@article {pmid42786172,
year = {2026},
author = {Prins, V and Tedersoo, L and Mikryukov, V and Paiste, P and Sepp, M and Grossart, H and Kisand, V and Laas, A and Tammert, H and Abarenkov, K and Agan, A and Agasild, H and Agha, R and Alatalo, J and Alvarez-Manjarrez, J and Ameryk, A and Anderson, J and Anslan, S and Antão-Geraldes, A and Antosiak, A and Funck, JA and Arias-Real, R and Ariyan, M and Bahram, M and Bansal, S and Bao, R and Beck, S and Bernotas, P and Berry, N and Bertilsson, S and Birnbaum, C and Bonk, M and Borges, AV and Botez, F and Brearley, FQ and Brookes, J and Bruno, D and Budzyńska, A and Bullerjahn, G and Bundschuh, M and Calheiros-Nogueira, B and Calore, R and Capelli, C and Caputo, L and Carballeira, R and Chronis, I and Čiampor, F and Čiamporová-Zaťovičová, Z and Craig, D and Csabai, Z and Cukrov, N and da Silva, L and de Eyto, E and Delgado, J and Dimante-Deimantovica, I and Domaizon, I and Dondajewska-Pielka, R and Dornan, T and Drenkhan, R and Drouillard, K and Duarte, S and Dulya, O and Dzhulai, A and Dziga, D and Egeter, B and Espenberg, M and Färkkilä, S and Fazi, S and Feckler, A and Fenoy, E and Fernandes, I and Ferreira, S and Ferreira, V and Fleituch, T and Fornaroli, R and Freiwald, A and Frenken, T and Gaffney, P and García-Oliva, O and Geara, H and Gkelis, S and Gohar, D and Gołdyn, R and Grandjean, F and Gsell, A and Gutiérrez-Cánovas, C and Haase, P and Hagh-Doust, N and Harris, T and Hashem, A and Havens, S and Heidari, B and Higgins, S and Moghaddam, MH and Ibrahim, A and Jerinkić, D and Jones, S and Kagami, M and Kahar, S and Kangro, K and Kariman, K and Kataržytė, M and Kepfer-Rojas, S and Khan, H and Knoll, LB and Knorrn, A and Kõljalg, U and Konstantinou, D and Kotta, J and Kowalczewska-Madura, K and Kozak, A and Kulawig, B and Kupagme, J and Kušan, I and Laarmaa, R and Laas, P and Langenheder, S and Lanzén, A and Lateef, A and Ligi, M and Löffler, T and Lortou, U and Lujza, K and MacConnell, T and Maček, I and Macreadie, P and Maileht, K and Marazzi, F and Marcello, L and Markovskaja, S and Martin, A and Martínez, S and Mata, V and Matočec, N and McKay, R and McKindles, K and Mehrshad, M and Menéndez, M and Merino, N and Mešić, A and Moctar, S and Moza, M and Nõges, P and Nõges, T and O'Hanlon, R and Öğlü, B and Oja, J and Okello, W and Orav-Kotta, H and Orr, P and Osemwegie, I and Padisák, J and Pajunen, V and Panou, M and Papatheodoulou, A and Pavlovska, M and Pearman, J and Pehlak, H and Peng, X and Pereira, A and Pereira, R and Pernecker, B and Picazo, F and Pinnow, S and Pochekutova, P and Põlme, S and Pontevedra-Pombal, X and Pošta, A and Prekrasna-Kviatkovska, Y and Pruuli, J and Pruuli, M and Pruuli, T and Radoja, N and Rahimlou, S and Rannap, R and Rasconi, S and Rasmussen, A and Remmers, W and Reyes, L and Rhodes, G and Roe, C and Rojas-Castillo, O and Roslin, T and Runnel, K and Rusch, J and Rybak, M and Rychtecký, P and Sahadevan, S and Saitta, A and Salehi-Najafabadi, A and Santi, I and Sarapuu, J and Schäfer, RB and Schneeweiss, A and Scholz, B and Selmeczy, G and Smederevac-Lalić, M and Sommaruga, R and Stetler, J and Stoica, E and Stoll, S and Strand, D and Tamm, M and Tapolczai, K and Tarand, J and Teurlincx, S and Thompson, J and Thomson-Laing, G and Tiirmann, L and Tkalčec, Z and Trbojević, I and Trevathan-Tackett, S and Tsiarta, N and Tuvikene, A and Tuvikene, L and Vacaflores-Argandoña, M and Vahter, T and Vaino, K and Val, AL and Vandergoes, M and Vasemägi, A and Vask, A and Vasquez, M and Veríssimo, J and Vesamäki, J and Virta, L and Visser, P and Viza, A and Vrålstad, T and Ward, CS and Waryszak, P and Wierenga, J and Wilson, P and Wood, S and Woźniczka, A and Wurzbacher, C and Zingel, P and Znachor, P and Dela Cruz, TEE and Panksep, K},
title = {The FunAqua dataset of global fungal biodiversity in aquatic ecosystems.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42786172},
issn = {2052-4463},
mesh = {*Biodiversity ; *Fungi/genetics/classification ; *Ecosystem ; *Water Microbiology ; DNA Barcoding, Taxonomic ; Geologic Sediments/microbiology ; },
abstract = {Advances in high-throughput DNA sequencing technologies have accelerated research on aquatic microorganisms, their diversity, and ecological functions. This has also significantly advanced research on fungi that shape aquatic ecosystems and food webs. Here, we present the FunAqua dataset, which describes global fungal biodiversity in aquatic ecosystems based on eukaryotic long-read metabarcoding data from 1,076 sediment and 1,299 filtered water samples collected across 1,452 sampling sites in 87 countries. We targeted the internal transcribed spacer (ITS) region. In total, 50,152 fungal OTUs were recorded. The sequencing data is accompanied by comprehensive sample metadata, including physicochemical data of water and sediments. The FunAqua dataset provides a new resource for analysing and better understanding the biodiversity of fungi in different types of aquatic habitats across biogeographical regions. The dataset described in this data paper will be periodically updated with additional metabarcoding data.},
}

*Biodiversity
*Fungi/genetics/classification
*Ecosystem
*Water Microbiology
DNA Barcoding, Taxonomic
Geologic Sediments/microbiology

@article {pmid42786257,
year = {2026},
author = {Farsi, DN and Cotter, PD and O'Sullivan, O},
title = {Fermented protein foods as modulators of the gut-muscle axis: mechanisms, evidence, and future directions.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42786257},
issn = {2399-3642},
mesh = {Humans ; *Muscle, Skeletal/physiology/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Fermented Foods ; *Dietary Proteins/metabolism ; },
abstract = {Skeletal muscle has a profound influence on metabolic health, functional capacity and resilience across the lifespan. Beyond dietary protein and physical activity, the gut microbiome may have the capacity to impact skeletal muscle mass and function through the bidirectional network termed the gut-muscle axis (GMA). Fermented protein foods (FPFs) are protein rich matrices transformed by microbial activity that integrate modified protein structures, bioactive peptides, and live microorganisms, or components thereof, which could modulate skeletal muscle physiology. Here, we review mechanistic, preclinical and human evidence concerning the potential of FPFs to influence skeletal muscle health through GMA modulation. Although emerging human studies suggest favourable effects on metabolic regulation, inflammatory pathways and gut microbial ecology, direct evidence that FPFs impact muscle protein synthesis, muscle mass or function remains limited. Furthermore, the literature is characterised by considerable heterogeneity in interventions and outcome measures. Studies integrating comprehensive microbiome characterisation, multi-omics approaches and direct skeletal muscle phenotyping are needed to determine whether FPFs confer advantages over conventional protein foods or more established microbiome targeted strategies such as probiotic supplementation. Such studies will be essential to elucidate their role in targeted nutritional strategies for ageing, metabolic disease, muscle atrophy, and physical performance.},
}

Humans
*Muscle, Skeletal/physiology/metabolism
Animals
*Gastrointestinal Microbiome
*Fermented Foods
*Dietary Proteins/metabolism

@article {pmid42786922,
year = {2026},
author = {van Straalen, KR and Chandran, NS and Fletcher, JM and Giamarellos-Bourboulis, EJ and Rosi, E and Jemec, GBE},
title = {Pathogenesis of hidradenitis suppurativa: From susceptibility to chronicity.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70765},
pmid = {42786922},
issn = {1468-3083},
abstract = {Hidradenitis suppurativa (HS) is a chronic, recurrent inflammatory skin disease characterized by painful nodules, abscesses, draining tunnels and scarring, with substantial effects on quality of life. Although the therapeutic landscape has expanded with biologics targeting TNF, IL-17A and IL-17A/F, many patients do not achieve sustained disease control, and chronic, draining tunnels remain difficult to treat. Recent data support a more integrated view of HS as a heterogeneous, stage-dependent disease in which inherited susceptibility, modifiable risk factors, epithelial dysfunction, immune activation and microbial ecology converge. In this review, we summarize clinically relevant advances in HS epidemiology, genetics, immunopathogenesis and microbiome research. Global studies highlight substantial variation in prevalence, sex distribution and clinical phenotype across populations, suggesting differences in risk architecture and disease expression. Genetic studies have moved the field beyond rare γ-secretase-associated familial disease towards a polygenic model involving follicular and epithelial regulatory programmes, antigen presentation and immune regulation. Single cell and spatial studies further indicate that HS pathogenesis evolves from epithelial stress and perifollicular inflammation in HS-prone skin, through IL-1-, TNF-, neutrophil- and IL-17-associated acute inflammation, towards chronic immune-stromal niches characterized by epithelialized tunnels, B cells, plasma cells, tertiary lymphoid structures, NETosis and fibrosis. In parallel, microbiome studies suggest that dysbiosis, particularly anaerobe-rich and biofilm-like communities within tunnels, acts primarily as an amplifier of chronicity rather than as a proven initiating event. Together, these findings support a shift from single-pathway models towards stage-specific and patient-stratified approaches aimed at earlier diagnosis, rational treatment selection and prevention of irreversible tissue damage.},
}

@article {pmid42787064,
year = {2026},
author = {Guimarães, GNF and Barrett, DW and Gonzalez-Lima, F},
title = {Combined abdominal and transcranial photobiomodulation is associated with fecal microbiome restructuring: a systems microbiology pre-post case report.},
journal = {Frontiers in systems biology},
volume = {6},
number = {},
pages = {1920618},
pmid = {42787064},
issn = {2674-0702},
abstract = {Photobiomodulation (PBM) has been proposed as a non-invasive strategy capable of modulating mitochondrial, inflammatory, vascular, and gut-brain axis-related pathways. However, its potential effects on fecal microbiome ecology in neurobehavioral conditions remain poorly characterized. This case report describes paired fecal microbiome findings before and after a 90-day combined abdominal and transcranial PBM protocol in a 6-year-old female with autism spectrum disorder and chronic constipation. PBM was delivered daily using a 1064-nm near-infrared LED device with 54 mW/cm[2] irradiance, applied for 10 min over the right prefrontal cortex and for 10 min over the infraumbilical and right lower abdomen. Fecal samples collected before and after the intervention were analyzed by 16 S rRNA amplicon sequencing. The baseline sample showed limited taxonomic resolution, with 93.14% assigned to "Other/unclassified," whereas the post-intervention sample showed a more taxonomically resolved microbial profile, including Firmicutes (53.37%), Bacteroidetes (29.66%), Actinobacteria (7.97%), Verrucomicrobia (4.21%), Euryarchaeota (2.89%), Proteobacteria (1.14%), and a markedly reduced unclassified fraction (0.03%) at the phylum level. At the genus level, the post-intervention profile showed detection or increased representation of taxa commonly discussed in relation to gut microbial ecology, mucosal biology, and short-chain fatty acid metabolism, including Faecalibacterium (7.03%), Bifidobacterium (4.25%), Bacteroides (18.82%), Alistipes (5.38%), preserved Akkermansia (3.92%-4.21%), and low-abundance Roseburia. Taxa with context-dependent or uncertain significance, including Sarcina, Collinsella, Parabacteroides, and residual unclassified genera, were also observed and are reported transparently. Caregiver behavioral observations included improved bowel regularity, reduced abdominal distension, more stable mood, reduced irritability and impulsivity, improved communication, and greater social tolerance. The intervention was well tolerated with no reported adverse effects. As a single-patient pre-post case report without sham control, repeated baseline sampling, or functional metagenomic confirmation, these findings cannot establish causality. Nevertheless, they provide a biologically plausible systems-level observation linking combined abdominal and transcranial PBM with a shift in fecal microbiome structure and gastrointestinal-behavioral regulation, supporting future controlled studies integrating longitudinal microbiome profiling, metabolomics, inflammatory biomarkers, autonomic measures, and validated behavioral outcomes.},
}

@article {pmid42787116,
year = {2026},
author = {Doster, E and Pinnell, LJ and Parker, JK and Wolfe, CA and Morley, PS},
title = {Different DNA input amounts and library preparation kits yield comparable resistome characterization using target-enriched metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1907850},
pmid = {42787116},
issn = {1664-302X},
abstract = {INTRODUCTION: Target-enriched metagenomic sequencing improves detection of antimicrobial resistance genes (ARGs) relative to standard shotgun metagenomics, but whether DNA input amount influences resistome characterization has not been systematically evaluated.

METHODS: We evaluated target-enriched sequencing using fecal microbial communities from multiple host species and compared results across library preparation kits, DNA input amounts, and sequencing approaches. Composite fecal samples from livestock and humans and individual canine samples were processed using three library preparation kits and DNA input amounts ranging from 50 to 800 ng.

RESULTS: Target-enriched libraries from composite samples were compared with shotgun metagenomic sequences generated from the same samples. Target-enriched sequencing achieved a 7.9-fold increase in on-target read proportions and detected 12-fold more unique antimicrobial resistance gene groups than shotgun metagenomics. Resistome composition was driven primarily by sample source, which explained 66%-79% of within-species variance, while library preparation kit accounted for 13%-26% and DNA input amount had no consistent effect. Kit-associated differences were systematic and affected primarily low-abundance resistance classes but were small relative to biological variation among samples.

DISCUSSION: These findings demonstrate that target-enriched metagenomic sequencing substantially improves resistome detection and provides comparable resistome characterization DNA input amounts ranging from 50 to 800 ng. Differences associated with library preparation were small relative to biological variation, supporting the flexibility of using differing DNA inputs for resistome characterization.},
}

@article {pmid42787428,
year = {2026},
author = {Patil, S and Rudragouda, CS},
title = {Coffee phytobiome dynamics: integrating multitrophic interactions and plant physiology for climate-resilient production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1951767},
pmid = {42787428},
issn = {1664-302X},
abstract = {Coffee (Coffea arabica L. and Coffea canephora Pierre ex A. Froehner) is a globally important perennial plantation crop that sustains the livelihoods of millions of smallholder farmers while making substantial contributions to agricultural economies worldwide global agricultural economies. Nevertheless, sustainable coffee production is increasingly constrained by climate change, declining soil fertility, emerging pests and diseases and the environmental costs associated with intensive use of synthetic agrochemicals. Recent advances in plant microbiome research have transformed the understanding of coffee from an individual organism to a holobiont, where the host plant and its associated microorganisms operate as an integrated biological system. The coffee phytobiome encompasses diverse microbial communities inhabiting the rhizosphere, rhizoplane, endosphere, phyllosphere, anthosphere, carposphere and spermosphere, together with complex multitrophic interactions involving shade trees, soil fauna, insects and the surrounding environment. These interactions collectively regulate nutrient acquisition, carbon assimilation, water-use efficiency, hormonal balance, stress tolerance, immune responses and overall plant productivity. This review critically examines current advances in multitrophic plant-microbe interactions that influence physiological adaptation in coffee, with particular emphasis on sustainable production under Indian agroecological conditions. It highlights the functional functions of plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), endophytic microorganisms and other beneficial microbes in enhancing root development, nutrient cycling, and resilience to biotic and abiotic stresses. Furthermore, the review evaluates recent progress in metagenomics, metatranscriptomics, metabolomics and microbiome engineering for harnessing indigenous microbial resources. Finally, it outlines future research priorities integrating plant physiology, microbial ecology, systems biology, and precision agriculture to develop climate-resilient, resource-efficient, and environmentally sustainable coffee production systems.},
}

@article {pmid42787483,
year = {2026},
author = {Zarkasi, KZ and Kamal, MHA and Ronidean, MD and Zaludin, MSM and Daud, MF and Purwantisari, S and Ghazali, AHA and Salim, H},
title = {Metagenomic Profiling of Barn Owl (Tyto javanica javanica) Regurgitated Pellets Reveals Spatially Structured Environmental Microbiota in Paddy Agroecosystems.},
journal = {Ecology and evolution},
volume = {16},
number = {9},
pages = {e74429},
pmid = {42787483},
issn = {2045-7758},
abstract = {The tropical barn owl (Tyto javanica javanica) is a major biocontrol agent against rodents in paddy fields. While raptors are frequently monitored for zoonotic diseases, they may also facilitate beneficial microbial redistribution. This study evaluated bacterial communities in barn owl regurgitated pellets to assess their role as environmental biosensors and vectors for microbe dispersal. We collected 90 fresh pellets from three paddy field locations during the growing season. Samples underwent bacterial enumeration and metagenomic sequencing of the 16S rRNA V3-V4 domains via the Illumina MiSeq platform. Results revealed significant spatial variation in bacterial communities across locations (PERMANOVA, F(2, 87) = 3.14, p < 0.05). Firmicutes (28.1%-63.2%) and Proteobacteria (17.7%-45.6%) dominated all sites. Notably, Sporosarcina sp., known for eco-friendly biocementation and soil enhancement, was highly abundant across all locations (up to 40.6%). The high abundance of Escherichia sp. at the AV site (32.1%) highlighted the pellet's ability to capture transient environmental and prey-derived coliforms. Ultimately, these pellets act as critical environmental proxies capturing localized microbiota. This supports the perspective that barn owls contribute significantly more to microbial ecological redistribution than to disease spread, offering valuable agricultural ecological services.},
}

@article {pmid42787749,
year = {2026},
author = {Sun, X and Ma, X and Ma, Y and Wang, X and Li, X and Ji, M},
title = {The oral immune and inflammatory network under circadian clock control.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1894302},
pmid = {42787749},
issn = {1664-3224},
mesh = {Humans ; *Circadian Clocks/immunology ; Animals ; *Inflammation/immunology ; Microbiota/immunology ; *Circadian Rhythm/immunology ; *Mouth/immunology/microbiology ; Homeostasis ; *Mouth Diseases/immunology ; Signal Transduction ; },
abstract = {Circadian rhythms are essential regulators of immune homeostasis, coordinating immune cell functions, inflammatory responses, and tissue repair. Although extensive studies have revealed the importance of circadian regulation in systemic immunity, most mechanistic insights are derived from peripheral immune systems and non-oral tissues. The oral cavity is a unique immune interface continuously exposed to complex microbial communities; however, the role of circadian regulation in oral immune homeostasis and disease development remains poorly understood. This review summarizes the mechanisms by which circadian clocks regulate oral immunity, focusing on immune cell functions, inflammatory responsiveness, tissue homeostasis, and interactions between circadian clock components and inflammatory signaling networks. We further discuss the emerging temporal dynamics of the oral microbiome and the potential effects of host circadian rhythms, feeding schedules, and chrono-nutrition on microbial ecology and immune balance. Current evidence linking circadian disruption with oral diseases, including periodontitis, dental caries, apical periodontitis, Sjögren's syndrome, temporomandibular joint inflammatory disorders, and oral squamous cell carcinoma, is also reviewed, with emphasis on distinguishing direct oral evidence from extrapolated mechanisms. Finally, we highlight circadian-based therapeutic strategies and existing limitations, underscoring the need for longitudinal studies, multi-omics approaches, and personalized circadian interventions in oral medicine.},
}

Humans
*Circadian Clocks/immunology
Animals
*Inflammation/immunology
Microbiota/immunology
*Circadian Rhythm/immunology
*Mouth/immunology/microbiology
Homeostasis
*Mouth Diseases/immunology
Signal Transduction

@article {pmid42788817,
year = {2026},
author = {Ganesan, BK and Mishra, A and Hota, D and Maiti, R},
title = {Non-antibiotic therapeutic approaches for antimicrobial resistance: current evidence and future directions.},
journal = {Expert review of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17512433.2026.2739560},
pmid = {42788817},
issn = {1751-2441},
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is a global health challenge that reduces the effectiveness of existing antibiotics, leading to increased morbidity, mortality and healthcare costs worldwide. The lack of the development of novel classes of antibiotics has led to an increased interest in non-antibiotic therapeutic approaches that focus on bacterial virulence, host-pathogen interactions, microbial ecology, and resistance mechanisms.

AREAS COVERED: This review summarizes the current evidence on non-antibiotic therapeutics including bacteriophages, antimicrobial peptides, anti-virulence agents, monoclonal antibodies, microbiome-based therapies, CRISPR-Cas systems, nanoparticles, photodynamic therapy, repurposed non-antibiotic drugs and combination strategies. We performed a literature search on PubMed, Embase, Scopus, Web of Science, and Google Scholar until May 2026. Though several approaches have demonstrated promising biological activity and favorable safety profiles, clinical evidence remains limited and heterogeneous.

EXPERT OPINION: Non-antibiotic therapeutics are vital adjunctive, salvage and precision approaches to the challenge of AMR. However, most strategies are still at an early translational stage with a paucity of high-quality randomized clinical evidence. Barriers include delivery, manufacturing complexity, regulatory uncertainty, cost, and lack of long-term safety data. Further progress will depend on standardization of production, better delivery platforms, well-designed multicentric clinical trials, and incorporation into antimicrobial stewardship and precision medicine frameworks.},
}

@article {pmid42790302,
year = {2026},
author = {Zhao, J and Duan, M and Cui, P and Xiong, X and Miao, P and Wang, D and Yan, X and Yu, P and Zeng, Z and Lin, Y and Masuda, Y and Honjoh, KI and Miyamoto, T and Xiao, F},
title = {Next-generation fermented foods from non-conventional proteins: Linking fermentation dynamics, flavor chemistry, and gut microbiome modulation.},
journal = {International journal of food microbiology},
volume = {462},
number = {},
pages = {112076},
doi = {10.1016/j.ijfoodmicro.2026.112076},
pmid = {42790302},
issn = {1879-3460},
abstract = {The urgent need to diversify protein sources beyond animal agriculture has propelled non-conventional proteins (e.g., insects, microalgae, single-cell organisms, novel plants) to the forefront of food innovation. However, their adoption is limited by off-flavors, anti-nutritional factors, and low digestibility. Fermentation can address these drawbacks and may impart health-relevant benefits, though human evidence remains limited. This review defines next-generation fermented foods (NGFFs) as rationally fermented non-conventional protein substrates achieving superior sensory, nutritional, and gut health outcomes and possessing the potential to replace existing food products. We synthesize the cascading effects of controlled fermentation on these matrices, connecting fermentation dynamics with flavor chemistry and gut microbiome modulation. We dissect substrate compositional peculiarities, proteolysis kinetics, metabolic fluxes, and microbial ecology under tailored conditions, showing how process parameters steer formation of desirable volatiles and elimination of off-note compounds. We explore the prebiotic and probiotic potential of the resulting ferments, with preliminary evidence for gut microbial restructuring, short-chain fatty acid enhancement, and intestinal barrier reinforcement. From these interdependencies, we propose an integrated process-property-health (PPH) nexus to rationalize NGFF design. Finally, we discuss how artificial intelligence, synthetic biology, and life-cycle assessment can accelerate translation to sustainable, consumer-accepted food systems, providing a holistic framework for harnessing fermentation to unlock alternative proteins' full potential. Critically, we identify persistent knowledge gaps, unresolved conflicts in literature, and methodological limitations that constrain current understanding, and we propose prioritized research directions to advance the field from descriptive case studies toward predictive, mechanistic design of next-generation fermented foods.},
}

@article {pmid42791354,
year = {2026},
author = {Humolli, D and Piel, D and Ransome, J and Bausch, K and Tschudin-Sutter, S and Ortelli, M and Dehio, C and Veening, JW and Harms, A},
title = {Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42791354},
issn = {2058-5276},
support = {Ambizione Fellowship PZ00P3_180085//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; Starting Grant TMSGI3_211369//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; NCCR AntiResist (grant number 180541)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; NCCR AntiResist (grant number 180541)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; NCCR AntiResist (grant number 180541)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {The arms race of bacteriophages and their bacterial hosts has inspired major breakthroughs in biotechnology and shaped phages as fierce predators with great clinical potential to fight multidrug-resistant bacterial pathogens. However, the large amount of genes of unknown function in phage genomes remains a major obstacle for the molecular understanding of phage-host interactions. Here we present HIDEN-SEQ (hidden Acr-enabled transposon-insertion sequencing), a transposon-insertion sequencing method for phages that systematically links viral genes to selectable phenotypes. Using model phage T4, we show that HIDEN-SEQ readily reproduces the gene essentiality map established over decades of research. Our method is easily portable across diverse non-model phages and reveals conditionally essential genes in multiple bacterial hosts and growth conditions, including previously unknown antidefence factors that we matched to specific antiviral defences. We anticipate that HIDEN-SEQ will be leveraged to reveal functions of viral genes with direct relevance for microbial ecology, biotechnology and phage therapy.},
}

@article {pmid42791611,
year = {2026},
author = {Zhang, WX and Li, HR and Guo, X and Zhang, W},
title = {Lepidopteran pests and phytopathogenic fungi: The overlooked interface of insect‒microbe interactions.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70352},
pmid = {42791611},
issn = {1744-7917},
support = {32471609//National Natural Science Foundation of China/ ; 32101277//National Natural Science Foundation of China/ ; },
abstract = {Lepidopteran pests and phytopathogenic fungi are major biotic threats to crop health and productivity, yet their interactions remain poorly integrated into current frameworks of insect-microbe and plant disease ecology. Lepidopteran pests and fungal pathogens often share common ecological niches on host plants, particularly damaged tissues and microbe-rich interfaces. Chewing damage, frass deposition and movement by lepidopteran pests can create opportunities for fungal dispersal and invasion. This review synthesizes current knowledge on lepidopteran pest-phytopathogenic fungus-plant (LPP) tripartite interactions. It first outlines the biological features of lepidopteran pests, phytopathogenic fungi, and host plants that provide the ecological basis for their co-occurrence. Direct interactions are then examined, including competition for plant-derived resources, pest-mediated fungal facilitation, mutualistic associations, and antagonistic effects of fungi on lepidopteran survival or development. Plant-mediated indirect interactions are further discussed, focusing on how pest feeding or fungal infection reshapes host-plant physiology, defense responses, and ecological signaling. Finally, interaction-guided strategies are considered from three perspectives: breeding crop varieties with coordinated resistance, applying RNAi-based approaches to target key pest or fungal genes, and manipulating plant- or insect-associated microbial communities. Overall, understanding the pest-fungus interactions shifts the paradigm from isolated threat management toward holistic interventions, providing a mechanistic foundation for next-generation sustainable crop protection.},
}

@article {pmid42791728,
year = {2026},
author = {Yerlikaya, Z and Karabulut, B and Cankaya, E and Girgin, M and Polat Dincer, PF and Eroksuz, H},
title = {Comparative Lung Bacterial Community Profiles in Pneumonic and Non-Pneumonic Akkaraman Lambs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/ani16182871},
pmid = {42791728},
issn = {2076-2615},
abstract = {Ovine pneumonia is a multifactorial respiratory disease, yet bacterial community alterations associated with pathologically confirmed pneumonia in lambs remain poorly characterised. This study investigated the lung bacterial microbiota of non-pneumonic and pneumonic Akkaraman lambs by integrating gross and histopathological examination with 16S rRNA gene amplicon sequencing. The final dataset comprised lung samples from 15 non-pneumonic and 14 pneumonic lambs. Alpha diversity did not differ significantly between groups, whereas bacterial community composition differed significantly for both Bray-Curtis (R[2] = 0.093, p = 0.001) and weighted UniFrac (R[2] = 0.117, p = 0.006) distances, with no significant differences in multivariate dispersion. At the genus level, Mannheimia showed significantly higher relative abundance in pneumonic lungs after false-discovery-rate correction and was the only genus also identified as differentially abundant by ANCOM. Mycoplasma, Fusobacterium, and Trueperella showed greater relative representation in pneumonic lungs, whereas Acinetobacter and Psychrobacter showed the opposite pattern. Prevalence analysis further demonstrated contrasting taxon distributions between groups. Overall, naturally occurring pneumonia was associated with distinct alterations in lung bacterial community composition rather than a generalised loss of within-sample diversity, with Mannheimia representing the strongest pneumonia-associated genus-level signal.},
}

@article {pmid42793777,
year = {2026},
author = {Zhang, J and Shu, L},
title = {Colposcopic Imaging Carries Most of the Signal: Externally Validated Tri-Modal Integration of Imaging, Vaginal Microbiome, and Coagulation-Immune Data in HPV-Associated Co-Infection.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {18},
pages = {},
doi = {10.3390/diagnostics16182992},
pmid = {42793777},
issn = {2075-4418},
support = {Y20240600//Wenzhou Municipal Science and Technology Bureau/ ; },
abstract = {Background/Objectives: To determine whether a coagulation-immune index, vaginal microbiome composition, and colposcopic imaging carry non-redundant information about HPV-associated lower genital tract co-infection when integrated within a single learned model. Methods: This retrospective three-center study analyzed 560 women referred for colposcopy: 420 formed the development cohort, and 140 were a withheld external cohort from a third center. All three modalities were sampled within one visit. Participants were classified as HPV-negative, HPV-positive without co-infection, or HPV-positive with co-infection, the latter confirmed by nucleic acid amplification for Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, or Mycoplasma genitalium, with overlapping taxa masked a priori. TIM-Fusion combined a ConvNeXt-Tiny image encoder, a feature-tokenizer transformer for the D-dimer-to-lymphocyte ratio, and a perceptron for centered log-ratio abundances through modality-confidence weighting and bottleneck cross-attention. Results: On the external cohort, TIM-Fusion achieved a macro-AUC of 0.92 (95% CI 0.86 to 0.96) and accuracy of 0.90 across the three categories, exceeding the image-only baseline at 0.81, the tabular-only baseline at 0.76, and the best pairwise combination at 0.86. All thirteen comparisons, differences of 0.03 to 0.16, retained significance under Holm correction. Ablation attributed 0.05 (0.01 to 0.10) to bottleneck fusion, the only component with an interval excluding zero; withholding imaging, microbiome, or the ratio cost 0.13, 0.06, and 0.04. Imaging was therefore the dominant contributor, its removal costing three times as much as either of the other modalities. Entering D-dimer and lymphocyte count separately rather than as a ratio gave 0.89 (0.82 to 0.93), so the ratio form is an estimation convenience at this sample size and not a requirement. Co-infection-class AUC was 0.87 (0.75 to 0.94) on 26 events. In a secondary analysis restricted to the 84 HPV-positive external participants, binary discrimination of co-infection was 0.86 (0.76 to 0.93) with sensitivity 0.85 and specificity 0.91, lower than the one-versus-rest figure, which includes HPV-negative women in the negative class. Conclusions: Colposcopic morphology carries most of the discriminatory signal, while vaginal microbial ecology and coagulation-immune status each add information the others do not. Discrimination of co-infection status itself is more modest than the macro-averaged figure suggests, since within the HPV-positive stratum alone it falls to 0.86 on 26 events.},
}

@article {pmid42774681,
year = {2026},
author = {Van Rossum, U and Heyndrickx, M and Demaître, N and Rasschaert, G and Boon, N and Cools, A and De Reu, K},
title = {Laboratory and pilot-farm evaluation of cleaning and disinfection protocols for biofilms in livestock drinking water systems.},
journal = {Biofilm},
volume = {12},
number = {},
pages = {100397},
pmid = {42774681},
issn = {2590-2075},
abstract = {Persistent biofilms harboring pathogens can compromise drinking water quality in livestock housing, leading to animal health issues and reduced production. Microbial water quality can be maintained through various treatments and/or by cleaning and disinfecting drinking water systems to remove dirt and biofilms. However, despite routine monitoring of drinking water quality, biofilm persistence after treatment is often overlooked in practice. This study evaluated commonly used (cleaning and) disinfection protocols (peroxides, peracetic acid, chlorine dioxide, formic acid, chlorine, and enzymatic) for drinking water systems, both in vitro and in situ. Four selected three- or four-species communities were grown on polycarbonate and stainless-steel coupons in a stirred Centers for Disease Control (CDC) biofilm reactor. The in situ study was conducted on a pilot broiler farm during four consecutive six-week production cycles, with both water and biofilm samples collected during each cycle. Our in vitro study showed that the disinfectants reduced multispecies viable biofilm cells, but the effects varied with microbial composition. The in situ results showed little effect of the cleaning and disinfection protocols. Consequently, targeted intervention strategies, supported by regular monitoring of water quality and biofilm presence, are essential for making treatment decisions to minimize the risk of water contamination.},
}

@article {pmid42777354,
year = {2026},
author = {Tellez-Isaias, G},
title = {From environmental perception to reproductive allocation: the microbiome-membrane-mitochondria axis in poultry.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107841},
doi = {10.1016/j.psj.2026.107841},
pmid = {42777354},
issn = {1525-3171},
abstract = {Reproductive performance has traditionally been interpreted through the physiology of reproductive organs, endocrine regulation, and genetics. Although these approaches have substantially advanced poultry production, they do not fully explain why reproduction consistently reflects the overall physiological condition of the organism. This review proposes an integrative conceptual framework in which reproductive success emerges from the coordinated activity of the entire host-microbiome ecosystem, not from the reproductive system alone. We examine current evidence supporting the concept that the intestinal microbiome functions as a major ecological and metabolic partner that can contribute to whole-organism homeostasis through effects on intestinal barrier integrity, immunometabolism, endocrine signaling, microbial metabolite production, and mitochondrial bioenergetics. In this model, microbially derived signals, including short-chain fatty acids, bile acid metabolites, tryptophan derivatives, polyamines, vitamins, extracellular vesicles, and microbial-associated molecular patterns, form an extensive communication network linking the intestinal ecosystem with distant tissues. Central to this model is the recognition of mitochondria as major bioenergetic and signaling integrators within the host-microbiome system. Beyond ATP production, mitochondria participate in redox homeostasis, immune activation, metabolic adaptation, endocrine responses, steroidogenesis, and cellular quality control, thereby integrating microbial, nutritional, immune, and environmental signals into cellular responses. Diverse stressors, including dysbiosis, heat stress, pathogens, mycotoxins, oxidative stress, nutritional imbalance, and chronic inflammation, converge upon mitochondrial and immunometabolic pathways that can alter systemic resource allocation and reproductive resilience. Reproductive performance is therefore considered here as an emergent, condition-dependent physiological outcome rather than as a hierarchically superior biological function. The intestinal microbiome does not directly regulate reproduction; instead, it contributes to the systemic conditions that can support reproductive investment, whereas microbial communities within the reproductive tract may interact more directly with reproductive tissues and gametes. The revised framework further emphasizes reciprocal communication: endocrine and reproductive states can reshape metabolism, immunity, intestinal physiology, mitochondrial function, and microbial ecology. Finally, maternal programming and optimization of host-microbiome interactions are considered as potential strategies for strengthening reproductive resilience across generations.},
}

@article {pmid42779556,
year = {2026},
author = {Ehiosun, KI and Chapleur, O and Mazéas, L},
title = {Diagnosing Anaerobic Digesters' Function and Performance: From Meta-Omics to Integrated Meta-Omics Analyses.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70417},
pmid = {42779556},
issn = {1758-2229},
support = {ANR-22-CE43-0014-01//Agence Nationale de la Recherche/ ; },
mesh = {Multiomics ; Anaerobiosis ; Metabolomics/methods ; *Bioreactors/microbiology ; Biofuels ; Metagenomics/methods ; Methane/metabolism ; Proteomics ; *Bacteria/metabolism/genetics ; },
abstract = {Anaerobic digestion (AD) of organic wastes by microorganisms into biomethane contributes significantly towards bioenergy generation. However, the bioprocess remains challenging due to its complex microbial ecology, dynamic biochemical pathways and sensitivity to perturbations. Over the past decade, using meta-omics like metataxonomics, metagenomics, metatranscriptomics, metaproteomics and metabolomics to diagnose its functioning has become necessary and common. However, a single meta-omics method can only provide limited biological understanding of the bioprocess. This led to the use of multi-meta-omics analyses in tandem; however, most studies still examine and interpret each meta-omics separately, limiting their ability to uncover functional interactions across molecular levels. Currently, the frontier is integrated meta-omics, where multi-meta-omics and process data are systematically combined into a single and interpretable system to unlock mechanistic understanding, diagnostic and predictive control of AD. This review critically examines specific application of meta-omics in AD, discussing their strengths, limitations and distinct position in integrated meta-omics approach. Importantly, it explores the computational frameworks, methodologies and challenges of integrated meta-omics. Discovering diagnostic biomarkers with high predictive power and transferability across AD systems through cross-omics validation is highlighted. As workflows standardise and technologies mature, integrated meta-omics would significantly contribute to the advancement of AD bioprocess for bioenergy.},
}

Multiomics
Anaerobiosis
Metabolomics/methods
*Bioreactors/microbiology
Biofuels
Metagenomics/methods
Methane/metabolism
Proteomics
*Bacteria/metabolism/genetics

@article {pmid42779984,
year = {2026},
author = {Kitsios, G and Sy, MA and Bain, WG and Hensley, M and Qin, S and Wang, X and Inman, KW and Dela Cruz, C and Robinson, K and Nouraie, SM and Shah, FA and Benos, P and McVerry, BJ and Morris, A},
title = {Microbiome Profiling Reveals Prognostic Heterogeneity in Staphylococcus aureus Pneumonia.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {42779984},
abstract = {BACKGROUND: Staphylococcus aureus is a leading cause of severe pneumonia in mechanically ventilated patients. Clinical cultures identify pathogen presence but may not reflect lower respiratory tract microbial ecology. Whether culture-confirmed S. aureus pneumonia encompasses compositional heterogeneity with prognostic implications remains unknown.

METHODS: We performed 16S rRNA gene sequencing and shotgun nanopore metagenomics on endotracheal aspirate samples from mechanically ventilated patients with culture-confirmed S. aureus pneumonia in a prospective ICU registry. We quantified Staphylococcus abundance, assessed correlations with culture characteristics and host inflammatory biomarkers, and examined associations with 60-day mortality using Kaplan-Meier and Cox hazards analyses.

RESULTS: Among 109 patients, semi-quantitative culture growth and methicillin resistance showed no associations with outcomes. 16S sequencing (n=54) revealed marked heterogeneity in Staphylococcus relative abundance (range 0-96.7%), with only 33% demonstrating dominance (>50%). Dominance was associated with worse 60-day survival (50% vs. 80%,p=0.013) and remained independently predictive after adjusting for age, sex, and methicillin resistance (adjusted HR 3.24 [95%CI 1.12-9.36],p=0.030). Patients with dominance exhibited elevated pentraxin-3 (p=0.01) and reduced fractalkine (p=0.02). Nanopore metagenomics (n=28) validated these findings, with high absolute S. aureus read counts independently predicting mortality (adjusted HR 11.23 [95%CI 2.25-55.9],p=0.003). In an exploratory analysis of virulence genes (n=19), staphylokinase detection was associated with the hyperinflammatory phenotype (p=0.003) and mortality (p=0.046).

CONCLUSIONS: Metagenomic profiling reveals clinically meaningful heterogeneity within culture-confirmed S. aureus pneumonia, masked by conventional diagnostics. Staphylococcus dominance identifies a high-risk phenotype with elevated bacterial burden, dysregulated host responses, and increased mortality, challenging the assumption that culture positivity represents a uniform clinical entity.},
}

@article {pmid42781463,
year = {2026},
author = {Longhinos, NB and Mahesh, P and Bindhu, DV and Sunil, A and Nair, A and Kuppusamy, DR and Hariharan, AM and Sruthi, V and Nair, BG and Pal, S and Subhash, S},
title = {Rhizosphere microbiome engineering with PGPR to combat soil-mediated climate change.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1880722},
pmid = {42781463},
issn = {1664-302X},
abstract = {The synergistic effects of accelerated climate change and anthropogenic land-use shifts increasingly compromise the functional integrity of terrestrial ecosystems. To preserve soil health and ensure global food security, a transition toward biointensive, climate-smart agriculture is imperative. This review provides a comprehensive synthesis of the multifaceted role of plant growth-promoting rhizobacteria (PGPR) as "rhizosphere architects," bridging global biogeochemical cycles with intricate molecular and digital interventions. Microbe mediated mitigation of atmospheric stressors is evaluated by monitoring increases in soil carbon sequestration and concomitant reductions in greenhouse gas (GHG) emissions. Central to ecosystem recovery is the physiochemical regeneration of marginal and polluted soils, where PGPR facilitate the detoxification of xenobiotics, including heavy metals, microplastics, and organic contaminants, while promoting the structural restoration of degraded edaphic environments. At the tripartite plant-microbe-soil interface, the synergistic regulation of root system architecture (RSA) is investigated alongside the emerging role of epigenetic modifications, such as DNA methylation and histone acetylation, as critical drivers of transgenerational stress memory against extreme climatic conditions. These molecular and structural shifts are functionally correlated with rhizosphere enzymatic activity, including specific enzyme fluxes (e.g., urease, phosphatase, and dehydrogenase), which serve as biochemical proxies for soil health restoration. To address the historical inconsistency of field inoculants, a translational framework is proposed that integrates Industry 4.0 technologies, such as AI-assisted bioformulation design and IoT-based precision monitoring, for real-time microbiome management. By discussing the translational hurdles of microbial competition and regulatory frameworks, this synthesis underscores how the fusion of microbial ecology and digital agriculture provides a robust pathway toward resilient terrestrial ecosystems and sustained agricultural productivity in the Anthropocene.},
}

@article {pmid42781585,
year = {2026},
author = {Ginnan, N and Jones, R and Wu-Woods, J and Pervaiz, T and El-Kereamy, A and Ashworth, VETM and Hamid, MI and Dawson, EK and Strauss, SL and Stajich, J and Rolshausen, P and Roper, C},
title = {Orchard management alters citrus root and rhizosphere microbiomes with functional consequences for plant performance.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag248},
pmid = {42781585},
issn = {2730-6151},
abstract = {Agricultural management practices act as ecological disturbances that can restructure soil and plant-associated microbial communities, but the functional consequences of these microbial shifts on crop performance remain poorly understood. Here, we examined how common orchard inputs, including wood mulch, glyphosate, and humic acid, affect citrus root and rhizosphere microbiomes, leaf nutrient trajectories, and tree performance over a 3-year field experiment. Mulch emerged as the dominant driver of fungal community composition and taxonomic turnover, enriching for saprophytic fungi. Conversely, bacterial communities responded primarily to interactions among applications, particularly mulch × glyphosate, which was associated with significant depletions of bacterial genera in roots and rhizospheres. These microbiome changes corresponded with reduced tree carbon assimilation, transpiration, and yield, and altered leaf nutrients dynamics. To verify whether the microbial shifts were contributing to these plant phenotypic changes, we conducted a greenhouse experiment using field-derived soil microbiota. Active microbiota from mulch-treated soils reduced citrus seedling establishment and root growth relative to microbiota from nonmulched soils, whereas heat-killed controls eliminated these negative effects, demonstrating a causal relationship between management-induced microbiota changes and decreases in plant performance. The effect of mulch-associated microbiota on root growth further depended on glyphosate history, paralleling field observations. Humic acid increased root growth regardless of microbiota activity and moderated decreases in shoot growth by mulch-associated microbiota. Together, these results show that management practices can restructure citrus microbiomes and generate community-level traits that influence plant performance, highlighting the importance of incorporating microbial ecology and microbiome information when devising crop management strategies.},
}

@article {pmid42782137,
year = {2026},
author = {Szymanski, CM and Rogers, AM and Glendenning, LM and Warmath, D and Mousa, JJ and Daugherty, TM and Zeltner, N and McAlpine, JL and Tribble, DR and Cook, GA and Boons, G-J and Papri, N and Hayat, S and Jahan, I and Islam, Z and Richardson, RJ and Whitehead-Tillery, CE and Bell, JA and Mansfield, LS},
title = {Transformative advances in Guillain-Barré syndrome research.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043626},
doi = {10.1128/msphere.00436-26},
pmid = {42782137},
issn = {2379-5042},
abstract = {The Guillain-Barré Syndrome Innovation Alliance held its inaugural meeting focused on creating treatment solutions for Guillain-Barré syndrome (GBS), an autoimmune disease increasingly recognized as a postinfectious neuropathy and the most common cause of paralysis since vaccines for polio. These collaborators, funded by the Department of War, Congressionally Directed Medical Research Programs, and the National Institute of Allergy and Infectious Diseases, span institutes/universities, including the University of Georgia, Michigan State University, Florida State University, the University of Utrecht, the International Centre for Diarrhoeal Disease Research, and the Uniformed Services University of the Health Sciences. Group efforts span biochemistry, epidemiology, immunology, medicine, microbiology, microbial ecology, glycobiology, neurology, neuroscience, pharmacology, and multiomics data science/computational biology. Our team is committed to the advancement of two core objectives: expanding understanding of biological mechanisms of GBS and developing more efficacious, targeted therapies. We are dedicated to finding alternative therapies for patients unresponsive to intravenous immunoglobulin and to creating affordable options to eliminate financial barriers to care.},
}

@article {pmid42783894,
year = {2026},
author = {Choudhary, G and Hamdani, A and Unno, H and Kimura, M and Venmathi Maran, BA},
title = {A Review on Climate Change Redefining Tetrodotoxin Accumulation and Ecological Dynamics in Pufferfishes.},
journal = {Marine drugs},
volume = {24},
number = {9},
pages = {},
doi = {10.3390/md24090300},
pmid = {42783894},
issn = {1660-3397},
mesh = {Animals ; *Tetrodotoxin/metabolism/toxicity ; *Climate Change ; *Tetraodontiformes/metabolism ; Food Chain ; Ocean Acidification ; },
abstract = {Pufferfishes (Tetraodontidae) accumulate tetrodotoxin, a potent neurotoxin, primarily through microbial and trophic pathways rather than endogenous biosynthesis, linking their toxicity directly to marine microbial ecology and food-web structure. Anthropogenic climate change, ocean warming, deoxygenation, and acidification are reshaping the environmental conditions that govern TTX production, transfer, and accumulation. This review synthesizes evidence from 62 studies (28 with quantitative data) identified through a PRISMA-ScR-compliant search. We organize findings around three mechanistic pathways: (1) warming-associated proliferation of TTX-producing bacteria and consequent shifts in environmental TTX availability, (2) climate-driven range shifts and hybridization that generate novel and unpredictable toxicity phenotypes, and (3) physiological responses of pufferfishes to warming, hypoxia, and acidification that may alter toxin allocation. We identify priority research needs, long-term monitoring, multi-stressor experiments, and standardized LC-MS/MS-based surveillance and outline an integrated framework for anticipating climate-driven shifts in pufferfish toxicity.},
}

Animals
*Tetrodotoxin/metabolism/toxicity
*Climate Change
*Tetraodontiformes/metabolism
Food Chain
Ocean Acidification

@article {pmid42783907,
year = {2026},
author = {D'Arelli, A and Sosa, S and Dall'Ara, S and Cangini, M and Carlin, M and Antonelli, P and Dall'Occo, A and Scapin, N and Arcangeli, G and Losasso, C and Tubaro, A and Pelin, M},
title = {Optimization and Intra-Laboratory Validation of the Neuro-2a Assay for Tetrodotoxin Detection in Mussels.},
journal = {Marine drugs},
volume = {24},
number = {9},
pages = {},
doi = {10.3390/md24090314},
pmid = {42783907},
issn = {1660-3397},
support = {RF-2021-12373885//Ministero della Salute/ ; },
mesh = {Animals ; *Tetrodotoxin/analysis/toxicity ; *Bivalvia/chemistry ; Mice ; Saxitoxin/analysis ; Cell Line, Tumor ; Limit of Detection ; Reproducibility of Results ; Food Contamination/analysis ; Seafood/analysis ; Veratridine/pharmacology ; Biological Assay/methods ; },
abstract = {Tetrodotoxin (TTX) is a potent marine neurotoxin responsible for severe seafood poisoning in humans, characterized by neurological symptoms that may be fatal. Originally identified as a natural contaminant of pufferfish (Tetraodontidae family), over the last few years TTX and its analogs have also been detected in other edible marine organisms, including mollusks, gastropods and crustaceans. Consequently, there is a need for rapid, sensitive, and reliable methods for TTX detection in seafood. In this study, a functional assay based on the use of mouse neuroblastoma Neuro-2a cells has been optimized and characterized for TTX detection in mussels. The assay is based on the toxin's ability to block voltage-gated sodium channels, thereby counteracting the sodium-dependent cytotoxicity induced by veratridine and ouabain. The linear range of the TTX standard curve fell between 0.44 and 33 ng/mL, with limits of TTX detection (LOD) and quantitation (LOQ) of 0.132 ng/mL and 0.439 ng/mL, respectively, and good intra- and inter-day repeatability (RSDr= 15 and 11%, respectively). The assay also detected saxitoxin, which shares the same mechanism of action as TTX, but was less sensitive towards 4,9-anhydro-TTX. The minimum mussel extract dilution of 1:100 did not result in matrix-related interference, allowing accurate TTX quantitation, with a LOQ of 0.54 µg TTX equivalents/kg mussel meat. Given its sensitivity, the optimized Neuro-2a assay represents a promising tool for toxicity-based TTX quantitation in mussels before their consumption.},
}

Animals
*Tetrodotoxin/analysis/toxicity
*Bivalvia/chemistry
Mice
Saxitoxin/analysis
Cell Line, Tumor
Limit of Detection
Reproducibility of Results
Food Contamination/analysis
Seafood/analysis
Veratridine/pharmacology
Biological Assay/methods

@article {pmid42784843,
year = {2026},
author = {Zhao, X and Li, B and Zhai, F and Gao, J and Yang, X and Qin, X and Li, T},
title = {Mechanisms of yield improvement in dryland wheat under plastic film mulching: Insights from soil fungal communities and function.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag110},
pmid = {42784843},
issn = {1574-6968},
abstract = {Plastic film (PF) mulching is an important method for winter wheat cultivation. In this study, the effects of PF mulching on wheat yield were analysed. Compared with non-mulched control, grain yield increased by 70% in PF treatment. Soil available phosphorus (AP) and electrical conductivity (EC) increased by 104.70% and 5.55%, respectively. PF mulching was associated with shifts in the relative abundance of several fungal taxa, including increases in Talaromyces, Trichoderma, and Schizothecium. The overall abundance of taxa classified as potential plant pathogens decreased by 37.73%. However, some taxa that include known plant pathogens, such as Didymella and Bipolaris, showed increased abundance, suggesting the need for careful disease management under mulching conditions. Co-occurrence network analysis indicated that fungal interactions became less complex in PF treatment, accompanied by an increased proportion of positive correlations. Redundancy analysis showed that soil EC and AP were significantly associated with wheat yield and with the relative abundance of specific fungal taxa. PF mulching was associated with changes in soil properties and fungal community structure, which may contribute to improved wheat yield. It provides insights into the potential role of fungal communities in mulching systems and highlights the importance of considering pathogen risks in wheat production.},
}

@article {pmid42762968,
year = {2026},
author = {Sun, Y and Du, Y and Liang, Y and Zhang, Y and Wu, F and Feng, J and Shen, R and Luo, J and Yu, J and Liu, B and Zhao, L},
title = {Steering ecological interactions in microbial chain elongation: functions and impacts of carbon- and iron-based materials.},
journal = {Biotechnology advances},
volume = {93},
number = {},
pages = {109047},
doi = {10.1016/j.biotechadv.2026.109047},
pmid = {42762968},
issn = {1873-1899},
abstract = {The increasing accumulation of organic waste and the demand for renewable chemicals highlight the production of medium-chain fatty acids (MCFAs) as an effective strategy for waste valorization. Microbial chain elongation (CE) converts short-chain fatty acids (SCFAs) into MCFAs. However, its efficiency in mixed cultures is frequently limited by unstable carbon flow, restricted electron transfer, and shifts in functional microbial communities. While exogenous materials are increasingly applied to regulate CE, their mechanisms of action have not been as systematically reviewed as traditional process optimization strategies. This review examines how material-mediated CE enhances MCFA production by facilitating metabolic pathways, directing microbial enrichment, and promoting electron transfer. Specifically, the discussion focuses on carbon-based materials, iron-based materials, and engineered composites, detailing their role in electron shuttling, interfacial redox buffering, microbial attachment, and functional microbial community assembly. Furthermore, we summarize material design principles, their enhancement effects, and the key factors governing operational stability in practical mixed-culture systems. Rather than focusing solely on the enrichment of single functional microbes, this review emphasizes the application of exogenous materials to direct microbial community assembly and enhance interfacial microbe-material interactions. These mechanisms provide a basis for understanding and regulating caproate selectivity during organic waste conversion. Finally, by incorporating economic and environmental considerations, we propose strategies for scaling up material-assisted CE from the laboratory to practical applications. Ultimately, this review builds a framework connecting material properties, microbial ecology, and process efficiency, facilitating the selective conversion of organic waste into MCFAs.},
}

@article {pmid42765949,
year = {2026},
author = {Wittwer, AE and Sumerta, IN and Cristetti, F and Howell, KS},
title = {Microbial ecology of fermented foods.},
journal = {FEMS yeast research},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsyr/foag050},
pmid = {42765949},
issn = {1567-1364},
abstract = {Over thousands of years, a wide variety of food fermentations in human diets have developed in different geographical regions, cultures, and traditions. The desirable conversions of food components that occur during fermentation rely on a diverse array of micro-organisms which interact with one another and with their environments. Notably, many yeast, bacterial and filamentous fungal taxa are key members of the microbiomes of fermented food products. Strategies employed by these micro-organisms to ensure their survival typically include maximising reproductive rates, and this affects patterns of microbial succession and key metabolic dependencies. The principles of microbial ecology can be used to understand growth, activity and interactions in these diverse communities. In this review, we summarise the historical significance and factors influencing key microbial functions in palm wine, wine, sourdough, and tempeh, selected for their varied raw materials and fermentation techniques. Despite differences, in fermented foods abiotic and environmental influences from natural or human-controlled sources act to define a food's microbial ecology and therefore the final product's properties. Modern production of traditional and novel foods by microbes should consider the principles of microbial ecology to understand and control fermentation outcomes.},
}

@article {pmid42765955,
year = {2026},
author = {Xue, R and Li, J and Hu, S and Ding, J and Wang, C and Ke, W and Li, C and Corvini, P and Cui, L},
title = {Microbial physiological trait shifts link heavy metal remediation to enhanced soil carbon storage potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag250},
pmid = {42765955},
issn = {1751-7370},
abstract = {Widespread and chronic heavy metal pollution resulting from industrial activities has compromised the sustainability of soil ecosystems. Increasing and stabilizing soil carbon storage is central to soil development, but how remediation reshapes soil carbon cycling processes during the mitigation of heavy-metal contamination remains unclear. Here, we tracked genome-scale microbial metabolism, community turnover, and phenotype-level physiological responses during a 120-day remediation of heavy metal-contaminated soils with several decades of pollution histories and resolved their dynamic interplay with microbial carbon use efficiency (CUE) and CO2 emissions. We found that heavy-metal stress accelerated microbial respiratory carbon loss from soils, with contaminated soils exhibiting significantly higher cumulative CO2 emissions than both nearby uncontaminated and remediated soils. Metagenomic profiles were enriched in oxidative-stress defense and metal-detoxification functions, consistent with elevated maintenance costs that may contribute to enhanced respiration. In contrast, remediation significantly reduced soil CO2 emissions while increasing microbial growth rate and CUE, indicating a shift toward greater soil carbon storage potential. Raman-based in situ monitoring further showed that biomolecules associated with microbial growth, including phospholipids, nucleic acids, and proteins, increased progressively throughout the remediation process. Structural equation modelling further revealed that microbial physiological traits, particularly metabolic activity and intracellular biomolecular composition, exerted stronger direct effects on CUE than community traits, including community stability and life-history strategy. These results identify microbial physiological traits as a key link between environmental stress and soil carbon cycling. Together, these findings suggest that remediating heavy metal-contaminated soils may represent an underappreciated pathway for enhancing terrestrial carbon sequestration.},
}

@article {pmid42769501,
year = {2026},
author = {Al-Rshaidat, M and Alsayed, A and Al-Rshaidat, O and Imraish, A and Abazid, H and Zihlif, M},
title = {Genetic factors associated with COVID-19 severity and mortality: TYK2 and NOTCH4.},
journal = {Biomedical reports},
volume = {25},
number = {5},
pages = {125},
pmid = {42769501},
issn = {2049-9442},
abstract = {The clinical manifestations and outcomes of coronavirus disease (COVID-19) vary among patients. Emerging evidence indicates that host genetic factors may influence disease severity. Genome-wide association studies (GWAS) have identified several genetic loci, including TYK2 and NOTCH4, as contributors to COVID-19 pathogenesis. The present study examined the association between genetic variants of TYK2 (rs74956615) and NOTCH4 (rs3131294) and the severity and mortality of COVID-19 in a Jordanian cohort. The present study included 362 patients with COVID-19 who were admitted to a hospital in Amman, Jordan. Clinical severity was categorized according to the WHO guidelines (non-severe, severe and critical), and outcomes were classified as survivors or non-survivors. Blood samples were collected, and DNA was extracted. Genotyping of TYK2 and NOTCH4 single-nucleotide polymorphisms was performed using PCR and Sanger sequencing. The frequencies of heterozygous and variant alleles of TYK2 and NOTCH4 were significantly higher in patients with critical disease than in non-survivors (P<0.001). Logistic regression analysis revealed that individuals with heterozygous or variant alleles of NOTCH4 had 15.3 times higher odds of developing severe/critical conditions (P=0.010), while those with variant alleles of TYK2 and NOTCH4 had approximately eight times higher odds of mortality (P<0.001 for both). TYK2 and NOTCH4 variants are markedly associated with increased COVID-19 severity and mortality, indicating their potential as genetic biomarkers for risk stratification. These findings support the importance of host genetics in disease progression and may guide future personalized treatment strategies for this condition.},
}

@article {pmid42769506,
year = {2026},
author = {Karrick, CE and Veglia, AJ and Meiling, S and Maxwell, K and Huebner, LK and Holstein, DM and Mydlarz, L and Brandt, M and Apprill, A and Muller, EM and Correa, AMS},
title = {Key coral symbiont lineages (family Symbiodiniaceae) are differentially associated with stony coral tissue loss disease.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag228},
pmid = {42769506},
issn = {2730-6151},
abstract = {Stony coral tissue loss disease (SCTLD) has caused unprecedented coral mortality across the Caribbean, and its etiology remains unresolved. SCTLD affects >30 coral species that differ in their associations with dinoflagellate endosymbionts (family Symbiodiniaceae), and symbiont lineage-level dynamics may underlie variation in holobiont disease response. We analyzed 491 apparently healthy and SCTLD-affected corals in Florida (USA) and the United States Virgin Islands, representing 9 coral species sampled in situ or during an SCTLD transmission experiment. Based on the internal transcribed spacer-2 (ITS-2) region of rDNA, we identified 114 Symbiodiniaceae ITS-2 type profiles spanning 6 genera. Symbiodiniaceae composition varied significantly by coral species, disease susceptibility group, tissue health state, and region. In the corals Orbicella annularis and Colpophyllia natans, lesion-adjacent tissues had enriched relative abundance of a Durusdinium lineage, whereas Symbiodinium and Cladocopium lineages were relatively more abundant in apparently healthy tissues. Accounting for biogeography and host identity, our results suggest that in corals harboring multiple Symbiodiniaceae lineages, more susceptible lineages are lost first, leaving relatively resistant lineages in lesion-adjacent tissue until sloughing occurs. These findings indicate SCTLD acts as a selective filter on coral symbiont assemblages. Our results provide the first multi-species, multi-region evidence of fine-scale associations between Symbiodiniaceae lineages and SCTLD, establishing a framework for testing lineage-specific disease susceptibility in future experiments.},
}

@article {pmid42772429,
year = {2026},
author = {Siddiqua, KS and Farooqui, SA and Zhang, Y and Wang, L and Zhang, G and Jiang, F and Wen, TC},
title = {Nanoparticle pharmacomicrobiomics: Reprogramming the microbiome-immune axis for cancer immunotherapy.},
journal = {Pharmacological research},
volume = {233},
number = {},
pages = {108481},
doi = {10.1016/j.phrs.2026.108481},
pmid = {42772429},
issn = {1096-1186},
abstract = {The composition and functional activity of the gut microbiome are important host-associated factors that influence the efficacy and responsiveness of cancer immunotherapy. Traditional microbiome modulation methods lack precision, consistency, and extensive clinical applicability. Engineered nanoparticles (NPs) represent an emerging platform for investigating more controllable approaches to microbiome-associated therapeutic modulation. NPs possess physicochemical characteristics that can influence the gut microbial ecosystem. This review introduces the concept of "nanoparticle pharmacomicrobiomics" as an emerging framework that links NP design to defined microbial shifts and their potential pharmacological and immunological consequences. Through integrated literature synthesis, bibliometric co-occurrence analysis, clinical trial synthesis, and mechanistic interpretation, we develop a conceptual framework that describes potential relationships among NP properties, microbial ecology, metabolite signalling, immune modulation, and cancer immunotherapy. We emphasize the integration of nanomaterials, microbiome science, and immunology as an emerging interdisciplinary direction in oncology. This framework provides a conceptual basis that may facilitate the development of future strategies that integrate nanotechnology with microbiome and immune modulation to improve precision cancer immunotherapy.},
}

@article {pmid42773291,
year = {2026},
author = {Zhao, W and Feng, Q and Zhang, H and Ma, R and Shi, S and Fan, C and Qi, F and Zhou, J},
title = {Hydrochemical associations with microbial community structure in the Reshuigou hot springs, northeastern Qinghai-Tibet Plateau.},
journal = {Extremophiles : life under extreme conditions},
volume = {30},
number = {1},
pages = {},
pmid = {42773291},
issn = {1433-4909},
support = {522807250007//Research and Demonstration of Hybrid Energy Storage Technology for New Energy Absorption and Supply in Qinghai Province/ ; },
mesh = {*Hot Springs/microbiology/chemistry ; *Microbiota ; Tibet ; *Water Microbiology ; *Bacteria/classification/isolation & purification ; },
abstract = {Geothermal hot springs provide important windows into the links among deep hydrothermal circulation, water-rock interaction, and microbial ecology in extreme environments. This study investigated six hot-spring water samples from Reshuigou, Guide County, Qinghai Province, by integrating hydrochemical analysis, PHREEQC mineral saturation calculations, microbial community profiling, RDA, PCoA environmental fitting, and Spearman correlation analysis. The Reshuigou waters were characterized by medium to high temperature, weak alkalinity, reducing conditions, and moderate to relatively high mineralization. Their hydrochemical facies were consistently of the Na+K/Cl-SO4 type, reflecting deep-circulation water-rock interaction, sulfate and chloride inputs, silicate dissolution, and ion exchange. The microbial communities were dominated by Proteobacteria, Aquificota, Deinococcota, Chloroflexi, and Bacteroidota, with Hydrogenobacter, Thermus, Herbaspirillum, and Delftia as important genera. Phylum- and genus-level RDA accounted for 71.9 and 77.4% of the constrained community variation, respectively. Spearman analysis further showed an inverse relationship between Chloroflexi and ORP, a positive relationship between Chloroflexi and HCO3[-], and positive covariation of Proteobacteria with several major ions and mineralization indicators. Taken together, the results show that a shared deep-geothermal background establishes the regional community baseline, whereas temperature, redox state, mineralization, major-ion composition, and local discharge conditions jointly structure microbial differentiation among spring sites.},
}

*Hot Springs/microbiology/chemistry
*Microbiota
Tibet
*Water Microbiology
*Bacteria/classification/isolation & purification

@article {pmid42773349,
year = {2026},
author = {Maghsoudlou, M and Tserendorj, D and Abbaszade, G and Kavasi, N and Völgyesi, P and Tóth-Bodrogi, E and Sahoo, SK and Štrok, M and Inoue, K and Kovács, T and Szabó, C},
title = {Strontium isotopic signatures and source apportionment in urban soils of Salgótarján: unraveling the impact of industrial emissions.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42773349},
issn = {1614-7499},
abstract = {Urban soil contamination is primarily associated with human activities, especially industrial by-products, which have introduced high concentrations of heavy metal(loid)s from diverse sources over centuries of city development. This study investigated the distribution of strontium and its stable isotopic ratios ([87]Sr/[86]Sr) in urban soils of Salgótarján, a former industrial city in northern Hungary, with a focus on anthropogenic contamination, particularly from a former coal-fired power plant (CFPP). Fifteen urban soil samples from kindergartens, playgrounds, parks, and roadsides, in the northeastern part of the city were analyzed for Sr concentration, isotopic composition, and physicochemical properties. The analytical results revealed considerable variations in Sr concentrations (17.5-51.3 mg kg[-][1]), and [87]Sr/[86]Sr ratios (0.710303-0.719559), indicating mixed natural and anthropogenic inputs. A two-end-member [87]Sr/[86]Sr isotopic model was applied to semi-quantitatively estimate source contribution, identifying coal ash as a major contamination source in soils near the former CFPP. However, certain samples gathered far from the CFPP exhibited even stronger anthropogenic influence, suggesting an additional source, likely from smelter slag (known additional industrial source in the environment) and/or unknown technogenic soils (human-transformed soils). In contrast, other samples at greater distances from the CFPP showed minimal or no coal ash contribution, instead reflecting local soil inputs (i.e., natural/artificially made quartz-rich soils), introduced during land use changes. Our study highlights the effectiveness of [87]Sr/[86]Sr isotopic tracing in urban contamination assessment, offering a robust tool for understanding and managing urban environment quality.},
}

@article {pmid42759709,
year = {2026},
author = {Zhang, E and Wang, Z and Xu, H and Wu, J and Xu, ZD and Liang, Y},
title = {Galanin signaling in stress-induced brain-gut axis dysregulation: Receptor-specific mechanisms and context-dependent pharmacology.},
journal = {Peptides},
volume = {201},
number = {},
pages = {171518},
doi = {10.1016/j.peptides.2026.171518},
pmid = {42759709},
issn = {1873-5169},
abstract = {Stress-related dysregulation of the brain-gut axis may help explain the frequent co-occurrence of gastrointestinal disorders and neuropsychiatric phenotypes, including anxiety and depression. Acute and chronic stress can alter gastrointestinal motility, visceral sensation, mucosal barrier integrity, and central affective circuits through the hypothalamic-pituitary-adrenal (HPA) axis, the autonomic nervous system (ANS), immune and inflammatory signaling, and changes in gut microbial ecology. Galanin is distributed across central stress-related nuclei, the enteric nervous system, visceral afferent pathways, and mucosal immune cells, positioning the galanin system as a potential integrator of bidirectional brain-gut signaling. This review examines the expression, receptor biology, and regulatory actions of galanin and its three receptors-galanin receptor 1 (GalR1), galanin receptor 2 (GalR2), and galanin receptor 3 (GalR3)-in stress-induced brain-gut axis dysregulation, while galanin-like peptide (GALP) and spexin provide additional endogenous-ligand context for interpreting GalR pharmacology. The galanin system is neither uniformly protective nor uniformly detrimental. Its functional effects depend on ligand identity, receptor subtype, cell type, anatomical site, stress stage, and inflammatory state, as well as receptor complexes and downstream signaling bias. This context-dependent framework may help identify settings in which galanin-pathway modulation is most mechanistically plausible according to stress stage, inflammatory status, visceral sensitivity, and barrier function. Future studies should prioritize subtype-directed, tissue-restricted, and signaling-biased strategies while maintaining a clear distinction between experimental pharmacological utility, preclinical therapeutic potential, and clinical applicability.},
}

@article {pmid42760115,
year = {2026},
author = {Zhao, Q and Ding, Y and Yan, S and Ma, H and Wang, Y and Guo, S and Luo, X and Pang, Y and Jiang, C and Wang, K},
title = {A durably colonising engineered native symbiont enables sustained intestinal delivery for metabolic dysfunction and colitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339637},
pmid = {42760115},
issn = {1468-3288},
abstract = {BACKGROUND: Engineered bacterial therapeutics represent a promising strategy for sustained intestinal delivery of therapeutic molecules, but their efficacy is limited by inefficient colonisation, safety concerns and the need for repeated administration or auxiliary delivery systems.

OBJECTIVE: To develop a safety-optimised native bacterial chassis capable of long-term gut colonisation and sustained therapeutic delivery for intestinal inflammatory and metabolic diseases.

DESIGN: Native murine Escherichia coli isolates were screened for antibiotic susceptibility, genetic tractability and long-term intestinal colonisation. The selected strain, MEc30, was further optimised by deleting the putative virulence-associated clb and irp loci. MEc30 was then engineered to produce nicotinic acid (MEc30-NA) or deliver murine interleukin-10 (MEc30-mIL-10), and therapeutic efficacy was evaluated in a high-fat diet-induced metabolic dysfunction model as well as Il10 [-/-] and dextran sulphate sodium (DSS)-induced colitis models.

RESULTS: MEc30 achieved stable lifelong colonisation of the murine intestine after a single oral administration, without antibiotic preconditioning or auxiliary delivery systems and did not detectably disturb host physiology or gut microbial ecology. Deletion of clb and irp abolished potential colibactin- and yersiniabactin-associated biosafety risks while preserving bacterial growth and colonisation capacity. MEc30-NA continuously produced nicotinic acid in the gut, activated epithelial GPR109a-associated barrier signalling, improved glucose and lipid metabolism, reduced systemic inflammation and avoided the sharp peak exposure associated with conventional nicotinic acid administration. MEc30-mIL-10 enabled sustained intestinal interleukin-10 delivery, suppressed inflammatory macrophage activation, improved barrier integrity and alleviated colitis in both Il10[-] [/] [-] and DSS-induced mouse models.

CONCLUSION: This study identifies MEc30 as a durable and safety-optimised native E. coli chassis for sustained intestinal therapeutic delivery. Engineered native symbionts may provide a long-acting live biotherapeutic strategy for metabolic diseases and chronic intestinal inflammation.},
}

@article {pmid42761071,
year = {2026},
author = {Zhou, M and Yasuda, S and Miura, H and Xu, T and Kuroiwa, M and Xu, X and Terada, A},
title = {Electron acceptor-dependent duality of nitrous oxide metabolism in Thiobacillus during sulfur autotrophic denitrification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1903473},
pmid = {42761071},
issn = {1664-302X},
abstract = {Sulfur-driven autotrophic denitrification (SADN) is a promising biotechnology for nitrogen removal from low-carbon wastewater; however, nitrous oxide (N2O) emissions remain a significant environmental concern. This study systematically investigated the effects of different nitrogen oxide electron acceptors on denitrification performance, microbial community succession, distribution of the N2O reductase gene nosZ clade, and the ecological functions of Thiobacillus using sequential enrichment cultivation. Among the tested conditions, the nitrate (NO 3 -)-fed system achieved the highest denitrification and sulfur oxidation rates, with the lowest net N2O accumulation, whereas the nitrite (NO 2 -)-fed condition led to severe N2O accumulation due to an imbalance between N2O production and reduction. High-throughput sequencing and quantitative PCR analyses revealed that Thiobacillus became the primary sulfur-oxidizing denitrifier in the presence of NO 3 - , NO 2 - , and nitric oxide, accompanied by substantial enrichment of nirS and clade I nosZ genes. In contrast, N2O-fed conditions promoted a more functionally diverse community enriched with clade II nosZ bacteria, including Azonexus and Dechloromonas. Metagenomic analyses recovered three distinct Thiobacillus metagenome-assembled genomes (MAGs 10, 11, and 25), each with distinct denitrification and sulfur oxidation capacities. MAG 10 contains genes for complete sulfur oxidation and denitrification, including clade I nosZ and nirS genes. Conversely, the nosZ gene was not detected in MAG 11, whereas the norB/norC genes were present, indicating their potential role as an N2O producer. MAG 25 exhibits N2O-responsive functional enrichment upon N2O feeding, reflecting a specialized ecological strategy centered on sulfur oxidation coupled with N2O reduction. Overall, these findings show that electron acceptors play a key role in shaping microbial succession, nosZ clade distribution, and the dual roles of Thiobacillus in N2O cycling depending on conditions. This study provides new insights into microbial ecology and offers potential strategies for mitigating N2O emissions in SADN processes.},
}

@article {pmid42762633,
year = {2026},
author = {Shaker, D and Liu, W and Le Coustumer, P and Stoll, S},
title = {Towards a better understanding of protein affinity for polystyrene nanoplastics: Investigation of surface charge effects, interaction mechanisms and aggregation kinetics.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {269},
number = {},
pages = {116184},
doi = {10.1016/j.colsurfb.2026.116184},
pmid = {42762633},
issn = {1873-4367},
abstract = {This study investigates the mechanisms governing nanoplastic-protein interactions, aggregation, and colloidal stability between bovine serum albumin (BSA) and polystyrene nanoplastics (PS NPls) with opposite surface charges under controlled conditions at pH 7.4. Positively charged amidine latex (180 ± 20 nm) and negatively charged sulfate latex (220 ± 20 nm) PS NPls were characterized over pH 3-10, then studied in ultrapure water (UPW) and 10 mM HEPES. When BSA concentration was varied at fixed PS NPls concentration (30 mgL[-1]), cationic PS NPls (+) rapidly adsorbed BSA, inducing charge neutralization and aggregation at low BSA (≈ 4 mg L[-1]) through reduced electrostatic repulsion and protein bridging. At higher BSA concentration (20 mg L[-1]), surface saturation led to protein corona formation, charge inversion, and colloidal restabilization. Anionic PS NPls (-) remained dispersed, with no detectable aggregation or charge inversion by DLS and ζ-potential. In a BSA-rich model system (50 mg L[-1]) with varying PS NPls concentrations, low cationic PS NPls concentrations (< 4 mg L[-1]) produced stable BSA aggregates, while higher concentrations (> 4 mg L[-1]) yielded well-dispersed corona-coated particles. These interaction states formed rapidly and remained stable over 48 h. PS NPls (-) showed no significant interaction or kinetic evolution. Similar trends in UPW and HEPES indicate that ionic screening modulated but did not alter the charge-dependent mechanisms. Together, these findings highlight the central role of surface charge in controlling PS NPls-protein interactions and provide a mechanistic basis for future studies in complex biological media.},
}

@article {pmid42756118,
year = {2026},
author = {Xiong, S and Yao, R},
title = {Klebsiella pneumoniae in inflammatory bowel disease and rectal cancer: from gut inflammation to a potential driver of carcinogenesis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1948813},
pmid = {42756118},
issn = {1664-302X},
abstract = {The gut microbiota is a critical modulator of intestinal inflammation and colorectal cancer (CRC), yet the specific microbial drivers that bridge inflammatory bowel disease (IBD) to rectal carcinogenesis remain poorly defined. Klebsiella pneumoniae (K. pneumoniae) has recently emerged as a compelling candidate at this nexus; however, several critical questions remain unresolved: (i) whether K. pneumoniae colonization is a cause or a consequence of rectal carcinogenesis; (ii) how strain level heterogeneity determines pathogenic versus commensal outcomes; and (iii) which rectal microenvironmental factors selectively amplify its carcinogenic potential. Moreover, the potential utility of persistent colonization with carcinogenic K. pneumoniae strains as a predictive biomarker and target for chemoprevention warrants further investigation. This review systematically addresses these questions by integrating findings from microbial ecology, virulence factor biology, host immunology, and oncogenic signaling. We dissect the dual role of K. pneumoniae along the inflammation cancer axis, focusing on its capacity to promote T helper 17 (Th17) driven inflammation, disrupt the epithelial barrier, and directly alkylate host DNA via colibactin-like genotoxins. We propose a mechanistic framework in which chronic K. pneumoniae colonization acts as a bridge between IBD activity and rectal tumorigenesis, and we critically evaluate the potential of phage therapy, virulence inhibitors, and microbiome-based biomarkers to intercept this process. Finally, we highlight key knowledge gaps and outline future directions required to establish causality and translate these insights into clinical strategies for IBD associated rectal cancer prevention.},
}

@article {pmid42756370,
year = {2026},
author = {Jiao, Y and Zhao, Y and Zhang, Z and Sun, H and Wang, Y and Bai, X and Piao, C and Lei, X and Zhang, N and Xu, H},
title = {Sishen wan modulates gut microbial and short-chain fatty-acid imbalances and ameliorates behavioral and inflammatory abnormalities in mice with chronic sleep deprivation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1944977},
pmid = {42756370},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic sleep deprivation (CSD) disrupts mood-related behavior, gut microbial ecology, and inflammatory homeostasis. Sishen Wan (SSW), a medicinal plant formula used clinically for chronic diarrhea, has shown microbiota- and inflammation-modulating effects in colitis models, but its protective effects under sleep-deprivation conditions remain unclear.

METHODS: The chemical profile of SSW was characterized by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Male C57BL/6 J mice underwent CSD using a modified multiple-platform method and received three doses of SSW or fluoxetine. Behavioral performance, histopathology, gut microbiota composition, and short-chain fatty acid (SCFA) concentrations in feces, serum, and hippocampal tissue were assessed. Fecal material from Control, Model, and high-dose SSW (SSW-H) donors was transplanted into antibiotic-pretreated recipients. Serum untargeted metabolomics, hippocampal transcriptomics, RT-qPCR, and resting-state functional magnetic resonance imaging were used to characterize metabolic, transcriptional, and brain-function changes.

RESULTS: CSD reduced sucrose preference and open-field activity, prolonged immobility in the tail-suspension and forced-swim tests, aggravated colonic and hippocampal injury, and increased pro-inflammatory cytokines. SSW-H produced the most consistent improvements. CSD also reduced gut microbial richness and diversity, altered community composition, and lowered fecal acetate, propionate, and butyrate and serum acetate. SSW-H shifted the community toward the Control profile, increased Akkermansia, reduced several Model-enriched taxa, and increased major fecal SCFAs and serum acetate. Recipients of Model-donor feces developed reduced sucrose preference and activity, prolonged immobility, and colonic and hippocampal abnormalities. In contrast, recipients of SSW-H-donor feces showed milder behavioral and histological changes and a microbial profile distinct from that of FMT-Model recipients. SSW-H was also associated with partial normalization of lipid-, amino-acid-, and one-carbon-metabolism-related serum features, modulation of hippocampal immune pathways involving chemokines, cytokines, and NF-κB signaling, and attenuation of several CSD-associated regional brain abnormalities.

CONCLUSION: SSW alleviated CSD-associated behavioral abnormalities, tissue injury, and inflammation, with the high dose showing the most consistent effects. These improvements were accompanied by changes in gut microbial composition and SCFA profiles.},
}

@article {pmid42756730,
year = {2026},
author = {Ilicic, D and Vallet, M and Salimi, F and Buaya, AT and Thines, M and Grossart, HP},
title = {Temperature modulates infection-associated metabolic responses in bloom-forming freshwater diatoms.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag240},
pmid = {42756730},
issn = {2730-6151},
abstract = {Warmer waters are reshaping unseen interactions at the base of aquatic food webs, with potential consequences for microalgal bloom dynamics and carbon transfer to higher trophic levels. Two major groups of aquatic parasites-chytrids and oomycetes-infect the same algal host, and changes in temperature can alter the dynamics of these infections and determine their success. Using laboratory-controlled synthetic communities, we investigated the effect of temperature on chytrid and oomycete infection dynamics in the bloom-forming freshwater diatom Ulnaria ulna. Our findings reveal complex dynamics, with temperature shaping infection prevalence and host growth differently between the two infection systems. Notably, chytrid infection prevalence increased at lower temperatures, challenging the general applicability of the cold-water refuge theory in this host-parasite system, whereas oomycete infection dynamics showed a contrasting temperature response. Using UHPLC-HRMS analysis, we identified significant metabolic changes associated with parasite infection, while temperature further modulated these responses differently in chytrid- and oomycete-infected cultures. Chytrid infections were associated with metabolites potentially linked to stress- or defense-related responses, whereas oomycete infections exhibited metabolic signatures potentially associated with nutrient scavenging and manipulation of host metabolism. These different metabolic responses suggest that warming not only alters parasite success, but also modifies the biochemical composition of infected host-parasite systems, with possible implications for trophic transfer efficiency and carbon cycling. Together, these findings establish a conceptual framework linking temperature with infection-associated metabolic changes and provide first insights into how temperature affects parasitic infections of microalgae and their biochemical consequences for aquatic food webs.},
}

@article {pmid42696302,
year = {2026},
author = {Sun, X and Zhang, IH and Babbin, AR and Weissman, JL and Zakem, EJ},
title = {Lifestyle differentiation among marine denitrifying microorganisms.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag232},
pmid = {42696302},
issn = {1751-7370},
support = {LS-FMME-00871981//University of Pennsylvania and the Simons Foundation/ ; OCE-2342986//National Science Foundation/ ; OCE-2142998//National Science Foundation/ ; #2125142//National Science Foundation/ ; OCE-2019589//Center for Chemical Currencies of a Microbial Planet/ ; //NSF Center for Chemical Currencies of a Microbial Planet/ ; //Simons Foundation Early Career Investigator in Aquatic Microbial Ecology and Evolution Award/ ; },
mesh = {*Denitrification ; *Seawater/microbiology ; Nitrates/metabolism ; *Bacteria/metabolism/genetics/classification ; Ecosystem ; *Aquatic Organisms/metabolism/genetics ; },
abstract = {Microorganisms carrying out denitrification in marine anoxic zones drive bioavailable nitrogen loss. Sequencing datasets have demonstrated the modularity of denitrification, with most populations having the genetic capability for only a subset of the pathway (NO3-➔NO2-➔NO➔N2O➔N2). Although previous work provided ecological explanations for this diversity among the functional modules, large trait variations exist within each functional module, and this within-module diversity and its biogeochemical implications remain unexplored. Here, we combine genomic data and modeling to explore how metabolic "lifestyle" strategies influence denitrifier community structure. We build a comprehensive genomic database of marine denitrifiers, and identify lifestyle differentiation among denitrifier functional groups. We then extend a mathematical ecosystem model by resolving two microbial functional types for each module representing a metabolic trade-off: a copiotroph, optimized for fast growth, and an oligotroph, optimized for high nutrient affinity. In the model, as the supply of organic matter relative to nitrate increases, the degree of copiotrophy among the community increases and then decreases. This suggests that oligotrophs are associated with either organic-matter- or nitrate-limiting conditions, whereas copiotrophic lifestyles are associated with an intermediate regime. Our model further associates NO2- reducers with oligotrophy and NO3- reducers with copiotrophy, particularly those producing the greenhouse gas nitrous oxide (N2O), linking N2O production to substrate-replete conditions, which is consistent with our genome-based lifestyle estimates. Results provide insight into denitrifier ecological niches and thus the biogeochemical conditions that are associated with the production of intermediates, such as N2O, improving our understanding of how nitrogen cycling will change in a warming ocean.},
}

*Denitrification
*Seawater/microbiology
Nitrates/metabolism
*Bacteria/metabolism/genetics/classification
Ecosystem
*Aquatic Organisms/metabolism/genetics

@article {pmid42754709,
year = {2026},
author = {Selten, G and Lamouche, F and Gómez-Repollés, A and López, JL and Zhang, XM and Smart, C and Blahovska, Z and Zarate Camargo, G and Kelly, S and de Jonge, R and Radutoiu, S},
title = {Functional capacities drive recruitment of bacteria into plant root microbiota.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42754709},
issn = {2058-5276},
support = {OPP11772165//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; NNF24SA0096909//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF24SA0096909//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 024.004.14//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
abstract = {Root-associated microbiomes are shaped by the plant, yet vary across environments and hosts, challenging prediction and engineering. Here, to uncover principles of bacterial selection at the root-soil interface, we applied a systems-level approach using reconstitution studies with communities of isolates from Arabidopsis, barley and Lotus grown in soil. Functional divergence among the microbiota of the host plants reflected distinct strategies: in Arabidopsis and barley, recruitment was primarily shaped by inoculum, while Lotus root environment favoured fewer, functionally diverse isolates, akin to a 'Swiss army knife' strategy. Despite taxonomic variability, root microbiomes encoded overlapping functions. Across major taxa, isolates with broad but distinct functional repertoires within their families were consistently more abundant. Using a genome-to-function framework that is function centric, taxonomically inclusive and host-context aware, we identified 266 functions enriched across all root microbiomes. This functional backbone emerged as a core signature of plant-associated bacteria, providing a solid foundation for microbiome engineering in agriculture.},
}

@article {pmid42755161,
year = {2026},
author = {Guo, H and Zhang, C and Wang, R and Yang, Y and Wang, G and Cui, S and Lu, W and Yang, B and Lyu, X and Tian, P and Tian, F and Zhao, J and Zhai, Q},
title = {Dietary and nutritional strategies for reducing disease risk associated with antibiotic-induced dysbiosis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2728330},
doi = {10.1080/19490976.2026.2728330},
pmid = {42755161},
issn = {1949-0984},
mesh = {*Dysbiosis/chemically induced/microbiology/diet therapy ; Humans ; *Anti-Bacterial Agents/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; Animals ; *Diet ; Bacteria/classification/metabolism/drug effects ; },
abstract = {Antibiotic exposure is a major driver of gut microbiota dysbiosis, and its effects extend beyond transient diversity loss. Persistent alterations in microbial composition and metabolites disrupt intestinal barrier integrity, immune homeostasis, and host metabolic signaling, thereby increasing the risk of chronic diseases. Here, we review the evidence linking antibiotic-induced dysbiosis to disease susceptibility and argue that post-antibiotic recovery should target microbial functions and metabolic network restoration. We also examine a range of nutritional strategies, including dietary adjustments, prebiotics, probiotics, and bioactive nutrients, for their capacity to support beneficial commensal bacteria, restore key microbial metabolites, and enhance the gut ecosystem resilience. However, inter-individual variability in response complicates the development of universal protocols, and limited long-term clinical outcome data make it difficult to determine the clinical value of these interventions. Integrating nutritional science, microbial ecology, and precision medicine will be essential for developing effective personalized interventions.},
}

*Dysbiosis/chemically induced/microbiology/diet therapy
Humans
*Anti-Bacterial Agents/adverse effects
*Gastrointestinal Microbiome/drug effects
Prebiotics/administration & dosage
Probiotics/administration & dosage
Animals
*Diet
Bacteria/classification/metabolism/drug effects

@article {pmid42749571,
year = {2026},
author = {Armstrong, R and Timmis, KN},
title = {The textile web as a probiotic interface.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.08.007},
pmid = {42749571},
issn = {1878-4380},
abstract = {Microbiome of the Built Environment research exhibits a marked 'hard-surface bias', overlooking the dynamic soft materials that dominate human-microbial exchange. We propose a theoretical reorientation: the home as a textile web of dynamic, porous microbial reactors. Grounded in immunology's Danger Theory and the principle of 'tissue-based class control', these soft interfaces function as an external tissue analog. By treating textiles as designable interfaces (ranging from airway exchange nodes to laundry bioreactors), architecture becomes a site for proactive probiotic rituals. This framework leverages competitive exclusion to support externalized mucosal 'guard duty', transitioning from prophylactic sterility to a choreography of domestic care. Notably, this reframing recognizes that hygiene encompasses more than infection prevention: domestic cleaning rituals also shape the microbial ecology that educates the immune system. Ultimately, we frame the living home as a tolerogenic exoskeleton, biologically calibrated to protect and prime the human holobiont.},
}

@article {pmid42752591,
year = {2026},
author = {Rocha, PRF and Tirichine, L},
title = {Electrical signalling beyond diffusion-limited microbial interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag238},
pmid = {42752591},
issn = {1751-7370},
abstract = {Ecological communication is traditionally interpreted through diffusion-limited chemical signalling. Here, we argue that bioelectricity provides a complementary dimension of microbial ecological interaction, arising from ion-driven electrical signalling between responsive cells and extracellular electron transport through redox-active or conductive pathways. These mechanisms operate over distinct physical regimes, with ion-driven signalling mediating information-bearing interactions when electrical or electrochemical perturbations are sensed and decoded by biological recipients, whereas extracellular electron transport enables metabolic and redox coupling. We define "handover distance" as the effective functional interaction range over which a biologically generated electrical or electrochemical perturbation can elicit a measurable response in a biological recipient. In analogy to the phycosphere, which describes the diffusionlimited chemical interaction radius surrounding microorganisms, handover distance provides an experimentally testable means of linking cellular electrophysiology to the spatial range of biological interactions. This Perspective proposes that bioelectrical interactions represent an underappreciated dimension of microbial ecology that complements established chemical communication across complex environments.},
}

@article {pmid42753439,
year = {2026},
author = {Wang, B and Zhu, K and Wang, Z and Sun, W and Zha, Y and Wang, H and Zhang, Y and Zhang, Y and Song, Y and Zhang, H},
title = {Biogeographical pattern of persistent organic pollutant-transformation genes and their hosts across global inland waters.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143613},
doi = {10.1016/j.jhazmat.2026.143613},
pmid = {42753439},
issn = {1873-3336},
abstract = {Persistent organic pollutants (POPs) remain widespread in inland waters despite decades of regulation, yet the global distribution and ecological controls of microbial POP transformation potential remain largely unresolved. Here, we analyzed 1593 metagenomic samples from inland waters across six continents to investigate the biogeography, microbial hosts, and environmental drivers of POP transformation genes (POPTGs). We identified four major POP categories, with polychlorinated POP transformation genes dominating both water and sediment habitats. Sediments harbored significantly higher POPTG richness and abundance than water columns, highlighting their role as global reservoirs of POP transformation capacity. Unexpectedly, POPTG diversity displayed hump-shaped latitudinal pattern. Proteobacteria were the dominant POPTG carriers, and widespread host taxa generally possessed broader transformation repertoires. Nearly half of POPTG-carrying species were shared between habitats, while frequent associations with mobile genetic elements suggested potential horizontal dissemination of transformation traits. Structural equation modeling revealed that host diversity, anthropogenic pressure, and mean annual temperature collectively explained 38% of POPTG abundance variation, with host diversity exerting the strongest effect. Our findings establish a global framework linking microbial ecology with POP transformation potential and provide insights into predicting natural attenuation and remediation capacity of inland waters under environmental change.},
}

@article {pmid42744179,
year = {2026},
author = {Cui, Y and Yang, Y and Yu, H and Yang, D and Yang, D and Han, H and Dai, X},
title = {Coupling interfacial thermodynamics and microbial ecology drives carrier-induced microgranulation in activated sludge systems.},
journal = {Environmental research},
volume = {308},
number = {Pt 2},
pages = {125679},
doi = {10.1016/j.envres.2026.125679},
pmid = {42744179},
issn = {1096-0953},
abstract = {High-concentration powder carrier bio-fluidized bed (HPB) technology provides a promising strategy for rapid cultivation of microgranules; however, the interfacial mechanisms governing carrier-induced granulation remain poorly explored. In this study, three typical carriers (diatomite, montmorillonite, and fly ash) were employed to investigate microgranule formation in HPB systems. By integrating expanded Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, extracellular polymer substances (EPS) and electrochemical characterization, microbial community analysis, and nitrogen transformation functional genes, the mechanisms linking interfacial interactions to microgranule development were systematically elucidated. Among tested carriers, diatomite exhibited the strongest granulation-promoting effect, increasing particle size by 63.3% and biomass growth by 24.7% within 30 d. Surface thermodynamic analysis revealed that diatomite possessed the lowest adhesion Gibbs free energy (-16.90 mJ m[-2]), compared with -9.42 and -3.95 mJ m[-2] for montmorillonite and fly ash, respectively. The Lewis acid-base (AB) interaction free energy of the diatomite-sludge interface reached -13.43 mJ m[-2], accounting for more than 79% of the total adhesion free energy, indicating that AB interactions were primarily responsible for diatomite's superior microbial adhesion capacity. Consistent with thermodynamic advantage, the interaction energy barrier disappeared on day 30 in the diatomite system, 10 d earlier than in the fly ash system, with the reversible adhesion distance decreased to 5.61 nm, facilitating rapid aggregate formation. The accelerated microgranules' development was also accompanied by enhanced protein/polysaccharide (PN/PS) and electrochemical activity, with increasing from 1.40 to 2,29, 1185 to 1454 μF, respectively. Simultaneously, nitrifying, denitrifying, and granulation-associated microorganisms were selectively enriched. Correspondingly, the abundances of amoABC, hao, narB, and nosZ reached 188%, 179%, 163%, and 151% of control levels, respectively. These findings demonstrate the exceptional granulation performance of diatomite originates from its favorable interfacial thermodynamic properties, which promote microbial adhesion, extracellular electron transfer, and functional microbial assembly, thereby accelerating microgranule formation in HPB systems.},
}

@article {pmid42744694,
year = {2026},
author = {Geerlings, NMJ},
title = {Cable bacteria use extracellular electron transfer.},
journal = {Trends in biochemical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibs.2026.08.007},
pmid = {42744694},
issn = {0968-0004},
abstract = {Recent work by Aiyer and colleagues demonstrates that cable bacteria can conserve energy and grow under anoxic conditions by transferring electrons to electrodes via extracellular electron transfer. This transfer is both direct and riboflavin-mediated. Two distinct outer cell-surface redox centers, likely outer-membrane cytochromes, are involved in the electron transfer.},
}

@article {pmid42744850,
year = {2026},
author = {El-Banna, AF and Junca, H and Steube, A and Wissenbach, DK and Settmacher, U and Schneider, C and Tekbaş, A},
title = {A prospective randomized controlled pilot study of gut microbiome modulation by Nigella sativa seed oil and thymoquinone metabolism in healthy volunteers: implications for gastrointestinal surgery.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42744850},
issn = {2045-2322},
mesh = {Humans ; *Plant Oils/pharmacology/administration & dosage ; *Benzoquinones/metabolism/urine/pharmacology/administration & dosage ; Adult ; Male ; Pilot Projects ; Female ; Prospective Studies ; *Gastrointestinal Microbiome/drug effects ; Nigella sativa/chemistry ; Healthy Volunteers ; Feces/microbiology ; Dietary Supplements ; Carum/chemistry ; Seeds/chemistry ; Young Adult ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Maintaining gut microbial balance may influence outcomes in gastrointestinal surgery. Dietary supplementation has the potential to selectively modify its composition. Nigella sativa seed oil (NSSO), which contains the bioactive compound thymoquinone (TQ), has antimicrobial and immunomodulatory properties, but human data on NSSO-associated gut microbiome changes and urinary TQ detectability after repeated oral exposure remain limited. In this prospective, single-center, randomized open-label pilot study, eight healthy adults were assigned to a treatment group (n = 4) receiving TQ-containing NSSO capsules (two capsules, three times daily for 20 days) or a control group (n = 4) without supplementation. Fecal samples were collected at five time points and analyzed by 16 S rRNA gene sequencing. Alpha and beta diversity, exploratory differential abundance, and machine learning analyses were performed. Food diaries were reviewed descriptively. Urine samples obtained at two time points were analyzed using Gas Chromatography Mass Spectrometry (GC-MS) to detect TQ and its metabolites. No significant differences in alpha or beta diversity were observed between groups, proving a stable microbiome composition. However, specific taxa increased or decreased, among them Mediterraneibacter lactaris (p = 9 × 10[-5]) and Terrisporobacter mayombei (p = 3 × 10[-4]), respectively. TQ and/or TQ-H2 were qualitatively detected in urine samples from the treatment group after repeated NSSO intake. This pilot study suggests that repeated NSSO intake is feasible for longitudinal microbiome and urinary metabolite sampling and provides preliminary evidence for taxon-specific changes in healthy adults. Urinary detection of TQ/TQ-H2 confirms detectability following repeated NSSO intake but does not permit pharmacokinetic conclusions. These findings may guide the design of future blinded, placebo-controlled, diet-controlled perioperative microbiome studies.Trial Registration: The trial was retrospectively registered at ClinicalTrials.gov (NCT07450807) on 4 March 2026.},
}

Humans
*Plant Oils/pharmacology/administration & dosage
*Benzoquinones/metabolism/urine/pharmacology/administration & dosage
Adult
Male
Pilot Projects
Female
Prospective Studies
*Gastrointestinal Microbiome/drug effects
Nigella sativa/chemistry
Healthy Volunteers
Feces/microbiology
Dietary Supplements
Carum/chemistry
Seeds/chemistry
Young Adult
RNA, Ribosomal, 16S/genetics

@article {pmid42745450,
year = {2026},
author = {Luo, X and Lan, Y and Guo, J and Liu, J and Gao, M and Yuan, Y and Li, M and Zheng, S},
title = {A Two-Step SeCys Oxidation Pathway Bridging Soil Selenium Bioavailability and Rice Selenium Biofortification.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70417},
pmid = {42745450},
issn = {1462-2920},
support = {32370130//National Natural Science Foundation of China/ ; NYWSWZX2025-2027-09//Major Special Project for the Development of Agricultural Microorganism Industry in Hubei Province/ ; },
mesh = {*Oryza/metabolism/microbiology/chemistry ; *Selenium/metabolism ; Oxidation-Reduction ; *Biofortification ; *Soil/chemistry ; Biological Availability ; Soil Microbiology ; *Bacterial Proteins/metabolism/genetics ; Selenious Acid/metabolism ; },
abstract = {Addressing global selenium (Se) deficiency requires enhancing soil Se bioavailability, a process largely governed by microbial oxidation whose molecular mechanisms remain elusive. Here, we systematically elucidated the SeCys2 oxidation mechanism of Comamonas testosteroni JL40 and its role in promoting rice Se biofortification. Strain JL40 employed a novel two-step oxidative pathway, converting SeCys2 sequentially to Se nanoparticles (SeNPs) and then to selenite (Se(IV)). SeoA-D were identified to catalyse Se oxidation by integrated proteomic, genetic and enzymatic analyses. Of these, SeoA and SeoB catalysed the complete two-step oxidation; SeoD exclusively mediates the first step of SeCys2 to SeNPs, while SeoC drives the second step of Se(0) to Se(IV). This system demonstrates broad host diversity and environment distribution and represents a prevalent mechanism for Se activation in the environment. Acting in concert with sulphur-oxidising metabolic gene clusters, they facilitated Se-S cross-metabolism, assembling into Se-oxidising activity as a previously unrecognised functional trait. Crucially, strain JL40 stably colonised the rice rhizosphere, where it enhanced soil Se bioavailability by 150%, increased grain Se content by 87.5%, and concurrently improved plant physiological traits and reshaped rhizosphere microbial networks. This work reveals a key Se-cycle pathway and directly enables sustainable biofortification, bridging microbial ecology and crop nutrition.},
}

*Oryza/metabolism/microbiology/chemistry
*Selenium/metabolism
Oxidation-Reduction
*Biofortification
*Soil/chemistry
Biological Availability
Soil Microbiology
*Bacterial Proteins/metabolism/genetics
Selenious Acid/metabolism

@article {pmid42745690,
year = {2026},
author = {Duan, X and Wang, L and Koski, TM and An, L and Efferth, T and Fu, Y},
title = {Drought Stress Mediated Changes in Food Crops: Mechanisms and Remediation Strategies.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77194},
pmid = {42745690},
issn = {2198-3844},
support = {2024YFD2201105//National Key R&D Program of China/ ; 2025XAGG0057//Science and Technology Innovation Program of Xiongan New Area/ ; BLRC2023A01//5·5 Engineering Research & Innovation Team Project of Beijing Forestry University/ ; },
abstract = {Climate change has intensified drought frequency and severity, threatening global food security, particularly for staple crops like maize, wheat, and soybean. As central secondary metabolites, flavonoids orchestrate cellular redox homeostasis, stress signal transduction, and metabolic plasticity during plant drought responses. Previous reviews are confined to isolated molecular cascades and separate treatment of flavonoid metabolism, rhizosphere microecology, and agronomic mitigation strategies, failing to establish an integrated multi-scale regulatory framework. To fill this fragmented gap, this review integrates advances in plant physiology, microbial ecology, and nanobiotechnology to construct a cross-scale framework of flavonoid-mediated drought resistance in major food crops. We systematically summarize species-specific flavonoid regulatory networks and metabolic reprogramming triggered by drought-induced oxidative stress, dissect rhizosphere microbiome effects on flavonoid biosynthesis and drought signaling, and elaborate novel mechanisms whereby nanomaterials reshape flavonoid metabolism and boost drought tolerance via tuning ROS homeostasis. Furthermore, this work integrates soil amendment and precision irrigation to decipher synergistic drought-resistance crosstalk among agronomic practices, crop metabolism, and root-associated microbiota. Collectively, this review unifies molecular, microbial, technological, and agronomic perspectives to establish a multi-scale, interdisciplinary framework for crop drought adaptation. It delivers fundamental theoretical support for climate-resilient agriculture and outlines priority research avenues to safeguard global food security.},
}

@article {pmid42747194,
year = {2026},
author = {Aguayo, S and Leiva-Sabadini, C and Saavedra, P and Thalhuber, D and Helliwell, E and Merritt, J and Kreth, J},
title = {From Biogenesis to Host Modulation: The Expanding Biology of Oral Streptococcal Membrane Vesicles.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag049},
pmid = {42747194},
issn = {1574-6976},
abstract = {Bacterial extracellular membrane vesicles (bEVs) provide fundamental biological functions through communication, ecological adaptation, and mediation of host interactions. Gram-positive oral streptococci were long considered to be incapable of bEVs production due to their thick peptidoglycan. In contrast, recent advances in imaging, biochemical isolation, and multi-omics profiling have revealed that bEVs production is common and may represent a general trait of streptococci. This review summarizes current research on the biogenesis, cargo composition, and functional roles of bEVs, with an emphasis on oral streptococcal vesicles and their contributions to oral microbial ecology and host responses. We highlight methodological innovations for isolation and characterization of bEVs that have led to the discovery of species-specific bEVs cargo. Functionally, bEVs participate in diverse biological activities, including horizontal gene transfer, antimicrobial peptide delivery, virulence and redox modulation, and they profoundly influence host immunity by modulating cytokine signaling, epithelial barrier function, and immune pathways. Emerging evidence further suggests active roles in polymicrobial biofilm development and systemic dissemination of microbial signals relevant to health and disease. By integrating biochemical, structural, ecological, and immunological perspectives, this review provides a comprehensive overview of the current state of streptococcal and Gram-positive bEVs research and discusses its translational potential to support oral and general health.},
}

@article {pmid42748564,
year = {2026},
author = {Zhang, F and Wang, Y and Qian, J and Li, S and Deng, X and Lu, M and Liu, Y and Yang, X and Zhang, J and Ren, Z and Yang, X},
title = {Gut microbial community assembly exhibits compartment-specific responses to selection for high body weight in female chickens.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107712},
doi = {10.1016/j.psj.2026.107712},
pmid = {42748564},
issn = {1525-3171},
abstract = {Conventional poultry breeding primarily targets host growth traits, yet breeding may also reshape the gut microbiota through host-microbe interactions. Given the spatial heterogeneity of the chicken gastrointestinal tract, whether divergent selection for body weight is associated with compartment-specific microbial assembly and differences in the digestive ecosystem remains unclear. Here, using female primitive line and a high body weight (HBW) selected line, we systematically characterized differences in host gastrointestinal traits and gut microbial ecology associated with divergent selection history. Significant differences in gut morphology and local environmental conditions were observed between the two lines, together with region-specific shifts in microbial community assembly. Specifically, crop weight was greater and microbial assembly exhibited greater stochasticity in the HBW line, potentially reflecting differences in feeding-related gastrointestinal dynamics. In contrast, the small intestine displayed improved villus morphology and altered microbial assembly patterns, accompanied by enrichment of potentially beneficial taxa associated with nutrient utilization, including Monoglobus in the duodenum and Blautia in the ileum, indicating coordinated changes in host intestinal development and microbial ecological adaptation. The cecal community showed relatively stable assembly patterns but was enriched in metabolically relevant taxa such as Lachnospiraceae and Faecalibacterium, together with differences in predicted functional potential related to nutrient metabolism. Overall, this study shows that the HBW line is associated with distinct, compartment-specific patterns of gut microbial assembly, providing a conceptual framework for considering the gut microbiota in poultry breeding strategies.},
}

@article {pmid42523320,
year = {2026},
author = {Morabbi, SM and Bhowmik, N and Sutherland, S and Wylie, EA and Decker, RS and Daerwish, AA and Pérez, MP and Pascual, E and Lutter, EI and Philmus, B and Stubbendieck, RM},
title = {Differential Metabolite Production Underlies Disruption of the Cystic Fibrosis Airway Microbiota by Pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42523320},
issn = {2692-8205},
abstract = {Cystic fibrosis (CF) is a multisystem disease characterized by the accumulation of mucus in the airways that promotes pathogen colonization, leading to respiratory exacerbations, lung failure, and death. Culture-independent approaches have revealed that the CF airway harbors a complex microbiota, including opportunistic pathogens and bacteria that colonize the oropharynx. Here, we reanalyzed 5,260 16S rRNA gene microbiota datasets to infer ecological associations between members of the CF microbiota. We determined that pathogens are more likely to proliferate and dominate when present, while oropharyngeal bacteria are more likely to form persistent communities. Further, we found higher diversity and increasing numbers of inferred interactions were positively associated with lung function. In contrast, pathogens were negatively associated both with each other and with oropharyngeal bacteria, suggesting that they may disrupt the microbiota. To validate these predictions, we cultured 1,597 bacterial isolates from 96 people with CF and performed 12,542 coculture assays against eight representative CF pathogenic and oropharyngeal bacteria. 23% of these interactions resulted in growth inhibition. While Pseudomonas isolates were, on average, the most inhibitory, we observed variable activity among isolates. We then confirmed that Pseudomonas aeruginosa isolates, even those from the same donor and timepoint, exhibited significant differences in their metabolome and bioactivity profiles that correlated with acquisition of mutations. Together, our results suggest that pathogens may disrupt the CF microbiota and bloom in part through differential metabolite production. Furthermore, these data highlight that characterizing multiple isolates is necessary to capture the full landscape of chemically mediated interactions within microbial communities.},
}

@article {pmid42743742,
year = {2026},
author = {Guan, K and Xiao, Y and Xu, C and Zhang, H and Wu, S and Song, Z and Cao, S},
title = {Phosphorus alleviates age-associated osteoporosis in laying hens by reshaping bone metabolism and modulating cecal microbial communities.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107678},
doi = {10.1016/j.psj.2026.107678},
pmid = {42743742},
issn = {1525-3171},
abstract = {Osteoporosis in aged laying hens poses a major constraint on long-term egg production system. This study investigated the efficacy and underlying mechanisms of dietary phosphorus (P) in alleviating age-associated osteoporosis. A completely randomized design was employed, with 300 Hy-Line Brown laying hens (58 weeks of age) randomly assigned to one of three dietary treatments: a low-phosphorus diet (LP, 0.12% non-phytate phosphorus [NPP]), a regular-phosphorus diet (RP, 0.32% NPP), or the LP diet supplemented with 10,000 FTU/kg phytase (PHY, 0.12% NPP). Each treatment comprised 10 replicates of 10 hens. Following a 2-week adaptation period, the experiment lasted for 12 weeks. The results showed that dietary P reduction or phytase supplementation had no significant effect (P > 0.05) on egg production performance or egg quality throughout the experimental phase. However, at the end of the trial, hens fed the LP diet exhibited significantly lower serum P concentration and alkaline phosphatase (ALP) activity, along with reduced tibial P and magnesium (Mg) contents (P < 0.05), compared with the RP group. Conversely, serum calcium (Ca) level and tartrate-resistant acid phosphatase (TRACP) activity were significantly elevated in the LP group (P < 0.05). In contrast, phytase supplementation in the PHY group significantly increased serum ALP activity and tibial P and Mg contents relative to the LP group (P < 0.05). Notably, the PHY group also showed higher serum Ca concentration than the RP group (P < 0.05). Histomorphological examination revealed progressive cortical bone thinning accompanied by irregular erosion and increased demineralized areas in the tibiae of LP-fed hens, whereas only mild pathological changes were observed in the PHY group. Analysis of cecal microbiota indicated that dietary P modulation significantly altered microbial community structure: principal coordinate analysis (PCoA) showed distinct clustering for the LP and PHY group at week 8 and week 12, respectively (P < 0.05). Linear discriminant analysis effect size (LEfSe) further revealed that the LP group was enriched with pro-inflammatory taxa and microbes associated with nutrient metabolism stress. The RP group harbored a more complex and diverse microbial community, while the PHY group was characterized by an enrichment of beneficial bacteria involved in short-chain fatty acid (SCFA) production. Spearman correlation analysis demonstrated significant associations between specific bacterial genera and tibial health parameters. Genera such as Phascolarctobacterium, Rikenellaceae_RC9_gut_group, and Bacteroides were positively correlated with tibial mineral content and structural integrity, whereas Lactobacillus, Olsenella, and Prevotellaceae_Ga6A1_group showed negative correlations with these bone traits (P < 0.05). Collectively, these findings indicate that chronic P deficiency induces severe skeletal deterioration and gut microbiota dysbiosis in aged laying hens. Phytase supplementation partially counteracts the adverse effects of low-P diet by improving P utilization and reshaping the cecal microbiota toward a more beneficial composition. Nevertheless, long-term feeding of P-deficient diet even with phytase remains insufficient to fully preserve skeletal health. Therefore, ensuring adequate dietary P supply is essential for alleviating age-associated osteoporosis in aged laying hens, likely through integrated regulation of bone metabolic homeostasis and gut microbial ecology.},
}

@article {pmid42743793,
year = {2026},
author = {Andersen, JE and Iturbe-Espinoza, P and Ellegaard-Jensen, L and Sapkota, R and Winding, A},
title = {Protists introduce distinct temporal patterns in a synthetic bacterial community consistent with known feeding traits.},
journal = {Microbiological research},
volume = {314},
number = {},
pages = {128728},
doi = {10.1016/j.micres.2026.128728},
pmid = {42743793},
issn = {1618-0623},
abstract = {Through predation, protists act as strong determinants of bacterial communities, yet their role in shaping synthetic communities (SynCom) remains unclear. We present the effects of three predator protists - a ciliate (Colpoda steinii), a flagellate (Neobodo designis), and an amoeba (Acanthamoeba castellanii) on the temporal dynamics of bacterial SynCom using a microtiter plate-based design. We asked whether predation contributes to the maintenance of SynCom richness, alters trajectories, and whether these effects depend on the identity of the protist. Bacterial community structure and composition in absolute abundances were estimated by 16S rRNA gene metabarcoding. Protist 18S and bacterial 16S rRNA gene copy numbers were quantified by qPCR, respectively. Using five sampling points, we found that bacterial 16S rRNA gene abundance did not change significantly over time when cultured alone, whereas protist 18S rRNA gene abundance altered at later time points, decreasing in ciliates, remaining stable in amoebae, and increasing in flagellates. Further, using 16S rRNA gene metabarcoding, we found that protists significantly reshaped bacterial community structure across the temporal scale. Protist predation was associated with community richness and species-specific SynCom dynamics: C. steinii induced broad suppression, whereas N. designis exerted more restricted effects, both preferentially targeting initially dominant taxa, while A. castellanii showed a minor impact. These results highlight the importance of accounting for trophic interaction and point to prioritizing protists with a narrower feeding range when creating SynCom to maintain community diversity over time.},
}

@article {pmid42740563,
year = {2026},
author = {Feruza, J and Otajon, M and Shaxobiddin, M and Mamura, A and Aziz, K and Nargiza, K and Alimova, Z},
title = {The Oral Microbiome-Inflammaging Axis in Elderly Periodontitis: Emerging Immunopathogenic and Systemic Mechanisms.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70493},
pmid = {42740563},
issn = {1601-0825},
abstract = {BACKGROUND: Periodontitis prevalence increases with age, yet "elderly periodontitis" is not merely cumulative plaque exposure. Aging remodels mucosal immunity, elevates chronic inflammation, and promotes senescent cell accumulation with pro-inflammatory secretory phenotypes.

OBJECTIVE: To critically evaluate the self-reinforcing oral microbiome-inflammaging axis in elderly periodontitis.

METHODS: Narrative synthesis of mechanistic studies, human cohorts, and preclinical models investigating interactions between oral microbial ecology, immunosenescence, cellular senescence, and inflammaging.

RESULTS: Dysbiotic biofilms deliver persistent pressure interpreted by aged immune-stromal networks with heightened inflammatory gain. Mechanistic studies implicate aging-sensitive TLR9 sensing, age-amplified inflammasome-linked macrophage responses to P. gingivalis, and senescent niches that potentiate inflammation. Microbes directly induce senescence programs, including epithelial senescence and exosome-mediated paracrine immune senescence. Systemically, periodontitis induces multi-organ frailty-like phenotypes, neuroinflammatory changes, persistent gut dysbiosis, and altered metabolomes despite local therapy.

CONCLUSION: Elderly periodontitis represents a geroscience-relevant disorder where dysbiosis and biological aging jointly establish a self-sustaining inflammatory ecosystem. Priority gaps include longitudinal elderly cohorts integrating microbiome function with senescence markers and stratified trials combining biofilm control with host modulation.},
}

@article {pmid42740589,
year = {2026},
author = {Yu, J and Li, H and Zeng, H},
title = {Association of a Dietary Index for Gut Microbiota With Epilepsy Among US Adults Aged 40 and Over: A Cross-Sectional Study.},
journal = {Behavioural neurology},
volume = {2026},
number = {1},
pages = {e5311940},
pmid = {42740589},
issn = {1875-8584},
mesh = {Humans ; Cross-Sectional Studies ; Female ; *Epilepsy/epidemiology/microbiology ; Male ; *Gastrointestinal Microbiome/physiology ; *Diet ; Adult ; Middle Aged ; United States/epidemiology ; Nutrition Surveys ; Aged ; Prevalence ; },
abstract = {BACKGROUND: Epilepsy remains difficult to control in some patients, motivating interest in modifiable factors linked to seizure biology. Because diet can shape gut microbial ecology and gut-brain signaling, we examined whether the dietary index for gut microbiota (DI-GM) was associated with prevalent epilepsy in US adults aged ≥ 40 years.

METHODS: This cross-sectional study included 5025 participants from NHANES 2013-2016. DI-GM was constructed from 14 predefined dietary components reflecting microbiota-supportive or microbiota-adverse intake. NHANES sampling weights were applied. Multivariable logistic regression evaluated associations between DI-GM and prevalent epilepsy. Restricted cubic splines, subgroup analyses, and weighted quantile sum (WQS) regression were used to examine dose-response shape, effect heterogeneity, and component contributions.

RESULTS: In the fully adjusted model, DI-GM showed an inverse association with prevalent epilepsy (OR per 1-point increase, 0.80; 95% CI, 0.69-0.93; p = 0.008). Compared with Q1, Q4 had lower epilepsy odds (OR, 0.29; 95% CI, 0.10-0.87; p = 0.033). The spline analysis did not support nonlinearity (p = 0.663). The inverse association was mainly seen among adults without hypertension or diabetes, with significant interaction by hypertension (p < 0.001) and diabetes status (p = 0.003). WQS results highlighted cranberries, chickpeas, avocados, soybeans, and lower processed meat intake as major contributors.

CONCLUSIONS: Higher DI-GM adherence was associated with lower odds of prevalent epilepsy, particularly in metabolically healthier subgroups. Prospective and intervention studies are needed to test temporality and clinical relevance.},
}

Humans
Cross-Sectional Studies
Female
*Epilepsy/epidemiology/microbiology
Male
*Gastrointestinal Microbiome/physiology
*Diet
Adult
Middle Aged
United States/epidemiology
Nutrition Surveys
Aged
Prevalence

@article {pmid42741332,
year = {2026},
author = {Wang, QH and Liu, YF and Wang, B and Xiao, Q and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Oil composition determines microbial preference for carbon source between hydrocarbons and Necromass in water droplets within crude shale oil.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag242},
pmid = {42741332},
issn = {2730-6151},
abstract = {Water droplets entrapped in crude oil have recently been recognized as unexpected but metabolically active microbial habitats in shale oil reservoirs. However, the key environmental drivers that shape the community composition and metabolic profiles of these droplet microorganisms remain poorly understood. Here, we investigated three shale oil samples from Jiangsu oilfield, all of which contained abundant water droplets (>10[5] droplets/ml oil) of ancient formation water origin. Integrated microscopy, metagenomics, and metabolomics revealed that the physicochemical properties of the enclosing oil, primarily API gravity and viscosity, are associated with droplet size and may influence the droplet microbiomes. These factors appear to jointly drive a fundamental metabolic dichotomy, where in light oil with low-salinity water, communities are enriched with hydrocarbon degraders together with molecular signatures of active petroleum hydrocarbon metabolism. In more viscous, light-to-medium oil with high-salinity water, however, communities shift towards necromass recycling and strong genetic adaptations to osmotic stress. Our findings demonstrate that microbial life in water droplets enclosed in shale oil is widely found in the shale oil reservoirs examined, and selected by carbon quality and environmental pressure. This study provides a mechanistic framework for understanding microbial ecology and biogeochemical processes in shale oil reservoirs and offers insights for microbial enhanced oil recovery in heavy oil reservoirs.},
}

@article {pmid42741352,
year = {2026},
author = {Monge-Loría, M and Brady, C and Wu, H and Aron, A and Garg, N},
title = {Computational mass spectrometry and genome mining guided discovery of metallophores produced by Microbulbifer.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag238},
pmid = {42741352},
issn = {2730-6151},
abstract = {Iron is an essential component of cellular biology. Thus, iron's low bioavailability is a key evolutionary pressure guiding microbial dynamics in the marine environment. Among marine bacteria, Microbulbifer is a chemically underexplored and functionally versatile bacterial genus, which is commonly associated with sponges, algae, corals, and sediments. Previously, genome analyses have revealed that Microbulbifer spp. can degrade polymers and synthesize natural products. Despite their recognized potential to produce secondary metabolites, siderophores are yet to be identified in Microbulbifer, and their iron acquisition strategies remain largely unknown. Here, we developed a comprehensive mass spectrometry-based query language code to determine siderophore production by Microbulbifer spp. in mono- and mixed cultures. Using this workflow, we discovered a new metallophore, which we named bulbichelin, as well as a suite of previously unreported petrobactins containing an unprecedented longer chain length acylation on the central spermidine moiety. We applied genome mining methods to describe the biosynthesis of these compounds. Using metal infusion mass spectrometry, we show that bulbichelins bind a variety of metals. Notably, neither of these compounds were produced in a co-culture of Microbulbifer with coral-derived pathogen Vibrio coralliilyticus Cn52-H1. Understanding how siderophores shape interspecies interactions between Microbulbifer spp. and other marine organisms will aid in unraveling the chemical and catalytic versatility of this genus and adaptation in nutrient deplete marine environment.},
}

@article {pmid42742455,
year = {2026},
author = {Chen, J and Ren, S and Tong, Z and Guan, Z and Zhang, W and Ren, S and Ma, L and Kong, L and Chong, H and Wang, Z and Yong, X and Yan, S and Wang, Y and Zhou, J},
title = {An integrated culturomic and genomic database and analysis platform for methanogenic archaea.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42742455},
issn = {1758-0463},
support = {U24A20543//National Natural Science Foundation of China/ ; 32371538//National Natural Science Foundation of China/ ; JASTIF, CX [23]1038//Jiangsu Agriculture Science and Technology Innovation/ ; XTSW4C01//Jiangsu Synergetic Innovation Center for Advanced Bio-Manufacture/ ; },
mesh = {*Genome, Archaeal/genetics ; *Databases, Genetic ; *Archaea/genetics/metabolism ; *Genomics/methods ; Biocuration ; *Methane/metabolism ; },
abstract = {Methanogenic archaea research is challenged by limited strain resources, fragmented genomic data, inconsistent genome quality, substantial uncultured lineages, and difficulties in laboratory culturing, hindering advances in biogas production, climate mitigation, and microbial ecology. These archaea play crucial roles in global carbon cycling and anaerobic environments, yet scattered data and unculturable strains limit systematic studies and applications. To address this, we created MethArDB (Methanogenic Archaeal Genome Database), a specialized database for methanogenic archaea, compiling 3919 genomes, 87 host-associated plasmids, and 42 phages, with standardized quality classifications (complete, scaffold, draft), protein sequences, and metadata on geography, habitats, metabolism, and inheritable elements. Integrated MethArCT (Methanogenic Archaeal Culturomics Toolkit) employs a dual-threshold orthologous/paralogous protein analysis to evaluate metabolic pathway completeness, predicting cultivation parameters and suggesting candidate cultivation strategies, including potential medium formulations and conditions, to support strain isolation. Overall, MethArDB and MethArCT form an integrated platform combining genomics and culturomics to facilitate methanogenic archaea research. Database URL: http://methardb.cn.},
}

*Genome, Archaeal/genetics
*Databases, Genetic
*Archaea/genetics/metabolism
*Genomics/methods
Biocuration
*Methane/metabolism

@article {pmid42743290,
year = {2026},
author = {Stoll, MF and Dentz, M and Stocker, R and Jimenez-Martinez, J},
title = {Porous medium heterogeneity favors chemotaxis to nutrient hotspots in flow.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {38},
pages = {e2616336123},
doi = {10.1073/pnas.2616336123},
pmid = {42743290},
issn = {1091-6490},
support = {956457//EC | Horizon 2020 Framework Programme (H2020)/ ; 956457//EC | Horizon 2020 Framework Programme (H2020)/ ; 205321_207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 51NF40_225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; NA//Eidgenössische Technische Hochschule Zürich (ETH)/ ; NA//Eidgenössische Technische Hochschule Zürich (ETH)/ ; },
mesh = {*Chemotaxis/physiology ; Porosity ; *Nutrients/metabolism ; *Azospirillum brasilense/physiology ; Hydrodynamics ; Soil Microbiology ; },
abstract = {Natural porous environments, such as soils and aquifers, are often highly heterogeneous, exposing microorganisms to variable fluid flow and nutrient landscapes. Chemotactic bacteria can locate nutrient hotspots and thereby accelerate subsurface reactions, yet how chemotaxis is affected by pore-scale flow remains poorly understood. Here, we show that pore-scale heterogeneity enhances the foraging benefits afforded to bacteria by motility and chemotaxis, compared to nonmotile cells advected by the flow. Using a microfluidic porous medium with localized steady nutrient sources, mimicking those found in natural porous media, we systematically test the effects of hydrodynamic heterogeneity, flow magnitude, and bacterial traits on nutrient exposure and pore-scale transport by directly tracking single cells of the soil bacterium Azospirillum brasilense. By introducing an advantage index that quantifies nutrient exposure compared to that of nonmotile cells, we find that the chemotactic gain in nutrient exposure increases with hydrodynamic heterogeneity by 1.5-fold. The underlying mechanism is due to swimming bacteria preferentially occupying low-velocity regions, where they can swim against the flow to climb the chemical gradient. The heterogeneous flow field in porous systems additionally causes chemotaxis to remain advantageous across a wider range of flow rates than in uniform, grain-free systems at the same mean fluid speed. These findings highlight how, due to the strong heterogeneity in the flow field, the quenching effect of flow on chemotaxis is much weaker in porous media than in homogeneous environments, with implications for biogeochemical cycling and predictive modeling of the transport of chemotactic bacteria and contaminants in porous media.},
}

*Chemotaxis/physiology
Porosity
*Nutrients/metabolism
*Azospirillum brasilense/physiology
Hydrodynamics
Soil Microbiology

@article {pmid42714937,
year = {2026},
author = {McDougall, FK and Paranagama, K and Boardman, WSJ and Wyres, K and Power, ML},
title = {Detection of opportunistic bacterial pathogens with intrinsic amoxicillin- and cephalosporin-resistance in wild koala faecal microbiomes.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {9},
pages = {},
pmid = {42714937},
issn = {1465-2080},
mesh = {Animals ; *Phascolarctidae/microbiology ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Amoxicillin/pharmacology ; *Cephalosporins/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/drug effects/isolation & purification/genetics/classification ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial ; Animals, Wild/microbiology ; *Gastrointestinal Microbiome/drug effects ; Third Generation Cephalosporins ; },
abstract = {Opportunistic bacterial pathogens frequently associated with human clinical infections, including antimicrobial-resistant strains, are infiltrating the microbiomes of wild animals, where they have the potential to negatively impact wildlife health. Bacterial genes conferring resistance to amoxicillin have previously been reported in koala (Phascolarctos cinereus) faecal DNA. Koalas are facing several key threats, including wildfires, and affected individuals may receive amoxicillin therapy to treat burn wounds. This study aimed to identify the species of amoxicillin-resistant bacteria in koala gut microbiomes and determine if they are opportunistic pathogens. Faecal samples collected from 98 wild-caught koalas were cultured using amoxicillin-supplemented media to isolate amoxicillin-resistant Gram-negative enteric bacteria. Isolates were screened using 16S rRNA PCR and Sanger sequencing to identify opportunistic pathogenic species, which then underwent whole-genome sequencing and antimicrobial susceptibility testing. Intrinsically amoxicillin-resistant opportunistic pathogens were obtained from 9.2% (9/98) of koala faecal samples and comprised Klebsiella oxytoca (6/98, 6.1%), Klebsiella pneumoniae (1/98, 1.0%) and Citrobacter spp. (2/98, 2.0%). Seven of nine amoxicillin-resistant opportunistic pathogens also exhibited cephalosporin resistance. Four K. oxytoca isolates belonged to lineages associated with human clinical infections, which also have the potential to cause disease in koalas, including fatal systemic infections in pouch young. The presence of amoxicillin- and cephalosporin-resistant strains may also increase the risk of gut dysbiosis and opportunistic infections when penicillins or cephalosporins are required to treat bacterial infections in koalas, highlighting the importance of good antimicrobial stewardship. The study findings demonstrate the One Health perspective of microbial pathogens and the intertwined microbial ecology between humans and wildlife.},
}

Animals
*Phascolarctidae/microbiology
*Feces/microbiology
*Anti-Bacterial Agents/pharmacology
*Amoxicillin/pharmacology
*Cephalosporins/pharmacology
RNA, Ribosomal, 16S/genetics
*Bacteria/drug effects/isolation & purification/genetics/classification
Microbial Sensitivity Tests
*Drug Resistance, Bacterial
Animals, Wild/microbiology
*Gastrointestinal Microbiome/drug effects
Third Generation Cephalosporins

@article {pmid42715205,
year = {2026},
author = {Nauwynck, W and Faust, K and Boon, N},
title = {Accessible, robust ultrahigh-throughput microbiome analysis via integration of uniform droplet-templated emulsification and FACS.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0356887},
pmid = {42715205},
issn = {1932-6203},
mesh = {*Flow Cytometry/methods ; Emulsions/chemistry ; *Microbiota ; *High-Throughput Screening Assays/methods ; },
abstract = {Microbial phenotypes vary at the single-cell level, shaping key community traits like resilience and adaptability. Yet, current methods either lack resolution (e.g., culturing, sequencing), are too costly, or technically complex, limiting widespread use. To address this gap, we introduce and validate a workflow called DE-SWIRL (Double Emulsion-Sorting Workflow with sImple, Rapid emuLsification), an accessible, low-cost workflow enabling ultrahigh-throughput (~107 microcultures/experiment) screening of individual microbial cells. DE-SWIRL integrates a published droplet-templated emulsification protocol producing uniform double emulsions from monodisperse single emulsions with Fluorescence-Activated Cell Sorting (FACS). We validated that double emulsions of 6 and 24 pL can be reliably formed, with ~45% droplet survival. To address persistent large-particle contaminants, we validated a gating strategy and show it enables accurate screening and sorting. When starting from a monodisperse single emulsion population, oil layer variability is higher for droplet-templated emulsification than for on-chip microfluidics, but maintains a comparably uniform core emulsion while offering substantial time savings. We demonstrate DE-SWIRL's utility by isolating viable strains from a synthetic community with up to 99% sorting purity and isolating droplet cocultures from a mixed community. This workflow provides a fast, accessible, and affordable workflow for screening entire microbiomes at a single-cell level using a fluorescent assay of interest.},
}

*Flow Cytometry/methods
Emulsions/chemistry
*Microbiota
*High-Throughput Screening Assays/methods

@article {pmid42719130,
year = {2026},
author = {Dai, Y and Li, H and Wang, H and He, Y and Cai, K and Wu, X and Zou, H and Wang, Y and Cai, L and Wu, X and Shamsi, IH},
title = {Insights into the changes of soil microorganism communities and carbon cycle metabolic functions caused by the application of L-glufosinate-ammonium.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1920057},
pmid = {42719130},
issn = {1664-302X},
abstract = {L-glufosinate-ammonium (L-GLA), a widely used herbicide, exerts detrimental non-target effects on crops, soil microorganisms, and ecosystems. However, its impacts on soil microbial communities and metabolic functions remain poorly understood. In this study, we applied L-GLA at two concentrations-600 g a.i. hm[-2] (low, L) and 3,000 g a.i. hm[-2] (high, H)-to yellow-brown soil and investigated its effects on microbial community composition, carbon cycle-related metabolic functions, and soil metabolites using integrated metagenomics and soil environmental pseudotargeted metabolomics at 30 and 60 days post-application. The degradation rate of L-GLA was concentration-dependent, with half-lives of 18.8 days (L) and 29.7 days (H). Both doses significantly reduced soil organic matter (SOM) and available potassium (AK) content, and markedly altered microbial community richness, structure, and composition. L-GLA exposure also disrupted the complexity of soil microbial co-occurrence networks and the activities of carbon-cycle-related enzymes. Metabolomic analysis further revealed significant (p < 0.05) and dose-dependent alterations in the soil metabolite profile. Correlation analysis indicated strong associations between characteristic microbial taxa and differential metabolites. Our findings provided critical insights into how L-GLA influences the soil microecological environment and contributed to a deeper understanding of soil microbial ecology in the context of modern agricultural practices.},
}

@article {pmid42724485,
year = {2026},
author = {Zhang, H and Zhang, T and Pan, Z and Zhang, Y and Liang, T and Liu, H and Wang, B and Yu, Y and Wang, S},
title = {Microbiota-associated metabolic networks in gut-kidney communication and renal immune regulation: mechanisms and therapeutic potential.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1899977},
pmid = {42724485},
issn = {1664-302X},
abstract = {Kidney disease development and progression involve not only local inflammation, immune dysregulation, and fibrosis but also alterations in gut microbiota composition and metabolic function. Microbiota-associated metabolic signals connect the intestinal ecosystem, host metabolism, and the renal immune microenvironment through their associations with intestinal barrier integrity, renal tubular epithelial homeostasis, immune cell function, and inflammatory-fibrotic responses. Depending on their biological origin, receptor engagement, target-cell specificity, and disease context, these signals may either support immune homeostasis and tissue repair or contribute to persistent inflammation and tissue remodeling. Representative mediators include short-chain fatty acids, tryptophan-derived metabolites, bile acid-related signaling molecules, indoxyl sulfate, p-cresyl sulfate, trimethylamine N-oxide, succinate, and other host-microbiota-associated metabolites. Their biological effects, however, cannot be interpreted independently of renal function because circulating metabolite levels are also influenced by impaired renal clearance, systemic inflammation, dietary factors, and host metabolism. Conversely, kidney dysfunction reshapes intestinal barrier integrity, microbial ecology, and metabolic output, establishing a dynamic gut-kidney metabolic-immune feedback network. In this Review, we summarize current evidence linking microbiota-associated metabolic networks to renal immune remodeling across different kidney diseases, highlighting metabolite origin, shared target-cell responses, disease-specific and context-dependent mechanisms, and current evidence limitations. We further discuss therapeutic strategies targeting this axis and emphasize key translational challenges, including distinguishing causal metabolic drivers from secondary metabolic alterations and developing precision interventions based on metabolic and immune phenotypes.},
}

@article {pmid42724737,
year = {2026},
author = {Raval, R and Hejmadi, S and Hettiarachchi, M and Chandna, S and Mehta, AC},
title = {Gut-lung axis in chronic respiratory diseases: a narrative review of emerging insights.},
journal = {Journal of thoracic disease},
volume = {18},
number = {8},
pages = {967},
pmid = {42724737},
issn = {2072-1439},
abstract = {BACKGROUND AND OBJECTIVE: The gut-lung axis is a bidirectional network through which intestinal microbial ecology, mucosal immunity, epithelial barrier function, microbial metabolites, and neurohumoral signalling influence pulmonary inflammation. This narrative review summarizes the mechanistic basis of gut-lung communication, compares the strength of evidence across major chronic respiratory diseases (CRDs), and evaluates emerging microbiome-targeted interventions.

METHODS: PubMed, Embase, and Google Scholar were searched for peer-reviewed English-language literature published from January 2010 through June 2024 using combinations of terms related to the gut-lung axis, microbiome, asthma, chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), short-chain fatty acids (SCFAs), intestinal permeability, bile acids, tryptophan metabolites, vagal signalling, and glucagon-like peptide-1 (GLP-1). Human and animal original studies, randomized trials, cohort studies, mechanistic studies, and relevant narrative or systematic reviews were considered; case reports, non-English articles, and studies without respiratory outcomes were excluded. Reference lists of key papers were also hand-searched.

KEY CONTENT AND FINDINGS: Evidence is strongest for biologically plausible immune and metabolic pathways linking intestinal dysbiosis to pulmonary disease. In asthma, early-life depletion of SCFA-producing taxa may impair regulatory T-cell development and promote allergic sensitization. In COPD, gut dysbiosis, increased intestinal permeability, and systemic endotoxin exposure are more consistently associated with inflammatory phenotype and exacerbation burden. Evidence in ILD remains preliminary but supports a possible role for gut-derived pathogen-associated molecular patterns in profibrotic signalling. After lung transplantation (LT), antibiotic exposure, immunosuppression, and microbial loss may interact with allograft inflammation and chronic lung allograft dysfunction (CLAD). Dietary modulation, probiotics, prebiotics/synbiotics, post-biotics, and fecal microbiota transplantation (FMT) remain investigational, with heterogeneous and generally limited clinical evidence.

CONCLUSIONS: Current data support mechanistic plausibility but do not justify routine microbiome-directed treatment of CRDs. Future trials should standardize microbiome profiling, incorporate metabolomic and disease-specific clinical endpoints, and stratify responders to define where gut-lung axis interventions can add clinically meaningful benefit.},
}

@article {pmid42725769,
year = {2026},
author = {Van Rossum, U and Heyndrickx, M and Demaître, N and Sadiq, FA and Boon, N and Rasschaert, G and Cools, A and De Reu, K},
title = {Biofilm formation and multispecies interactions of bacteria recovered from drinking water systems in broiler houses and piglet nursery units.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0108426},
doi = {10.1128/spectrum.01084-26},
pmid = {42725769},
issn = {2165-0497},
abstract = {The presence of biofilms on the surfaces of drinking water systems in livestock housing can compromise the microbiological quality of drinking water. Understanding the biofilm microbiome and the biofilm-forming capacity of its dominant species is therefore essential, particularly for identifying species that coexist and enhance biofilm formation through interactions. This study investigated 248 bacterial isolates representing the dominant microbiota of biofilm samples collected from drinking water systems in broiler houses and pig nursery units. Biofilm formation was assessed in both single-species cultures and 341 multispecies combinations. Of the tested isolates, 80% formed biofilms in single culture; however, only 25% were classified as strong biofilm formers. In multispecies combinations with up to four species or isolates, antagonistic or competitive interactions were dominant, whereas biofilm mass enhancement was observed in only a limited number of combinations. These included opportunistic pathogens, with Citrobacter freundii and Staphylococcus nepalensis identified as key species driving the interactions. Our research highlights the importance of specific microbial interactions in biofilm development and provides a potentially practice relevant four-species model to guide future research aimed at improving strategies for controlling biofilms in livestock drinking water systems.IMPORTANCEEnsuring the quality of drinking water on livestock production farms benefits animal production and health. Persistent biofilms on water line surfaces can lead to microbial contamination, resulting in lower-quality drinking water. This study examines bacteria commonly found in biofilms within livestock drinking water systems in pig nursery units and broiler houses. Most bacterial isolates can form biofilms in monoculture. Specific interactions among certain species primarily mediate bacterial interactions that enhance biofilm biomass in multispecies communities. Identifying these key interactions enables the development of a synthetic model to guide research on controlling biofilms in livestock drinking water systems.},
}

@article {pmid42728625,
year = {2026},
author = {Schroeder, BG and Bhattacherjee, R and Bonatelli, ML and da Rocha, UN and Sträuber, H and Harms, H and Nikolausz, M},
title = {Anaerobic mono-digestion of wheat straw in a three-stage semi-continuous system inspired by a beetle larva gut.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {19},
number = {1},
pages = {},
pmid = {42728625},
issn = {2731-3654},
support = {nº 88887.161417/2017-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {Based on the efficient digestive system of the larva of the sun beetle (Pachnoda marginata) in utilizing lignocellulose-rich biomass, a reactor system was designed to partially mimic processes that occur in the larval gut. We aimed developing a process with this system for anaerobic mono-digestion of wheat straw to produce volatile fatty acids (VFAs) and biogas. Three stirred tank reactors connected in series were customized with polyurethane foam and operated at 37 °C. The first two reactors were designed to mimic the midgut of the larva with enhanced VFA production and the third one to resemble the hindgut and optimized for methanogenesis. The system was fed in a semi-continuous regime with ground wheat straw in an alkaline medium. Enrichment cultures from midgut and hindgut of the larva were used as inocula and three conditions with increasing organic loading rate were tested. The highest biomass to methane conversion occurred at the lowest organic loading rate and highest retention time, when a methane yield of 148 mLNorm g[-1]VS was obtained and VS degradation reached 44%. The microbial community was enriched toward cellulose and hemicellulose degrading taxa, including Dysgonomonadaceae, Lachnospiraceae, Marinilabiliaceae and Ruminococcaceae. The methanogenic community shifted from predominance of Methanosarcina to Methanobacterium and Methanoculleus. A comparison with other studies investigating straw utilizing bioreactors confirmed that a core microbiome composed of the phyla Firmicutes, Bacteroidetes and Proteobacteria effectuates the anaerobic digestion of lignocellulose-rich materials, regardless of the source of the inoculum and the process conditions. The designed process was stable and capable to convert wheat straw into methane and carboxylates. Further adaptations are suggested to improve the anaerobic digestion and decrease assembly and operating costs.},
}

@article {pmid42729561,
year = {2026},
author = {Ji, F and Wang, S and Wang, L and Zhao, Y and Zhong, J and Wang, R and Qu, J and Lu, Y and Yuan, N and Zhang, Q},
title = {The impact of short-term intensive fasting on physical health and gut microbiota in obese individuals.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1873000},
pmid = {42729561},
issn = {2296-861X},
abstract = {OBJECTIVES: This study aimed to characterize how a 7-day complete water-only fast followed by structured refeeding was associated with changes in body weight, hydration-dependent bioelectrical-impedance estimates, physical test performance, cardiovascular indicators, and gut microbial ecology in adults with obesity and normal-weight controls.

METHODS: Seventy-two eligible volunteers formed prespecified BMI sampling strata (normal weight, n = 36; obesity, n = 36), from which 14 participants were randomly selected within each stratum before the intervention and before outcome collection (N = 28). All selected participants completed a supervised 7-day water-only fast followed by a 7-day structured refeeding period. Physical indicators were assessed pre-fasting, post-fasting, and post-refeeding and analyzed using two-factor mixed-design repeated-measures models; gut microbiota (16S rRNA) was profiled pre- and post-fasting.

RESULTS: BMI-group-by-time interactions were significant for body weight and BMI (both p < 0.001) but not for BIA-derived fat mass, body-fat percentage, or muscle mass (all p > 0.05). Dynamometer-recorded grip, knee-flexion, and knee-extension scores increased over time (all time-effect p < 0.001), but none showed a BMI-group-by-time interaction (all p ≥ 0.340). Gut microbial alpha diversity remained largely stable apart from an FDR-significant ACE-index reduction in the normal-weight group (q = 0.021); most taxonomic findings did not survive FDR correction, and beta-diversity analysis showed no community-level convergence between groups.

CONCLUSION: Supervised seven-day water-only fasting followed by structured refeeding was associated with reduced body weight, particularly in participants with obesity. Changes in body composition were BIA-derived estimates, while higher dynamometer scores represented measured test performance that may have been influenced by familiarization. Gut-microbiota alpha diversity was largely stable, with exploratory compositional changes supporting further investigation in controlled studies.},
}

@article {pmid42733080,
year = {2026},
author = {Li, C and Wang, Y and Zhou, ASK and Pan, X and Zhu, Y and Zhang, X and Chen, T and Xiong, A and Ho, YW and Liu, J and Zhou, Z and Wang, J and Adyel, TM and Fang, JK and Bank, MS and Rillig, MC and Jin, LN},
title = {Unraveling the coastal marine plastisphere archaeome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42733080},
issn = {2041-1723},
mesh = {*Archaea/genetics/classification ; *Seawater/microbiology ; Crenarchaeota/genetics/classification ; Phylogeny ; Euryarchaeota/genetics/classification ; Metagenomics ; Ecosystem ; Biodiversity ; Methane/metabolism ; },
abstract = {Plastic pollution has created an expanding anthropogenic microbial niche, the plastisphere, raising questions about microbial ecology and associated impacts. Archaea, the third domain of life with fundamental ecological and evolutionary significance, remain poorly understood in this habitat. Here, using paired plastic debris and bulk-water samples from coastal marine ecosystems, key archaeal habitats increasingly threatened by plastic pollution, we characterize the plastisphere archaeome through archaeal amplicon sequencing and metagenomics. We show that the archaeome is significantly reshaped in the plastisphere, exhibiting higher taxonomic diversity, greater community heterogeneity, and selective enrichment of Euryarchaeota and Crenarchaeota. Archaeal genes involved in methane, nitrogen, and sulfur cycling are enriched in the plastisphere. Taxonomic and functional divergence between the plastisphere and bulk water increases with anthropogenic chemical stress. These findings suggest that plastic pollution could alter marine archaeal diversity, biogeography, and biogeochemical potential, extending understanding of plastisphere impacts to the archaeal domain.},
}

*Archaea/genetics/classification
*Seawater/microbiology
Crenarchaeota/genetics/classification
Phylogeny
Euryarchaeota/genetics/classification
Metagenomics
Ecosystem
Biodiversity
Methane/metabolism

@article {pmid42734183,
year = {2026},
author = {Chen, W and Pan, Y and Chen, M and Zhou, S and Liu, X and Sun, M and Yang, Z and Zhi, Y},
title = {Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726620},
pmid = {42734183},
issn = {1949-0984},
mesh = {Humans ; *Stroke/complications/metabolism ; Metabolomics ; Metagenomics ; *Depression/metabolism/etiology/microbiology ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Inflammation/metabolism ; Middle Aged ; Aged ; Cytokines/blood ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Biomarkers/blood ; },
abstract = {Post-stroke depression (PSD) is a common complication that significantly impacts patient prognosis. This study aimed to systematically characterize the associations among gut microbial ecology, metabolic profiles, and inflammatory responses across different severities of PSD. We conducted metagenomic sequencing, non-targeted metabolomics, and serum cytokine analysis (IL-1β, IL-6, IL-10, IL-18, TNF-α, IFN-γ, and CRP) in 91 patients with varying degrees of PSD and non-PSD controls. Bioinformatics analyzes were employed to construct multi-omics association networks and machine learning models. Results indicated that PSD patients exhibited significantly increased gut microbiota alpha-diversity, suggesting dysbiosis. Mild depression was characterized by compensatory neural signaling activation, whereas the moderate depression group exhibited abnormalities in tryptophan/indole metabolism, oxidative stress-related metabolic imbalances, and functional decompensation. Further analyzes suggested that Alistipes, Blautia_A, Evtepia gabavorous, and Lachnospira were associated with inflammatory features, GABA-related metabolic alterations, aromatic amino acid/indole metabolism, and lipid-amino acid metabolism, respectively. Under a more rigorous 10-fold cross-validation framework, the performance of different multi-omics combination models showed heterogeneity; however, some combinations still demonstrated superior discriminatory ability compared to single-omics approaches. This study provides multi-omics clues suggesting associations between different PSD severity levels and features such as increased Alistipes abundance, reduced antioxidant capacity, and altered tryptophan metabolism. It provides candidate biomarker combinations that may be useful for PSD stratification and suggests that the gut microbiome may represent a potential target for future PSD intervention. In summary, PSD may be associated with dynamic alterations along the "gut-brain-inflammation-metabolism" axis. These findings provide integrated evidence for microbial, metabolic, and inflammatory abnormalities across different PSD severity levels, but still require validation in larger samples, longitudinal cohorts, and mechanistic studies.},
}

Humans
*Stroke/complications/metabolism
Metabolomics
Metagenomics
*Depression/metabolism/etiology/microbiology
Female
Multiomics
Male
*Gastrointestinal Microbiome
Inflammation/metabolism
Middle Aged
Aged
Cytokines/blood
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology
Biomarkers/blood

@article {pmid42736476,
year = {2026},
author = {Li, L and Ma, L and Zhang, Z},
title = {Global Research Trend of Axillary Osmidrosis: A Bibliometric and Visualized Analysis.},
journal = {Aesthetic plastic surgery},
volume = {},
number = {},
pages = {},
pmid = {42736476},
issn = {1432-5241},
abstract = {BACKGROUND: Axillary osmidrosis is a common condition with significant psychosocial implications. Despite growing research interest in recent years, no bibliometric analysis has been conducted in this field. This study aims to provide a knowledge framework and identify research hotspots in this domain using bibliometric methods.

METHODS: Publications related to axillary osmidrosis from 1990 to 2025 were retrieved from the Web of Science Core Collection and PubMed. Bibliometric analyses were conducted using VOSviewer, Bibliometrix package of R, and Microsoft Excel.

RESULTS: A total of 252 publications on axillary osmidrosis were included. China led in both publication output (n = 119) and total citations (n = 1321). Chang Gung Memorial Hospital was the most prolific institution (n = 12). Aesthetic Plastic Surgery ranked first in both publication output and h-index among journals. Highly cited literature primarily focused on foundational research, including odor components, microbiological mechanisms, and genetic susceptibility. Keyword analysis revealed a thematic shift from foundational research on odor chemistry, microbial ecology, and genetics toward clinical application of minimally invasive therapies and patient-centered outcome assessments.

CONCLUSIONS: Research on axillary osmidrosis has entered a phase of rapid development, with increasing focus on minimally invasive treatments and individualized care. Future efforts should prioritize cross-regional collaboration, high-quality clinical trials, and translation of mechanistic insights into clinical practice.

LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .},
}

@article {pmid42737277,
year = {2026},
author = {Zhang, S and Guo, Y and Zhao, J and Zhao, J and Guo, Y and Yan, W},
title = {Lacticaseibacillus paracasei LPB27: Effectively Enhances the Immune System by Improving the Intestinal Environment.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737277},
issn = {2304-8158},
support = {2023YFF1103802//National Key Research and Development Program of China/ ; ZK10202501//Key Projects and Major Training Programs of Beijing Union University/ ; },
abstract = {Lacticaseibacillus paracasei LPB27 is a novel probiotic isolated from the intestines of healthy infants and young children. In this study, healthy mice were used as a model to systematically investigate the immune regulatory effects of LPB27 mediated by the microbiota-gut-immune axis, with a focus on evaluating its immune-enhancing potential. The safety evaluation showed that, at a dose of 0.50 g/kg/day, LPB27 caused no observable toxicity or adverse reactions. The evaluation of immune function indicated that in terms of cellular immunity, high-dose LPB27 increased the delayed-type hypersensitivity response and lymphocyte proliferation by 69% and 35%, respectively; in terms of humoral immunity, the number of hemolytic plaques and hemolysin titer increased by 42% and 36%, respectively; in terms of innate immunity, the carbon clearance capacity, CRBC phagocytosis rate, and macrophage phagocytic index increased by 13%, 33%, and 66%, respectively. Serum IgA, IgG, and IL-6 levels were significantly elevated in the high-dose group, whereas TNF-α was significantly reduced. Overall, LPB27 supplementation enhanced multiple immune indicators in mice. By comparing the gut microbiota composition at different time points, the study found that continuous intake of LPB27 was associated with an enrichment of multiple beneficial bacterial genera, including Akkermansia, Lactobacillus, Muribaculum, and Lachnospiraceae_NK4A136_group, together with a reduction of potentially pathogenic taxa, indicating an overall improvement in the intestinal microbial ecology. Changes in the abundance of these beneficial taxa were positively correlated with the predicted activation of metabolic pathways related to the synthesis of immune-related proteins. These findings support the further development of LPB27 as an immune-regulating ingredient.},
}

@article {pmid42737331,
year = {2026},
author = {Olanbiwoninu, AA and Awotundun, TA and Afolabi, JF and Fashogbon, RO and Fagunwa, O},
title = {Ethnogeographic Distribution of Nigerian Fermented Foods and the Prospects for Bioeconomy Improvements.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737331},
issn = {2304-8158},
abstract = {Fermented foods and beverages represent a cornerstone of Nigerian food culture, yet their scientific documentation remains fragmented, and their potential within global bioeconomy frameworks is largely unrealised. This review addresses two interrelated gaps: the absence of a comprehensive ethnogeographic analysis of Nigerian fermented foods that integrates ecological, cultural, and agricultural drivers of regional diversity, and the limited examination of these foods as models for circular bioeconomy development. Using a narrative synthesis of peer-reviewed literature spanning 1986-2025, we systematically map the distribution of fermented tuber, cereal, legume, dairy, and fruit products across Nigeria's major geopolitical zones, demonstrating that agroecological endowment, ethnic composition, trade routes, and cross-cultural interactions shape regional variation. Beyond their socio-cultural significance, Nigerian fermented foods contribute meaningfully to food security by extending shelf life, enhancing nutrient bioavailability, and reducing post-harvest losses. This review further positions ogi (fermented maize gruel) and garri (fermented cassava granules) as model systems for circular bioeconomy integration, demonstrating how by-product valorisation can generate value-added outputs, including animal feed, bioethanol, biodegradable packaging, and organic acids. Key challenges, including food safety deficits, absence of standardised production protocols, and limited regulatory frameworks, are critically assessed. Three priority research directions are identified: metagenomics-based microbiome profiling, development of culturally appropriate starter cultures, and formulation of gender-responsive regulatory instruments. Nigerian fermented foods, properly documented and integrated into innovation systems, represent an underutilised asset for sustainable food system transformation in Sub-Saharan Africa.},
}

@article {pmid42738923,
year = {2026},
author = {Klain, A and Cascone, S and Grella, C and Cattivera, V and Fabiano, C and Galletta, F and Manti, S and Senatore, AA and Licari, A and Miraglia Del Giudice, M and Marseglia, GL and Indolfi, C and , },
title = {Prenatal, Perinatal and Postnatal Exposures and Clinical Factors of Food Allergy Prevention: A Review for the First 1000 Days of Life from the SIAIP Primary and Secondary Prevention of Allergic Diseases Commission.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42738923},
issn = {2072-6643},
mesh = {Humans ; *Food Hypersensitivity/prevention & control ; Female ; Pregnancy ; Infant ; Infant, Newborn ; Breast Feeding ; *Prenatal Exposure Delayed Effects ; Risk Factors ; Diet ; Developmental Origins of Health and Disease ; },
abstract = {Food allergy prevention is no longer understood as the simple avoidance of allergenic foods. The first 1000 days (from conception to, approximately, 24 months of age) include prenatal, perinatal and postnatal windows in which diet, epithelial barrier integrity, microbial ecology, immune maturation and family-level implementation interact. This narrative review was developed as a Commission-proposed SIAIP-oriented clinical framework, rather than a formal guideline or consensus statement. Evidence from guidelines, systematic reviews, randomised trials, birth cohorts and mechanistic studies was organised by developmental window and interpreted according to endpoint validity, confounding, feasibility and clinical readiness. Prenatal factors include maternal allergen non-avoidance, whole-diet quality, micronutrient and fatty acid status, antibiotic exposure, environmental context and maternal microbiome. Perinatal factors include mode of delivery, intrapartum and neonatal antibiotics, gestational maturity, early colonisation, breastfeeding initiation and routine vaccination. Postnatal factors include eczema, skin barrier inflammation, the timing and regularity of allergen introduction, breastfeeding management, infant diet diversity, siblings, daycare, pets, smoke and pollution, physical activity and equitable implementation. The strongest actionable evidence remains eczema-linked risk recognition and timely, sustained oral exposure to peanut and well-cooked egg. Maternal and environmental factors are clinically important, but many are contextual rather than prescriptive; they should guide non-restrictive, non-blaming counselling rather than deterministic risk labelling.},
}

Humans
*Food Hypersensitivity/prevention & control
Female
Pregnancy
Infant
Infant, Newborn
Breast Feeding
*Prenatal Exposure Delayed Effects
Risk Factors
Diet
Developmental Origins of Health and Disease

@article {pmid42739013,
year = {2026},
author = {Buzatu, GD and Dodocioiu, AM and Ciupeanu-Călugaru, ED and Radulescu, D and Trască, ET},
title = {Dietary Nitrate Bioactivation at the Diet-Microbiota-Host Interface: The Enterosalivary Cycle, Food Matrix, Microbial Determinants and Health Implications-A Narrative Review Supported by a Structured Literature Search.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42739013},
issn = {2072-6643},
mesh = {Humans ; *Nitrates/metabolism ; *Diet ; *Gastrointestinal Microbiome/physiology ; Nitrites/metabolism ; Nitric Oxide/metabolism ; *Intestinal Mucosa/metabolism ; Animals ; },
abstract = {Background/Objectives: Dietary nitrate, long framed through food-safety concerns about N-nitroso compound formation, is now also recognised as a substrate of the nitrate-nitrite-nitric oxide pathway. This review aims to define the mechanistic, dietary and host conditions under which nitrate bioactivation becomes functionally relevant, with particular attention to its microbial determinants and to the level of inference the evidence actually supports. Methods: We conducted a narrative review supported by a structured literature search (PubMed, Scopus and Web of Science; 1 January 1976 to 14 February 2026; full-text, peer-reviewed, English-language, human-relevant sources; 148 sources retained, of which 93 contributed to the evidence synthesis), with narrative synthesis of mechanistic, interventional, observational and regulatory sources addressing dietary source and food matrix, enterosalivary metabolism, oral and gut microbial function, and health-related outcomes. A PRISMA-style flow diagram summarises the documented screening and inclusion process, and the complete database-specific search strategies are provided in Supplementary Table S1; no meta-analysis was performed because of substantial heterogeneity in designs and outcomes. Results: Within the canonical enterosalivary pathway, nitrate-to-nitrite bioactivation is predominantly microbiota-dependent and downstream conversion is chemically conditional: within the enterosalivary cycle, nitrate-reducing bacteria on the tongue dorsum generate the nitrite required for downstream nitric oxide formation, and its conversion in the stomach depends on pH and on matrix constituents. Dietary source and food matrix therefore govern both the delivered dose and the chemistry that follows, so vegetables, beetroot products, inorganic salts, drinking water and processed meat are not interchangeable exposure models. The oral microbiota is the principal microbial determinant of the response, whereas the gut microbiota acts as a context-dependent modifier of intestinal redox tone, barrier function and microbial ecology, supported by markedly weaker human evidence. Nitrate-rich sources reproducibly raise nitrate and nitrite biomarkers, with variable effects on blood pressure, vascular function and exercise efficiency, limited or inconsistent effects on cognition, cerebral blood flow and metabolic endpoints, and a safety profile whose interpretation depends on food matrix, dose, exposure pattern and host context rather than concentration alone. Conclusions: We propose the Source-Matrix-Microbiota-Host (SMMH) framework, in which biological impact depends on the interaction between dietary source and dose, food matrix, microbial nitrate-reducing capacity and host susceptibility, rather than on nitrate dose alone, and in which pathway-level, physiological and clinical evidence are kept explicitly distinct. The evidence base is mechanistically robust for the oral microbiota, considerably less defined for the gut microbiota, and variable at the level of validated clinical endpoints; it does not yet support source-independent guidelines or population-level recommendations.},
}

Humans
*Nitrates/metabolism
*Diet
*Gastrointestinal Microbiome/physiology
Nitrites/metabolism
Nitric Oxide/metabolism
*Intestinal Mucosa/metabolism
Animals

@article {pmid42739046,
year = {2026},
author = {Szabó, J and Maróti, G and Solymosi, N and Andrásofszky, E and Tuboly, T and Bersényi, A and Bruckner, G and Fébel, H},
title = {Effects of Dietary Glucose, Fructose, and Monosaccharide-to-Lard Energy Ratios on Cecal Microbiota Composition and Ecological Organization in Rats.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42739046},
issn = {2072-6643},
mesh = {Animals ; *Fructose/administration & dosage/pharmacology ; *Cecum/microbiology ; Male ; *Glucose/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Monosaccharides/administration & dosage/pharmacology ; *Dietary Fats/administration & dosage ; Rats, Sprague-Dawley ; *Dietary Carbohydrates/administration & dosage ; Bacteria/classification ; Diet ; Energy Intake ; },
abstract = {Background: Although dietary fat and carbohydrates are major determinants of gut microbiota composition, their interactive effects across changing dietary monosaccharide-to-lard energy ratios remain incompletely understood. This study descriptively examined treatment-level cecal microbiome profiles across dietary gradients in which lard (L) was progressively replaced with glucose (G) or fructose (F). Methods: A carbohydrate-free, lard-rich control diet was formulated, and lard was progressively replaced with glucose or fructose while maintaining a constant protein-to-energy ratio. Cecal contents from eight rats per dietary group were pooled in equal amounts, yielding one composite microbiome sample per treatment. Pooled samples were characterized by shotgun metagenomic sequencing. Sequencing/classified read counts (CRs) and relative abundance (RA) were treated as complementary sequencing-derived representations rather than measures of absolute bacterial abundance. Microbiome outcomes were interpreted descriptively at the treatment level. Results: Across the pooled treatment profiles, CRs and RA showed non-linear patterns and did not consistently change in parallel, providing complementary descriptions of treatment-level taxonomic responses. CR patterns indicated a combined effect of L and monosaccharide content, with several mixed L-monosaccharide diets showing lower CRs than both the L6.03 reference and the lard-free endpoints. Differences between the G and F series were most apparent at low L and high monosaccharide levels, particularly under lard-free conditions, although their magnitude and direction varied among taxa. Hierarchical clustering and exploratory correlation networks provided complementary descriptions of treatment-level community organization. Conclusions: The pooled treatment-level microbiome profiles revealed non-linear responses to changing dietary L-monosaccharide composition, with CRs and RA providing partly different information on taxonomic patterns. Differences between the G and F series were most apparent at low L and high monosaccharide levels, particularly under lard-free conditions.},
}

Animals
*Fructose/administration & dosage/pharmacology
*Cecum/microbiology
Male
*Glucose/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
Rats
*Monosaccharides/administration & dosage/pharmacology
*Dietary Fats/administration & dosage
Rats, Sprague-Dawley
*Dietary Carbohydrates/administration & dosage
Bacteria/classification
Diet
Energy Intake

@article {pmid42739438,
year = {2026},
author = {Liu, M and Feng, X and Wang, H and Tan, Z and Liang, X and Wang, Q and Wang, Y and Wang, J},
title = {Effects of the Lower Irrigation Limit and Drip Irrigation Flow Rate on Root Traits and Bacterial Community Structure of Tomatoes Grown in Coconut Coir.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42739438},
issn = {2223-7747},
support = {52509081//the National Natural Science Foundation of China/ ; 8254048//the Natural Science Foundation of Beijing/ ; 2023B02024-2//the Research and Demonstration of Key Technologies for Green Development of Ecological Agriculture in Gobi/ ; No. 2024TSYCTD0019//the Tianshan Talent Science and Technology Innovation Team Project of Xinjiang Uygur Autonomous Region/ ; 2023AB071//the Science and Technology Plan Project of Xinjiang Production and Construction Corps/ ; No. 2024TSYCQNTJ005//the Tianshan Talent Youth Support Program of Xinjiang Uygur Autonomous Region/ ; 2026-2030//the Agricultural Science and Technology Innovation Program/ ; },
abstract = {Water management is a key factor affecting crop physiology and rhizosphere microbial ecology in protected agriculture. However, the responses of root development and bacterial community structure to different lower irrigation limits and drip irrigation flow rates in coir substrates remain poorly understood. This study investigated greenhouse-grown tomatoes in the Gobi region under three lower irrigation limits (30%, 50%, and 70% of substrate water-holding capacity) and two drip irrigation flow rates (1 and 2 L·h[-1]). Substrate moisture, root traits, bacterial community structure, co-occurrence networks, and functional potential were evaluated. Increasing the lower irrigation limit maintained higher and more stable substrate moisture and generally enhanced root length, root surface area, root tip number, and root activity. W3Q1 promoted greater spatial expansion of the root system, whereas W2Q2 produced the largest root volume and maintained relatively high root activity. Irrigation combination significantly altered bacterial community structure but had limited effects on bacterial richness. W2Q1 enriched Bacillota-related taxa, whereas W2Q2 enriched Pseudomonadota and exhibited greater bacterial network connectivity and modularity. FAPROTAX-based functional prediction indicated that the bacterial communities were mainly associated with chemoheterotrophy, organic matter decomposition, and nitrogen transformation. Overall, the lower irrigation limit primarily regulated substrate moisture and root traits, whereas the effects of drip irrigation flow rate were trait- and irrigation-limit-dependent, with significant main and interaction effects on root volume. These findings provide a basis for optimizing precision irrigation in coir-substrate tomato cultivation in arid greenhouse systems.},
}

@article {pmid42714191,
year = {2026},
author = {Dyczko, D and Jawień, P and Kiewra, D},
title = {Mosquito diversity in an urban landscape: species composition and a new record of Culiseta longiareolata ław, Poland.},
journal = {Annals of parasitology},
volume = {72},
number = {},
pages = {},
doi = {10.17420/ap72.553},
pmid = {42714191},
issn = {2299-0631},
mesh = {Animals ; Poland ; *Culicidae/classification/physiology ; *Biodiversity ; Cities ; Seasons ; Animal Distribution ; },
abstract = {Climate change, globalisation, and land use transformation are driving the redistribution of mosquito species (Diptera: Culicidae), with urban areas becoming hotspots for both native and invasive taxa. This study assessed mosquito species diversity in Wrocław, SW Poland, based on CDC trap collections from 14 sites between May and October 2024. A total of 17,104 adult mosquitoes were collected, of which 16,728 (97.8%) were identified to species level. Fifteen species across five genera were recorded, with Aedes vexans dominating the assemblage (68.7%), followed by Coquillettidia richiardii (9.8%). Molecular analyses confirmed all morphologically identified species. Mosquito abundance peaked in July and August, although some locations showed earlier seasonal maxima. Species such as Ae. vexans, Cq. richiardii, and Culex pipiens s.l./Cx. torrentium were present at all sites, while others were more localised. Notably, Culiseta longiareolata, previously unrecorded in Poland, was detected at a single urban site, contributing to recent evidence of a northward shift in its European distribution. Although based on only two individuals, this finding may indicate an early signal of a northward range of extension rather than evidence of established populations. These results underscore the value of continuous urban mosquito surveillance for documenting changes in species composition, detecting potential range shifts, and assessing public health risks under changing environmental conditions.},
}

Animals
Poland
*Culicidae/classification/physiology
*Biodiversity
Cities
Seasons
Animal Distribution

@article {pmid42714846,
year = {2026},
author = {Cui, Y and Zhang, B and Jiang, X and Rehemujiang, H and Xu, G and Li, Y and Wang, B},
title = {Perilla seed oil reshapes the rumen microbiome and increases fermentation end-products in vitro.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag233},
pmid = {42714846},
issn = {1365-2672},
abstract = {AIMS: The effect of Perilla frutescens seed oil (PSO) on an in vitro rumen microbial ecosystem was evaluated by integrating fermentation measurements, microbiome profiling, metagenomics, and untargeted metabolomics.

METHODS AND RESULTS: Rumen inoculum was incubated for 24 h with a control TMR substrate (CK), TMR supplemented with 23.7 mg of Perilla seeds per bottle (PS), or TMR supplemented with 8.5 μL of Perilla seed oil per bottle (PSO), with the PS and PSO treatments providing equivalent amounts of seed oil. Fermentation kinetics and volatile fatty acids were measured, and microbial and metabolic responses were characterized using 16S rRNA gene sequencing, metagenomics, KEGG and CAZy annotation, untargeted metabolomics and MetOrigin2 source tracing. PSO increased maximum gas production and total volatile fatty acid concentrations while maintaining pH within the physiological range. Community diversity was unchanged, but PSO altered microbial composition, including increases in Firmicutes, Verrucomicrobia, Vagococcus, Clostridium and Lactobacillus and decreases in Shigella sonnei and Methanosarcina sp. Ant1. PSO also altered microbial functional profiles and increased several lipid- and vitamin-associated metabolites, including linoleic acid, 13-HODE, 9-oxoODE, pantothenic acid and thiamine, while reducing lactate.

CONCLUSIONS: PSO changed rumen microbial community structure and functional potential in parallel with increased fermentation end-products and extensive metabolic shifts. These in vitro findings identify microbial and metabolic responses that warrant validation in vivo.},
}

@article {pmid42712928,
year = {2026},
author = {Bautista, J and Hernández-León, R and Valencia-Valverde, A and López-Cortés, A},
title = {The gut microbiome-cardiometabolic axis: insights into obesity, type 2 diabetes, and hypertension.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1948038},
pmid = {42712928},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Obesity/microbiology/metabolism ; *Hypertension/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; },
abstract = {Alterations in gut microbial ecology have been linked to obesity, type 2 diabetes (T2D), and hypertension, but their biological significance remains difficult to separate from diet, medication use, adiposity, and other host factors. We synthesize evidence on intestinal barrier dysfunction, microbial translocation, low-grade inflammation, and microbiota-derived metabolites as interconnected mechanisms across these disorders. SCFAs, bile acids, trimethylamine N-oxide, tryptophan derivatives, branched-chain amino acid metabolites, and phenylacetylglutamine influence epithelial function, immune activation, insulin signaling, lipid handling, vascular tone, and renal physiology. Cross-cohort comparisons identify the greatest taxonomic overlap between obesity and T2D, whereas hypertension is characterized more consistently by shifts in community structure than by reproducible disease-specific taxa. Dietary modification, prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation produce modest and variable benefits, often shaped by baseline microbial features and clinical phenotype. The mechanistic and comparative data position the microbiome as a context-dependent contributor rather than an independent cause of cardiometabolic dysfunction. Progress requires longitudinal cohorts, repeated sampling, integrated multi-omics, standardized protocols, diverse populations, and prospective validation of functional biomarkers and treatment-response signatures before translation into clinical practice.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/metabolism
*Obesity/microbiology/metabolism
*Hypertension/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Animals

@article {pmid42713785,
year = {2026},
author = {Thakur, R and Dhar, H and Kiran, S and Gulati, A},
title = {Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70416},
doi = {10.1002/mbo3.70416},
pmid = {42713785},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation & purification ; *Tea/microbiology ; Metagenomics ; Sequence Analysis, DNA ; Biodiversity ; Phylogeny ; DNA, Bacterial/genetics/chemistry ; China ; DNA, Fungal/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; DNA, Ribosomal Spacer/genetics/chemistry ; },
abstract = {This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.},
}

*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Fungi/classification/genetics/isolation & purification
*Tea/microbiology
Metagenomics
Sequence Analysis, DNA
Biodiversity
Phylogeny
DNA, Bacterial/genetics/chemistry
China
DNA, Fungal/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
DNA, Ribosomal Spacer/genetics/chemistry

@article {pmid42705711,
year = {2026},
author = {Du, J and Du, X and Wang, Y and Zhou, C and Zhang, Y and Teng, W and Wang, J and Zhuang, S and Cao, J},
title = {Microbial and flavor modulation of Jinhua ham at the fermentation stage by a synthetic mold and yeast community.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120202},
doi = {10.1016/j.foodres.2026.120202},
pmid = {42705711},
issn = {1873-7145},
mesh = {*Fermentation ; Odorants/analysis ; Animals ; Penicillium/metabolism ; *Food Microbiology/methods ; *Meat Products/microbiology/analysis ; *Taste ; Volatile Organic Compounds/analysis ; *Yeasts/metabolism ; Penicillium chrysogenum/metabolism ; Aldehydes/analysis ; Rhodotorula ; },
abstract = {This study investigated the effect of individual inoculation with Penicillium (Penicillium aethiopicum & Penicillium chrysogenum, PP), yeast (Candida parapsilosis & Rhodotorula mucilaginosa, CM) and their co-inoculation (MI) on the microbial ecology and flavor of Jinhua ham. Inoculation established target fungal populations (>6.0 log CFU/g) successfully increased lipase activity (peak in MI) and inhibited lipid oxidation, peroxide values and Aspergillus community to <10% compared to the control. PP accelerated the release of free fatty acid, especially unsaturated fatty acids, driving total volatile aldehyde concentrations by 5.0-, 1.5-, and 2.2-fold in PP, CM, and MI, respectively, compared to the control. Consequently, hams in the PP group exhibited stronger green and meaty odor scores, lower off-odor scores, and enhanced W1S, W2S and W3S sensor responses. In contrast, CM and MI increased monounsaturated fatty acids, alcohols, aldehydes, carboxylic acids, esters and pyrazines contents with stronger mellow, green & meaty odor scores, as verified by robust W1W, W1S, W3S and W5S sensor responses than the control. These findings indicate that targeted Penicillium or yeast multi-species combination strategies promoted the formation of desirable aldehydes, ketones, esters and pyrazines contents and produced green, meaty and mellow flavor profile of Jinhua ham.},
}

*Fermentation
Odorants/analysis
Animals
Penicillium/metabolism
*Food Microbiology/methods
*Meat Products/microbiology/analysis
*Taste
Volatile Organic Compounds/analysis
*Yeasts/metabolism
Penicillium chrysogenum/metabolism
Aldehydes/analysis
Rhodotorula

@article {pmid42709016,
year = {2026},
author = {Duysburgh, C and Govaert, M and Azmi, P and Finn, R and Simmons, N and Marzorati, M},
title = {Comparison of the Bioaccessibility of Two Formulations of Magnesium Bisglycinate Using an In Vitro Simulation of the Upper Gastrointestinal Tract.},
journal = {Journal of dietary supplements},
volume = {23},
number = {5},
pages = {690-704},
doi = {10.1080/19390211.2026.2727023},
pmid = {42709016},
issn = {1939-022X},
mesh = {Humans ; *Magnesium/pharmacokinetics ; Biological Availability ; *Upper Gastrointestinal Tract/metabolism ; *Dietary Supplements ; *Glycine/pharmacokinetics/analogs & derivatives ; Intestinal Absorption ; Models, Biological ; Gastrointestinal Transit ; Capsules ; },
abstract = {Modern diets are often deficient in magnesium, making magnesium supplementation an important consideration for overall human health. However, the efficiency of magnesium release and absorption in the small intestine varies among different magnesium formulations. The objective of this study was therefore to assess whether using the same magnesium salt type in different formulations could affect efficiency of magnesium release and passive diffusion in the simulated human intestine. This study utilized an in vitro simulation of the upper gastrointestinal tract under fasted conditions to evaluate capsule dissolution and levels of bioaccessible and dialyzable magnesium during transit for two magnesium bisglycinate supplements containing a similar magnesium content (Chelamax[®] and Albion[®]). For this purpose, the validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) technology platform was used and magnesium fractions were determined by inductively coupled plasma optical emission spectroscopy following sample extraction. Analytical validation proved that the model was fit for purpose (94-102% recovery, RSD ≤ 2.4%, R2 > 0.999, LOQ 0.04 mg/kg). Visual capsule scoring found that the Chelamax[®] product dissolved later in gastrointestinal transit than the Albion[®] product. Magnesium bioaccessibility was higher for the Chelamax[®] versus Albion[®] product in early phases of the gastrointestinal tract (i.e. duodenum), resulting in 17% higher overall Mg availability after the small intestinal incubation was complete. The level of dialyzable magnesium at the end of the small intestinal incubation was significantly higher with the Chelamax[®] versus Albion[®] product (53 mg vs. 39 mg; p = 0.0009). These results demonstrate that the Chelamax[®] product showed significantly higher in vitro efficiency of potentially absorbable magnesium, even upon using the same magnesium salt type, suggesting the crucial role of product formulation. Even though a proven valid in vitro methodology for the prediction of effectiveness of magnesium availability was used, future in vivo studies should confirm these findings.},
}

Humans
*Magnesium/pharmacokinetics
Biological Availability
*Upper Gastrointestinal Tract/metabolism
*Dietary Supplements
*Glycine/pharmacokinetics/analogs & derivatives
Intestinal Absorption
Models, Biological
Gastrointestinal Transit
Capsules

@article {pmid42709402,
year = {2026},
author = {van Neerbos, FAC and Cusumano, A and Lievens, B and de Bobadilla, MF},
title = {Honeydew microbial ecology: A neglected frontier in multitrophic networks.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag104},
pmid = {42709402},
issn = {1574-6941},
abstract = {Honeydew, the sugary excretion produced by sap-feeding Hemiptera, is one of the most common carbohydrate resources in many plant-based food webs. Honeydew supports a wide range of organisms, including ants, pollinators, (hyper-)parasitoids wasps, predatory insects, and microbes. As a sugar-rich resource, honeydew is frequently colonized by specific microbes (i.e., bacteria and fungi), which consume its sugars and other nutritional constituents. Recent research suggests that microbes within honeydew may modify its traits. Thereby driving microbial succession and acting as important "hidden players" in multitrophic ecological interactions. Yet its role as a dynamic microbial habitat remains largely unexplored. Here, we synthesize current evidence on the microbial ecology of honeydew and propose that honeydew is a dynamic rapidly changing microbial habitat. We further propose a four-stage successional model to frame its temporal dynamics. We discuss how the honeydew microbiome alters nutritional composition. Further, we discuss how the honeydew microbiome may mediate multitrophic interactions through the emission of volatile organic compounds that attract natural enemies of honeydew-producing insects. We propose that this process may pose a trade-off between the microbial secondary metabolism and its dispersal capacity of some microbes. We aim to stimulate research that will establish honeydew microbial ecology as a new frontier in plant-insect-microbe interactions.},
}

@article {pmid42705452,
year = {2026},
author = {Tummala, R and Kondapalli, N and Katari, V and Manandhar, I and Dalal, K and Adapala, R and Paruchuri, S and Joe, B and Thodeti, C},
title = {TRPV4 deletion remodels the gut microbiota and increases colonic ammonia levels.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124671},
doi = {10.1016/j.lfs.2026.124671},
pmid = {42705452},
issn = {1879-0631},
abstract = {AIMS: The transient receptor potential vanilloid 4 ion channel is widely expressed in the gastrointestinal tract and contributes to epithelial barrier regulation, mechanosensation and innate immune signaling. However, its role in shaping gut microbiota composition and intestinal metabolic homeostasis remains unclear. This study aimed to determine whether deletion of TRPV4 influences gut microbial composition and intestinal ammonia levels.

MATERIALS AND METHODS: Fecal microbiota from wild type and TRPV4 knockout mice were analyzed using taxonomic profiling and microbial diversity approaches. Alpha diversity and beta diversity metrics were used to evaluate microbial richness, evenness, phylogenetic diversity and community structure. Ammonia concentration and pH were measured in cecal and colonic contents.

KEY FINDINGS: Phylogenetic diversity differed significantly between wild type and TRPV4 knockout mice whereas microbial richness and evenness were not altered. Beta diversity analysis revealed marked differences in microbial community composition between genotypes. The ratio of Bacillota to Bacteroidetes was reduced by approximately 50 % in TRPV4 knockout mice due to decreased Bacillota and increased Bacteroidetes abundance. In addition, TRPV4 knockout mice exhibited significantly elevated ammonia levels in both the colon and cecum compared with wild type mice.

SIGNIFICANCE: Deletion of TRPV4 alters gut microbial community structure and intestinal nitrogen metabolism without affecting overall microbial richness or evenness. These findings identify TRPV4 as a novel regulator of gut microbiota composition and metabolic homeostasis and suggest that ion channel dependent signaling contributes to the regulation of gut microbial ecology and metabolite balance.},
}

@article {pmid42701922,
year = {2026},
author = {Zhang, L and Tian, Q and Du, C},
title = {γ-Butyrolactones and γ-butenolides as autoregulatory systems: key mediators of intraspecific, interspecific, and interkingdom communication in Streptomyces.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42701922},
issn = {1432-072X},
support = {Grant No.: 32572911//National Natural Science Foundation of China/ ; Grant No.: LH2024C096//Heilongjiang Provincial Natural Science Foundation/ ; },
mesh = {*4-Butyrolactone/analogs & derivatives/metabolism/chemistry ; *Streptomyces/metabolism/genetics/physiology ; *Quorum Sensing ; Gene Expression Regulation, Bacterial ; Anti-Bacterial Agents/biosynthesis ; Signal Transduction ; },
abstract = {Streptomyces represent a phylogenetically coherent group of aerobic, Gram-positive, high-GC-content bacteria occupying diverse terrestrial and aquatic environments. They are renowned for their exceptional capacity to biosynthesize structurally diverse secondary metabolites, many of which serve as clinically essential antibiotics, antifungals, immunosuppressants, and anticancer agents, with broad applications in pharmaceuticals, agriculture, food, and industrial biotechnology. Quorum sensing (QS) represents a fundamental regulatory paradigm governing both intraspecies coordination and interspecies crosstalk in Streptomyces. Within this framework, gamma-butyrolactones (GBLs) and gamma-butenolides (GBNs) function as structurally analogous, receptor-specific signaling molecules that autoregulate antibiotic biosynthesis, morphological differentiation, and stress adaptation. However, despite growing insights into their intraspecies functions, the ecological range, molecular determinants, and functional outcomes of GBL- and GBN-mediated interspecies communication remain largely underexplored. This review summarizes recent advances in the chemical diversity and regulatory mechanisms of microbial GBLs and GBNs. Based on current empirical evidence, we categorize their interspecies communication functions into four distinct themes: experimentally validated ligand-receptor pairs, exogenous compound-mediated receptor responses, extract- or coculture-mediated complementation, and Streptomyces-fungi communication hypotheses. Furthermore, we propose a forward-looking research agenda integrating multi-omics, synthetic biology, and microbial ecology to decipher the mechanistic foundation of interspecies QS networks-ultimately facilitating the rational activation of silent biosynthetic gene clusters, the discovery of novel bioactive natural products, and the mitigation of antimicrobial resistance.},
}

*4-Butyrolactone/analogs & derivatives/metabolism/chemistry
*Streptomyces/metabolism/genetics/physiology
*Quorum Sensing
Gene Expression Regulation, Bacterial
Anti-Bacterial Agents/biosynthesis
Signal Transduction

@article {pmid42702405,
year = {2026},
author = {Šulčius, S and Kuznecova, J and Kasperovičienė, J and Alzbutas, G and Šimoliūnas, E and Voss, M and Jürgens, K and Dziga, D},
title = {Cyanophage lysis reshapes nitrogen cycling and microbiome composition in diazotrophic cyanobacterium Aphanizomenon flos-aquae.},
journal = {Harmful algae},
volume = {159},
number = {},
pages = {103186},
doi = {10.1016/j.hal.2026.103186},
pmid = {42702405},
issn = {1878-1470},
mesh = {*Aphanizomenon/virology/metabolism/physiology/genetics ; *Bacteriophages/physiology ; *Microbiota ; Nitrogen Fixation ; *Nitrogen Cycle ; Nitrogen/metabolism ; },
abstract = {Although it is presumed that viruses play a significant role in nutrient cycling and bacterial community dynamics, this has only rarely been addressed in studies of diazotrophic cyanobacteria. In this study, we therefore examined how cyanophage infection affects the expression of nitrogen (N) cycling genes, N2 fixation rates, and population structure in the diazotrophic cyanobacterium Aphanizomenon flos-aquae, a prevalent bloom-forming species in temperate brackish and freshwater ecosystems. We also assessed the influence of A. flos-aquae lysis on co-occurring bacterial assemblages throughout an incubation experiment. We found that nitrogen fixation, its release, and the relative availability of different nitrogen forms (e.g. ammonium versus nitrate/nitrite) varied substantially during cyanophage infection, population lysis, and recovery phases. Interestingly, resistant A. flos-aquae subpopulation emerged during viral infection, showed increased expression of N fixation (e.g. nitrogenase (nifH) and heterocyst differentiation regulator (hetR)) and assimilation (e.g. glutamine (glnA) and glutamate (gltB) synthase) genes, as well as higher cell-specific N2 fixation rates. These changes were accompanied by a fast recovery of A. flos-aquae population structure (e.g. filament length and heterocyte-to-vegetative cell ratio) to pre-infection level, indicating A. flos-aquae ability to quickly compensate for short-term population decline. Lysis of the cyanobacterial host significantly altered the successional trajectory and increased diversification of the co-occurring bacterial community. The compositional changes corresponded well with the prevalent inorganic nitrogen form, implying a substantial, nitrogen-driven reorganization of the microbial network and its interactions within the A. flos-aquae microbiome. This study improves our understanding of nitrogen cycling and microbial dynamics within cyanobacteria-driven communities disturbed by viral infections and lysis.},
}

*Aphanizomenon/virology/metabolism/physiology/genetics
*Bacteriophages/physiology
*Microbiota
Nitrogen Fixation
*Nitrogen Cycle
Nitrogen/metabolism

@article {pmid42702754,
year = {2026},
author = {Sengupta, S and Ghorai, S and Bose, S and Hazra, S and Mukhopadhyay, A and Majumdar, A and Roychowdhury, T},
title = {Integrating Plant Physiology and Microbiome Engineering for Climate-Resilient Crops: Bridging Knowledge Gaps in Multi-Stress Tolerance.},
journal = {Physiologia plantarum},
volume = {178},
number = {5},
pages = {e71088},
pmid = {42702754},
issn = {1399-3054},
mesh = {*Crops, Agricultural/physiology/microbiology ; *Stress, Physiological/physiology ; *Microbiota/physiology ; Climate Change ; *Plant Physiological Phenomena ; },
abstract = {Climate change is intensifying the frequency and co-occurrence of abiotic and biotic stresses, posing significant challenges to global crop productivity and stability. Conventional approaches based on single-stress responses are increasingly insufficient for addressing complex field environments where plants experience multiple simultaneous stresses. This review synthesizes current knowledge on plant physiological responses, microbiome interactions, and emerging technological interventions to develop an integrative framework for climate-resilient agriculture. It highlights how stress perception, hormonal regulation, metabolic adjustments, and epigenetic mechanisms collectively shape plant adaptation under multi-stress conditions. The review further examines the role of plant-associated microbiomes in enhancing nutrient acquisition, regulating stress signaling, and improving resilience through mechanisms such as phytohormone modulation, antioxidant activity, and induced systemic resistance. Advances in microbiome engineering, including synthetic microbial communities and computational prediction frameworks, are discussed as promising strategies for improving stress tolerance. In addition, emerging tools such as nanotechnology-assisted delivery systems and biosensing platforms are considered for precision management of plant-microbe systems. By identifying critical knowledge gaps in multi-stress physiology, microbiome assembly, and field-level predictability, this review proposes an interdisciplinary approach that integrates plant physiology, microbial ecology, and technological innovations to support sustainable crop production under changing climatic conditions.},
}

*Crops, Agricultural/physiology/microbiology
*Stress, Physiological/physiology
*Microbiota/physiology
Climate Change
*Plant Physiological Phenomena

@article {pmid42703030,
year = {2026},
author = {de Lorenzo, V},
title = {Environmental Release of Genetically Intervened Microorganisms: Towards a New Narrative.},
journal = {Microbial biotechnology},
volume = {19},
number = {9},
pages = {e70441},
pmid = {42703030},
issn = {1751-7915},
support = {CL6-2021-UE 101060625//HORIZON EUROPE Excellent Science/ ; },
mesh = {*Microorganisms, Genetically-Modified/genetics ; Genetic Engineering/legislation & jurisprudence ; *Containment of Biohazards ; Biotechnology/legislation & jurisprudence ; },
abstract = {The deliberate release of genetically engineered microorganisms for environmental applications has remained largely blocked since the early days of recombinant DNA technology, when limited ecological knowledge, lack of success stories and public apprehension shaped a culture of caution and restrictive regulation. Despite profound advances in microbial ecology, synthetic biology and genetic design, current frameworks still rely on outdated assumptions and legacy regulations that equate engineered microbes with inherent danger and demand unrealistic forms of absolute containment. This review examines how laboratory-trained microorganisms exist on a continuum with naturally evolved life, and that their risks are neither categorically different nor greater. Rather than pursuing unachievable containment, governance should shift towards traceability, stewardship and long-term monitoring through genomic barcodes, digital twins and transparent oversight. The vision moves from domination and control to care and partnership recognizing engineered microbes as live amendments capable of restoring degraded ecosystems. Achieving this transformation requires new terminology, phased field-trial frameworks, improved scaling methods, and the integration of epistemological perspectives that emphasize reciprocity and coexistence with nature. Reframing biotechnology in this way could finally unlock the capacity of engineered microorganisms to contribute responsibly and effectively to planetary repair in an era of escalating environmental crises.},
}

*Microorganisms, Genetically-Modified/genetics
Genetic Engineering/legislation & jurisprudence
*Containment of Biohazards
Biotechnology/legislation & jurisprudence

@article {pmid42704537,
year = {2026},
author = {de Freitas Germano, J and Leite, G and Pimentel, M},
title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42704537},
issn = {1534-312X},
mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; },
abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.

RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.},
}

Humans
Multiomics
*Intestine, Small/microbiology
Proteomics/methods
*Blind Loop Syndrome/diagnosis/microbiology
Breath Tests/methods
Gastrointestinal Microbiome
Metagenomics/methods
Syndrome

@article {pmid42704659,
year = {2026},
author = {Cahill, N and Kovarova, A and Alfahl, Z and O'Connor, L and Morris, D},
title = {Antimicrobial resistance in wastewater-impacted coastal waters: implications for environmental surveillance and public health.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {9},
pages = {},
pmid = {42704659},
issn = {1465-2080},
mesh = {*Wastewater/microbiology ; Ireland ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/drug effects/isolation & purification ; *Seawater/microbiology ; *Bacteria/genetics/drug effects/isolation & purification/classification ; Public Health ; Anti-Bacterial Agents/pharmacology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; beta-Lactamases/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a global public health concern, and wastewater-impacted aquatic environments are recognized as reservoirs and dissemination pathways for antimicrobial-resistant bacteria (ARB) and genes (ARGs). However, harmonized environmental AMR surveillance frameworks that integrate culture-based ARB enumeration with molecular ARG monitoring across wastewater and receiving surface waters remain limited. This pilot study, conducted in Ireland as part of a European harmonized monitoring initiative, assessed ARB and ARG abundances in wastewaters and surface waters. Wastewater treatment plant influent (n=3), effluent (n=3) and surface waters upstream and downstream of the discharge point (n=3 each) were sampled on three occasions in late 2024. Culture-based methods enumerated total and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, while quantitative real-time PCR quantified 16S rRNA and five AMR-associated genes (intI1, ermB, aadA1, bla CTX-M-1 and vanA). Total E. coli concentrations were highest in influent (~10[5]-10[6] c.f.u. dl[-1]), decreased in effluent (~10[3]-10[5] c.f.u. dl[-1]) and lowest in surface waters (~10[1]-10[2] c.f.u. dl[-1]). ESBL-producing E. coli were consistently detected in influent (~10[4] c.f.u. dl[-1]) and effluent (~10[1]-10[3] c.f.u. dl[-1]) but were not recovered from seawater. ARG abundances were highest in influent, reaching up to ~10[11] copies dl[-1] for intl1, remained elevated in effluent (up to ~10[10] copies dl[-1]) and were ~2-3 orders of magnitude lower in surface waters relative to effluent. Downstream seawater exhibited higher ARG levels than upstream freshwater despite low culturable E. coli. Peak ARG concentrations in effluent and surface waters were observed following a period of heavy rainfall; however, the limited number of sampling events precluded assessment of any statistical association. These findings highlight the impact of wastewater discharges on environmental AMR dissemination and suggest that faecal indicator-based monitoring may underestimate emerging risks, supporting integration of AMR indicators into EU water quality frameworks.},
}

*Wastewater/microbiology
Ireland
*Environmental Monitoring
*Drug Resistance, Bacterial/genetics
Escherichia coli/genetics/drug effects/isolation & purification
*Seawater/microbiology
*Bacteria/genetics/drug effects/isolation & purification/classification
Public Health
Anti-Bacterial Agents/pharmacology
Pilot Projects
RNA, Ribosomal, 16S/genetics
Water Microbiology
beta-Lactamases/genetics

@article {pmid42698632,
year = {2026},
author = {Park, J and Cheon, S and Choi, YS and Kim, J and Ahn, SJ and Chung, JE},
title = {Anaerobic antibiotic exposure and risk of maculopathy: a nationwide dual design study.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1840229},
pmid = {42698632},
issn = {1663-9812},
abstract = {The pathogenesis of maculopathy remains incompletely understood, and emerging evidence implicates the gut-eye axis in retinal and macular diseases. Given that antibiotics with anti-anaerobic activity may disrupt gut microbial ecology, this study investigated their association with the risk of incident maculopathy. We conducted a nationwide population-based study using the National Health Insurance Service-National Sample Cohort of South Korea. A retrospective cohort study was used to assess cumulative systemic anaerobic antibiotic exposure during a 5-year baseline period and subsequent incident maculopathy from 2007 to 2019. After 1:1 propensity score matching, hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards regression. A nested case-control study was also conducted using risk-set sampling and 1:10 propensity score matching. Anaerobic antibiotic exposure during the 365 days before the index date was assessed, and odds ratios (ORs) and 95% CIs were estimated using conditional logistic regression. Duration-response relationships were evaluated using formal trend analyses. Sensitivity analyses included age restriction, Fine-Gray competing risk models, extended exposure assessment windows, lag-time analyses, and a negative control comparator analysis using first-generation cephalosporins. In the retrospective cohort study, 326,436 anaerobic antibiotic users were matched to 326,436 non-users. Anaerobic antibiotic use was associated with an increased risk of incident maculopathy in the fully adjusted model (HR, 1.07; 95% CI, 1.03-1.12), with a significant duration-response trend and the highest risk observed for ≥57 days of cumulative use (HR, 1.24; 95% CI, 1.09-1.42). In the nested case-control study, 55,776 cases were matched to 557,760 controls. Anaerobic antibiotic use within 365 days before the index date was associated with increased odds of maculopathy (OR, 1.04; 95% CI, 1.02-1.07), also showing a significant duration-response trend. Sensitivity analyses and first-generation cephalosporin comparator analyses, generally supported the robustness of the findings. Systemic exposure to antibiotics with anti-anaerobic activity was associated with an increased risk of incident maculopathy, with a duration-response pattern across cumulative exposure categories. These findings suggest further investigation into gut microbiome disruption and the gut-eye axis as potential pathways involved in maculopathy.},
}

@article {pmid42699672,
year = {2026},
author = {Wu, D and Dong, T and Chen, X and Lin, Z and Pan, Q and Wei, J and Liang, J and Wei, J},
title = {Insights into microbiome and ARGs diversity in patients with upper and lower respiratory tract infections by targeted next-generation sequencing.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21615},
pmid = {42699672},
issn = {2167-8359},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Male ; Middle Aged ; Adult ; *Bacteria/genetics/drug effects/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Drug Resistance, Bacterial/genetics ; Coinfection/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Respiratory tract infections (RTIs) cause substantial global morbidity and mortality, with antimicrobial resistance presenting an increasing challenge to the effective management. Characterizing the differences in microbiome composition and antimicrobial resistance genes (ARGs) between upper respiratory tract infections (URTIs) and lower respiratory tract infections (LRTIs) may inform site-specific diagnostic and therapeutic strategies. We retrospectively analyzed 1,340 URTIs samples (nasopharyngeal swab) and 699 LRTIs samples (bronchoalveolar lavage fluid) admitted to a single medical center to characterize the epidemiology of the respiratory microbes and ARGs using targeted next-generation sequencing (tNGS). Microbiome diversity, ARGs profiles, and coinfection patterns were compared between LRTIs and URTIs groups. Random forest machine learning was employed to identify discriminating species. LRTIs patients exhibited significantly higher microbiome abundance and ARGs diversity than URTIs patients (P < 0.001. Beta-lactam, multidrug, phenicol, and fluoroquinolone resistance genes were significantly more abundant in LRTIs (P < 0.01). Bacteria-virus coinfections predominated in both LRTIs (39.3%) and URTIs (54.6%). Thirty species were identified as potential discriminators between LRTIs and URTIs, with an Area Under Curve (AUC) of 0.852 in the training set. These findings reveal distinct microbial and ARGs profiles between URTIs and LRTIs patients, and provide a foundation for understanding site-specific microbial ecology in RTIs for clinical diagnosis and antimicrobial stewardship.},
}

Humans
*Respiratory Tract Infections/microbiology
*Microbiota/genetics
Female
High-Throughput Nucleotide Sequencing
Retrospective Studies
Male
Middle Aged
Adult
*Bacteria/genetics/drug effects/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Drug Resistance, Bacterial/genetics
Coinfection/microbiology
Anti-Bacterial Agents/pharmacology

@article {pmid42694744,
year = {2026},
author = {Rajakaruna, S and Howard-Varona, C and Urvoy, M and AminiTabrizi, R and Ayala-Ortiz, C and Gittrich, M and Solonenko, N and Burris, M and Sanderson, C and Noel, C and Leopold, J and Quillin, L and Doshi, K and Walker, LR and Sullivan, MB and Tfaily, MM},
title = {Metabolome restructuring reveals distinct virocell infection strategies in bacteriophage-host interaction.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag223},
pmid = {42694744},
issn = {2730-6151},
abstract = {Viral infection transforms microbial cells into metabolically reprogrammed "virocells," yet the metabolic architecture underlying this transition remains poorly resolved. Here we investigate how bacteriophages reshape host metabolism in Cellulophaga baltica across time and phage types, uncovering coordinated metabolic reorganization during infection that includes pathway-level patterns consistent with membrane remodeling, amino-acid recycling, and redistribution of cellular resources. Temporal analyses further distinguished infection strategies: efficient phages produced structured, phased metabolic shifts indicative of controlled host reprogramming, whereas inefficient infection triggered abrupt metabolic collapse. These results suggest that the organization and timing of host metabolome restructuring represent defining features of the virocell state and may reflect underlying viral life-history strategies. These biological patterns were made accessible by an integrative annotation framework that combines previously validated computational tools, substantially expanding interpretable metabolite coverage beyond conventional approaches. This approach reveals coherent infection signatures that would otherwise remain hidden, demonstrating how expanded metabolite interpretability can uncover functional principles of virus-host interactions. The analytical strategy presented here is readily transferable to other virus-host systems and complex microbial communities, providing a path toward mechanistic interpretation of untargeted metabolomic data in microbial ecology.},
}

@article {pmid42695145,
year = {2026},
author = {Van Etten, J and Han, S and Burns, JA and Lhee, D and Willoughby, AC and Stephens, TG and Chille, E and Sleith, RS and Bhattacharya, D and Yoon, HS},
title = {Crawling under the radar: Two novel Paulinella species expand knowledge about the ecology and evolution of a primary plastid-containing amoeba lineage.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70230},
pmid = {42695145},
issn = {1529-8817},
support = {80NSSC19K1542/NASA/NASA/United States ; RS-2022-NR068987//National Research Foundation of Korea/ ; RS-2022-NR070837//National Research Foundation of Korea/ ; RS-2025-25434508//National Research Foundation of Korea/ ; NJ01180//USDA National Institute of Food and Agriculture Hatch Formula/ ; 2410274//National Science Foundation/ ; 2410358//National Science Foundation/ ; RS-2025-02304428//Korea Institute of Marine Science and Technology promotion/ ; },
abstract = {The genus Paulinella represents a rare, independent case of primary endosymbiosis, providing a unique system to study the early stages of organelle evolution. Here, we expand current understanding of primary plastid endosymbiosis through the discovery and characterization of two novel photosynthetic amoebae, Paulinella marae sp. nov. and Paulinella murrayi sp. nov., isolated from a brackish water habitat in North Carolina, United States. Complete chromatophore genomes and mitochondrial data revealed conserved gene content but notable structural variation, including genome rearrangements and inversion events. Phylogenetic analyses uncovered significant discordance between nuclear and organelle datasets, likely driven by substitution saturation, limited taxon sampling, and differing evolutionary signals across loci. Ecological observations over multiple years indicate that both species are in low abundance but consistently present, and when coupled with hobbyist data, support the hypothesis that photosynthetic Paulinella species are globally distributed yet under-sampled. These results increase known species diversity within the clade from four to six and highlight the importance of integrating field-based observations with genomic approaches. Overall, this work advances Paulinella as a model for studying ongoing primary endosymbiosis, lineage divergence, and the ecological strategies of low-abundance microbial eukaryotes.},
}

@article {pmid42696299,
year = {2026},
author = {Román, R and Maestre, FT and Couradeau, E},
title = {Rainfall-induced microbial resuscitation reveals functional decoupling across biocrust succession.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag231},
pmid = {42696299},
issn = {1751-7370},
abstract = {Dryland ecosystems rely on infrequent rainfall pulses to activate soil microbial communities, yet the fraction and identity of microbes resuscitating after hydration remain unclear. We applied bioorthogonal non-canonical amino acid tagging coupled with fluorescence-activated cell sorting (BONCAT-FACS) and 16S rRNA gene sequencing to identify translationally active bacteria in early (L-BSC) and late (D-BSC) successional cyanobacteria-dominated biocrusts subjected to 3 mm simulated rainfall under light and dark conditions. Our results reveal that only a small subset of the microbial community resumes activity within six hours, with higher active cell abundances in mature crusts. Microbial activity patterns were largely independent of light exposure and showed partial decoupling from total community composition, indicating that presence does not predict short-term function. These findings suggest that biocrust maturity shapes microbial activation dynamics and that functional responses to precipitation pulses are governed by a conserved pool of fast responders, informing predictions of dryland soil microbiome resilience under changing precipitation regimes.},
}

@article {pmid42696594,
year = {2026},
author = {Glasl, B and Kitzinger, K and Luter, HM and Legin, A and Schuster, S and Salas, E and Heldwein, N and Damjanovic, K and Rutsch, M and Vekeman, B and Geerlings, NMJ and Pjevac, P and Séneca, J and Watzka, M and Wanek, W and Speth, DR and Wagner, M},
title = {Branched-chain amino acid assimilation enables mixotrophy of ammonia-oxidizing archaeal sponge symbionts.},
journal = {Science advances},
volume = {12},
number = {36},
pages = {eaef9450},
doi = {10.1126/sciadv.aef9450},
pmid = {42696594},
issn = {2375-2548},
mesh = {Animals ; *Ammonia/metabolism ; *Symbiosis ; *Archaea/metabolism/physiology ; *Amino Acids, Branched-Chain/metabolism ; *Porifera/microbiology/metabolism ; Oxidation-Reduction ; },
abstract = {Marine sponges and ammonia-oxidizing archaea (AOA) represent one of the earliest animal-microbe symbioses. AOA are considered metabolically constrained chemolithoautotrophs that remove nitrogenous waste within the sponge holobiont. Here, we expand this view by demonstrating that symbiotic AOA assimilate branched-chain amino acids (BCAA) as additional carbon and nitrogen sources. By combining stable isotope probing with fluorescence and chemical imaging, we trace the assimilation of [13]C- and [15]N-labeled BCAA (leucine, isoleucine, and valine) in the sponge holobiont Ianthella basta at single-cell resolution. We show that the ability to take up, degrade, and biosynthesize BCAA is a common adaptation among symbiotic AOA lineages. This ability may enable symbiotic AOA to modulate BCAA concentrations in their auxotrophic sponge hosts. Modulation of BCAA availability by symbionts may regulate the leucine-sensitive mTOR (mechanistic target of rapamycin) signaling pathway in sponges.},
}

Animals
*Ammonia/metabolism
*Symbiosis
*Archaea/metabolism/physiology
*Amino Acids, Branched-Chain/metabolism
*Porifera/microbiology/metabolism
Oxidation-Reduction

@article {pmid42697479,
year = {2026},
author = {Luo, Y and Jiang, Y and Tingting, Z},
title = {Targeting Nrf2 in oxidative liver injury: expanding the role of gut microbiota and metabolites.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.09.006},
pmid = {42697479},
issn = {2090-1224},
abstract = {BACKGROUND: Liver diseases are a major cause of illness and death worldwide. Oxidative stress is a pivotal driver in the pathogenesis of a spectrum of liver diseases, including alcoholic liver disease (ALD), metabolic dysfunction-associated fatty liver disease (MAFLD), drug-induced liver injury (DILI), and hepatocellular carcinoma (HCC). The transcription factor Nrf2, a master regulator of cellular antioxidant responses, plays a central yet context-dependent role in modulating this injury. Additionally, the gut-liver axis is a critical regulator of hepatic homeostasis.

AIM OF REVIEW: This review presents recent advances to propose a refined gut-microbiota-Nrf2 axis as a key mechanistic link in the treatment of liver injury. We detail how specific gut-derived microbial metabolites, such as short-chain fatty acids (SCFAs), tryptophan derivatives, and urolithins, directly or indirectly activate the hepatic Keap1/Nrf2 signaling pathway. This activation orchestrates a cytoprotective program that enhances the redox balance, promotes detoxification, and induces selective autophagy, thereby protecting against oxidative liver injury. Conversely, we examine the dual role of Nrf2, highlighting how its dysregulated and constitutive activation in established HCC can paradoxically promote tumor progression and ferroptosis resistance. Finally, we evaluate the therapeutic potential of targeting this axis using microbiome-modulating strategies, including probiotic and prebiotic supplementation, fecal microbiota transplantation (FMT), dietary intervention, and synergy with Nrf2-targeting drugs.

This review provides an integrated framework that connects gut microbial ecology with host redox signaling, offering novel mechanistic insights and translational perspectives for the prevention and treatment of oxidative liver diseases.},
}

@article {pmid42697798,
year = {2026},
author = {Ho, PM and Nazeer, RR and Askenasy, I and Quinn, RA and Welch, M},
title = {Microbial content versus microbial interaction: the impact of medications on CF airway microbial ecosystems.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.08.011},
pmid = {42697798},
issn = {1873-5010},
abstract = {BACKGROUND: The airways of people with cystic fibrosis (pwCF) are often colonized by a variety of different microbes. Although much effort has been put into cataloguing the impact of medication on the identities and abundances of these microbes, far less has been directed towards examining this from an ecological perspective, i.e., examining how medications affect the network and types of interactions between microbes.

METHODS: In the current work, we generated an ecological model of the CF airway microbiome and examined how medications affect interactions between co-habiting airway microbiota in six pwCF. Ecological interactions were inferred from a generalized Lotka-Volterra model, and the impact of medications was determined by principal component(s) regression analysis.

RESULTS: For the majority of the subjects studied, antimicrobial interventions had relatively little impact on the CF airway microbial ecology, and even appeared to stabilize ecological interactions between the microbiota. However, the microbial ecosystem in some individuals was more sensitive to external perturbations. More surprisingly, we found that some non-antimicrobial medications, and also certain carriers and excipients affect the ecosystem.

CONCLUSIONS: Medications affect the ecology of the CF airway microbiota. These impacts appear to be very patient-specific. We also note that some nominally non-bioactive ingredients in medications can also potentially impact the CF airway ecosystem. Our data highlight the importance of collecting patient-specific data and in employing suitable computational frameworks for disentangling medication-microbiota interactions in vivo.},
}