultimately, this approach contributes to advancing electrochemical biotechnology toward practical deployment in energy-efficient wastewater treatment systems.},
}

@article {pmid41686264,
year = {2026},
author = {Wu, CY and Cheng, HY and Lin, YC and Wang, YC and Meng, YZ and Hsieh, YE and Liu, AC and Yang, SH},
title = {Role of Core Microbiome Shifts in Octocoral Litophyton Under Diurnal Temperature Fluctuations.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02715-4},
pmid = {41686264},
issn = {1432-184X},
support = {NSTC 112-2611-M-002 -020//National Science and Technology Council/ ; NTUCCP- 115L891306//National Taiwan University/ ; },
abstract = {Climate change is projected to raise sea surface temperatures and intensify diurnal temperature fluctuations (DTF), threatening the survival of both scleractinian corals and octocorals. Litophyton, a common octocoral in Taiwan's shallow reefs, is frequently exposed to large DTF and summer heat stress, making it a suitable model to study thermal resilience. Coral-associated bacterial communities are known to shift under thermal stress, and key bacterial taxa may play crucial roles in host acclimation. This study aimed to address two questions: (1) Can higher DTF mitigate cumulative heat stress in octocorals? (2) If so, what physiological and microbial community changes accompany this effect? To answer these questions, we conducted tank experiments under constant warming and two short-term DTF regimes (± 5 °C and ± 7 °C; baseline 25-27.8 °C), along with a no-fluctuation control. We measured physiological stress indicators, including superoxide dismutase (SOD) and catalase (CAT) activities, and monitored bacterial community dynamics. Our results show that DTF helped maintain stable photosynthetic efficiency (Fv/Fm) compared to constant warming. Notably, significant differences in ROS activity were only observed in the ± 5 °C group, rather than in the larger ± 7 °C group, indicating a measurable alleviation of thermal stress and greater plasticity in Litophyton coping with temperature changes. Moreover, 29.4% more significantly abundant in the ± 7 °C group compared to the control in the core microbiome Endozoicomonas preceded detectable physiological changes in the host, suggesting a potential role in early stress mitigation. These findings deepen our understanding of octocoral holobiont resilience under fluctuating thermal regimes and highlight Endozoicomonas diversity as a potential indicator of Litophyton health.},
}

@article {pmid41685888,
year = {2026},
author = {Gilson, M and Bayon-Vicente, G and Krings, S and Toubeau, L and Wattiez, R and Leroy, B},
title = {Fundamental aspects of sucrose metabolism reveal a trophic link between Rhodospirillum rubrum and Rhodobacter capsulatus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0371725},
doi = {10.1128/mbio.03717-25},
pmid = {41685888},
issn = {2150-7511},
abstract = {Purple non-sulfur bacteria (PNSB) are well known to have an exceptional metabolic versatility. However, while the growth of PNSB on sugar-rich streams has been extensively explored, their ability to metabolize sugars is poorly understood. Here, we explore the metabolic mechanisms of sucrose, glucose, and fructose utilization in two phototrophic PNSB, Rhodospirillum rubrum and Rhodobacter capsulatus. Our findings demonstrate distinct carbohydrate assimilation capacities, as well as the use of different metabolic strategies for each species. Moreover, a trophic link was identified between the two species during co-cultivation, resulting from the production of fermentation by-products by Rh. capsulatus, which are then reassimilated by Rs. rubrum. Finally, we demonstrate that the synergy observed between Rs. rubrum and Rh. capsulatus can be successfully scaled up in a photobioreactor system. Our study highlights how fundamental knowledge of metabolism and the establishment of a trophic link between two PNSB species might be useful for the development of biobased economy and resource recovery strategies.IMPORTANCEThe diverse metabolic capacities found in microbial communities expand the possibilities of microbial biotechnological exploitation. In this study, we demonstrate that Rhodospirillum rubrum and Rhodobacter capsulatus, two purple non-sulfur bacteria, adopt different metabolic strategies for sugar assimilation. These differences allow them to benefit from each other, resulting in enhanced carbon yield and productivity compared to pure cultures. We also showed that the trophic link between both species can be scaled up in a photobioreactor system. Understanding these interactions expands the potential for designing microbial consortia optimized for the valorization of carbohydrate-rich waste streams using purple non-sulfur bacteria.},
}

@article {pmid41683185,
year = {2026},
author = {Song, D and Song, L and Zhong, X and Wu, Y and Zhang, Y and Yang, L},
title = {Integrated Molecular Informatics and Sensory-Omics Study of Core Trace Components and Microbial Communities in Sauce-Aroma High-Temperature Daqu from Chishui River Basin.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683185},
issn = {2304-8158},
support = {MTXYTD202501//Science and Technology Innovation Team of Moutai Institute/ ; QianKeHeJiChu-ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; ZunShiKeHe HZ Zi[2023]112//The Fund of Zunyi Technology and Big data Bureau, Moutai Institute Joint Science and Technology Research and Development Project/ ; mygccrc[2022]011, mygccrc[2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute & Guangdong Li'er'an Chemical Industry Group Co., Ltd/ ; },
abstract = {Flavor-relevant trace volatiles and microbial communities were examined in six sauce-aroma high-temperature Daqu samples. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) quantified 210 trace volatile compounds across 14 chemical classes. Orthogonal partial least squares discriminant analysis (OPLS-DA) with variable importance in projection (VIP) screening was integrated with sensory scoring, correlation analysis, and molecular docking to an olfactory receptor model. Volatile profiles showed clear stratification in total abundance. Pyrazines dominated the high-total group. Tetramethylpyrazine served as a major driver. Sensory evaluation indicated that aroma explained overall quality best. (E)-2-pentenal and dimethyl trisulfide showed significant positive associations with aroma and overall scores. In the olfactory receptor, the polar residue module that provides directional constraints for Daqu odor activation was formed by Ser75, Ser92, Ser152, Ser258, Thr74, Thr76, Thr98, Thr200, Gln99, and Glu94. The hydrogen-bond or charge network was further reinforced by Arg150, Arg262, Asn194, His180, His261, Asp182, and Gln181. The core discriminant set comprised acetic acid, hexanoic acid, (E)-2-pentenal, nonanal, decanal, dimethyl trisulfide, trans-3-methyl-2-n-propylthiophane, 2-hexanone oxime, ethyl linoleate, propylene glycol, 2-ethenyl-6-methylpyrazine, 4-methylquinazoline, 5-methyl-2-phenyl-2-hexenal, and 1,2,3,4-tetramethoxybenzene. Sequencing revealed higher bacterial diversity than fungal. Bacillus and Kroppenstedtia were dominant bacterial genera. Aspergillus, Paecilomyces, Monascus, and Penicillium were major fungal genera. Correlation patterns suggested that Bacillus and Monascus were positively linked to acetic acid and 1,2,3,4-tetramethoxybenzene. Together, these results connected chemical fingerprints, sensory performance, receptor-level plausibility, and microbial ecology. Concrete targets are provided for quality control of high-temperature Daqu.},
}

@article {pmid41683077,
year = {2026},
author = {Jiang, X and Li, X and Song, P and Dou, Y and Xue, J and Wu, Z and Ma, S and Wei, W and Zheng, W and Dou, S and Dong, L},
title = {Analysis of Microbial Interactions During the Production of Chinese Ethnic Fermented Foods.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683077},
issn = {2304-8158},
support = {No.2025-MSLH-016//Liaoning Provincial Science and Technology Plan Joint Plan (Natural Science Foundation-General Program)/ ; 2014020134//Natural Science Foundation of Liaoning Province/ ; JYTMS20230376//Liaoning Provincial Department of Education University Basic Scientific Research Surface Project/ ; },
abstract = {Food fermentation is an ancient bioprocess characterized by complex biochemical transformations driven primarily by microbial communities. Across the diverse regions of China, various ethnic groups have developed a rich array of traditional fermented foods through long-term practical experience. These foods are integral to local culinary heritage and provide valuable systems for studying microbial ecology and function. From the perspective of microbial interactions, this review summarizes key concepts and major interaction types-including mutualism, commensalism, and competition-and describes how bacteria, yeasts, and molds interact via metabolic division of labor to drive substrate conversion, flavor formation, preservation, and biosynthesis of functional compounds. Focusing on four representative ethnic fermented foods-Dong fermented fish, Mongoslian milk curd, Miao sour soup, and Manchurian kombucha-we analyze how microbial interactions contribute to product quality, safety, and sensory attributes. Given current challenges in industrializing traditional fermented foods, such as poor standardization and variable quality, we propose future research directions centered on modern microbiome tools, designed microbial consortia, and process optimization. This work aims to provide a scientific foundation and practical strategies for modernization and quality improvement of traditional fermented foods.},
}

@article {pmid41681446,
year = {2026},
author = {Onbaşılar, EE and Yalçın, S and Batur, B and Yalçın, S and Kılıçlı, İB and Bakıcı, C and Bakır, B and Kartal, YK and Sel, T},
title = {Effects of Xylanase and Protease Supplementation on Growth Performance, Meat Quality, Gut Health, Cecal Fermentation, and Bone Traits in Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030465},
pmid = {41681446},
issn = {2076-2615},
abstract = {This study investigated the effects of dietary xylanase and protease supplementation, applied individually or in combination, on growth performance, intestinal characteristics, gut fermentation, meat quality, and skeletal traits in broiler chickens. A total of 540-day-old male broiler chicks were allocated to six experimental groups and fed a control corn-soybean meal-based diet or diets supplemented with xylanase, protease, or a xylanase-protease combination. Enzyme supplementation significantly improved body weight gain and feed efficiency, particularly between days 22 and 42, and reduced intestinal digesta viscosity. Improvements in gut morphology were reflected by increased villus height and villus-to-crypt ratios, accompanied by higher cecal total volatile fatty acid concentrations, increased Lactobacillus populations, and reduced coliform counts. In contrast, breast meat physicochemical composition and antioxidant status were not affected by dietary treatments. Skeletal development was positively influenced, with improvements observed in selected morphometric and structural bone traits. Overall, dietary xylanase and protease supplementation enhanced broiler performance and skeletal development primarily through improved digestive efficiency and favorable modulation of gut morphology, microbial ecology, and intestinal fermentation, without adverse effects on meat quality.},
}

@article {pmid41681371,
year = {2026},
author = {Tang, D and Chen, S and Tang, C and Li, X and Li, M and Li, X and Zhang, K and Ma, J},
title = {The Analysis of Transcriptomes and Microorganisms Reveals Differences Between the Intestinal Segments of New Zealand Rabbits.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030390},
pmid = {41681371},
issn = {2076-2615},
support = {2021YFYZ0009//Main livestock and poultry molecular breeding platform (Breeding research project)/ ; CARS-43-A-3//Supported by the earmarked fund for China Agriculture Research System/ ; },
abstract = {This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine.},
}

@article {pmid41680172,
year = {2026},
author = {Lu, Q and Wang, K and Gu, S and Ma, J and Cui, D and Chi, Z and Li, B and Zai, X and Wang, N and Wang, T and Dou, Z and Zhang, F and Geisen, S and Raaijmakers, JM and Song, C and Zuo, Y},
title = {Siderophore-producing Bacillus and free-living nematodes are associated with soil suppressiveness to banana root-knot nematodes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69647-y},
pmid = {41680172},
issn = {2041-1723},
support = {No. 32372810//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 32302668//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 42577142//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The control of soil-borne diseases is crucial for ensuring global food security. Here, we investigate the impact of the root-knot nematode (Meloidogyne) on banana continuous cropping over a period of 11 years. The results show significant root infestation initially, but disease incidence declined markedly from the 7th cropping year onwards. Soil community profiling revealed that this intriguing onset of nematode suppressiveness was associated with changes in free-living nematode populations and rhizosphere microbiome composition. Rhizosphere microbiome analyses and strain isolation pinpointed Bacillus velezensis as a keystone taxon in soil suppressiveness to Meloidogyne. Genomics, metabolomics and bioassays validated the suppressive effects of B. velezensis against Meloidogyne and identified the siderophore bacillibactin as key metabolite with repellent and nematicidal activities. By integrating long-term field studies with multi-omics approaches, this study uncovered co-occurring increases in specific rhizobacterial genera and free-living nematodes associated with reduced root-parasitic nematode populations, offering valuable insights for sustainable agriculture.},
}

@article {pmid41679819,
year = {2026},
author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M},
title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124886},
doi = {10.1016/j.carbpol.2026.124886},
pmid = {41679819},
issn = {1879-1344},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation & purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; },
abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.},
}

*Gastrointestinal Microbiome/drug effects
*Galactans/chemistry/pharmacology/isolation & purification
Fermentation
*Agaricales/chemistry
Molecular Docking Simulation
Fatty Acids, Volatile/metabolism
Prebiotics

@article {pmid41679575,
year = {2026},
author = {Kovarova, A and Ryan, K and Tumeo, A and McDonagh, F and Clarke, C and Cormican, M and Miliotis, G},
title = {Emergence of dual β-lactam and Colistin resistance via blaFRI-8 and mcr-10.2 co-carriage on an IncFII family plasmid in Enterobacter vonholyi.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105899},
doi = {10.1016/j.meegid.2026.105899},
pmid = {41679575},
issn = {1567-7257},
abstract = {OBJECTIVES: Enterobacter vonholyi isolate E323169 represents a rare case of co-carriage of the antimicrobial resistance genes (ARGs) blaFRI-8, mcr-10.2, isolated from a clinical rectal swab. E323169 represents one of only 11 known E. vonholyi genomes. To date, within the NCBI Pathogen Detection resource, blaFRI-8 was identified in three assemblies and mcr-10.2 in two. In that dataset, blaFRI-8 co-occurred with an mcr-10 hit only once (Enterobacter asburiae). This study analyzes the genomic, phenotypic and epidemiological importance of this rare co-occurrence.

METHODS: Species identification for E323169 was initially assigned by MALDI-TOF and subsequently confirmed using a multifactorial genomic workflow. Antimicrobial susceptibilities were determined by MIC assay. The genome of E323169 was sequenced on an Illumina-NextSeq-1000, assembled, and annotated for ARGs, virulence factors, and plasmid replicons detection. Comparative phylogenomics used all canonical E. vonholyi RefSeq assemblies, and NCBI metadata were analysed for plasmid distributions of blaFRI-8 and mcr-10.2.

RESULTS: E323169 carried six ARGs: four chromosomally encoded (blaACT-91, fosA, oqxA10, oqxB9) and two plasmid-borne (blaFRI-8 and mcr-10.2) co-located on IncFII(p14)_1_p14 replicon. Additional plasmid replicons: Col(MG828)_1 and ColRNAI_1 were also identified. By mining the NCBI Pathogen Detection pipeline, we identified blaFRI-8 on IncFII replicon in E. asburiae JBIWA002, and mcr-10.2 on a multi-replicon (IncFIB/IncFII) plasmid in E. kobei 11,778-yvys.

CONCLUSION: This report, to our knowledge, represents the first E. vonholyi isolate co-harboring blaFRI-8 and mcr-10.2 on a single IncFII family plasmid in a non Enterobacter cloacae complex species, showing the widening host range of plasmid-mediated resistance to carbapenems/colistin. These findings suggest IncFII-family plasmids as recurrent scaffolds for the accumulation of high-impact resistance determinants in Enterobacter and suggest that monitoring IncFII backbones may provide an early warning signal for future convergence events.

IMPACT STATEMENT: The detection of Enterobacter vonholyi across human, animal, plant, and environmental sources underscore its relevance within a One Health framework, highlighting the potential for cross-sectoral circulation of antimicrobial resistance. The convergence of blaFRI-8 and mcr-10.2 on an IncFII plasmid in E. vonholyi exposes an unrecognized reservoir of last-line resistance in a species prone to misidentification. Together, these findings emphasize the importance of integrating genomic surveillance into routine diagnostics to identify hidden reservoirs of carbapenem and colistin resistance and to strengthen infection prevention strategies before wider dissemination occurs.},
}

@article {pmid41677726,
year = {2026},
author = {Zeng, T and Zuo, L and Yu, Q and Wu, Q and Bao, Z and Xiong, H and Luo, M and Li, B},
title = {Role and Mechanisms of Gut Microbiota in Infectious Diseases: Recent Evidence from Animal Models.},
journal = {Biology},
volume = {15},
number = {3},
pages = {},
pmid = {41677726},
issn = {2079-7737},
support = {XGKJ2024010037//Xiaogan Municipal Bureau of Science and Technology (Hubei Province， China)/ ; 2025K009//Hubei Small Town Development Research Center, Hubei University of Engineering/ ; },
abstract = {Infectious diseases present persistent and complex challenges to global public health, with conventional antibiotic therapies increasingly limited by antimicrobial resistance, microbiota disruption, and adverse effects. There is a critical need to explore complementary strategies that augment host defense mechanisms without exacerbating these limitations. Accumulating evidence underscores the integral role of the gut microbiota-a diverse microbial ecosystem within the gastrointestinal tract-in regulating systemic immunity and pathogen susceptibility. This review synthesizes recent advances from animal models to delineate the multi-faceted mechanisms by which commensal microbes and their metabolites confer protection against enteric and respiratory infections. Key processes include competitive exclusion for nutrients and ecological niches, production of antimicrobial compounds, reinforcement of intestinal barrier integrity, and orchestration of local and systemic immunity via gut-lung axes. We further discuss the potential of microbiota-targeted interventions to enhance treatment efficacy and patient outcomes. By integrating mechanistic insights with translational applications, this review aims to inform the rational design of next-generation anti-infective strategies grounded in microbial ecology and host immunobiology.},
}

@article {pmid41675709,
year = {2025},
author = {Lin, W and Niu, M and Mu, C and Wang, C and Ye, Y},
title = {Key species drive community and functional stability of segment-specific gut microbiomes after the swimming crab molting.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e51},
pmid = {41675709},
issn = {2996-9514},
abstract = {Molting is a crucial process for crab growth and development. However, the impacts of molting on the structure and function of the gut bacterial community in swimming crab Portunus trituberculatus are poorly understood. Then, dynamic changes in the microbiotas of gut segments (foregut, midgut, and hindgut) after molting were investigated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. We highlight the segment-specific responses in bacterial community compositions, alpha-diversity, and co-occurrence patterns, emphasizing the significant impact of hindgut bacteria on the analysis of the whole gut. The identification of enriched and emerged species and their source, coupled with insights into functional stability and multifunctionality, adds granularity to our understanding of postmolt microbial ecology. We offer potential keys to driving microbial community succession. These findings provide essential insights into the stability and dynamics of gut microbiota, which are crucial for both ecological understanding and sustainable management of crab probiotic regulation.},
}

@article {pmid41674154,
year = {2026},
author = {Măgălie, A and Marantos, A and O'Brien, JM and Schwartz, DA and Marchi, J and Lennon, JT and Weitz, JS},
title = {Phage infection fronts trigger early sporulation and viral entrapment in bacterial populations.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag023},
pmid = {41674154},
issn = {1751-7370},
abstract = {Bacteriophage (phage) infect, lyse, and propagate within bacterial populations. However, physiological changes in bacterial cell state can protect against infection even within genetically susceptible populations. One such example is the generation of endospores by Bacillus and its relatives, characterized by a reversible state of reduced metabolic activity that protects cells against stressors including desiccation, energy limitation, antibiotics, and infection by phage. Here we tested how sporulation at the cellular scale impacts phage dynamics at population scales when propagating amongst B. subtilis in spatially structured environments. Plaques resulting from infection and lysis were approximately 3-fold smaller on lawns of spore-forming bacteria vs. non-spore-forming bacteria. Analysis of plaque growth revealed that final plaque size was reduced due to an early termination of expanding phage plaques rather than the reduction of plaque growth speed. Microscopic imaging of the plaques revealed "sporulation rings", i.e., spores enriched around plaque edges relative to phage-free regions. We developed a series of mathematical models of phage, bacteria, spore, and small molecules that recapitulate plaque dynamics. We show evidence that phage infections trigger the formation of sporulation rings that reduce the productivity of phage infections and halt plaque spread even when resources are available for infection and lysis further away from plaque centers. Moreover, sporulation rings are also enriched in viable virospores, suggesting that although dormancy limits phage infections at population scales in the near-term, viruses may co-opt phage-avoidance strategies to re-emerge over the long-term, opening new avenues to explore the entangled fates of phages and their bacterial hosts.},
}

@article {pmid41673345,
year = {2026},
author = {Lafont, A and Violle, C and Ranchou-Peyruse, M and Guignard, M and Mura, J and Fargetton, T and Cézac, P and Ranchou-Peyruse, A},
title = {Successional Trajectories of Deep Subsurface Microbiomes in Response To Experimental Dihydrogen Injection.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02697-3},
pmid = {41673345},
issn = {1432-184X},
support = {ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; },
abstract = {Converting pre-existing gas storage facilities to dihydrogen storage raises critical questions about storage quality and dihydrogen consumption by prokaryotes. To investigate biologically driven changes during such transitions, we analyzed data from five dihydrogen pulse experiments conducted in pressurized bioreactors that replicate deep aquifer pressure and temperature conditions. Our goal was to determine whether consistent community-level responses to dihydrogen injection could be identified. We found that dihydrogen exposure consistently led to a decline in fermentative ASVs, likely driven by environmental filtering. Hydrogenotrophic sulfate reducers initially dominated in some experiments, with total sulfate depletion observed in certain cases, followed by the emergence of methanogenic archaea. In some instances, a succession pattern involving Thermodesulfovibrio and Methanothermobacter appeared across taxonomically distinct communities, suggesting deterministic ecological processes. Additionally, we observed potential dispersal limitation and selection pressures, possibly linked to pH shifts caused by autotrophy. These findings underscore the importance of considering microbial dynamics in dihydrogen storage strategies in deep aquifers and suggest that, despite initial variability, predictable ecological succession may occur under specific geochemical conditions.},
}

@article {pmid41673333,
year = {2026},
author = {Lu, L and Wang, X and Qin, Y and Xiao, Y and Zhang, Y and Ma, H and Wang, D and Li, Z},
title = {Hydrological Fragmentation Driving Microbial Carbon Necromass Reduction in Columnar Sediments: Evidence from CAZyme Genomic Signatures in Cascade Reservoirs.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02705-6},
pmid = {41673333},
issn = {1432-184X},
support = {52470202//National Natural Science Foundation of China/ ; U2340222//National Natural Science Foundation of China/ ; NBWL202200489 and 202403005//China Three Gorges Corporation/ ; 309GJHZ2024110GC//Chinese Academy of Sciences/ ; },
abstract = {Microbial necromass carbon (MNC), a key component of soil organic carbon, plays a vital role in aquatic carbon sequestration. Its accumulation and transformation are highly sensitive to environmental changes, particularly in reservoir sediments-critical zones for organic matter storage and biogeochemical cycling. This study investigated the vertical distribution and regulatory mechanisms of MNC in cascade reservoir systems through sediment analysis and metagenomic sequencing. Our findings reveal that MNC constitutes 15 ~ 35% of total sediment organic carbon (SeOC) , with fungal-derived necromass consistently dominating over bacterial contributions. Metagenomic data highlight distinct functional potentials in carbon cycling, showing that bacterial necromass exhibits higher lability than fungal necromass, as evidenced by shifts in carbohydrate-active enzyme (CAZyme) gene abundances-particularly those involved in glucan and peptidoglycan degradation. Notably, cascade damming introduced spatial heterogeneity in MNC distribution , with downstream reservoirs experiencing reduced MNC accumulation due to altered hydrological connectivity and nutrient regimes. These results underscore the pivotal role of MNC in aquatic carbon storage while highlighting the complex interplay between environmental factors, microbial metabolic traits, and anthropogenic disturbances in regulated river systems. Therefore, our findings demonstrate that fungal necromass is a dominant and relatively stable component of sediment carbon, and its dynamics must be integrated to accurately assess and predict carbon sequestration in dammed rivers.},
}

@article {pmid41671169,
year = {2026},
author = {Saati-Santamaría, Z and Pérez-Mendoza, D and Khashi U Rahman, M and de Sousa, BFS and Montero-Calasanz, MDC and Rey, L and Roy, S and Sanjuán, J and García-Fraile, P},
title = {Evolutionary mechanisms underlying bacterial adaptation to the plant environment.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag005},
pmid = {41671169},
issn = {1574-6976},
abstract = {Plants and bacteria have coevolved over hundreds of millions of years, forming complex associations ranging from mutualism to pathogenicity that are essential for plant survival and ecosystem function. Bacterial adaptation to plant environments involves dynamic evolutionary mechanisms including horizontal gene transfer, gene regulation, and metabolic specialization, enabling bacteria to persist and specialize within diverse plant-associated niches. Here we review how evolutionary forces such as selection, drift, and gene flow shape bacterial genomes, regulatory networks, and ecological strategies in response to plant-imposed pressures, underpinning both beneficial and pathogenic lifestyles. Understanding these processes provides a unified evolutionary framework for bacterial adaptation to plants and highlights their implications for sustainable agriculture and microbiome-based innovations.},
}

@article {pmid41668299,
year = {2026},
author = {Frings, DM and Mellinger, JM and Drace, KM},
title = {Microbial Diversity Across Chemolithotrophic and Phototrophic Biofilms in Cold Sulfur Springs.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70223},
pmid = {41668299},
issn = {2045-8827},
mesh = {*Biofilms/growth & development ; *Sulfur/metabolism ; RNA, Ribosomal, 16S/genetics ; Alabama ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phototrophic Processes ; *Microbiota ; Phylogeny ; *Biodiversity ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; Chemoautotrophic Growth ; Cold Temperature ; *Natural Springs/microbiology ; Sequence Analysis, DNA ; Oxidation-Reduction ; },
abstract = {Sulfur-rich environments host specialized microbial communities that drive key biogeochemical processes, particularly sulfur cycling. While sulfur-oxidizing microbiota from hydrothermal vents and volcanic systems are well studied, microbial communities in cold terrestrial sulfur springs remain less understood. In this study, we used 16S rRNA gene sequencing to examine how sulfur availability and environmental conditions shape microbial assemblages across different biofilm types in a cold sulfur spring system at Blount Springs, Alabama (33.9301° N, 86.7928° W). Sulfur-oxidizing chemolithotrophs, including Sulfurovum and Halothiobacillus, represented the majority of the recovered reads in sulfur-rich white biofilms, while purple phototrophic biofilms were enriched with anoxygenic sulfur-oxidizing bacteria, such as Chromatium and Chlorobium. Nonsulfur biofilms from adjacent environments displayed greater microbial diversity, including a high abundance of photosynthetic diatoms, like, Melosira. Notably, Sulfurovum was abundant across both sulfur-rich and phototrophic niches, suggesting ecological flexibility and a central role in sulfur metabolism. These findings highlight the influence of sulfur chemistry and light availability in structuring microbial communities and contribute to a broader understanding of microbial adaptation and sulfur cycling in cold sulfur spring ecosystems.},
}

*Biofilms/growth & development
*Sulfur/metabolism
RNA, Ribosomal, 16S/genetics
Alabama
*Bacteria/classification/genetics/metabolism/isolation & purification
Phototrophic Processes
*Microbiota
Phylogeny
*Biodiversity
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
Chemoautotrophic Growth
Cold Temperature
*Natural Springs/microbiology
Sequence Analysis, DNA
Oxidation-Reduction

@article {pmid41668183,
year = {2026},
author = {Zhang, Y and Jing, G and Chen, R and Gong, Y and Li, Y and Wang, Y and Wang, X and Zhang, J and Mao, Y and He, Y and Zheng, X and Wang, M and Yuan, H and Xu, J and Sun, L},
title = {RamEx: an R package for high-throughput microbial ramanome analyses with accurate quality assessment.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02339-3},
pmid = {41668183},
issn = {2049-2618},
abstract = {BACKGROUND: Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped.

RESULTS: Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets-including pathogenic bacteria, probiotic strains, and yeast fermentation populations-demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic-associated fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++ acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour.

CONCLUSIONS: By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx. Video Abstract.},
}

@article {pmid41675503,
year = {2025},
author = {Gu, S and Shao, J and He, R and Xiong, G and Qu, Z and Shao, Y and Yu, L and Zhang, D and Wang, F and Xu, R and Guo, P and Xi, N and Li, Y and Wu, Y and Wei, Z and Li, Z},
title = {Forging the iron-net: Towards a quantitative understanding of microbial communities via siderophore-mediated interactions.},
journal = {Quantitative biology (Beijing, China)},
volume = {13},
number = {2},
pages = {e84},
pmid = {41675503},
issn = {2095-4697},
abstract = {Iron is a critical yet limited nutrient for microbial growth. To scavenge iron, most microbes produce siderophores-diverse small molecules with high iron affinities. Different siderophores are specifically recognized and uptaken by corresponding recognizers, enabling targeted interventions and intriguing cheater-producer dynamics. We propose constructing a comprehensive iron interaction network, or "iron-net", across the microbial world. Such a network offers the potential for precise manipulation of the microbiota, with conceivable applications in medicine, agriculture, and industry as well as advancing microbial ecology and evolution theories. Previously, our successful construction of an iron-net in the Pseudomonas genus demonstrated the feasibility of coevolution-inspired digital siderophore-typing. Enhanced by machine learning techniques and expanding sequencing data, forging such an iron-net calls for multidisciplinary collaborations and holds significant promise in addressing critical challenges in microbial communities.},
}

@article {pmid41667848,
year = {2026},
author = {González-Azcona, C and Solano-González, F and Jiménez-Ruiz, S and Santos, N and Marañón-Clemente, I and Álvarez-Gómez, T and Eguizábal, P and Alonso, CA and Benito, D and Zarazaga, M and Torres, C and Lozano, C},
title = {High Nasal Carriage of MRSA-mecC in Wild Rabbits in the Iberian Peninsula: a Wildlife Reservoir?.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02713-6},
pmid = {41667848},
issn = {1432-184X},
}

@article {pmid41666926,
year = {2026},
author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P},
title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.12.051},
pmid = {41666926},
issn = {1097-4172},
abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.},
}

@article {pmid41666603,
year = {2026},
author = {Cristino, S and Caligaris, L and Salaris, S and Derelitto, C and Bonincontro, C and Marino, F and Grottola, A and Girolamini, L},
title = {Legionella petroniana sp. nov., a novel species isolated in Bologna, Italy: taxonomic, genomic and ecological insights in the era of environmental change.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126694},
doi = {10.1016/j.syapm.2026.126694},
pmid = {41666603},
issn = {1618-0984},
abstract = {This study presents the characterization of a novel Legionella species isolated in Italy over three different years from one company and two hospitals. Starting from standard techniques such as culture of water samples, agglutination test, MALDI-TOF MS and gene sequencing analysis used to identify the isolates, genomic and metabarcoding approaches were subsequently employees to further characterize the species. Legionella contamination ranged from 400 to 700 CFU/L. The tiny colonies displayed atypical morphology compared to typical Legionella features, although they grew on BCYE medium supplemented with L-cysteine. Microscopic and phenotypic analyses revealed Gram-stain negative, Ziehl-Neelsen-negative, rod-shaped, motile cells capable of growing at 32-37 °C, including on selective media such as GVPC and MWY. The isolates tested positive for oxidase and gelatinase activity. Fatty acid profiling identified the dominant components as Summed Features 3 (C16:1 ω7c/C16:1 ω6c, 28.9%), C16:0 iso (18.4%), and C15:0 anteiso (15.4%). Ubiquinone Q13 was the major quinone. Sequence analysis of the mip and rpoB genes showed 98.2% and 95.1% similarity, respectively, to L. feeleii (WO-44C ATCC 35072[T]). Whole genome sequencing (WGS) revealed a GC content of 41.5%, a dDDH value of ≤54.9%, and an ANI of 94.06% with L. feeleii (WO-44C ATCC 35072[T]), supporting the classification of a novel species within the genus Legionella. Furthermore, taxonomic resolution of water samples revealed the presence of 168 bacterial genera, including several respiratory, opportunistic, and zoonotic pathogens, as well as seven Legionella species. The name Legionella petroniana sp. nov. is proposed, with strain 31fI33[T] (=DSM 114357[T]=CCUG 76442[T]) designated as type strain.},
}

@article {pmid41663799,
year = {2026},
author = {Gao, S and Zhao, W and Guan, X and Zhao, Z and Wang, B and Xiao, Y and Zhang, G and Pan, Y and Sun, H and Jiang, P and Mi, R and Jiang, J and Zhou, Z},
title = {Stronger Adaptability of Eukaryotic Communities than Prokaryotes in Seawater across an Extensive Salinity Gradient.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {28},
number = {1},
pages = {32},
pmid = {41663799},
issn = {1436-2236},
support = {U24A200104//National Natural Science Foundation of China/ ; XLYC2203191//Liaoning Revitalization Talents Program/ ; 2023JH1/10200007//Science and Technology Project of Liaoning Province/ ; 2023RJ007//Dalian Science and Technology Talent Innovation Support Program/ ; 2025HQ1304//Fundamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; },
mesh = {*Salinity ; *Seawater/microbiology/chemistry ; *Eukaryota/physiology/genetics/classification ; *Prokaryotic Cells/physiology ; *Adaptation, Physiological ; *Microbiota ; Biodiversity ; },
abstract = {Researching microbial ecology in extreme environments is crucial for advancing the basic ecological theory and exploring their potential applications in biotechnology. The salt drying system provides an accessible but harsh environment that covers a maximum salinity gradient. In this study, we conducted a comparative analysis of the salinity adaptation and assembly mechanisms of prokaryotic and eukaryotic communities in several salt drying tanks using high-throughput amplicon sequencing and multiple ecological analyses. The beta diversity analysis, based on the unweighted and weighted Unifrac distances, revealed significant variations in microbial community compositions along the salinity gradient, with stronger influences on prokaryotes. Species turnover was the primary mechanism driving the beta diversity patterns, which was regulated by the local species pool. Further comparisons of multiple niche and adaptation indices indicated that seawater eukaryotic communities exhibited stronger salinity adaptability than prokaryotes. In addition, the beta deviation index suggested that heterogeneous processes shaped the microbial communities. Moreover, the neutral community model showed higher dispersal ability of eukaryotes than prokaryotes. Also, they were stochastic and deterministic dominant communities along the salinity gradient, respectively. Overall, our findings contributed significantly to understanding the microbial ecology in relation to salinity gradients.},
}

*Salinity
*Seawater/microbiology/chemistry
*Eukaryota/physiology/genetics/classification
*Prokaryotic Cells/physiology
*Adaptation, Physiological
*Microbiota
Biodiversity

@article {pmid41661138,
year = {2026},
author = {Bäcker, M and Doekes, HM and Garza, DR and Meijer, J and van Vliet, S and Allen, RJ and Hogeweg, P and Dutilh, BE and van Dijk, B},
title = {Spatial structure: Shaping the ecology and evolution of microbial communities.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf067},
pmid = {41661138},
issn = {1574-6976},
abstract = {Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.},
}

@article {pmid41660022,
year = {2026},
author = {Shaji, A and Ramachandran, AK and Chandrasekaran, N and Savarimalai, KC and Adhira, R},
title = {A cross-sectional metagenomic analysis of the microbial ecology in symptomatic apical periodontitis - An in vivo study.},
journal = {Journal of conservative dentistry and endodontics},
volume = {29},
number = {1},
pages = {60-64},
pmid = {41660022},
issn = {2950-4708},
abstract = {BACKGROUND: Symptomatic apical periodontitis (SAP) is a painful inflammatory disease driven by root canal infection. A detailed understanding of its microbial ecology, compared to a noninfectious baseline, is needed.

AIMS: This study aimed to characterize the microbial ecology of SAP using 16S ribosomal (RNA) 16S rRNA metagenomic sequencing and compare it to control teeth undergoing root canal treatment after trauma.

MATERIALS AND METHODS: This cross-sectional study included 10 patients with SAP and 10 control patients. Pulpal samples were collected aseptically. Microbial DNA was extracted, and the full-length 16S rRNA gene was sequenced through Oxford Nanopore Technology. Analysis was performed using QIIME2.

STATISTICAL ANALYSIS USED: Microbial abundances and diversity indices were compared using an independent samples t-test or Mann-Whitney U-test (P < 0.05 significant).

RESULTS: The SAP microbiome was dysbiotic and enriched in anaerobes. Veillonella parvula was highly abundant in SAP (mean 13.1%) but absent in controls. Species like Dialister pneumosintes and Prevotella melaninogenica were found almost exclusively in SAP. Commensals including Faecalibacterium prausnitzii were significantly reduced.

CONCLUSION: SAP is associated with a distinct microbial signature defined by the enrichment of anaerobic pathobionts and a loss of commensals, revealing a polymicrobial, dysbiotic community.},
}

@article {pmid41659429,
year = {2026},
author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT},
title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.27.701854},
pmid = {41659429},
issn = {2692-8205},
abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae . At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella , and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae . By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.},
}

@article {pmid41655393,
year = {2026},
author = {Tao, S and Gao, J and He, B and Zhang, T and Chen, B and Yin, Y and Shi, J and Mao, Y and Hu, L and Jiang, G},
title = {Understanding microbial mercury methylation via metabolic pathways: Processes associated with one-carbon metabolism.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141373},
doi = {10.1016/j.jhazmat.2026.141373},
pmid = {41655393},
issn = {1873-3336},
abstract = {Microbial mercury methylation is the key step responsible for the high toxicity and bioaccumulation potential of mercury. Since metabolic pathways serve as a bridge between mercury methylation and microbial activity, studying mercury methylation from the perspective of metabolic pathways will offer valuable insights into its underlying mechanism and integration into microbial metabolism. This review aims to summarize current understanding of the metabolic pathways that supply methyl groups for mercury methylation and to elucidate the relationships between them. The acetyl-coenzyme A pathway is extensively studied and well recognized for its role in methyl group transfer. The Wolfe cycle, representing the methanogenesis pathway in methanogenic archaea, has recently been identified as a distinct source of methyl groups contributing to mercury methylation. In addition, at the chemical level, S-adenosyl-L-methionine from the methionine biosynthesis pathway has been shown to donate a methyl group to mercury via the HgcAB complex, although this process has not yet been validated in vivo. Finally, the dimethylsulfoniopropionate degradation pathway is proposed as a speculative and potential route for mercury methylation. By integrating these pathways, we provide a comprehensive overview of their interconnections, demonstrating that microbial mercury methylation is embedded within the broader framework of one-carbon metabolism. The close association between methylation and one-carbon flux suggests that mercury methylation may function as an interspecies competition strategy that enhances microbial survival in mercury-rich environments. This pathway-centered perspective advances our understanding of the biochemical basis of microbial mercury methylation and may inform future research into its environmental controls and microbial ecology.},
}

@article {pmid41654744,
year = {2026},
author = {Wünschmann, T and Ghaderiardakani, F and Homeier-Bachmann, T and Quartino, ML and Wichard, T and Busch, A},
title = {Genomic and functional characterization of Pseudosulfitobacter pseudonitzschiae BPC-C4-2: a growth-promoting symbiont in Antarctic Ulva communities.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12626-w},
pmid = {41654744},
issn = {1471-2164},
}

@article {pmid41653958,
year = {2026},
author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ},
title = {Household Environmental Characteristics Influence House Dust Metagenome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123889},
doi = {10.1016/j.envres.2026.123889},
pmid = {41653958},
issn = {1096-0953},
abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5,821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.},
}

@article {pmid41653300,
year = {2026},
author = {Zenelt, W and Hoffmann, A and Sadowska, K and Krawczyk, K},
title = {Insects as a New Source of Plant Growth Promoting Bacteria - Review.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02692-0},
pmid = {41653300},
issn = {1432-184X},
}