@article {pmid41610050,
year = {2026},
author = {Moreno-Mirón, JM and Ruiz-Argüelles, GJ and Gallardo-Pérez, MM and Moreno-Mirón, A and Rivera-Aguilar, AP and Gale, RP},
title = {The Gastro-Intestinal Microbiota in Haematology.},
journal = {Acta haematologica},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000550689},
pmid = {41610050},
issn = {1421-9662},
abstract = {BACKGROUND: The gastro-intestinal microbiota is a key regulator of systemic immunity and inflammatory tone and it contributes to normal haematopoiesis through microbial metabolites, barrier integrity, and host-microbe immune signalling. Disruption of this has been increasingly linked to the development, clinical course, and treatment-related complications of haematological disorders, including clonal haematopoiesis of indeterminate potential (CHIP), leukaemias, and plasma cell neoplasms (PCNs).

SUMMARY: This review synthesises current evidence on how gut microbiota composition and function intersect with haematopoietic regulation and haematological disease biology. We summarise proposed mechanisms - including microbe-derived metabolites (e.g., short-chain fatty acids), pattern-recognition receptor signalling, intestinal permeability, and cytokine-mediated inflammation - that may influence haematopoietic stem and progenitor cell behaviour and immune cell differentiation. We then discuss disease-specific associations of dysbiosis with CHIP, leukaemias, and PCN, as well as the impact of common haematology interventions (antibiotics, chemotherapy, immunomodulatory therapies, and transplantation) on microbial ecology and downstream clinical outcomes. Finally, we highlight methodological challenges and outline priorities for longitudinal, mechanistic, and multi-omics studies to enable microbiota-informed risk stratification and therapeutic modulation.

KEY MESSAGES: (1) The gut microbiota influences haematopoiesis via immune signalling, microbial metabolites, and maintenance of mucosal barrier function. (2) Dysbiosis is associated with CHIP, leukaemias, and PCN, and may contribute through chronic inflammation and altered immune homeostasis. (3) Haematological therapies frequently reshape the microbiota; these changes may affect infection risk, treatment tolerance, and outcomes. (4) Current evidence is largely associative; rigorously designed longitudinal and interventional studies are needed to establish causality and guide clinical translation.},
}

@article {pmid41853994,
year = {2026},
author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C},
title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70245},
doi = {10.1111/1758-2229.70245},
pmid = {41853994},
issn = {1758-2229},
support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; },
mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; },
abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.},
}

*Ecosystem
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Metagenome
*Lakes/microbiology
*Fresh Water/microbiology
Metagenomics
Transcriptome

@article {pmid41854259,
year = {2026},
author = {Almela, P and Hamilton, TL},
title = {Enhancing DNA recovery in low-biomass snow algae samples: a comparative study of extraction methods and their effect on community composition.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0003126},
doi = {10.1128/aem.00031-26},
pmid = {41854259},
issn = {1098-5336},
abstract = {High-throughput sequencing is a powerful tool for environmental microbiology and can be particularly important for examining community structure and function for organisms that are difficult to culture or environments that are difficult to mimic, like snow. Nucleic acid extraction significantly impacts these analyses, often introducing more variation between samples than PCR or sequencing. Snow algae are widespread on mountain and polar snowfields, where they contribute to biogeochemical cycling and accelerate melt. Despite increasing research on snow algae, DNA extraction remains challenging, as the thick, resilient walls of snow algal cysts can limit cell lysis, and differences among extraction methods may therefore affect the estimates of community composition and richness. Here, we compared three common extraction methods (Qiagen DNeasy PowerSoil Pro, Qiagen DNeasy PowerWater, and phenol-chloroform) alongside ultrasonication in samples with varying snow algae abundance. The extraction method strongly influenced the resulting microbial profiles assessed by amplicon sequencing of rRNA genes. Ultrasonication improved DNA yield in low-biomass samples and enhanced the recovery of DNA from resilient cells, including mature-phase snow algae, likely due to improved cell lysis. Our findings provide insights to improve standardization and facilitate comparison among studies in snow and ice environments.IMPORTANCEHigh-throughput sequencing has transformed environmental microbiology, allowing for detailed, culture-independent analyses of microbial communities. However, multiple methodological factors, including DNA extraction, can introduce variability in results, making cross-study comparisons challenging. This research contributes to improving our understanding of snow algae, which play a role in alpine and polar ecosystems by influencing biogeochemical cycles and snow reflectivity. By evaluating common DNA extraction techniques for snow algae, this study helps improve the reliability and reproducibility of sequencing data, supporting broader efforts toward methodological standardization in microbial ecology.},
}

@article {pmid41855561,
year = {2026},
author = {Berne, C and Debidour, M and Paniconi, M and Danis, N and Sprowls, ED and Kavanagh, K and Gilbert, L and Brun, Y},
title = {Exploring the diversity of bacterial holdfast polar adhesins from Québec aquatic environments.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0310},
pmid = {41855561},
issn = {1480-3275},
abstract = {Biofilms are complex microbial communities that adhere to surfaces, often in response to their environment. Irreversible attachment in these biofilms is mediated by bacterial adhesins, and, in many Alphaproteobacteria, those adhesins are located at the cell pole. To examine the prevalence and natural variation of polar adhesins, 76 water samples were collected across Québec through a citizen science initiative. Environmental isolates were screened for their ability to form biofilms, and strains exhibiting polar attachment were selected. A subset of 21 representative strains was used for phenotypic assays and whole-genome sequencing. Phylogenetic analysis showed that most belonged to the order Caulobacterales, and microscopic characterization indicated variability in the polysaccharide composition of polar adhesins in these environmental strains. By integrating comparative genomics with phenotypic assays, this work establishes a unique framework for linking microbial ecology to molecular mechanisms of adhesion. Our results highlight intra-order natural variations in polar adhesin structure and composition. Such variations may be signatures of adaptive adhesive performances across diverse environments. These findings not only advance the understanding of biofilm biology but also open avenues for bio-inspired applications, including the development of next-generation adhesives and anti-biofouling materials.},
}

@article {pmid41855876,
year = {2026},
author = {Lou, J and Zhu, Z and Zheng, Y and Chen, J and Su, Q and Zhu, J},
title = {Response mechanism of the DAMO-associated denitrification system to oxytetracycline stress.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129409},
doi = {10.1016/j.jenvman.2026.129409},
pmid = {41855876},
issn = {1095-8630},
abstract = {Antibiotics and denitrifying anaerobic methane oxidation (DAMO) processes frequently coexist in natural ecosystems and wastewater treatment systems. This study investigated the performance and microbial ecology of a denitrification system coupled with Nitrite-dependent anaerobic methane oxidation (N-DAMO) under oxytetracycline (OTC) stress. Specifically, 1 mg/L OTC enhanced nitrogen removal efficiency by 15% relative to the control, whereas 10 mg/L OTC exerted a significant inhibition of 58%. The Michaelis-Menten kinetic model predicted that the system could tolerate the maximum OTC concentration of 26.76 mg/L. Mechanistically, the secretion of protein-rich extracellular polymeric substances (EPS) served as a protective barrier against toxicity. The abundance of the DAMO bacterium Candidatus Methylomirabilis correlated negatively with OTC concentration. At 1 mg/L OTC, denitrification was enhanced through the enrichment of Thauera. However, 10 mg/L OTC damaged EPS structure and suppressed microbial activity, and led to a decrease in the abundance of related functional bacteria and an increase in the abundance of antibiotic resistant bacteria such as Hyphomicrobium and Thermomonas. Metagenomic analysis revealed that denitrification genes (e.g., norB, norC) were upregulated with 1 mg/L OTC, whereas high-concentration OTC induced pronounced enrichment of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), with frequently co-localization within the same hosts. This suggests an increased potential for horizontal gene transfer (HGT) occurred within the DAMO community, which may contribute to the dissemination of ARGs. These findings provide new insights into the adaptive mechanisms of N-DAMO systems under antibiotic stress and highlight their potential for nitrogen removal in contaminated environments.},
}

@article {pmid41856914,
year = {2026},
author = {Sorouri, B and Bernardin, J and Favier, AI and Garces, KR and McMullen, JG and McGuire, RM},
title = {Microbial ecology for all: A vision of accessibility, unity, and responsibility.},
journal = {Ecology},
volume = {107},
number = {3},
pages = {e70342},
doi = {10.1002/ecy.70342},
pmid = {41856914},
issn = {1939-9170},
support = {2305844//National Science Foundation/ ; 2305876//National Science Foundation/ ; 2305992//National Science Foundation/ ; },
mesh = {*Ecology ; Ecosystem ; Biodiversity ; Microbiota ; },
abstract = {Microorganisms are ubiquitous in nature, representing a significant portion of global biodiversity and playing vital roles in ecosystem functions, biogeochemical cycles, and organismal health. The growing recognition of microbial importance and their potential to address ecological and global challenges has inspired a renewed interest and innovation in microbial ecology. This field has benefited immensely from sequencing technologies that allow scientists to explore diversity at scales previously unimaginable. While the rapid growth of the field has offered significant positive advancements and foreshadows promising potential, there are aspects that need careful consideration. New technology has led to exponential growth in available microbial data, yet not everyone has easy access to sequencing technology, data mining and analysis tools, or the time to acquire new skills. Thus, we are at a crossroads in ensuring that these resources are accessible for all, and that traditional methods of microbiology are still appreciated as tools to progress the field in meaningful ways. As early-career researchers, we want to raise these points as principles for shaping the future of microbial ecology. Here, we outline a vision for a more accessible, united, and responsible microbial ecology field, one with applications equipped to address the needs of both society and the environment. To democratize the field, we advocate to destigmatize microbes and increase awareness of their beneficial roles by integrating microbes into early education. We believe unity and collaboration among microbial ecologists, as well as with professionals and community members in other STEM fields, are essential for advancing the field. Data should be accessible and standardized for collaboration, and greater integration across disciplines is essential to address future ecological challenges effectively and innovatively. It is our responsibility to ensure that we are asking relevant research questions with the potential to engage with socio-environmental issues and prioritize sustainable practices. As a collective field, our research should strive to not only expand scientific knowledge but also support community resilience and policy-making for a sustainable future. Together, this vision will promote a more equitable, diverse, and collaborative future for microbial ecology; and has applications for the broader ecology field.},
}

*Ecology
Ecosystem
Biodiversity
Microbiota

@article {pmid41857392,
year = {2026},
author = {Zhai, X and Jin, J and Yu, M and Liu, R and Li, J and Liu, Y and Zhang, XH and Liu, J},
title = {Spatial Heterogeneity of Microbial Communities and Biogeochemical Function in Water Column of Site F Cold Seep, South China Sea.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02722-5},
pmid = {41857392},
issn = {1432-184X},
support = {202172002//the Fundamental Research Funds for the Central Universities/ ; LSKJ202203206//the Science & Technology Innovation Project of Laoshan Laboratory/ ; ZR2022YQ038, ZR2024JQ006//Shandong Province Natural Science Foundation/ ; },
}

@article {pmid41859237,
year = {2026},
author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H},
title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag011},
pmid = {41859237},
issn = {2730-6151},
abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.},
}

@article {pmid41859451,
year = {2026},
author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L},
title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755652},
pmid = {41859451},
issn = {1664-302X},
abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.},
}

@article {pmid41860215,
year = {2026},
author = {Chaudhary, A and Lin, H and Guo, L and Poretsky, R},
title = {Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0026326},
doi = {10.1128/aem.00263-26},
pmid = {41860215},
issn = {1098-5336},
abstract = {Bacterial communities in freshwater ecosystems play a critical role in biogeochemical and food web dynamics. However, our understanding of environmental controls on bacterial community function, particularly in large lakes, is limited. We characterized Lake Michigan water chemistry, bacterial community function, and substrate preferences to better understand bacteria-water chemistry relationships. Using metatranscriptomics, we investigated bacterioplankton gene expression in surface waters across a nearshore-to-offshore transect during 2017-2018. Additionally, we measured nutrients, dissolved organic carbon (DOC), chromophoric dissolved organic matter (DOM), as well as changes in major fluorescent DOM components across this transect. The results highlighted similarities in inorganic N and P measurements and a minor reduction in DOC levels from nearshore to offshore. However, significant changes in the composition of DOM were observed across the transect, including a higher presence of terrestrially derived and high-molecular-weight DOM in the nearshore. These differences in DOM quality were associated with the differential expression of several gene families between nearshore and offshore bacterioplankton. Notably, genes involved in the acquisition of various DOM, N, and P substrates, including peptidases, proteases, and transporter genes for amino acids, nucleobases, sugars, urea, and inorganic phosphate, were over-represented in the offshore bacterioplankton. A focused analysis of all the transporter gene expression for C, N, and P substrates revealed similar trends-higher expression of DOM transporter genes in the offshore versus nearshore. When viewed in the context of changing DOM quality across the transect, these results imply that offshore bacterial communities are more substrate-limited (particularly C) than in nearshore and are investing more energy in acquiring DOM substrates.IMPORTANCEVarious environmental, geological, and climatic factors influence bacterial community dynamics in freshwater ecosystems in complex and interactive ways. It thus becomes challenging in microbial ecology studies to disentangle the specific effects of these factors on microbial community function. Spatial environmental gradients in large lake ecosystems can provide a unique opportunity to test important questions about bacterial function and water chemistry relationships in a relatively consistent geological and climatic framework. Lake Michigan, one of the five largest lakes in the world, is one such example. The lake has witnessed significant ecological changes in the last few decades, and the impact of these changes on the physico-chemical environment and bacterioplankton function is not fully understood. In a relatively novel approach for freshwater systems, this study assesses Lake Michigan bacterial metabolism using robust transcriptomics techniques in the context of rich environmental data, including characterization of the lake chromophoric DOM and fluorescent DOM pool.},
}

@article {pmid41846126,
year = {2026},
author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE},
title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141760},
doi = {10.1016/j.jhazmat.2026.141760},
pmid = {41846126},
issn = {1873-3336},
abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.},
}

@article {pmid41846605,
year = {2026},
author = {Allner, R and Decewicz, P and Allner, T and Bluszcz, A and Dziewit, L},
title = {Development of molecular biomarkers for monitoring of arable crops colonization with Methylobacterium symbioticum SB0023/3, a methylotrophic bacterium commonly used as a biostimulant in agriculture.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1718185},
pmid = {41846605},
issn = {1664-462X},
abstract = {INTRODUCTION: The intensive use of synthetic fertilizers has led to increased nitrous oxide emissions, declining soil fertility, and reduced biodiversity. Biological alternatives, such as the use of endophytic bacteria to improve plant growth, are promising alternatives but require reliable monitoring tools to assess colonization success and biological effectiveness under field conditions. One of the most commonly used microbial biostimulants is Methylobacterium symbioticum SB0023/3; thus, monitoring the efficacy of inoculation and maintenance of this strain is required for adequate evaluation of fertilization practices.

METHODOLOGY: The resequencing of the genome of M. symbioticum SB0023/3, followed by comparative genomics and functional annotation were performed. Specific real-time PCR primers were developed and validated for strain-specific detection. The colonization of various crops (wheat, corn, rapeseed, peas, and tomatoes) was tested under controlled conditions using developed molecular markers.

RESULTS: The resequencing of the SB0023/3 genome revealed novel genetic content and updated previous records. The resequenced genome showed 121 novel regions with 165 protein-coding genes and five tRNA. Based on the newly obtained genome, two highly specific biomarker genes (copG and ubik) were identified and, together with the (Methylobacterium spp./methylotrophs-specific) xoxF gene, validated for their strain/genus-specificity. The developed real-time PCR assays using copG and ubik biomarkers demonstrated high specificity for M. symbioticum SB0023/3, distinguishing it from related species. In contrast, the xoxF gene showed relaxed specificity and cannot be used for SB0023/3 detection. Successful endophytic colonization was confirmed in all tested crops, with high detection rates exceeding 80% in tomatoes. Classical culturing on a novel nitrogen-free medium additionally confirmed colonization, with the same validating the real-time PCR assays.

DISCUSSION: This study provides a robust, genome-informed molecular detection system for monitoring M. symbioticum SB0023/3 in crops. The presented approach enables direct detection from plant tissues, facilitating studies on colonization dynamics and biosafety. This methodology can be extended to other microbial biostimulants, supporting sustainable agricultural practices.},
}

@article {pmid41848198,
year = {2026},
author = {Skoupý, S and Stanojković, A and Johansen, JR and Casamatta, DA and McGovern, C and Jungblut, AD and Fastner, J and Dvořák, P},
title = {Population and herbarium genomics provide a comprehensive framework for a revision of Microcoleus (Cyanobacteria).},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70145},
pmid = {41848198},
issn = {1529-8817},
support = {//European Community Research Infrastructure Action under the FP7 "Capacities" Program/ ; 23-06507S//Grantová Agentura České Republiky/ ; },
abstract = {Microcoleus is a cosmopolitan, filamentous cyanobacterium and a key component of biological soil crusts-complex microbial communities essential for primary production in diverse terrestrial environments. Here, we performed a taxonomic revision of several species of Microcoleus based on a large population genomic dataset. The dataset was based on a Microcoleus speciation continuum characterized by variable levels of gene flow between the species. The putative species ranged from cryptic to distinctly morphologically defined lineages. We identify the type herbarium specimen and obtained a genome for the type species M. vaginatus and herein describe 10 novel species of Microcoleus. We provide epitypifications for the previously described species M. vaginatus and M. attenuatus. This research contributes to a more comprehensive understanding of terrestrial cyanobacterial biodiversity and cryptic species in cyanobacteria. It highlights the need for an extensive genomic and phenotypic dataset in the taxonomy of Cyanobacteria.},
}

@article {pmid41850628,
year = {2026},
author = {Tumeo, A and Kovářová, A and McDonagh, F and Ryan, K and Clarke, C and Miliotis, G},
title = {Patient colonization with Phytobacter spp. co-harboring blaIMP-4, blaSHV-12, and mcr-9.1 highlights its role as an under-recognized reservoir of antimicrobial resistance.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108562},
doi = {10.1016/j.ijid.2026.108562},
pmid = {41850628},
issn = {1878-3511},
abstract = {We report two uncommon identifications of patient colonization with multidrug-resistant, carbapenemase-encoding Phytobacter in Ireland. Phytobacter is a recently delineated genus within the Enterobacterales that is frequently misidentified in clinical laboratories. Two isolates were recovered from rectal swabs in 2024 and were initially identified as Phytobacter ursingii by MALDI-TOF. Whole-genome sequencing with in silico species typing (average nucleotide identity and digital DNA-DNA hybridization) resolved them as Phytobacter diazotrophicus E787336 and P. ursingii E980862. We reconstructed a genus-wide maximum-likelihood core-genome phylogeny and profiled all publicly available Phytobacter genomes to contextualize antimicrobial resistance (AMR) and plasmid content. Across the dataset, we detected 22 plasmid replicon types and a resistome comprising 71 genes, over half predicted to be plasmid-borne. These included carbapenemases in 26.5% (9/34) of the genomes, and disinfectant-associated resistance determinants in 29.5%. E787336 and E980862 represent the first Phytobacter isolates identified to co-harbor plasmid-borne blaIMP-4, blaSHV-12, and mcr-9.1 in association with IncHI2A plasmid reconstructions. Phenotypic testing confirmed resistance to aztreonam, aminoglycosides, cephalosporins, fluoroquinolones, and piperacillin-tazobactam, yet susceptibility to carbapenems and colistin. These findings expand the clinical and genomic evidence that Phytobacter can act as an under-recognized colonizer and reservoir for plasmid-borne AMR, including carbapenemases, and underscore the need for improved clinical identification, genomic surveillance, and preparedness for limited therapeutic options.},
}

@article {pmid41850929,
year = {2026},
author = {Garcés-Ruiz, M and Díaz-Otero, BG and Antonielli, L and Saraiva, JP and Karpouzas, D and Declerck, S},
title = {Machine learning for designing low-risk microbial consortia pesticides.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2025.12.027},
pmid = {41850929},
issn = {1879-3096},
abstract = {Microbial consortia, considered low-risk pesticides (LRPs), appear to be valuable tools for reducing our dependence on chemical pesticides. However, their use is limited by inconsistent product efficacy and registration difficulties. Artificial intelligence (AI) and machine learning (ML) offer solutions for designing and evaluating synthetic microbial communities (SynComs), predicting their compatibility, ecological stability, and biocontrol efficacy. The transition from laboratory discovery of SynCom-based LRPs to field application and commercialization could be significantly accelerated. Here, we review the methods and steps necessary to establish reliable SynComs and describe how AI and ML approaches could improve the construction and validation of SynCom-based LRPs to obtain more specific results that can contribute to their risk assessment.},
}

@article {pmid41851145,
year = {2026},
author = {Shen, J and Han, M and Sun, J and Yu, H and Yang, Y and Shen, K and Su, Y and Chen, X and He, H and Shao, H and Sun, J and McMinn, A and Wang, M and Liang, Y},
title = {Diversity and ecological potential of sediment viruses from Chinese continental shelf seas.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00940-w},
pmid = {41851145},
issn = {2055-5008},
abstract = {Continental shelves are important areas for global biogeochemical cycling, yet the roles of sediment viruses in these areas remain poorly understood. Here, 48 surface sediment samples from the Chinese continental shelf were analyzed, and 12,540 viral operational taxonomic units (vOTUs) were identified. Taxonomic classification found that 93.6% of the vOTUs could not be assigned at the family level, and protein-sharing networks showed that 60.4% were singletons. Viral community structure was shaped primarily by temperature and water depth. A total of 557 auxiliary metabolic genes (AMGs) were identified, including those involved in sulfur reduction and phosphorus acquisition (Pho-family proteins). Additionally, diverse antibiotic resistance genes (ARGs) were detected, suggesting anthropogenic influence. This study reveals the diversity, ecological function, and environmental drivers of viral communities in continental shelf sediments, providing new insights into viral contributions to microbial ecology and biogeochemical processes.},
}

@article {pmid41852400,
year = {2025},
author = {Fischer, A and Singh, JP and Van Hamme, J and Bottos, E and Fraser, LH},
title = {Investigating impacts from topsoil stockpile height on soil microbial communities.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1607677},
pmid = {41852400},
issn = {2813-4338},
abstract = {Mining activities are often severely disruptive to the landscape, and a significant barrier to reclamation following mining operations is the lack of quality topsoil. This project addresses knowledge gaps in the industry by exploring the compositional nature of topsoil stockpiles and their ability to facilitate post-mining revegetation after long-term storage. To do this, we conducted a microbial profiling of two topsoil stockpiles in the interior of British Columbia, Canada. Both stockpiles show depleted soil quality and significant changes compared to reference soils. Notably, there were declines in microbial diversity and significant shifts in community structure with increasing stockpile depths in one of the stockpiles. These results highlight the influence of topsoil-stockpile height on microbial communities in the soil, which ultimately influences the success of restoration. This research can help the industry to optimize restoration and expedite recovery in their mine-closure practices and provides insights into the general structure of the microbiome existing across a gradient in severely disturbed mining soils.},
}

@article {pmid41852403,
year = {2025},
author = {Helal, M and Bari, VK},
title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1549166},
pmid = {41852403},
issn = {2813-4338},
abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.},
}

@article {pmid41852418,
year = {2025},
author = {Berdy, BM and Williams, CE and Sizova, M and Jung, D and Tandogan, N and Goluch, ED and Epstein, S},
title = {Diverse cultivation strategies are necessary to capture microbial diversity in High Arctic lake sediment.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1619859},
pmid = {41852418},
issn = {2813-4338},
abstract = {While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.},
}

@article {pmid41853343,
year = {2023},
author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y},
title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1329925},
pmid = {41853343},
issn = {2813-4338},
abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.},
}

@article {pmid41853537,
year = {2024},
author = {Klimasmith, IM and Wang, B and Yu, S and Yoshikuni, Y and Kent, AD},
title = {Translating macroecological models to predict microbial establishment probability in an agricultural inoculant introduction.},
journal = {Frontiers in microbiomes},
volume = {3},
number = {},
pages = {1452476},
pmid = {41853537},
issn = {2813-4338},
abstract = {The use of potentially beneficial microorganisms in agriculture (microbial inoculants) has rapidly accelerated in recent years. For microbial inoculants to be effective as agricultural tools, these organisms must be able to survive and persist in novel environments while not destabilizing the resident community or spilling over into adjacent natural ecosystems. Despite the importance of propagule pressure to species introductions, few tools exist in microbial ecology to predict the outcomes of agricultural microbial introductions. Here, we adapt a macroecological propagule pressure model to a microbial scale and present an experimental approach for testing the role of propagule pressure in microbial inoculant introductions. We experimentally determined the risk-release relationship for an IAA-expressing Pseudomonas simiae inoculant in a model monocot system. We then used this relationship to simulate establishment outcomes under a range of application frequencies (propagule number) and inoculant concentrations (propagule size). Our simulations show that repeated inoculant applications may increase establishment, even when increased inoculant concentration does not alter establishment probabilities. Applying ecological modeling approaches like those presented here to microbial inoculants may aid their sustainable use and provide a monitoring tool for microbial inoculants.},
}

@article {pmid41841797,
year = {2026},
author = {Coskun, ÖK and Orsi, WD and Marshall, IPG and Muschler, KA and Mitschke, N and Ferdelman, TG and Gomez-Saez, GV},
title = {Hypoxia increases microbial carbon assimilation of taurine in a seasonally anoxic fjord.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag057},
pmid = {41841797},
issn = {1751-7370},
abstract = {Hypoxic zones are expanding globally altering marine biogeochemical cycles. Within these low-oxygen regions, microbial communities play a key role in the production, degradation, and transformation of dissolved organic sulfur (DOS) compounds. Taurine is a bioavailable DOS compound widely utilized by marine microbes with a central role in nutrients exchange, energy production and biomass generation. However, in stratified water columns with varying oxygen conditions, the specific microbial taxa assimilating taurine as a carbon source remain poorly characterized. Here, we applied quantitative stable isotope probing (qSIP) experiments using 13C-labeled organosulfur compounds (taurine and methionine) and 13C-glucose to identify active microbial utilizers in oxic and hypoxic waters in the seasonally anoxic Mariager Fjord (Denmark, Kattegat Sea). Our qSIP results were supported by physicochemical measurements and geochemical data. Taurine-derived 13C-carbon was assimilated into microbial biomass exclusively under hypoxic conditions, primarily by Flavobacteriaceae (Bacteroidota), indicating that taurine serves as a carbon source only when oxygen is limited. 13C-taurine and 13C-methionine assimilation were strongly associated, suggesting a flexible metabolic strategy for utilizing organosulfur compounds in hypoxic waters. In oxic waters, 13C-methionine and 13C-glucose were assimilated by distinct taxonomic groups, dominated by Bacteroidota and Verrucomicrobiota, respectively. Overall, our study identifies active microbial communities assimilating organosulfur compounds under varying oxygen levels in the seasonally anoxic Mariager Fjord, providing new insights into key microbial processes in low-oxygen coastal systems.},
}

@article {pmid41842987,
year = {2026},
author = {Reardon, CL and Manter, DK},
title = {Amplification Efficiency of Quantitative PCR Reactions is Improved by Addition of Non-Target DNA.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02719-0},
pmid = {41842987},
issn = {1432-184X},
}

@article {pmid41843121,
year = {2026},
author = {Dou, WH and Li, TC},
title = {Rapid Genomic Adaptation of Drosophila Melanogaster to Wolbachia Elimination.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02732-3},
pmid = {41843121},
issn = {1432-184X},
support = {ZR2024QC383//Natural Science Foundation of Shandong Province/ ; ZR2024QC222//Natural Science Foundation of Shandong Province/ ; },
}

@article {pmid41844028,
year = {2026},
author = {Sun, L and Huang, L and Jia, S and Wei, Y and Cao, Z and Zhang, P and Zhang, G},
title = {Enhancing wastewater denitrification in constructed wetlands: microbial mechanisms driven by lotus leaf-based carbon.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129368},
doi = {10.1016/j.jenvman.2026.129368},
pmid = {41844028},
issn = {1095-8630},
abstract = {The performance of constructed wetlands (CWs) in treating low C/N domestic wastewater is often constrained by limited carbon availability for denitrification. This study proposes an innovative approach using alkali-pretreated lotus leaves as a biodegradable, slow-release carbon source to enhance denitrification efficiency and uncover the underlying metabolic and microbial mechanisms. Results demonstrated that wet lotus leaves-especially those wet-4% NaOH-released carbon more efficiently than dried leaves, with a peak rate of 25.93 mg g[-1]·h[-1] (calculated as ΔCOD/Δt normalized to wet mass and measured within the first 20 h of the static experiment). This pretreatment also mitigated nitrogen and phosphorus leaching risks. Supplementation with 400 g of 4% NaOH-treated wet lotus leaves (CW2) significantly improved the TN removal efficiency, reaching a peak of 91.89 ± 3.56% during days 1-16, with an overall average of 85.63% ± 7.72%. Mechanistically, tryptophan-like DOM signals (EEM) suggest that small-molecule soluble organics released from plant-derived carbon sources can be rapidly taken up and utilized by denitrification-associated microorganisms, thereby supporting the denitrification process. Microbial characteristics analysis revealed that CW2 enriched microbial richness (Shannon = 6.96; Chao 1 = 2015.9) and shifted community composition toward denitrification-favorable taxa. Notably, Proteobacteria abundance increased from 21.5% to 38.5%, accompanied by the proliferation of key genera including Pseudomonas and Janthinobacterium. The taxa associated with nitrifiers, denitrifiers, and anammox bacteria collectively contributed to a more robust nitrogen removal pathway. These findings suggest that the supplementary carbon source-by regulating dissolved oxygen distribution, supplying bioavailable carbon, and establishing spatially structured redox gradients-strategically modulates microbial ecology and functional metabolism, offering a low-cost and sustainable solution for enhancing nitrogen removal in constructed wetlands.},
}

@article {pmid41844516,
year = {2026},
author = {Muratore, TJ and Chari, NR and Phillips, RP and Taylor, BN and Knorr, MA and Frey, SD},
title = {Increased root-derived carbon buffers soil carbon loss under simultaneous warming and nitrogen addition.},
journal = {Ecology},
volume = {107},
number = {3},
pages = {e70351},
doi = {10.1002/ecy.70351},
pmid = {41844516},
issn = {1939-9170},
support = {DEB-1832110//U.S. National Science Foundation (NSF) Long Term Ecological Research Program/ ; DEB-1456610//U.S. National Science Foundation (NSF) Long-Term Research in Environmental Biology/ ; 2106096//Macrosystems Biology and NEON-Enabled Science" (MSB-NES)/ ; 1950364//U.S. National Science Foundation (NSF) Directorate for Biological Sciences Division of Biological Infrastructure/ ; 3018//New Hampshire Agricultural Experiment Station/ ; Hatch NH-00701//New Hampshire Agricultural Experiment Station/ ; },
mesh = {*Soil/chemistry ; *Nitrogen/chemistry ; *Carbon/chemistry/metabolism ; *Plant Roots/metabolism/physiology ; *Global Warming ; Soil Microbiology ; *Carbon Cycle ; },
abstract = {Plant roots are primary drivers of soil organic matter dynamics, mediating belowground carbon (C) inputs, stabilization, and losses. Yet, how global changes such as rising temperatures and altered nitrogen (N) availability interact to affect these dynamics has rarely been tested empirically in the field. Here, we quantify how inputs to soil organic matter from fine-root production, root exudates, and root-associated fungi respond to long-term (16 years) soil warming (+5°C), nitrogen (N) enrichment (+5 g N m[-2] year[-1]), and their combination in a temperate hardwood forest. Warming alone reduced root-derived C inputs by 21% and increased microbial respiration by 46%, resulting in a net soil C loss of 135 g C m[-2] year[-1]. In contrast, N enrichment increased root-derived soil organic carbon (SOC) accumulation by 47% and reduced root respiration by 40%, contributing to a near-neutral soil C balance. When combined, warming × N addition increased root-derived SOC fourfold (from 70 to 281 g C m[-2] year[-1]), fully offsetting warming-induced C losses and maintaining soil C stocks at control levels. Root-derived SOC accumulation was positively related to fine-root production (r[2] = 0.42) and to maple:oak exudate ratios (r[2] = 0.31), highlighting species-specific control over C stabilization. These findings demonstrate that interacting global change factors can have balancing effects on root C allocation and microbial losses, highlighting soil N availability as a critical control determining whether warming accelerates SOC depletion or stabilizes new root-derived C.},
}

*Soil/chemistry
*Nitrogen/chemistry
*Carbon/chemistry/metabolism
*Plant Roots/metabolism/physiology
*Global Warming
Soil Microbiology
*Carbon Cycle

@article {pmid41844664,
year = {2026},
author = {Ruiz-Muñoz, B and Bretscher, KM and Carrión, VJ and Cazorla, FM and Gutiérrez-Barranquero, JA},
title = {Long-term organic farming shapes the avocado rhizosphere microbiota through the enrichment of drought-tolerant Bacillus spp.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00957-1},
pmid = {41844664},
issn = {2055-5008},
support = {PID2021-123713OB-I00//Ministerio de Ciencia, Innovacion y Universidades (Spain)/ ; },
abstract = {Long-term farming practices leave an imprint on soil microbiomes, but how these changes influence crop drought resilience remains poorly understood. Here, we examined avocado orchards managed organically or conventionally for two decades and recurrently exposed to drought, to assess how management history shapes the rhizosphere microbiota and its contribution to plant stress tolerance. Organic and conventional systems resulted in distinct soil physicochemical profiles that were associated with shifts in rhizosphere microbial community composition. Organic management was characterized by higher soil pH, phosphorus availability, water content, and C:N ratio, together with a consistent enrichment of spore-forming bacteria, especially members of the Bacillaceae family. We established a culture collection from the organic rhizosphere, dominated by Bacillaceae, and identified three top-performing strains: Bacillus halotolerans B19 and B21, and Bacillus subtilis B26. In greenhouse assays, B. halotolerans strains mitigated drought stress by preserving biomass and reducing leaf proline accumulation, while B. subtilis provided partial protection. Gene expression analysis revealed strain-specific responses that nonetheless converged on bdh (2,3-butanediol dehydrogenase) induction, highlighting a common mechanism for drought mitigation. Together, these findings establish a mechanistic link between long-term organic farming and microbial functions underpinning drought resilience in perennial agroecosystems, paving the way for climate-smart farming strategies.},
}

@article {pmid41845564,
year = {2026},
author = {Zhang, Y and Wang, DD},
title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644682},
doi = {10.1080/19490976.2026.2644682},
pmid = {41845564},
issn = {1949-0984},
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Proteomics ; Multiomics ; },
abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism
Humans
*Gastrointestinal Microbiome
Metagenomics
Animals
*Diet
Metabolomics
Bacteria/classification/genetics/metabolism/isolation & purification
Proteomics
Multiomics

@article {pmid41834869,
year = {2026},
author = {Ruff, SE and Murali, R and Rubin-Blum, M and Teske, AP},
title = {Editorial: Rising stars in geomicrobiology: microbial life in subsurface, seep and hydrothermal ecosystems.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1808625},
doi = {10.3389/fmicb.2026.1808625},
pmid = {41834869},
issn = {1664-302X},
}

@article {pmid41835129,
year = {2026},
author = {Milke, F and Garcia, SL and Simon, M and Pacheco-Valenciana, A and Lennartz, ST},
title = {Microbial cohorts: bringing ecological meaning to the modularity concept of co-occurrence networks.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag037},
pmid = {41835129},
issn = {2730-6151},
abstract = {Microbial communities are structured through complex interactions that are difficult to observe directly. Co-occurrence networks offer a way to infer community structure, revealing (not exclusively) potential biotic interactions. Such networks have been inferred for diverse biomes and repeatedly found to be modular, yet the ecological significance of this modularity remains underexplored. We tested whether clusters within co-occurrence networks ("cohorts"), are universal and ecologically meaningful units by assessing their ubiquity, stability, and environmental specificity across diverse ecosystems. Our meta-analysis spans 25 previously published 16S rRNA gene amplicon sequencing datasets (14 160 samples) and covers high environmental variability ranging from aquatic, terrestrial to anthropogenic environments. Microbial co-occurrence networks consistently exhibited high modularity across biomes. Inferred cohorts were ubiquitous and represented up to 90% of the community composition. Our findings demonstrate that modularity is a fundamental and generalizable feature of microbial community organization, indicating the existence of stable subcommunities. Highly similar cohorts were inferred even across different, unconnected environments and datasets, and showed consistent responses to environmental gradients, indicating that their composition is to a large degree deterministic and predictable. The overall cohort structure and environmental preferences were independent of the sample size and the inference algorithm, underlining the robustness and applicability of the results. Recognizing these microbial cohorts as a meaningful level of microbial organization will refine microbial community ecology, cultivation strategies, and predictive modelling of microbial dynamics.},
}

@article {pmid41836789,
year = {2026},
author = {Manzoor, M and Pussinen, PJ and Saarela, RK and Pitkälä, K and Hiltunen, K and Mäntylä, P},
title = {Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2641915},
pmid = {41836789},
issn = {2000-2297},
abstract = {BACKGROUND: The denture-associated oral microbiome (DAOM) may act as reservoirs of pathogenic microorganisms with potential health effects.

OBJECTIVES: To characterize the compositional and functional activity of the DAOM in dentate and edentulous older adults residing in long-term care facilities (LTCFs).

METHODS: Participants (51 dentate and 56 edentulous) aged ≥64 years were recruited from the Finnish Oral Health Studies in Older Adults. Clinical oral examinations were performed, and biofilm samples for shotgun metagenomics were collected from the acrylic surface of removable dentures. Diversity indices, taxonomic composition, and functional pathways were assessed to characterize DAOM.

RESULTS: Alpha diversity was similar, whereas beta diversity showed modest differences between groups. Dentate participants had a higher abundance of Streptococcus mutans, Veillonella parvula, and Parascardovia denticolens, whereas edentulous participants were enriched with Haemophilus parainfluenzae and Propionibacterium acidifaciens. Edentulous participants had reduced microbial network stability and interconnectedness but highly active microbial metabolic functions, particularly those associated with Streptococcus pneumoniae.

CONCLUSION: Although tooth loss does not markedly alter the overall microbial diversity of DAOM, it is associated with distinct taxonomic and functional shifts. Edentulous individuals have less stable and less interconnected microbial networks alongside heightened metabolic activity, reflecting notable changes in the DAOM of older adults living in LTCFs.},
}

@article {pmid41837593,
year = {2026},
author = {Mailem, RC and Tsai, PW and Tayo, L and Hsueh, CC and Hsieh, CY and Chen, BY},
title = {Uncovering the Redox and Immunoregulatory Basis of the Chinese Herbal Formula Ping An Fang Yu Yin using Network Pharmacology and In Silico Target Profiling.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128418247251211153057},
pmid = {41837593},
issn = {1873-4286},
abstract = {INTRODUCTION: Ping An Fang Yu Yin (PAFYY) is a traditional Chinese herbal tea formula commonly used to treat respiratory infections, including COVID-19. Previous research indicates potential antiinflammatory activities; however, the underlying mechanisms remain unclear. This study aimed to investigate the mechanisms underlying the therapeutic effects of PAFYY, specifically its electron-transport and bioenergetic properties, through network pharmacology, electrochemical analysis, and Microbial Fuel Cell (MFC) assessments.

METHODS: Active compounds and their respective targets were identified via database searches. Proteinprotein interaction networks were constructed using the STRING database and further analyzed using Cytoscape and MCODE software. Molecular docking was employed to assess the binding affinity between identified key compounds and their targets. Cyclic voltammetry (CV) and MFC assays evaluated the electrontransport characteristics of PAFYY water and ethanol extracts.

RESULTS: The analysis identified 298 active compounds associated with 1,940 biological targets, highlighting key targets including EP300, CREBBP, ESR1, AKT1, MAPK3, MAPK1, and STAT3. GO and KEGG pathway enrichment analyses revealed that PAFYY significantly influences immune system processes and neuronal signaling pathways. Molecular docking confirmed the anti-inflammatory and antiviral potential of the identified active compounds. Additionally, electrochemical studies demonstrated that PAFYY contains electroactive substances mediating electron-driven redox reactions.

DISCUSSION: Recent studies have demonstrated that traditional Chinese herbal teas contain electron shuttles capable of mediating electron transfer in electrogenic bacteria. Emerging evidence further indicates that electroactive plant polyphenols can modulate microbial ecology through redox-mediated mechanisms. Our findings suggest that PAFYY may act on the microbiota-immune axis, with its electron-shuttling constituents contributing not only to direct cellular effects and antioxidant activity but also to modulation of the gut microbiome in ways that support antiviral immunity and attenuate inflammation. These results may inform future research into the mechanistic basis of medicinal herbs, while highlighting the potential of MFCs as a functional screening platform for identifying bioactive redox compounds.

CONCLUSION: The anti-COVID-19 properties of PAFYY may be largely attributed to its electron-transport capabilities, mediated through electroactive compounds. These findings provide novel insights into the mechanistic basis of traditional Chinese medicine prescriptions, potentially enhancing their therapeutic application.},
}

@article {pmid41839398,
year = {2026},
author = {Kawuribi, V and Awere-Duodu, A and Adjei, FA and Osman, AH and Bomansaan, H and Madadi, MM and Tampuri, JU and Adu-Amankwaah, J},
title = {The Gut-Tumor Metabolic Axis: A Comprehensive Exploration of Bidirectional Crosstalk in Cancer Immunotherapy.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105280},
doi = {10.1016/j.critrevonc.2026.105280},
pmid = {41839398},
issn = {1879-0461},
abstract = {The gut-tumor metabolic axis represents a bidirectional immunometabolic network in which tumor-derived metabolites reshape microbial ecology, while gut microbiome-derived metabolites recalibrate systemic and intratumoral immunity, ultimately influencing cancer progression and immunotherapy outcomes. Tumor aerobic glycolysis generates excess lactate and acidity that suppress cytotoxic immune function, remodel the tumor immune microenvironment, and indirectly perturb intestinal microbial composition. In turn, microbial metabolites including short-chain fatty acids, bile acid derivatives, tryptophan catabolites, inosine, and trimethylamine N-oxide signal through defined host pathways such as GPR109A, AHR, and adenosine A2A receptors to regulate antigen presentation, T-cell differentiation, macrophage polarization, and immune checkpoint sensitivity. Preclinical and emerging clinical evidence demonstrates that dietary modulation, rational probiotics, and fecal microbiota transplantation can enhance immune checkpoint inhibitor efficacy in selected contexts. However, metabolite effects are highly context dependent, with dose, timing, tumor type, and immune state critically shaping therapeutic benefit or resistance. This review integrates mechanistic insights and clinical evidence, highlights translational challenges including safety, donor heterogeneity, and biomarker validation, and proposes a framework for biomarker-guided microbiome-based strategies to advance precision cancer immunotherapy.},
}

@article {pmid41840154,
year = {2026},
author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A},
title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {41840154},
issn = {1678-4405},
support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnología/ ; CAR-21861//Universidad Autónoma de Yucatán/ ; },
}

@article {pmid41841597,
year = {2026},
author = {Ye, Z and Kuang, J and Bates, CT and Escalas, A and Ning, D and Wu, L and Liu, S and Deng, S and Lei, J and Chen, X and Pett-Ridge, J and Saha, M and Hale, L and Wang, G and Tian, R and Fu, Y and Tang, Y and Firestone, M and Zhou, J and Yang, Y},
title = {Bioenergy Cropping Reduces the Spatiotemporal Scaling of Soil Bacterial Biodiversity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18964},
doi = {10.1002/advs.202518964},
pmid = {41841597},
issn = {2198-3844},
support = {KY-23ZK01//Hainan Institute of National Park/ ; 32161123002//National Natural Science Foundation of China/ ; //Office of Science/ ; DE-SC0014079//Office of Biological and Environmental Research Genomic Science program/ ; //UC Berkeley/ ; //Nobel Research Institute/ ; //University of Oklahoma/ ; //Lawrence Livermore National Laboratory (LLNL)/ ; AC52-07NA27344//Lawrence Berkeley National Laboratory/ ; SCW1555//Lawrence Berkeley National Laboratory/ ; EF-2025558//Lawrence Berkeley National Laboratory/ ; },
abstract = {Widespread bioenergy cropping can transform landscapes, strongly affecting biodiversity. However, the impact of bioenergy cropping on the spatiotemporal scaling of soil biodiversity remains virtually unknown, despite its profound implications for the functioning of the ecological community. Here, we investigated how bioenergy cropping influenced the spatiotemporal scaling of soil bacterial biodiversity in marginal soils (sandy loam and clay loam soils) in Oklahoma, USA. We detected strong, significant species-time-area relationships (STARs) and phylogenetic-time-area relationships (PTARs) in bacterial communities and their lineages, suggesting that STARs and PTARs exist in microbial ecology within the studied system. Also, spatiotemporal scaling rates (the slopes of STAR and PTAR models) varied substantially among bacterial lineages and were positively correlated with their 16S rRNA gene copy numbers, a genomic trait indicative of microbial growth potentials. Strikingly, bioenergy cropping significantly reduced spatiotemporal scaling rates by 6.8%-14.1%, with a more pronounced reduction observed in sandy loam soils, where those rates were significantly lower than in clay loam soils. The heterogeneity of soil phosphorus and carbon resulted in variations in bacterial spatiotemporal scaling rates. Collectively, our findings suggest that bioenergy cropping may alleviate rapid shifts in soil biodiversity across space and time, thereby stabilizing soil biodiversity and supporting its role as part of sustainable land management and climate mitigation strategies.},
}

@article {pmid41841793,
year = {2026},
author = {Dey, R and Coenen, AR and Solonenko, NE and Burris, MN and Mackey, AI and Galasso, J and Sun, CL and Demory, D and Muratore, D and Beckett, SJ and Sullivan, MB and Weitz, JS},
title = {Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag041},
pmid = {41841793},
issn = {1751-7370},
abstract = {Diverse phage-bacteria communities coexist at high densities in environmental, agricultural, and human-associated microbiomes. Phage-bacteria coexistence is often attributed to coevolutionary processes mediated by complex, pairwise infection networks. Here, using in vitro experiments and mathematical models, we explore how higher-order interactions function as a complementary, ecological feedback mechanism to stabilize phage-bacteria communities. To do so, we examine an environmentally-derived, synthetic phage-bacteria community comprised of five marine heterotrophic bacteria (Cellulophaga baltica and Pseudoalteromonas strains) and five associated phage. We used Bayesian inference to reconstruct free phage production in one-step growth experiments and then forecasted pairwise phage-bacteria community dynamics over multiple infection cycles. In contrast to model predictions of rapid bacterial population collapse, each bacterial strain persisted in the community. We hypothesized and then experimentally validated the relevance of infection attenuation at relatively high viral densities. We extended models into a community context, corroborating complex coexistence of all phage and bacteria. Life history traits inferred in community fits often differed from those inferred in a pairwise context, implicating higher-order interactions as an additional, ecological stabilization mechanism. Follow-up experiments confirm that phage traits (including burst size) can shift when infecting single vs. multiple strains. More broadly, these findings suggest that complex community coexistence of phage and bacteria may be more common than anticipated when including feedback mechanisms outside of the growth-dominated regimes of fitted pairwise models that do not reflect the full scope of ecologically relevant contexts.},
}

@article {pmid41826531,
year = {2026},
author = {Eckertová, T and Palyzová, A and Műllerová, M and Řezanka, T},
title = {Radioactive Springs and Archaeal Life in Deep Groundwater Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02720-7},
pmid = {41826531},
issn = {1432-184X},
support = {(VEGA project No. 1/0019/22//Scientific Grant Agency/ ; CZ.02.01.01/00/22_008/0004597//Grant Talking Microbes/ ; APVV-21-0356//Slovak Research and Development Agency/ ; RVO 61388971//Institutional Research Concept/ ; },
}

@article {pmid41826538,
year = {2026},
author = {Teban-Man, A and Erdem, ED and Berendonk, TU and Klümper, U and Coman, C and Szekeres, E},
title = {Hydrodynamics Shape Antibiotic Resistance in Wastewater-Impacted River Biofilms.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02725-2},
pmid = {41826538},
issn = {1432-184X},
}

@article {pmid41828603,
year = {2026},
author = {Reytor-González, C and Román-Galeano, NM and Aules-Curicama, LS and Cevallos-Villacis, CD and González, E and Jima Gavilanes, D and Horowitz, R and Simancas-Racines, D},
title = {The Oral-Gut-Immune-Nutrition Axis in Rheumatoid Arthritis: Molecular Mechanisms and Therapeutic Implications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
pmid = {41828603},
issn = {1422-0067},
mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; Diet ; Animals ; *Mouth/microbiology/immunology ; },
abstract = {Rheumatoid arthritis is a chronic systemic autoimmune disease that arises from complex interactions among genetic susceptibility, environmental factors, and immune dysregulation. Growing evidence indicates that microorganisms residing in the oral cavity and gastrointestinal tract, together with dietary factors, play a central role in shaping inflammatory and autoimmune responses in rheumatoid arthritis, forming an interconnected microbiome-immune-nutrition axis. Alterations in the composition and function of oral and intestinal microbial communities are associated with disruption of mucosal barrier integrity, activation of innate and adaptive immune pathways, increased differentiation of proinflammatory T lymphocyte subsets, and loss of immune tolerance that promotes autoantibody production. In addition, microbially derived metabolites, particularly short-chain fatty acids, provide a mechanistic link between microbial ecology, immune regulation, and bone metabolism. Diet represents a key upstream modulator of this axis. Dietary patterns rich in anti-inflammatory nutrients support microbial diversity and immunoregulatory metabolite production, whereas diets high in processed foods and saturated fats favor proinflammatory microbial profiles. Accumulating clinical evidence suggests that nutritional strategies and microbiome-targeted dietary interventions may reduce systemic inflammation and disease-related comorbidities when used alongside standard pharmacological treatments. Taken together, the microbiome-immune-nutrition axis represents a modifiable and clinically meaningful target in rheumatoid arthritis, emphasizing the need for interdisciplinary research and well-designed clinical trials to translate these insights into personalized approaches for disease management. The aim of this review is to integrate current mechanistic and clinical evidence on the interactions between the microbiome, immune system, and nutrition in rheumatoid arthritis, with a focus on their pathogenic relevance, therapeutic potential, and implications for personalized, diet-based interventions.},
}

Humans
*Arthritis, Rheumatoid/immunology/microbiology/therapy
*Gastrointestinal Microbiome/immunology
Diet
Animals
*Mouth/microbiology/immunology

@article {pmid41832088,
year = {2026},
author = {Schwalbe, M and Bosch, T and El Aidy, S},
title = {Gut motility as a driver of microbial community architecture and host-microbe evolution.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.12.016},
pmid = {41832088},
issn = {1878-4380},
abstract = {Digestive systems are dynamic, contractile ecosystems that continually shape the physical and chemical niches inhabited by gut microbes. Patterns of mixing and propulsion generate flow, shear, and nutrient gradients that select for microbial traits such as adhesion, biofilm formation, and metabolic timing. Microbial metabolites, in turn, influence smooth muscle excitability and enteric neural circuits, creating bidirectional feedback that structures microbial communities and affects host physiology. We argue that gastrointestinal motility, an ancient and nearly universal feature of metazoan digestive systems, functions as an evolutionary scaffold, linking microbial spatial organization with host neuromuscular diversification. Comparative evidence from cnidarians to mammals highlights how these interactions have shaped both microbial ecology and host adaptation, with relevance for understanding modern dysmotility-microbiome disorders.},
}

@article {pmid41832279,
year = {2026},
author = {Choran, N and Örmeci, B},
title = {Microfibres versus fragments: differential impacts of polyethylene terephthalate (PET) and polyamide (PA6) microplastics on anaerobic digestion efficiency and microbial ecology.},
journal = {Biodegradation},
volume = {37},
number = {2},
pages = {},
pmid = {41832279},
issn = {1572-9729},
mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; Methane/metabolism ; Biodegradation, Environmental ; Anaerobiosis ; *Microplastics/metabolism/chemistry ; *Caprolactam/analogs & derivatives/chemistry ; Polymers ; Bacteria/metabolism/drug effects ; },
abstract = {Rising microplastic (MP) pollution can significantly affect engineered treatment systems such as anaerobic digestion (AD). While prior studies have investigated the influence of individual polymers, varying concentrations and sizes on AD, the role of MP morphology and polymer interactions remains underexplored. This study investigated these factors using polyethylene terephthalate (PET) and polyamide 6 (PA6) MPs, both in isolation and in combination (1:1 ratio), introduced as microfibres (MFs) and fragments at three concentrations, 1, 5, and 15 mg/gTS. Results revealed morphology-dependent effects on methane production. MF exposure inhibited methane yield by 10-17% (p < 0.01), with PET and mixed polymers exhibiting a correlation to MP concentration. In contrast, fragments enhanced methane yield, particularly PA6 and mixed (PET and PA6) polymers increased methane output by 9 and 17% at the highest dose, respectively. Kinetic modelling further revealed that MFs consistently reduced methane production potential, apparent degradation and hydrolysis rate, whereas fragment trends were polymer-driven. Scanning electron microscopy (SEM) micrographs showed greater surface roughness in PA6, which enhanced microbial colonization compared to PET. Elevated reactive oxygen species (ROS) levels with MF addition, especially at the highest concentration, suggested higher oxidative stress and microbial inhibition. Microbial community analysis showed that exposure to MP fragments resulted in similar bacterial shifts across different polymer types, compared to the more diverse effects observed with MFs. Archaeal diversity was more affected by particle shape than polymer composition. All MP treatments favoured a shift toward hydrogenotrophic over aceticlastic methanogenesis. PET and mixed MF addition resulted in a substantial decline in the relative abundance of Actinobacteria (18-20%) from 42% in the control and other methanogenic taxa compared to their fragment counterparts. MF addition disrupted community structure, suppressed additive-degrading taxa, and increased acetogenic groups such as Synergistetes. Overall, the findings suggest that a comprehensive understanding of all influencing factors, including MP morphology, polymer type and concentrations, is important for effective AD system management.},
}

*Polyethylene Terephthalates/chemistry/metabolism
Methane/metabolism
Biodegradation, Environmental
Anaerobiosis
*Microplastics/metabolism/chemistry
*Caprolactam/analogs & derivatives/chemistry
Polymers
Bacteria/metabolism/drug effects

@article {pmid41834349,
year = {2026},
author = {Zhao, S and Fan, Z and Wu, Y and Liu, J and Tang, X and Qiu, Z and Zhu, M},
title = {Biocontrol potential of Talaromyces purpureogenus against the wheat powdery mildew fungus Blumeria graminis f. sp. tritici.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-11-25-2383-SC},
pmid = {41834349},
issn = {0191-2917},
abstract = {Talaromyces purpureogenus is known as a mycoparasite that is capable of suppressing plant pathogenic fungi. However, to date, there is little information about the impact of T. purpureogenus on powdery mildews. Based on morphological and molecular biological analyses, T. purpureogenus was identified and confirmed as a mycoparasite on the wheat powdery mildew fungus (Blumeria graminis f. sp. tritici, Bgt, recently clarified as B. graminis s. str.). T. purpureogenus effectively inhibited the colony formation and conidial distribution of Bgt. By inoculation with T. purpureogenus on Bgt, the abundance of Bgt notably decreased by 2.15-, 1.89-, 3.86-, and 25.90-fold at 2, 4, 6, and 8 days post inoculation (dpi), respectively, while the abundance of T. purpureogenus significantly increased by 4.16-, 12.11-, 11.07-, and 6.02-fold at the corresponding time points. In vitro, T. purpureogenus exudates significantly impaired the formation of Bgt appressoria. Therefore, T. purpureogenus acts as a potential biocontrol agent by suppressing the formation, distribution, and development of Bgt conidia, making it a viable alternative for controlling wheat powdery mildew. These results indicate that T. purpureogenus is an antagonistic parasite of wheat powdery mildew, providing new insights for the management of plant pathogenic fungi.},
}

@article {pmid41824189,
year = {2026},
author = {Azizian, A and Roomiani, L and Mehrgan, MS and Shekarabi, SPH},
title = {Advancing Fish Health: Systematic and Bibliometric Insights into Functional Feed Additives for Common Carp and Rainbow Trout.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41824189},
issn = {1867-1314},
}

@article {pmid41825203,
year = {2026},
author = {Fu, Q and Dai, H and Wang, J and Zheng, S and Zhou, Y and Liu, H and Xu, F and Cheng, C and Jiang, H and Qian, Y and Zhang, S and Liu, L and Zheng, H and Li, Y and Zhang, L and Chen, Y and Cheng, X and Yang, T},
title = {Multi-omics analysis of dynamic profiles in response to various nutrient loads provides novel insights into obesity.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {59},
number = {},
pages = {106607},
doi = {10.1016/j.clnu.2026.106607},
pmid = {41825203},
issn = {1532-1983},
abstract = {BACKGROUND& AIMS: Obesity is a global health issue driven by improper nutrient intake and metabolic dysregulation. The complexity of dietary components and the dynamic nature of postprandial metabolism limit our understanding of how different nutrient loads associated with obesity. This study aims to characterize the dynamic metabolic responses to nutrient intake using multi-omics approaches, assess the influence of dietary habits and gut microbiota, and evaluate the acute obesity-risk signature (AORS) associated with different macronutrients.

METHODS: We conducted a mixed meal tolerance test (MMTT) in 147 non-diabetic individuals (54 controls, 38 overweight, 55 obese). Blood samples were collected at multiple time points for untargeted metabolomics, lipidomics, proteomics, and hormone assays. Gut microbiota was profiled via metagenomic sequencing. A separate single macronutrient tolerance test (SMNTT) involving glucose, whey protein, butter, and olive oil was performed in 24 healthy volunteers to compare acute metabolic responses and derive an AORS based on postprandial multi-omics data.

RESULTS: Postprandial multi-omic analytes showed stronger associations with obesity indicators than fasting measures. Distinct temporal changes in metabolites, lipids, and proteins were observed across different BMI groups, with enrichment in pathways such as bile acid biosynthesis, triglyceride metabolism, and complement activation. Dietary habits and gut microbiota significantly influenced postprandial metabolic profiles, with specific metabolites and proteins mediating their effects on obesity. In SMNTT, glucose load exhibited the lowest AORS among isocaloric macronutrients (0.1082 ± 0.1917 %). Gut microbiota composition further modulated metabolic responses, with olive oil showing divergent AORS between Bacteroides- and Prevotella-dominated enterotypes (p = 0.043).

CONCLUSION: Postprandial multi-omics provides superior insights into obesity pathophysiology compared to fasting measurements. Our findings reveal that dietary habits and gut microbiota significantly influence postprandial metabolism and obesity risk, and demonstrate that different macronutrients confer distinct AORS values, which are further modified by an individual's gut microbiota composition. This underscores the potential for personalized nutritional strategies based on dynamic metabolic responses and microbial ecology.},
}

@article {pmid41824030,
year = {2026},
author = {Jankowska, K and Łukomska-Kowalczyk, M and Milanowski, R and Zakryś, B},
title = {Multiscale environmental analysis on autotrophic euglenid communities: insights from DNA metabarcoding.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02721-6},
pmid = {41824030},
issn = {1432-184X},
support = {OPUS 2016/23/B/NZ8/00919//Narodowe Centrum Nauki/ ; },
}

@article {pmid41823408,
year = {2026},
author = {Thorn, AV and Brinch, C and Aarestrup, FM and Munk, P},
title = {Urban sewage resistomes partially reflect clinical resistomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0003126},
doi = {10.1128/msystems.00031-26},
pmid = {41823408},
issn = {2379-5077},
abstract = {Antimicrobial resistance (AMR) poses a major global public health threat, and ongoing surveillance of antimicrobial resistance genes (ARGs) is critical to mitigate current and future risks. Sewage-based ARG surveillance is gaining traction, but insight into how it compares to surveillance by clinical bacterial isolates is limited, especially when it comes to ARG mutational variants. We compared ARGs identified in clinical bacterial isolates (n = 2,989) with those detected in sewage metagenomes (n = 468) across 33 countries. ARG variant detection data from clinical isolates and sewage metagenomes shared some regional patterns in detection, but many ARG variants were detected exclusively in either sewage metagenomes or clinical isolates. We found that across all samples, only 69% of ARG clusters detected in clinical isolates were also detected via read mapping in sewage. Some ARGs highly prevalent in clinical isolates were not detected in sewage. Among clinically widespread ARGs, prevalence varied across bacterial species and clinical isolate types depending on whether the ARGs were also detected in sewage. This could indicate that sewage surveillance is better suited for detection of clinically relevant ARGs prevalent in certain bacterial species and infection sites than others. Spearman correlation between ARG abundance in sewage and the proportion of clinical isolates from the same country with detection was 0.28 overall, with stronger correlations for certain ARGs. The results demonstrate that sewage ARG profiles correlate, to some extent, to the clinical AMR landscape, but do not capture the full spectrum of clinically relevant ARGs at currently realistic sequencing depths.IMPORTANCEAntimicrobial resistance (AMR) is a major public health threat. Surveillance of AMR is important and can be conducted via the detection of antimicrobial resistance genes (ARGs). Sewage can be used as a medium for surveillance as an alternative to analyzing individual bacterial isolates from health clinics. We compared detection in large global data collections of sewage metagenomes and clinical isolates. We found that while there were significant positive correlations between findings in sewage and clinical isolates, some widespread clinical ARGs were not detectable in sewage. This should be considered if establishing sewage surveillance systems.},
}

@article {pmid41823069,
year = {2026},
author = {Savini, F and Indio, V and Prandini, L and Tomasello, F and De Cesare, A and Oliveri, C and Seguino, A and Zanato, E and Serraino, A},
title = {Outside in: assessment of microbial composition of the crust of dry-aged beef and its relevance in relation to food business operator practices.},
journal = {Italian journal of food safety},
volume = {},
number = {},
pages = {},
doi = {10.4081/ijfs.2026.14620},
pmid = {41823069},
issn = {2239-7132},
abstract = {Dry aging of beef has recently been defined in Delegated Regulation 1141/2023, amending Regulation 853/2005. The delegated regulation lists specific measures to be applied when processing such a product. Specifically, a point is dedicated to the crust trimming that should be carried out in a hygienic manner, since the interventions performed at the end of the process might determine contamination of the edible parts. Nevertheless, despite the punctual application of good hygiene practices (GHP) and good manufacturing practices (GMP), a certain degree of contamination with pathogenic and spoilage microorganisms of the cut portions cannot be avoided, as demonstrated by some authors reporting contamination of the inner parts of dry-aged meat. In order to investigate the level of contamination occurring in field conditions during trimming and portioning, we performed two different trials: the sterility trial with the aim of evaluating the sterility of the inner parts of beef during aging and the contamination trial to assess the transfer of microbial populations from the outer to the inner part of the dry-aged beef. All tests were performed by means of cultural and non-cultural methods. Results of the sterility trial show that a very limited percentage of non-host DNA is present in the inner parts of the meat starting from the beginning of the test and that the detectable DNA increases slightly during the time of aging. Besides, the contamination trial results showed that the contamination of the trimmed meat is qualitatively and quantitatively related to the contamination of the crust. As a consequence, adherence to GHP and GMP during trimming and handling of dry-aged meat according to scientific literature is crucial to avoid/minimize cross-contamination since our data clearly demonstrate that processing practices are fully reflected in the final product quality.},
}

@article {pmid41821696,
year = {2025},
author = {Gao, X and Ju, Z and Wang, X and Wei, X and Gao, Y and Yang, C and Shi, Y and Huang, N and Liu, W and Jiang, Q and Wang, J and Zhang, Y and Xiao, Y and Huang, J},
title = {Dietary Supplement with Milk that Contains Different β-Caseins Influences Gut Microbiota and Serum Metabolites in Mice.},
journal = {Food science of animal resources},
volume = {45},
number = {5},
pages = {1491-1513},
pmid = {41821696},
issn = {2636-0780},
abstract = {The composition and metabolites of gut microbiota are shaped by dietary protein, consequently affecting host physiology, health, and diseases. This study aimed to elucidate the role of β-caseins in remodeling the composition of colon microbiota and the relationship between microbiota and serum metabolites. A total of 32 mice were randomly assigned to 4 groups and gavaged with A2, A1/A2, A1 milk, or saline for 5 wk. The supplementation of A1/A2 and A2 milk led to increased weight gain, while the A2 group exhibited an increase in goblet cell number and occludin expression in the colon. 16S ribosomal RNA gene analysis revealed differences in operational taxonomic units across groups, with Bacteroidetes and Firmicutes being predominant. Notably, A2 milk was associated with increased levels of Romboutsia and Anaerostipes compared to A1 milk. Untargeted metabolomics detected 537 and 371 metabolites in positive and negative ion modes, respectively. In the A2 group, 15 metabolites (e.g., vindoline, glycerol-3-phosphate, diphenylamine) were increased, while 13 metabolites (e.g., deoxyinosine, O-arachidonoyl ethanolamine) were decreased. Muribaculum, Ruminococcus, and Bifidobacterium genera showed significant associations with these metabolites. These findings suggest that β-casein supplementation in milk alters gut microbial ecology and metabolites, potentially impacting weight gain and colonic health positively.},
}

@article {pmid41821177,
year = {2026},
author = {Jordan, S and de Maayer, P and Smits, THM and Coutinho, TA},
title = {Enterobacter Species: Opportunistic Human and Plant Pathogens With Plant-Beneficial Traits.},
journal = {Molecular plant pathology},
volume = {27},
number = {3},
pages = {e70231},
doi = {10.1111/mpp.70231},
pmid = {41821177},
issn = {1364-3703},
support = {SNSF210305588900//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Enterobacter/pathogenicity/physiology/genetics ; Humans ; *Plant Diseases/microbiology ; *Plants/microbiology ; },
abstract = {UNLABELLED: Enterobacter species occur across diverse habitats and are best known for causing opportunistic and nosocomial infections in humans. The taxonomy of this genus is complex, with many species reassigned to and from this genus. Their interaction with plants is multifaceted. Strains of certain species cause opportunistic plant diseases.

HOST RANGE: Enterobacter species affect a wide range of plant hosts.

DISEASE SYMPTOMS: They cause a range of symptoms including leaf spots and blight, wilt and root diseases, decay and soft rot and cankers.

PLANT-BENEFICIAL TRAITS: Some Enterobacter species include strains that are plant growth promoters and occur either in the rhizosphere or as endophytes. Additionally, some strains can protect their hosts from pathogen attack and are regarded as promising biological control agents. Some strains also have potential for the bioremediation of various compounds.

GENOMIC FEATURES: Information on the pathogenicity and virulence mechanisms of plant-pathogenic Enterobacter species is limited. Comparison of diverse genomic features revealed no overall differences between plant-pathogenic and plant-beneficial strains.

CONCLUSION: While often reported as a plant pathogen, there is currently no evidence that Enterobacter is the primary cause of any of the reported diseases. In many cases, they would rather act opportunistically. This remains a significant concern, as a wide range of hosts are affected, and problems may intensify due to global warming. It is crucial to investigate these strains for plant pathogenicity and evaluate the risks to human health.},
}

*Enterobacter/pathogenicity/physiology/genetics
Humans
*Plant Diseases/microbiology
*Plants/microbiology

@article {pmid41821176,
year = {2026},
author = {Bıçakcı, G and Eren, Ö},
title = {Main effects of ascorbic acid levels and organic acid type on physicochemical properties, microbial populations, texture, and biogenic amine formation in sucuk.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70568},
pmid = {41821176},
issn = {1097-0010},
support = {BAP - 2013.09.01.676//Bolu Abant İzzet Baysal University/ ; },
abstract = {BACKGROUND: Sucuk is a traditional Turkish dry fermented sausage, the quality and safety of which depend on physicochemical, microbiological, and biochemical changes during fermentation and ripening. Organic acids, their salts, and antioxidants such as ascorbic acid (AA) are widely used in fermented meat products; however, information about their main effects on quality attributes and microbial ecology in sucuk is limited. This study evaluated the main effects of AA levels (0, 500, and 1000 mg kg[-1]) and selected organic acids or salts (acetic, lactic, citric, and sorbic acids, and potassium sorbate; 1000 mg kg[-1]) on sucuk quality and safety.

RESULTS: The pH, moisture, protein, fat content, lipolysis, proteolysis, thiobarbituric acid (TBA) values, and color parameters were not affected significantly by treatments (P > 0.05), whereas water activity was influenced significantly (P < 0.05). Increasing AA levels were associated with higher nitrate concentrations, whereas other anions, cations, and biogenic amine content did not differ among treatments. Higher AA levels, as well as sorbic acid and potassium sorbate treatments, increased shear force, shear work, hardness, and chewiness (P < 0.05). Lactic acid bacteria counts were affected significantly, whereas Micrococcus and Staphylococcus populations were not. Enterobacteriaceae and yeast and mold counts remained below the detection limit.

CONCLUSION: These results show that AA levels and organic acid or salt type influenced water activity, texture, and lactic acid bacteria populations selectively in sucuk without markedly affecting basic composition or biogenic amine content, providing practical guidance for improving microbial stability and technological quality in fermented sausages. © 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid41820526,
year = {2026},
author = {Chen, HL and Huang, JT and Guo, JJ and Wang, LS},
title = {Enteric nervous system in exercise physiology: a microbiota-neural interface.},
journal = {npj metabolic health and disease},
volume = {4},
number = {1},
pages = {},
pmid = {41820526},
issn = {2948-2828},
support = {2024MHBJ02//Bajian project of Minhang hospital/ ; },
abstract = {Exercise responses vary widely among individuals, yet the biological basis of this variability remains poorly understood. Microbiota-derived metabolites operate on timescales of hours to days, making them insufficient to explain rapid gastrointestinal and performance changes that emerge within minutes of exercise. We propose that the enteric nervous system (ENS) fills this regulatory gap by integrating mechanical, immune, and microbial signals in real time. We review evidence that the ENS modulates gut motility, barrier function, and microbial ecology during exercise, engages in bidirectional crosstalk with the microbiota, and relays gut-derived signals to muscle and brain via neural and humoral routes. We further introduce the concept of neuro-enteric phenotypes to account for inter-individual differences in exercise tolerance and adaptation.},
}

@article {pmid41819903,
year = {2026},
author = {Miftari, H and Nikolovska Nedelkoska, D and Rampanti, G and Harasym, J and Ferrocino, I and Ferati, I and Cardinali, F and Orkusz, A and Milanović, V and Franciosa, I and Garofalo, C and Aquilanti, L and Osimani, A},
title = {A taste of North Macedonia: Seasonal variation in the microbiota, physico-chemical traits, and morpho-textural profile of a traditional brined raw goat's milk cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {231},
number = {Pt 2},
pages = {118806},
doi = {10.1016/j.foodres.2026.118806},
pmid = {41819903},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Animals ; *Seasons ; Goats ; *Taste ; *Milk/microbiology/chemistry ; *Microbiota ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Salts/chemistry ; Food Handling/methods ; Bacteria/classification/genetics ; Hydrogen-Ion Concentration ; },
abstract = {This study provides a comprehensive characterization of a traditional Macedonian brined raw goat's milk cheese, focusing on how seasonal production (spring vs. autumn) shapes its physicochemical traits, morpho-textural properties, and microbial ecology. Cheese samples produced in autumn exhibited stronger acidification, higher titratable acidity, lower water activity, and higher NaCl content than spring cheeses, reflecting variability associated with artisanal, non-standardized processing. Texture profile analysis showed that cohesiveness and springiness were significantly affected by season, whereas hardness and adhesiveness remained comparable across batches. A combined culture-dependent and 16S rRNA gene-based metataxonomic approach revealed seasonally distinct microbiota. Viable microbial populations composed of mesophilic aerobes (up to 6.51 log cfu g[-1] at 60 days of ripening), presumptive mesophilic lactobacilli and lactococci (up to 6.51 and 7.18 log cfu g[-1] at 60 days of ripening, respectively), presumptive coagulase-negative and coagulase-positive staphylococci (up to 6.97 and 1.76 log cfu g[-1] at 60 days of ripening, respectively), and Enterobacteriaceae (up to 1.25 log cfu g[-1] at 60 days of ripening) were detected. Spring cheeses were characterized by higher relative abundances of Carnobacteriaceae, Enterococcus, Serratia, and Tetragenococcus halophilus, whereas autumn cheeses were dominated by Companilactobacillus and Lactococcus, alongside various Enterobacteriaceae. Beta-diversity analysis confirmed significant clustering of cheese microbiota by season. In total, 134 lactic acid bacteria isolates were obtained from the dairy environment, milk, brine, and cheese. These included Lactococcus lactis, Levilactobacillus brevis, multiple Enterococcus species, Pediococcus pentosaceus, Lacticaseibacillus paracasei, Marinilactibacillus psychrotolerans, and Companilactobacillus alimentarius. Many isolates showed strong proteolytic activity, several produced exopolysaccharides, and a subset exhibited lipolytic capacity, underscoring their technological potential. Screening for the histidine decarboxylase gene hdcA revealed that only the C. alimentarius isolate was positive, excluding this strain from consideration as an adjunct culture, whereas all other isolates were hdcA-negative and therefore suitable candidates from a histamine-safety perspective. Overall, this integrated analysis highlights the rich microbial diversity and seasonal variability of this artisanal cheese and supports the selection of safe autochthonous lactic acid bacteria for future product valorization.},
}

*Cheese/microbiology/analysis
Animals
*Seasons
Goats
*Taste
*Milk/microbiology/chemistry
*Microbiota
*Food Microbiology
RNA, Ribosomal, 16S/genetics
Salts/chemistry
Food Handling/methods
Bacteria/classification/genetics
Hydrogen-Ion Concentration

@article {pmid41818334,
year = {2026},
author = {Tong, C and Yu, R and Hu, A and Dong, R and Yang, W},
title = {Manure source distance and soil depth: a natural screening system for nutrient-solubilizing bacteria.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag072},
pmid = {41818334},
issn = {1365-2672},
abstract = {AIMS: To develop and validate an ecology-driven strategy that leverages natural manure-soil depth gradients as a screening system for the targeted isolation of nutrient-solubilizing bacteria (NSB) with high biofertilizer potential.

METHODS: A full-factorial sampling design was implemented across gradients of distance-from-manure (5 points, 8-m intervals) and soil depth (0-20, 20-40, 40-60 cm) in a coconut plantation. Culturable bacteria were isolated using a culture-dependent approach on a nutrient-rich medium, identified via 16S rRNA gene sequencing, and functionally screened in vitro for nitrogen fixation, phosphate solubilization (PS), and potassium solubilization (KS) capabilities.

RESULTS: Manure input and soil depth interacted to form a heterogeneous soil nutrient landscape, with available phosphorus (AP) identified as the most influential environmental factor shaping the bacterial community. Phosphate-solubilizing bacteria (PSB) were significantly enriched in low-P habitats, verifying the niche-based selection of functional bacteria. This gradient-based screening strategy enabled the targeted recovery of multifunctional NSB strains (e.g., Klebsiella and Enterobacter) with concurrent nitrogen fixation, phosphate and potassium solubilization capacities, which were isolated from specific microhabitats including deep, nutrient-depleted soil layers.

CONCLUSIONS AND IMPLICATIONS: This study demonstrates that intersecting manure and soil depth gradients form a powerful, predictable natural screening system for the targeted isolation of beneficial bacteria. This ecology-driven strategy effectively links microbial ecology to bioprospecting. It provides a curated library of isolates with defined ecological origins and a predictive framework for developing customized biofertilizers, thereby enhancing microbial resource mining efficiency and contributing to sustainable agriculture.},
}

@article {pmid41816689,
year = {2026},
author = {Jian, Z and Qian, Y and He, S and Zhao, R and Li, K and Cha, J and Ning, Z and Ye, Y and Bao, Z and Wang, K and Ge, C and Jia, J and Dou, T and Hu, Y and He, X and Zi, X},
title = {The gut resistome in poultry production: microbial ecology, antibiotic use, and sustainable control approaches.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768747},
pmid = {41816689},
issn = {1664-302X},
abstract = {Antibiotics remain central to modern poultry production, but their long-term and sometimes poorly managed use has markedly altered gut microbial ecology, effectively transforming the intestine into a substantial reservoir of antibiotic resistance genes (ARGs). In poultry, the composition of ARGs reflects not only resistant bacterial taxa but also the activity of mobile genetic elements, shifts in gut metabolic conditions, and features of the surrounding production system. This review synthesizes current understanding of both the structural and functional features of the poultry resistome, with particular attention to key bacterial hosts and the mobile genetic elements they carry. We further evaluate how different antibiotic-use patterns and additional co-selective pressures alter microbial communities and contribute to the persistence of ARGs. We also delineate the major transmission pathways that link breeder flocks, hatcheries, production facilities, and manure management, and interpret these connections within a One Health perspective. Particular emphasis is placed on microbial and nutritional interventions that influence gut microbial interactions, epithelial barrier integrity, and metabolic signaling. Drawing on these findings, we propose a resistome-microbiome-metabolome axis that links microbial taxa, resistance elements, and key metabolic signals, offering a conceptual framework for developing more targeted antimicrobial resistance mitigation strategies in poultry systems.},
}

@article {pmid41815892,
year = {2025},
author = {Avouris, DM and Maciel, F and Sharp, SL and Craig, SE and Dekker, AG and Di Vittorio, CA and Gardner, JR and Goldsmith, E and Gossn, JI and Greb, SR and Grunert, BK and Gurlin, D and Jampani, M and Khan, RM and Lowin, B and McKinna, L and Mouw, CB and Ogashawara, I and Calle, SR and Salls, W and Sánchez-Cabeza, JA and Schaeffer, B and Seegers, BN and Silander, J and Smail, EA and Wang, M and Werdell, J},
title = {Advancements in Satellite Observations of Inland and Coastal Waters: Building Towards a Global Validation Network.},
journal = {Remote sensing},
volume = {17},
number = {24},
pages = {4008},
pmid = {41815892},
issn = {2072-4292},
support = {EPA999999/ImEPA/Intramural EPA/United States ; },
abstract = {The use of satellite-based remote sensing imagery for water quality monitoring of inland and coastal waters has become widespread over the last few decades, with the expansion of, and investment in, operational Earth-observing missions. Satellite-based sensors are uniquely suited to provide synoptic, system-wide water quality parameter estimates that supplement traditional field-based sampling methods. The remote sensing of water quality parameter estimates is particularly valuable in systems with high temporal and spatial variability, as well as in areas that are difficult to access, or where agencies lack funding for routine monitoring. However, optically complex inland and coastal waters pose additional challenges for developing robust remote sensing retrieval models for optical properties and water quality parameters. One of the biggest challenges is collecting high quality field measurements that are used to calibrate and validate the retrieval algorithms. Here, we present the current status of satellite missions, field methods that include instruments used and commonly measured parameters, and repositories of historical field data that are relevant to inland and coastal water studies. We then present data requirements for model validation and highlight gaps in validation coverage. Finally, we provide considerations for future field campaigns to improve coordination with remote sensing data collection and ensure that field data is well suited for use in model or algorithm development.},
}

@article {pmid41814632,
year = {2026},
author = {Ferreti, JD and Ribeiro, B and Bonetti, JA and Camargo, LEA and Creste, S and Kuramae, EE and Monteiro-Vitorello, CB},
title = {Soil and Genotype Shape the Sugarcane Phytobiome for Enhanced Environmental Adaptation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70314},
doi = {10.1111/1758-2229.70314},
pmid = {41814632},
issn = {1758-2229},
support = {2022/03962-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 405314/2021-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 305961/2017-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Saccharum/microbiology/genetics/growth & development ; *Soil Microbiology ; Genotype ; *Soil/chemistry ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *Adaptation, Physiological ; Transcriptome ; },
abstract = {Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP-5503 and IACSP-6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48-h sprouted buds grown for 10 months, were analysed. Results showed that IACSP-5503 (adapted to low-fertility soils) and IACSP-6007 (less adapted) recruited endophytic microbiota in a soil-genotype-dependent manner. In sandy loam, IACSP-5503 promoted diverse plant growth-promoting bacteria (PGPB) (including Burkholderia, Leifsonia and Mycobacterium), associated with nitrogen fixation, hormone production and stress tolerance, while IACSP-6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP-6007 recruited more PGPBs (such as Pseudomonas, Bacillus and Klebsiella) linked to nutrient acquisition and defence responses. Both genotypes exhibited enhanced expression of defence- and antioxidant-related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil-dependent, genotype-specific microbial recruitment strategies, particularly in IACSP-5503, reflecting adaptive responses to nutrient-poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.},
}

*Saccharum/microbiology/genetics/growth & development
*Soil Microbiology
Genotype
*Soil/chemistry
*Bacteria/genetics/classification/isolation & purification
*Microbiota
*Adaptation, Physiological
Transcriptome

@article {pmid41821950,
year = {2025},
author = {De León, ME and Fox, EGP and Dunaj, S and Jenner, RA and Keiser, CN and Macrander, J and Nixon, SA and Nobile, CJ and Petras, D and Rodriguez-Roman, E and Saviola, AJ and Trim, SA and Varona, NS and Yeager, J and Ul-Hasan, S and Herzig, V and Colston, TJ},
title = {A review of the venom microbiome and its utility in ecology and evolution including future directions for emerging research.},
journal = {Symbiosis (Philadelphia, Pa.)},
volume = {95},
number = {1},
pages = {3-27},
pmid = {41821950},
issn = {0334-5114},
abstract = {Microbes play vital roles in ecological systems, yet their presence and functions within venom environments of venomous organisms remain understudied. Despite the prevalent belief in the sterility of venoms, recent findings reveal diverse microbial communities within venom systems. This review aims to explore the relationships between venoms and microbes, highlighting their potential roles in evolutionary processes, ecological interactions, and therapeutic advancements. Venoms, composed of toxins utilized in hunting or defense, represent a rich source of natural products with applications in drug discovery and therapy, exemplified by FDA-approved venom toxin-derived drugs. Understanding microbial resistance mechanisms against antimicrobial peptides can illuminate coevolutionary processes and guide therapeutic development. Integrating hologenomic evolution and microbial ecology frameworks will facilitate comprehensive research on venom-microbiome interactions, and reveal the evolutionary drivers of venom diversification. Investigating and investing in these relationships promises advancements in understanding evolution, ecology, and biotechnology, with implications for human health and ecological conservation. This review synthesizes existing knowledge, identifies many gaps in literature, and investigates critical unanswered questions in the field of venom microbiology, encouraging ongoing and future collaborative research.},
}

@article {pmid41813906,
year = {2026},
author = {Vass, M and Abramova, A and Bengtsson-Palme, J},
title = {Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09857-8},
pmid = {41813906},
issn = {2399-3642},
support = {KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2024-05922//Vetenskapsrådet (Swedish Research Council)/ ; },
abstract = {Aquatic ecosystems are major reservoirs of antibiotic resistance genes (ARGs) and hubs for microbial interactions that can facilitate their spread through horizontal gene transfer (HGT). While mobile genetic elements (MGEs), including plasmids and viruses, are recognized as important drivers of ARG mobility, the extent to which water column stratification constrains their vertical dissemination remains unresolved. Here, we analysed depth-resolved metagenomic data from stratified freshwater and marine systems to assess the role of HGT in ARG spread. We found that ARG diversity is consistently lower in marine than freshwater environments and that only a small fraction of ARGs is mobilized by plasmids and viruses. Importantly, we detected no evidence for recent HGT-mediated dissemination of ARGs across depth layers, despite genetic compatibility among co-occurring bacteria. Instead, ARGs appear largely confined to lineage-specific inheritance and within-layer persistence. These findings suggest that stratification acts as a barrier, limiting vertical ARG transfer while promoting within-layer accumulation. Given projections of intensified and prolonged stratification under climate change, our results imply reduced vertical connectivity of ARGs in aquatic environments, with potential consequences of further mitigation in its dynamics by water stratification.},
}

@article {pmid41812564,
year = {2026},
author = {Defoirdt, T},
title = {Interfering with the response of bacterial pathogens to host substances: An unexplored strategy to control bacterial diseases in aquaculture.},
journal = {Microbiological research},
volume = {308},
number = {},
pages = {128492},
doi = {10.1016/j.micres.2026.128492},
pmid = {41812564},
issn = {1618-0623},
abstract = {Bacterial infections represent a significant challenge in aquaculture, and the widespread use of antibiotics has accelerated the development of resistance, diminishing their efficacy and posing serious global public health concerns. Antivirulence therapy, disarming pathogens rather than killing them or inhibiting their growth, offers a promising alternative approach as it exerts reduced selective pressure on pathogens, thereby limiting the spread of resistance. Targeting the response of pathogens to host substances, molecules typically produced by host organisms, is an unexplored strategy for the development of novel disease control agents for aquaculture. Bacterial aquaculture pathogens have been shown to respond to host substances such as catecholamines, mucin, and bile acids and salts, leading to increased production of virulence factors (molecules or cell structures that enable pathogens to cause disease), and increased virulence to aquatic animals. This paper provides an overview of the impact of these host substances on the virulence of bacterial aquaculture pathogens and of currently known methods to interfere with this in order to control disease.},
}

@article {pmid41811973,
year = {2026},
author = {Martin, AN and Stuligross, C and Williams, NM and Noroian, HM and Vannette, RL},
title = {Floral microbes provisioned by Osmia lignaria establish in larval food stores, but do not affect bee development or survival.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag025},
pmid = {41811973},
issn = {1574-6941},
abstract = {Microbial dispersal and subsequent establishment among linked habitats can be used to examine drivers of community assembly and function. Flowers host microbial communities that can be acquired and vectored by bees to new flowers, establish within the adult bee gut, and enter food stores (e.g. pollen provisions) of developing larvae. Yet, whether microbes vectored by insects or applied for biocontrol can establish across these habitats and if they affect bee fitness remain unknown. Here, we applied microbes to flowers visited by blue orchard bees (Osmia lignaria) and compared microbial communities in flowers, adult bee guts, and pollen provisions before and after inoculation to determine microbial establishment, environmental filtering, and overlap across habitat types. We also inoculated provisions with microbes to test their effects on larval survival, development, and weight. Experimentally inoculated microbes were detected in all habitats, demonstrating that flowers are a source of microbial acquisition for adult and larval bees; however, the tested larval health metrics were largely unaffected by microbe supplementation.},
}

@article {pmid41811506,
year = {2026},
author = {Cervera, L and Álvarez-Torres, D and Barreto-Bailet, M and Béjar, J and Cuesta, A and Martín, MV and Jerez, S and Chaves-Pozo, E},
title = {Diagnosis of Betanodavirus Infection in the Gonad of Greater Amberjack Broodstocks Shows a Sex-Biased Infection and Immune Responses.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02733-2},
pmid = {41811506},
issn = {1432-184X},
}

@article {pmid41810611,
year = {2026},
author = {Rigali, S},
title = {When, where, and why specialised metabolites are produced: inferring function from expression control.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250024},
pmid = {41810611},
issn = {1744-1358},
support = {NA//Fonds De La Recherche Scientifique - FNRS (FNRS)/ ; },
abstract = {Although some microbial compounds have been repurposed for human use, microorganisms did not evolve their specialised metabolites with us in mind. Many natural products likely possess hidden activities, while others may be exploited in ways that ignore their most biologically relevant roles. Uncovering the true function of these compounds is essential not only for understanding microbial interactions in native environments but also for unlocking their most appropriate use. To facilitate prioritisation in discovering new natural products, computational tools have been developed to predict the function of compounds hidden in cryptic biosynthetic gene clusters. Yet beyond in silico predictions, understanding when, where, and why metabolites are produced is critical for both fundamental biology and targeted discovery. After all, what nature chooses to activate at a specific time or condition tells us what it is really for. Based on the principle 'function follows regulation', it is no coincidence that expression of metal chelators, phytotoxins, pigments, and antibiotics is controlled by metal availability, plant byproducts, radiations, and competitor sensing, respectively. Likewise, metabolite localisation and production timing also provide clues to function such as intracellular antiproliferative agents coordinating programmed cell death or pigments protecting against oxidative stress. These controlled expression patterns suggest a strategic approach for natural product discovery: focusing on culture conditions that mimic the environmental or developmental contexts under which metabolites are needed for the producer. Integrating expression control information offers a predictive framework to guide experimental design, increases the likelihood of identifying compounds with meaningful ecological roles, and anticipates their applications.},
}

@article {pmid41806463,
year = {2026},
author = {Atasever, Ü},
title = {Bile acid-microbiota interactions in multiple sclerosis: From experimental models to early clinical evidence.},
journal = {Journal of neuroimmunology},
volume = {415},
number = {},
pages = {578898},
doi = {10.1016/j.jneuroim.2026.578898},
pmid = {41806463},
issn = {1872-8421},
abstract = {This article examines the bidirectional relationship between bile acid metabolism and the intestinal microbiota and explores how disruptions in this interaction may contribute to the pathophysiology of multiple sclerosis. Bile acids are presented not merely as digestive end-products but as bioactive signaling molecules capable of regulating immune responses, maintaining epithelial and neural homeostasis, and influencing neuroinflammatory processes. Experimental work demonstrates that alterations in microbial composition affect bile acid diversity and circulation, while bile acids themselves shape gut microbial ecology through antimicrobial and signaling mechanisms. In preclinical models, specific bile acid species modulate the balance between pro-inflammatory and regulatory immune cells, suppress harmful activation states in astrocytes and microglia, and reduce neuroinflammation. Human studies show consistent disturbances in circulating bile acid profiles in individuals with multiple sclerosis, with some patterns associated with increased disability progression and markers of neurodegeneration. Early clinical interventions also indicate that therapeutic modulation of bile acid pathways is feasible and biologically active, although clinical efficacy remains to be established. Overall, the article highlights bile acid-microbiota interactions as a unifying conceptual framework linking environmental influences, metabolic status, immune dysregulation, and central nervous system injury. By integrating evidence from experimental models and emerging clinical observations, the authors propose that this metabolic and microbial axis may serve both as a source of novel biomarkers and as a target for future disease-modifying therapies.},
}

@article {pmid41757095,
year = {2026},
author = {Wang, F and Holmes, AJ and Browne, GV and He, X and Bockmann, MR and Davis, KM and Hughes, TE and Adler, CJ},
title = {Ecological and evolutionary dynamics of the oral microbiome across childhood.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41757095},
issn = {2692-8205},
abstract = {Childhood represents a critical period for oral microbiome development, yet evolutionary trajectories and the relative roles of host and environment remain unclear. Using a large longitudinal metagenomic dataset of 920 samples from a twin cohort spanning the first decade of life, we characterised microbial shifts and population dynamics of key bacterial groups. Microbiome diversity was initially reduced and highly heterogeneous and became increasingly complex and convergent with age. Microbial community state was associated with developmental age, environment and in late childhood was surprisingly strongly associated with host genotype. Strain-level analyses revealed species-specific temporal patterns of genetic variation particularly within Streptococcus, reflecting adaptive responses to host and environmental pressures. Fusobacterium exhibited consistently high replication rates, indicating sustained growth dynamics. Phylogenetic reconstruction further revealed host and niche specific genomic diversification of Saccharibacteria lineages. These findings establish childhood as a decisive period of oral microbial evolution and highlight the role of host-microbiome and epithelial interactions in shaping community structure, providing guidance for oral management strategies that promote lifelong oral health.},
}

@article {pmid41665259,
year = {2025},
author = {Gaisin, VA and Hadjicharalambous, C and Mujakić, I and Villena-Alemany, C and Li, J and Koblížek, M and Pilhofer, M},
title = {Thermophilic bacteria employ a contractile injection system in hot spring microbial mats.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag021},
pmid = {41665259},
issn = {1751-7370},
support = {CZ.02.01.01/00/22_008/0004624//OP JAK project Photomachines/ ; CoG 101000232/ERC_/European Research Council/International ; },
mesh = {*Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; *Chloroflexi/genetics/physiology/classification/metabolism ; Cryoelectron Microscopy ; Phylogeny ; Metagenomics ; *Bacteria/genetics ; Computational Biology ; Proteomics ; },
abstract = {Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or interactions with other organisms. Multiple novel CISs have been characterised in laboratory bacterial cultures recently; however, studying CISs in the context of the native microbial community remains challenging. Here, we present an approach to characterise a bioinformatically predicted CIS by directly analysing bacterial cells from their natural environment. Using cryo-focused ion beam milling and cryo-electron tomography (cryoET) imaging, guided by 16S rRNA gene amplicon sequencing, we discovered that thermophilic Chloroflexota bacteria produce intracellular CIS particles in a natural hot spring microbial mat. We then found a niche-specific production of CIS in the structured microbial community using an approach combining metagenomics, proteomics, and immunogold staining. Bioinformatic analysis and imaging revealed CISs in other extremophilic Chloroflexota and Deinococcota. This Chloroflexota/Deinococcota CIS lineage shows phylogenetic and structural similarity to previously described cytoplasmic CIS from Streptomyces and probably shares the same cytoplasmic mode of action. Our integrated environmental cryoET approach is suitable for discovering and characterising novel macromolecular complexes in environmental samples.},
}

*Hot Springs/microbiology
RNA, Ribosomal, 16S/genetics
*Chloroflexi/genetics/physiology/classification/metabolism
Cryoelectron Microscopy
Phylogeny
Metagenomics
*Bacteria/genetics
Computational Biology
Proteomics

@article {pmid41806051,
year = {2026},
author = {Tomachewski, D and Souza, RF and Lammel, DR and Schiebelbein, LM and Galvão, CW and Ribeiro, MF and Karas, LP and Galvão, F and Baura, VA and Rillig, MC and Etto, RM},
title = {Tree diversity shapes soil bacterial community structure under low abiotic heterogeneity in the Atlantic forest.},
journal = {Archives of microbiology},
volume = {208},
number = {5},
pages = {},
pmid = {41806051},
issn = {1432-072X},
}

@article {pmid41806036,
year = {2026},
author = {You, JH and Jeong, HJ and Park, SA and Kwon, H and Eom, SH and Kwon, M and Kang, NS},
title = {Feeding and growth of the new mixotrophic dinoflagellate Gymnodinium sp. GSTY2405 and the prey spectrum extension of its sister species Gymnodinium smaydae.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02739-w},
pmid = {41806036},
issn = {1432-184X},
support = {RS-2024-00452214//National Research Foundation of Korea/ ; RS-2021-NR058847//National Research Foundation of Korea/ ; 2026M00200//National Marine Biodiversity Institute of Korea/ ; },
}

@article {pmid41806019,
year = {2026},
author = {Su, ZZ and Hou, Y and Lin, JJ and Duan, YF and Obeten, AU and Dong, S and Huang, Q and Huang, H and Pan, Z},
title = {Extracellular vesicles from biofilm and planktonic Pseudomonas aeruginosa: proteomic profiles, iron chelation and functional Implications.},
journal = {Archives of microbiology},
volume = {208},
number = {5},
pages = {},
pmid = {41806019},
issn = {1432-072X},
}

@article {pmid41805951,
year = {2026},
author = {López-Puentes, D and Ojeda-Pérez, ZZ and Arias-Moreno, DM},
title = {Metagenomic Insights into the Microbial Composition and Functional Potential of Cocoa (Theobroma Cacao L.) During Fermentation and Drying in Colombia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02704-7},
pmid = {41805951},
issn = {1432-184X},
}

@article {pmid41805181,
year = {2026},
author = {Wallnisch, JL and Wünschmann, T and Baborski, A and Rau, M and Refisch, A and Opel, N and Allen, RJ and Busch, A},
title = {Draft genome of an Escherichia coli gut isolate from a sertraline-treated patient suggests potential antibiotic resistance induction.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0108725},
doi = {10.1128/mra.01087-25},
pmid = {41805181},
issn = {2576-098X},
abstract = {The draft genome of Escherichia coli ADAR08_002, from feces of a patient with major depressive disorder (MDD) treated long-term with sertraline, is 5,247,898 bp (GC 50.65%) in 273 contigs (N50 153,410 bp). It harbors mobile elements and antibiotic resistance, persistence, and metabolic adaptation genes, serving as a resource to study antidepressant impacts.},
}

@article {pmid41805117,
year = {2026},
author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE},
title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15254},
pmid = {41805117},
issn = {1520-5118},
abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.},
}

@article {pmid41803472,
year = {2026},
author = {da Silva Figueiredo, MI and Mello, IS and de Guimarães Bueno, L and Mendes, RRW and Dos Santos Almeida, JM and Eriksson, A and da Silva, GF and Soares, MA},
title = {Lactic acid bacteria isolated from mammalian feces exhibit distinct diversity and probiotic traits.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41803472},
issn = {1573-0972},
}

@article {pmid41803467,
year = {2026},
author = {Struk, M and Sakarika, M and Estévez, Á and Ganigué, R and Rabaey, K},
title = {Growth and protein content of Cupriavidus necator on organic acids derived from fermented grey starch.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {41803467},
issn = {1432-0614},
support = {No. 101081776//European Union's Horizon Europe research and innovation programme/ ; BOF.PDO.2025.0007.01//Ghent University/ ; BOF.BAF.2024.0502.01//Special Research Fund of Ghent University/ ; },
abstract = {Grey starch (GS) is a byproduct of potato processing and is conventionally valorised as low-grade animal feed or for biogas generation. In this manuscript, we systematically investigate the mixed culture fermentation of GS to organic acids and their subsequent aerobic upgrading to microbial protein via Cupriavidus necator. We focused on protein content, growth kinetics, biomass yield on individual, and mixed organic acids (C1-C6), using both synthetic media and real fermented effluents. High-throughput cultivation in microtiter plates was employed to evaluate performance across both straight-chain forms and isoforms of the acids. C. necator demonstrated growth on all tested individual substrates, although with distinct individual behaviour. Lactate, butyrate, and hexanoate supported the highest biomass yields, reaching up to 0.24 gCDW/gCOD (grammes of cell dry weight per grammes of COD fed). Lactate enabled the highest specific growth rate (0.6 h[-1]) with 29 ± 4% of protein. The maximum protein content (70 ± 11%) was observed on acetate at an initial concentration of 2 g/L. Depending on the acid, higher initial concentrations (2 and 4 g/L) led to increased cell dry weight but reduced growth rates or inhibition in some cases. Real fermented GS, primarily composed of lactate and butyrate, proved to be a viable substrate for microbial protein production. Undiluted fermented GS yielded the highest protein content (70 ± 9%), while a 1/4 dilution (2.6 gCOD/L) enabled the fastest growth (0.84 h[-1]) compared to all tested fermented GS and acid concentrations. These findings highlight the potential of GS-derived organic acids as feedstock for microbial protein production for feed and food. KEY POINTS: C. necator grows on all tested individual organic acids (C1-C6). Protein production varies by acid type and initial concentration. Grey starch was converted to organic acids for microbial protein production.},
}

@article {pmid41802809,
year = {2026},
author = {Jin, N and Sul, WJ and Do, HR and Kim, HS},
title = {ITS1-based profiling of the skin mycobiome in truncal acne reveals altered baseline ecology and heterogeneous doxycycline-associated patterns.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {2},
pages = {e2512013},
doi = {10.71150/jm.2512013},
pmid = {41802809},
issn = {1976-3794},
support = {2023R1A2C1007759//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; RS-2023-KH-136575//Ministry of Health and Welfare/ ; RS-2025-02217860//Ministry of Health and Welfare/ ; //Incheon St. Mary's Hospital/ ; //Catholic University of Korea/ ; },
mesh = {Humans ; *Doxycycline/therapeutic use/pharmacology ; *Acne Vulgaris/microbiology/drug therapy ; *Skin/microbiology ; *Mycobiome/drug effects/genetics ; Female ; Male ; Malassezia/genetics/isolation & purification/classification/drug effects ; Adult ; DNA, Ribosomal Spacer/genetics ; Young Adult ; *Fungi/genetics/classification/isolation & purification/drug effects ; Anti-Bacterial Agents/therapeutic use ; DNA, Fungal/genetics ; },
abstract = {Truncal acne represents a biologically distinct manifestation of acne vulgaris, yet its fungal ecology remains incompletely characterized. Previous work using internal transcribed spacer 2 (ITS2) sequencing suggested that truncal acne is associated with altered fungal richness and Malassezia species composition; however, fungal marker choice may influence ecological inference, particularly in sebaceous skin dominated by Malassezia. In this study, we characterized the truncal skin mycobiome of patients with truncal acne and healthy controls using internal transcribed spacer 1 (ITS1) amplicon sequencing. Skin swabs were collected from the upper back, and fungal communities were analyzed using QIIME 2 with taxonomic assignment against the UNITE v10.0 database. Baseline acne-control differences and doxycycline-associated patterns were evaluated using alpha- and beta-diversity metrics and differential abundance analyses. Doxycycline-associated patterns were assessed using paired, within-patient pre- and post-exposure comparisons. ITS1 profiling demonstrated that truncal acne was associated with altered baseline fungal ecology compared with controls, characterized by reduced alpha diversity and ASV-level differences within Malassezia-dominated communities. Beta-diversity analyses showed substantial overlap between acne and control samples, indicating limited global separation. Following doxycycline exposure, fungal communities remained Malassezia-dominant and did not demonstrate uniform convergence toward control profiles; instead, species- and ASV-level differences were heterogeneous across individuals and exposure durations. Together with prior ITS2-based findings, these results underscore the importance of marker-dependent perspectives when interpreting fungal ecology in sebaceous skin.},
}

Humans
*Doxycycline/therapeutic use/pharmacology
*Acne Vulgaris/microbiology/drug therapy
*Skin/microbiology
*Mycobiome/drug effects/genetics
Female
Male
Malassezia/genetics/isolation & purification/classification/drug effects
Adult
DNA, Ribosomal Spacer/genetics
Young Adult
*Fungi/genetics/classification/isolation & purification/drug effects
Anti-Bacterial Agents/therapeutic use
DNA, Fungal/genetics

@article {pmid41802390,
year = {2026},
author = {Mondal, A and Parvez, SS and Bera, D and Alam, M and Banik, A},
title = {Trichoderma in multitrophic plant-microbe interactions: a pan-genome guided roadmap for resilient physiology and sustainable bio-economy.},
journal = {Plant physiology and biochemistry : PPB},
volume = {232},
number = {},
pages = {111193},
doi = {10.1016/j.plaphy.2026.111193},
pmid = {41802390},
issn = {1873-2690},
abstract = {By 2050, the global population is projected to reach 9 billion, necessitating innovative approaches beyond traditional agricultural methods to ensure adequate food security. Several biological control agents have been used throughout the world to control plant diseases by re-programming natural prey-predator interactions. Trichoderma's biocontrol capabilities and plant growth-promoting effects have been extensively studied and documented, paving the way for its widespread adoption in agricultural practices. Here we performed a comprehensive pan-genome analysis of 25 industrially and agriculturally important Trichoderma strains, revealing an open pan-genome indicative of continuous genetic innovation. A combined total of 4960 core genes were shared between both industrial and biocontrol strains, which encode for fundamental functions with accessory and unique genes being enriched in adaptive functions. Industrial strains like T. reesei QM6a with 322 unique genes had enrichment of features for secretion of cellulase and lignocellulose degradation, validating their commercial dominance in industries producing enzymes and biofuels, while biocontrol-associated strains like T. harzianum CBS226.95 and T. virens Gv29-8 showed expanded accessory gene repertoires enriched in defense-related functions and secondary metabolism. Comparative biosynthetic gene cluster analysis across 25 genomes further demonstrated pronounced strain-level variation. Core-genome phylogeny revealed conserved ancestral relationships, whereas pan-genome phylogeny highlighted accessory gene-driven divergence among closely related strains. Remarkably, many strains had dual promise, being both industrial producers of enzymes and agriculturally desirable, highlighting their interdisciplinary applications. These results demonstrate the genomic malleability of Trichoderma and the adaptability of its evolution, facilitating agriculture and biotechnology, and provide a template for strain selection with precision and rational bioformulation design for promoting sustainable agriculture, environmental robustness, and green industry.},
}

@article {pmid41800395,
year = {2026},
author = {Li, J and Xiao, D and Gigena, ML and Wang, M and Li, P and Fu, R and Toure, MAM and Li, F},
title = {Dataset of microbial community evolution in synthetic black-clay-based soils during ecological reconstruction.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112593},
pmid = {41800395},
issn = {2352-3409},
abstract = {Ecological reconstruction of mine dump sites in cold-region environments is frequently constrained by limited availability of natural topsoil and harsh climatic conditions that hinder soil development and biological succession. In such settings, artificial soils derived from mineral substrates are increasingly used as alternatives to surface soil; however, their biological maturation relies strongly on microbial community establishment and evolution. This data article presents a microbial diversity dataset derived from black-clay-based artificial soils applied in a mine dump restoration system located in a cold and arid desert grassland. Soil samples were collected from restoration zones subjected to different microbial inoculation regimes, including full-process application of an ecological restoration bacteria consortium, single application, and untreated controls. To capture spatial and vertical heterogeneity, samples were obtained independently from upper aerobic layers and lower anaerobic layers across multiple sampling batches corresponding to different restoration stages. Microbial community composition was characterized using high-throughput sequencing of the bacterial 16S rRNA gene, generating raw sequence reads and a suite of processed datasets. These include taxonomic abundance tables, alpha- and beta-diversity metrics, distance matrices, hierarchical clustering outputs, shared operational taxonomic unit profiles, ecological niche breadth indices, beta-deviation measurements, and core community identification based on prevalence criteria. Network topology metrics derived from Zi-Pi analysis are also provided to support structural assessments of microbial associations. In addition, functional profiles were inferred from 16S rRNA gene data using PICRUSt2, producing pathway- and category-level functional prediction tables. All data files are organized with standardized metadata and fully documented analytical parameters to facilitate independent reuse. This dataset supports reanalysis of microbial community assembly, stratification, and temporal variation in artificial soil systems and can be applied in comparative studies, methodological benchmarking, and synthesis efforts related to mine-site restoration, artificial soil development, and microbial ecology in cold-region environments.},
}

@article {pmid41799378,
year = {2026},
author = {Kaur, M and Babu, R and Baweja, S and Gupta, R and Singh, SP and Pamecha, V and Bihari, C},
title = {Human Leukocyte Antigen Alleles and Oral Microbiome Association With Antibody-mediated Rejection in Living-donor Liver Transplant Patients.},
journal = {Journal of clinical and experimental hepatology},
volume = {16},
number = {3},
pages = {103494},
pmid = {41799378},
issn = {0973-6883},
abstract = {BACKGROUND/AIMS: Antibody-mediated rejection (ABMR) is an important cause of graft dysfunction after liver transplantation, yet the combined influence of human leukocyte antigen (HLA) immunogenetics and the oral microbiome on ABMR risk is not well defined.

METHODS: In this prospective cohort of 180 living donor-recipient pairs, pre-transplant 16S ribosomal ribonucleic acid sequences and high-resolution HLA genotyping were done. The human leukocyte antigen epitope mismatch algorithm quantified amino acid and solvent-accessible mismatches. Oral microbiome profiles were generated using the Divisive Amplicon Denoising Algorithm (DADA2) and quantitative insights into microbial ecology version 2 (QIIME2). Associations between HLA alleles and microbial taxa were assessed using generalized linear models and linear discriminant analysis effect size (LEfSe). ABMR was diagnosed as per Banff criteria over one year.

RESULTS: ABMR was diagnosed in 15 patients. These patients had significantly higher mismatch burdens at HLA-DPB1, DQB1, and DRB1 than non-ABMR recipients. Across the cohort, 68 HLA alleles demonstrated distinct microbial associations at phylum, family, and genus levels. Alleles such as HLA-DRB108, HLA-DPB1575, and HLA-C05 were linked to differential abundance of Actinobacteriota, Campylobacterota, and Fusobacteriota, respectively. Genus-level analyses revealed strong allele-specific associations with Veillonella, Enterobacter, Streptococcus, and other immunomodulatory taxa. LEfSe identified HLA-DQB106 and HLA-DQB1∗104 as associated with enrichment of Enterobacter, Citrobacter europaeus, Bacteroides plebeius, Rothia dentocariosa, Megasphaera, and Burkholderiaceae-microbial signatures also prominent in ABMR cases.

CONCLUSION: Class II HLA mismatch burden and allele-specific oral microbial signatures are closely linked to ABMR. Combined HLA-microbiome profiling may enhance early risk stratification and inform targeted peri-transplant microbial interventions.},
}

@article {pmid41799257,
year = {2026},
author = {Zhao, Y and Ren, Z and Xu, Q and Zhu, T and Hu, H and Fu, Y and Jiang, J and Zhai, Q},
title = {Factors influencing gut microbial colonization: A host-microbe-environment interaction perspective.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101361},
pmid = {41799257},
issn = {2665-9271},
abstract = {Gut microbial colonization is a dynamic balance shaped by host genetics and immunity, microbial ecology, and environmental exposures. This review synthesizes evidence on host barriers and immunity-mucus architecture, antimicrobial peptides, pattern recognition receptors, and secretory IgA-and on genetic loci such as LCT and ABO/FUT2 that modulate nutrient landscapes and strain selection. Microbial adaptability is summarized, including polysaccharide utilization loci and human milk oligosaccharide metabolism, bile salt hydrolase-mediated tolerance, extracellular polysaccharide-driven immune modulation, oxygen-gradient-linked metabolic partitioning, and adhesion mechanisms that secure niche occupancy. Environmental perturbations are evaluated, spanning dietary patterns, protein sources, polyphenols, food additives, pharmaceuticals, and lifestyle factors such as physical activity, circadian alignment, and smoking, which reshape resource competition, barrier integrity, and community resilience. Interaction frameworks that govern stability and dysbiosis are delineated, including competitive inhibition, cross-feeding, quorum sensing, cross-kingdom crosstalk among bacteria, fungi, and phages, and horizontal gene transfer that accelerates adaptation and resistance. Niche elasticity is proposed as a systems metric to quantify stability and recovery after perturbation. Translational strategies combine engineered probiotics, anti-adhesion approaches, and rationally designed phages and lysins with in situ multi-omics to enable mechanism-guided, personalized interventions for food science and microbial engineering.},
}

@article {pmid41798180,
year = {2026},
author = {Cakin, I and Millington, R and Pawar, S and Buckling, A and Smirnoff, N and Padfield, D and Duffy, J and Yvon-Durocher, G},
title = {A novel method to simultaneously estimate bacterial respiration and growth from oxygen dynamics.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag024},
pmid = {41798180},
issn = {2730-6151},
abstract = {Bacterial growth and respiration are fundamental metabolic processes that drive energy transformation and allocation within organisms and impact carbon sequestration at the ecosystem scale. However, these traits are usually measured independently; bacterial growth is quantified with endpoint biomass measurements, while respiration is determined by monitoring oxygen or carbon dioxide. Because the two physiological traits are collected at different temporal and volumetric scales (hours-to-days for growth versus minutes-to-hours for respiration), reconciling them is challenging and often introduces scale-mismatch bias, obscuring causal links between metabolism and environmental drivers. In this study, we develop a novel method for quantifying the rates of bacterial growth and respiration from a single dissolved-oxygen time series. Our approach introduces a model that couples exponential biomass growth with biomass-specific respiration, enabling simultaneous inference of growth rate and respiration rate from each oxygen trajectory. We applied our high-throughput method to 15 bacterial taxa isolated from natural environments. Our approach yielded growth estimates in close agreement with measurements based on popular methods using optical density or flow cytometry ([Formula: see text] > 0.9) with no evidence of taxon-specific bias. We also tested our approach in quantifying the effects of temperature on respiration, growth, and carbon use-efficiency in Pseudomonas sp. Our method yielded typical unimodal thermal response curves for growth and respiration where rates were highest at moderate temperatures, while carbon use efficiency increased with temperature, peaked around the growth thermal optimum (∼30°C-35°C), and declined at the highest temperature. By quantifying respiration and growth within a single assay and in high throughput, our approach effectively enables measurement of microbial metabolic strategies and adaptations to stress. It offers a noninvasive and scalable tool for high-throughput phenotyping and studies of environmental perturbations, enabling a new class of trait-based microbial ecology that links cellular physiology to broader ecosystem function.},
}

@article {pmid41797016,
year = {2026},
author = {Ghannem, S and Labiadh, H and Ishak, S and Louiz, S and Derguini, A and Idres, T and Grassi, E and Semprucci, F and Badraoui, R and Ben Hamadi, N and Chaudhary, AA and Alsalamah, SA and Bendif, H and Rebai, A and Boufahja, F},
title = {Investigation of the impacts of second-generation antihistamines on free-living marine nematodes and their interaction with ZnS nanoparticles: Mechanistic insights from community and population approaches and molecular interactions modeling.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107969},
doi = {10.1016/j.marenvres.2026.107969},
pmid = {41797016},
issn = {1879-0291},
abstract = {The current research investigates the impact of loratadine and its active metabolite desloratadine, applied at environmentally relevant concentrations (40 and 80 ng/L), using community-level, population-based, and molecular modeling approaches, on meiofauna from the Dammam coast, Saudi Arabia. The results indicate a significant reduction in the abundance of meiobenthic organisms, accompanied by a marked decline in nematode diversity across treatments, especially under combined exposures at higher concentrations. Additionally, trophic groups 1B and 2B, characterized by clavate tail morphologies, were the main contributors to the observed dissimilarity patterns across treatments. The mixture of 40 ng/L of antihistamines with ZnS nanoparticles (4.1 nm) enhanced catalase and GST activities in Metoncholaimus pristiurus. An increase in growth rate was also observed, along with larger pharyngeal lumens, suggesting higher food pumping under stress. Locomotion issues and decreased fertility are also suggested, with signs of masculinization. This highlights the intensified toxic effects of antihistamines following the addition of ZnS NPs. Overall, the findings suggest synergistic or additive interaction between loratadine, desloratadine, and ZnS nanoparticles. Their toxicokinetic properties, along with strong binding affinities and stable molecular interactions with GLD-3 and SDP receptors, provide a mechanistic basis and support ecotoxicological impacts of these antihistamines and ZnS NPs on nematodes.},
}

@article {pmid41795790,
year = {2026},
author = {Özkan Vardar, D and Ekmen, B and Çalı, A},
title = {Interactions between polystyrene-derived micro- and nanoplastics and the microbiota: a systematic review of multi-omics mouse studies.},
journal = {Journal of environmental science and health. Part C, Toxicology and carcinogenesis},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/26896583.2026.2636868},
pmid = {41795790},
issn = {2689-6591},
abstract = {Micro- and nanoplastics (MNPs), especially polystyrene-derived particles (PS-MPs/PS-NPs), have become a growing concern due to their increasing presence in the environment and their proven biological toxicity. Although PS particles have been identified in various human tissues, including feces, placenta, and blood, their impact on the gut microbiota and microbiota-driven metabolic pathways remains insufficiently synthesized. This systematic review aims to compile current in vivo evidence from mouse studies to assess how PS-MP/NP exposure influences gut microbial diversity, taxonomic composition, microbial metabolites, and subsequent physiological outcomes. A PRISMA-guided literature search identified 15 controlled mouse studies published between 2010 and 2024. Across these studies, PS exposure consistently induced gut dysbiosis, characterized by reductions or shifts in alpha-diversity, distinct beta-diversity clustering, loss of beneficial commensals such as Lactobacillus, Bifidobacterium, and members of Ruminococcaceae, and enrichment of opportunistic or pro-inflammatory taxa including Proteobacteria, Helicobacter, and Staphylococcus. Notably, MNPs particles induced more pronounced microbial disruption than micro-sized forms. Overall, current experimental evidence indicates that PS-MPs/PS-NPs induce multidimensional toxicity by simultaneously disrupting gut microbial ecology and host metabolic pathways. These findings emphasize the need for standardized methodologies in microplastic research and highlight the importance of clarifying the long-term health effects of human exposure to micro- and nanoplastics.},
}

@article {pmid41794478,
year = {2026},
author = {Chiarini, E and Buzzanca, D and Devizia, A and Giordano, M and Dipietro, F and Zeppa, G and Alessandria, V},
title = {Kombucha meets circular economy: A microbiome and metabolite perspective on second fermentation with plant by-products.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118597},
doi = {10.1016/j.foodres.2026.118597},
pmid = {41794478},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Kombucha Tea/microbiology/analysis/economics ; Food Microbiology ; Bacteria/metabolism/classification ; Yeasts/metabolism ; Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Kombucha is a traditional fermented beverage produced through the fermentation of sugared tea by a symbiotic culture of bacteria and yeasts (SCOBY). In recent years, the valorisation of plant-based by-products as fermentation substrates has gained attention as a sustainable approach to improving both the nutritional and economic efficiency of fermented beverages. The present study investigated the production of kombuchas supplemented with pineapple, fennel, and carrot by-products during the secondary fermentation phase, aiming to evaluate their influence on fermentation dynamics, microbial ecology, and the chemical and aromatic profiles of the final products. The experimental design integrated culture-dependent and culture-independent approaches, including amplicon sequencing, to characterize microbial community composition and evolution throughout fermentation. Chemical profiling was carried out using gas chromatography coupled with quadrupole mass spectrometry (GC-qMS) and high-performance liquid chromatography equipped with diode-array and refractive index detectors (HPLC-DAD/RI). The fermentation process was monitored during both the primary and secondary stages, and a shelf-life assessment was conducted over 14 days of refrigerated storage (4 °C) to evaluate product stability. Microbiological results indicated a predominance of Schizosaccharomyces spp., while Komagataeibacter spp. was the only bacterial genus identified. A significant reduction in α-diversity was observed over time, suggesting selective adaptation of the microbial community to the fermentation environment. β-diversity analysis revealed clear differences among samples collected after 8 and 22 days, reflecting the combined influence of time and substrate composition on microbial succession. Chemical analyses demonstrated an increase in acetic acid concentration and a progressive decline in pH throughout fermentation, consistent with the metabolic activity of acetic acid bacteria. Among volatile organic compounds (VOCs), alcohols and organic acids were the most abundant chemical classes detected. Several VOCs were associated with minor yeast genera, including Hannaella, Galactomyces, Aureobasidium, and Millerozyma, whereas Schizosaccharomyces spp. showed a strong correlation with specific aroma-active compounds, highlighting its key role in defining the sensory characteristics of the beverage. Overall, this study provides new evidence on how different vegetable by-products and microbial consortia influence the development of chemical and aromatic compounds in kombucha. The findings highlight the potential of using by-products as a sustainable, value-added strategy for producing fermented beverages, while also supporting the principles of the circular economy and resource-efficient food systems.},
}

*Fermentation
*Microbiota
*Kombucha Tea/microbiology/analysis/economics
Food Microbiology
Bacteria/metabolism/classification
Yeasts/metabolism
Volatile Organic Compounds/analysis
Gas Chromatography-Mass Spectrometry

@article {pmid41794468,
year = {2026},
author = {Wang, A and Qiu, C and Tang, J},
title = {Multidimensional synergy between yeast and lactic acid bacteria: mechanisms, quality formation, and precision fermentation strategies.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118586},
doi = {10.1016/j.foodres.2026.118586},
pmid = {41794468},
issn = {1873-7145},
mesh = {*Fermentation ; *Lactobacillales/metabolism/physiology ; Biofilms/growth & development ; *Microbial Interactions ; *Food Microbiology ; Quorum Sensing ; *Fermented Foods/microbiology ; *Yeasts/metabolism ; },
abstract = {The complex functional characteristics of fermented foods stem from dynamic microbial interactions rather than the activities of individual microorganisms. Traditional research has primarily focused on single-strain cultures and metabolic functions, whereas contemporary studies increasingly emphasize the pivotal role of interactions between different species in shaping fermentative ecosystems. This review explores the multifaceted interactions between yeast-lactic acid bacteria (LAB), focusing on three key aspects: (1) nutritional interactions and cross-feeding mechanisms; (2) molecular communication via metabolite exchange and quorum sensing; (3) collective adaptation strategies encompassing biofilm formation and environmental remodeling. Synergistic interactions promote metabolic complementarity, thereby enhancing substrate utilization efficiency and biosynthetic capacity beyond the limitations of single-strain cultures. Competitive interactions maintain ecological equilibrium within microbial communities while suppressing undesirable microorganisms. Quorum sensing mechanisms synchronize gene expression across entire populations, coordinating metabolic pathways and optimizing collective behavior. Biofilm formation creates structured microenvironments that enhance microbial resilience and metabolic specialization. Advanced methodologies, particularly multi-omics technologies and synthetic microbial ecology approaches, have become indispensable tools for unravelling these intricate interaction networks. Integrating genome-scale metabolic modelling with experimental validation offers unprecedented insights into the molecular mechanisms underpinning microbial interactions. This systems-level understanding enables the purposeful design of synthetic microbial communities and precise fermentation processes, highlighting the imperative shift from single-species optimization towards ecological management strategies. Future research should translate laboratory discoveries into industrial applications through standardized evaluation systems and dynamic regulatory strategies.},
}

*Fermentation
*Lactobacillales/metabolism/physiology
Biofilms/growth & development
*Microbial Interactions
*Food Microbiology
Quorum Sensing
*Fermented Foods/microbiology
*Yeasts/metabolism

@article {pmid41794110,
year = {2026},
author = {Wei, C and Hu, J and Wang, X and Chen, Y and Zhang, S and Peng, Y},
title = {Optimization of sulfate-reducing ammonium oxidation based on N/S: nitrogen and sulfur removal performance, microbial community, and response surface methodology.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124143},
doi = {10.1016/j.envres.2026.124143},
pmid = {41794110},
issn = {1096-0953},
abstract = {Sulfate-reducing ammonium oxidation (Sulfammox) offers a novel strategy for simultaneous nitrogen and sulfur removal. However, the microbial-driven metabolic pathways under different N/S and the optimal operational conditions remain unclear. This study operated three anaerobic sequencing batch reactors at N/S of 2.5, 2.0, and 1.5 to investigate the removal performance and microbial ecology. The reactor with an N/S of 1.5 (R3) achieved the highest removal efficiencies of 91.82% for NH4[+]-N and 47.95% for SO4[2-]-S, while the reactor with an N/S of 2.5 (R1) showed efficiencies below 15% for both, indicating that a lower N/S is critical for efficient removal. X-ray photoelectron spectroscopy confirmed the formation of elemental sulfur, indicating active sulfur transformation that alleviated sulfide inhibition and enhanced system stability. Batch tests identified optimal operating conditions: pH 8.0, hydraulic retention time 48 h, and COD 50 mg/L. When COD is greater than 300 mg/L, sulfate reduction dominated and inhibited the sulfammox process. Response surface methodology models (R[2]>0.98) predicted the optimal parameters in N/S 1.57, pH 7.66, HRT 46.53 h, and COD of 48.61 mg/L, achieving NH4[+]-N and SO4[2-]-S removal efficiencies of 93.13% and 47.35%. This represents 9.5% enhancement in NH4[+]-N removal over the pre-optimization phase. Microbial analysis revealed that N/S of 1.5 abundance of Desulfobacterota increased by 1.67%, driving sulfate reduction, while Chloroflexi constituted 26.07% in R3, the anammox bacterium Candidatus-Brocadia was inhibited, exhibiting a relative abundance of less than 0.1%. By elucidating sulfammox interactions, this study offers a practical, low-carbon and synergistic framework for the effective co-treatment of high NH4[+]-N and SO4[2-]-S wastewater.},
}

@article {pmid41792903,
year = {2026},
author = {Liang, MQ and Yuan, L and Liu, QH and Wu, J and Liu, DF and Sheng, GP},
title = {Membrane perturbation by the last-resort antibiotic polymyxin B drives biphasic regulation of horizontal gene transfer.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag046},
pmid = {41792903},
issn = {1751-7370},
abstract = {Although it is increasingly recognized that anthropogenic chemicals modulate horizontal gene transfer (HGT), the nature of these interactions is often more complex than a simple promotion or inhibition. The potential for a single chemical to exert opposing, concentration-dependent effects represent a critical and less-explored frontier in microbial ecology. Here, we investigate the last-resort antibiotic polymyxin B, a membrane-targeting peptide, and reveal a concentration-dependent, biphasic regulation of plasmid conjugation. Sub-inhibitory concentrations (0.125-0.5 mg/L) consistently inhibited the transfer of antibiotic resistance genes (ARGs) by up to 65.4%, whereas bactericidal concentrations (≥ 1 mg/L) strongly promoted it by up to 15.9-fold. This regulatory switch is driven by distinct physiological states: low-level exposure triggers defensive responses including reduced membrane permeability, whereas high-level exposure causes catastrophic membrane damage, inducing a synergistic stress response involving oxidative damage (>2-fold ROS increase) and a surge in cellular energy (up to 83.0% ATP increase) that facilitates HGT. High-concentration polymyxin B also promotes plasmid transfer in complex microbial communities derived from activated-sludge biofilms. Our findings reveal a new paradigm for the interaction between chemical stressors and microbial evolution, demonstrating that the ecological impact of contaminants on HGT cannot be predicted by monotonic models and highlighting the role of environmental hotspots in shaping the dissemination of antibiotic resistome.},
}

@article {pmid41791723,
year = {2026},
author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M},
title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70264},
doi = {10.1111/1462-2920.70264},
pmid = {41791723},
issn = {1462-2920},
support = {IITG/R&D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; },
mesh = {*Naphthalenes/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Systems Biology ; Computer Simulation ; *Environmental Pollutants/metabolism ; Microbial Consortia ; },
abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.},
}

*Naphthalenes/metabolism
Biodegradation, Environmental
*Bacteria/metabolism/genetics
Systems Biology
Computer Simulation
*Environmental Pollutants/metabolism
Microbial Consortia

@article {pmid41790321,
year = {2026},
author = {Sahoo, A and Maity, A and Das, B and Paul, RC and Paul, P and Chakraborty, P and Chaudhuri, BN and Ghosh, MM and Das, S and Tribedi, P},
title = {Combined application of Vancomycin and Levofloxacin potentiates the antimicrobial activity against MRSA: a response surface methodology-based study.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41790321},
issn = {1874-9356},
support = {TNU/R&D/MG/24/02//The Neotia University, India/ ; TNU/R&D/MP/2021/010//The Neotia University, India/ ; },
}

@article {pmid41789424,
year = {2026},
author = {Katrak, C and Reed, S and Carter, M and Khatib, M and Peterson, A and Martin, K and Kajfasz, JK and Abranches, J},
title = {Oral hygiene agents at work: effects on Streptococcus mutans and caries risk.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1768512},
pmid = {41789424},
issn = {2235-2988},
mesh = {Humans ; *Dental Caries/prevention & control/microbiology ; *Streptococcus mutans/drug effects/physiology/growth & development ; Biofilms/drug effects/growth & development ; *Oral Hygiene/methods ; Probiotics/pharmacology ; Dental Plaque/microbiology/prevention & control ; Chlorhexidine/pharmacology/therapeutic use ; Hydrogen Peroxide/pharmacology ; Fluorides/pharmacology/therapeutic use ; Prebiotics ; Zinc/pharmacology ; },
abstract = {Dental caries remains one of the most prevalent chronic polymicrobial diseases worldwide, driven by acidogenic and aciduric bacteria, most notably Streptococcus mutans, that thrive within oral biofilms. Conventional strategies for caries prevention rely on mechanical plaque removal combined with agents that inhibit bacterial growth, disrupt biofilm formation, or enhance enamel remineralization. Here, we synthesize current evidence regarding a range of key agents that are incorporated into modern oral hygiene products. In addition to describing the mechanisms and efficacy of these agents, we describe their distinct biochemical and ecological effects on S. mutans metabolism, acid tolerance, and biofilm development. The agents that are relevant in the present day include fluoride, hydrogen peroxide, chlorhexidine, zinc, prebiotics (such as arginine and xylitol), and probiotics. Fluoride remains the cornerstone of caries prevention through its dual effects on enamel fluorapatite formation and inhibition of bacterial glycolysis, while chlorhexidine and hydrogen peroxide provide broad-spectrum antimicrobial activity. Zinc exhibits multifaceted roles in metabolic inhibition and plaque reduction, whereas pre- and probiotics aim to restore ecological balance by favoring health-associated commensal species. Finally, the review highlights evidence supporting combinatorial and synergistic use of these agents, particularly fluoride pairings, which may yield additive or enhanced protective effects. Understanding the molecular mechanisms that drive the efficacy of these compounds and gaining insight into cumulative influence on oral microbial ecology will drive the development of future treatment strategies.},
}

Humans
*Dental Caries/prevention & control/microbiology
*Streptococcus mutans/drug effects/physiology/growth & development
Biofilms/drug effects/growth & development
*Oral Hygiene/methods
Probiotics/pharmacology
Dental Plaque/microbiology/prevention & control
Chlorhexidine/pharmacology/therapeutic use
Hydrogen Peroxide/pharmacology
Fluorides/pharmacology/therapeutic use
Prebiotics
Zinc/pharmacology

@article {pmid41788582,
year = {2026},
author = {Wang, E and Chen, C and Li, Q},
title = {Current obstacles for continuous cropping of Panax species and mitigation strategies.},
journal = {Journal of ginseng research},
volume = {50},
number = {2},
pages = {100925},
pmid = {41788582},
issn = {1226-8453},
abstract = {Panax species-represented here by Panax ginseng Meyer, Panax quinquefolius L., and Panax notoginseng (Burk.) F. H. Chen-are valued for their saponins and polysaccharides and thus have significant clinical and commercial value. Rising global demand has driven intensive, large-scale cultivation, but repeated monoculture has produced persistent continuous cropping obstacles that now threaten the sustainability of the industry. These obstacles are not attributable to a single factor. Rather, they arise from interacting processes including degradation of soil physical and chemical properties, accumulation of plant-derived toxins that inhibit growth (allelopathic autotoxicity), and shifts in the soil microbial community that impair soil health and plant resilience. Together, these changes lead to stunted growth, reduced yields, and increased disease incidence. This review synthesizes recent advances in understanding continuous cropping obstacles in Panax species. It evaluates evidence for the primary causal factors, assesses current mitigation strategies, and highlights areas where findings are robust or still uncertain. By integrating soil science, plant physiology, and microbial ecology, the review identifies practical approaches already in use and emerging technologies with potential to improve outcomes. Finally, we identify critical knowledge gaps and outline priority directions for future research aimed at clarifying mechanisms and translating that knowledge into an effective management framework. The ultimate goal is to provide a theoretical basis to guide the development of scalable, evidence-based practices that alleviate continuous cropping obstacles in the cultivation of Panax species.},
}

@article {pmid41788258,
year = {2026},
author = {Keles, E and Celik, O},
title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.},
journal = {Microbial cell (Graz, Austria)},
volume = {13},
number = {},
pages = {117-130},
pmid = {41788258},
issn = {2311-2638},
abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.},
}

@article {pmid41787281,
year = {2026},
author = {Van Rossum, U and Heyndrickx, M and Rasschaert, G and Demaître, N and Sadiq, FA and Boon, N and Cools, A and De Reu, K},
title = {Hidden threats: exploring biofilm communities in broiler houses and pig nursery units drinking water lines.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04790-6},
pmid = {41787281},
issn = {1471-2180},
support = {HBC.2021.1060//VLAIO-LA/ ; },
}

@article {pmid41787131,
year = {2026},
author = {Stanovcic, S and Milisavljevic, M and Azanjac, N and Kojic, S and Kojic, M},
title = {Biomolecules Generated During Programmed Cell Death (PCD) Enhance the Capacity of Proliferating Ustilago maydis Cells to Overcome the Negative Impacts of Non-PCD Necromass.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02736-z},
pmid = {41787131},
issn = {1432-184X},
support = {7730230//Science Fund of the Republic of Serbia/ ; },
}

@article {pmid41786226,
year = {2026},
author = {Li, Y and Wang, WJ and Zhang, S and Luo, Q and Qian, NF and Chen, DZ and Jin, RC and Feng, LJ and Yang, GF},
title = {Chaotic effects in completely autotrophic nitrogen removal over nitrite process: how minor dissolved oxygen variations reshape microbial community and functional genes to drive divergent nitrogen removal.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134333},
doi = {10.1016/j.biortech.2026.134333},
pmid = {41786226},
issn = {1873-2976},
abstract = {To elucidate how dissolved oxygen (DO) regulates nitrogen removal in the completely autotrophic nitrogen removal over nitrite (CANON) process, three continuous-flow reactors were operated under micro-aerobic conditions. Results revealed that minor DO variations (0.36-0.51 mg/L) triggered dramatic bifurcation in performance and microbial ecology, demonstrating chaotic effects characterized by nonlinear dynamics and sensitive dependence on initial conditions. A superior total nitrogen removal rate of 0.38 kg/m[3]/d and a NH4[+]-N removal efficiency of 86.7% were achieved at 0.36 mg/L DO. However, a slight increase to 0.51 mg/L DO significantly enhanced nitrite-oxidizing bacteria (NOB) activity and nitrate accumulation. Lower DO favored anammox bacteria and their essential genes (hzs/hdh), while elevated DO promoted NOB competition and oxidative stress responses, evidenced by Fe-Mn SOD gene upregulation and altered extracellular polymers composition. Our findings establish a direct link between minor DO fluctuations and macro-scale functional outcomes, providing a mechanistic framework for predicting and controlling CANON process.},
}

@article {pmid41778806,
year = {2026},
author = {Wasson, PA and McRose, DL},
title = {Nitrous oxide produced by denitrifying pseudomonads inhibits the growth of rhizosphere bacteria by inactivating the cobalamin-dependent methionine synthase.},
journal = {mBio},
volume = {},
number = {},
pages = {e0269925},
doi = {10.1128/mbio.02699-25},
pmid = {41778806},
issn = {2150-7511},
abstract = {Microbial communities are shaped by complex metabolic interactions, whereby the byproducts of one organism influence the physiology of others. This is exemplified in the microbial nitrogen cycle, where diffusion of free intermediates can drastically reshape the chemical landscape of the environment. One such intermediate, nitrous oxide (N2O), is often overlooked as biologically inert. However, emerging evidence suggests this gas may inhibit the activity of some cobalamin-dependent enzymes through a reaction with the cofactor. This raises the possibility that, through such an interaction, N2O-producing organisms may shape the microbial communities in which they reside, selecting against organisms that rely on these sensitive cobalamin enzymes. At the plant root, a hotspot of microbial activity, the impact of such interactions may be especially important. To investigate this, we focused on microbial N2O production and its effect on methionine biosynthesis, a ubiquitous bacterial process carried out by cobalamin-dependent (MetH) or independent (MetE) methyltransferases. In this study, we show that deleting metE and forcing reliance on MetH sensitizes the denitrifier Pseudomonas aeruginosa to exogenous and self-produced N2O. We extend these findings to plant-associated bacteria, where we find that a significant portion of an Arabidopsis thaliana rhizosphere culture collection relies exclusively on cobalamin-dependent methionine synthases and experimentally demonstrate their sensitivity to N2O. Finally, we show that the growth of one MetH-reliant rhizosphere isolate is suppressed in co-culture with N2O-producing P. aeruginosa. Together, these findings suggest that N2O producers can shape microbial ecology at the plant root.IMPORTANCEMicrobes that live on plant roots can make important contributions to plant health and often exist in tight-knit communities held together by chemical exchanges. This study investigates an interaction between two such metabolites: the climate-active gas nitrous oxide (N2O) and cobalamin. N2O can become toxic through a reaction with methionine synthase enzymes that use cobalamin as a cofactor. We asked whether the production of N2O by some bacteria curtails the growth of others that rely on these enzymes. Using genetic mutants of a model bacterium and natural isolates from the roots of the plant Arabidopsis thaliana, we showed that N2O-producing microbes suppress growth of their sensitive neighbors and that N2O sensitivity is common in rhizosphere bacteria. As natural and agricultural soils periodically experience bursts of N2O, our results suggest that exposure to this gas may shape the assembly of plant-beneficial microbial communities.},
}

@article {pmid41786065,
year = {2026},
author = {Wang, X and Liu, R and Liu, J and Lin, Y and Zhou, M},
title = {Gut microbiota-derived indole metabolites in depression: mechanisms and therapeutic potential.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {178720},
doi = {10.1016/j.ejphar.2026.178720},
pmid = {41786065},
issn = {1879-0712},
abstract = {Depression, a prevalent neuropsychiatric disorder with complex pathophysiology and often insufficient treatment efficacy, is increasingly associated with disruptions in the gut-brain axis. This review focuses on the underappreciated role of the microbial indole pathway, a key route in tryptophan metabolism orchestrated by the gut microbiota. We synthesize recent evidence demonstrating that gut microbiota-derived indole metabolites, such as indole-3-propionic acid (IPA) and indole-3-aldehyde (IAld), are significantly reduced in depression. These metabolites exert multifaceted antidepressant effects by enhancing intestinal and blood-brain barrier integrity, suppressing neuroinflammation, and promoting neuroplasticity. Furthermore, we explore the therapeutic potential of targeting this axis through interventions like specific probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation to restore microbial ecology and indole metabolite levels. By highlighting the microbiota-indole-brain pathway as a critical mechanistic and therapeutic frontier, this review provides a novel perspective on the pathogenesis and treatment of depression, moving beyond conventional monoaminergic theories.},
}

@article {pmid41785727,
year = {2026},
author = {Wang, C and Luo, M and Chen, Q and Zheng, L and Jiang, T and Dai, M},
title = {Hedyotis diffusa Willd. extract alleviates CCl4-induced liver fibrosis via modulation of the gut microbiota and FXR/SHP/CYP7A1-mediated bile acid metabolism.},
journal = {Journal of ethnopharmacology},
volume = {363},
number = {},
pages = {121450},
doi = {10.1016/j.jep.2026.121450},
pmid = {41785727},
issn = {1872-7573},
abstract = {Liver fibrosis is a critical stage in the progression of chronic liver diseases, yet effective therapeutic agents are limited. Hedyotis diffusa Willd., a traditional Chinese medicine herb with heat-clearing and detoxifying properties, has long been used to treat inflammatory disorders, hepatic dysfunction and malignancies. Although accumulating studies suggest that Hedyotis diffusa Willd. Extract (HDW) possesses hepatoprotective and antifibrotic potential, the underlying mechanisms, particularly those involving gut microbiota and bile acid (BA) metabolism along the gut-liver axis, remain largely undefined.

AIM OF THE STUDY: To investigate the protective effects of HDW against carbon tetrachloride (CCl4)-induced liver fibrosis in mice, and to determine whether its antifibrotic efficacy is mediated by modulation of the gut microbiota-bile acid-FXR/SHP/CYP7A1 axis.

MATERIALS AND METHODS: Liver fibrosis was induced by intraperitoneal injection of 10% CCl4 in olive oil for five weeks. Histopathological changes were evaluated using H&E, Sirius red and Masson staining. Liver function was assessed using serum levels of ALT, AST, ALP and γ-GT. Collagen deposition was evaluated by measuring hepatic hydroxyproline (HYP) and fibrosis-related markers (HAase, IV-C, LN and PC-III). Activation of hepatic stellate cells was determined by α-SMA and Col1a1 expression. The composition of the gut microbial was profiled using 16 S rRNA sequencing, and the necessity of gut microbiota for HDW efficacy was evaluated through an antibiotic (ABX) cocktail intervention. Targeted BA metabolomics quantified BA profiles, while RT-qPCR and Western blotting evaluated FXR/SHP/CYP7A1 pathway activity. Intestinal barrier integrity was assessed by villus morphology, tight junction protein levels (Claudin-1, ZO-1, Occludin), and serum lipopolysaccharide (LPS).

RESULTS: HDW treatment markedly alleviated CCl4-induced liver fibrosis, demonstrated by improved hepatic architecture, reduced serum transaminases and ALP/γ-GT, decreased hydroxyproline levels, and downregulation of α-SMA and Col1a1. HDW reshaped the gut microbial composition by enriching beneficial taxa, whereas ABX treatment markedly attenuated its antifibrotic effects, indicating that the therapeutic action of HDW is largely microbiota-dependent. HDW restored BA homeostasis and significantly increased fecal odeoxycholic acid. Consequently, hepatic FXR/SHP/CYP7A1 signaling was upregulated at both the mRNA and protein levels. Furthermore, HDW strengthened the intestinal epithelial barrier by enhancing tight junction integrity and reducing serum LPS.

CONCLUSION: HDW exerts significant antifibrotic effects in CCl4-induced liver fibrosis via a gut microbiota-dependent mechanism involving the restoration of BA metabolism and the activation of the hepatic FXR/SHP/CYP7A1 axis. Given its ability to modulate gut microbial ecology, BA homeostasis and intestinal barrier integrity simultaneously, HDW is a promising therapeutic candidate for targeting the gut microbiota in the treatment of liver fibrosis.},
}

@article {pmid41785576,
year = {2026},
author = {Poirier, S and Rondeau-Leclaire, J and Faticov, M and Roy, A and Lajeunesse, G and Lucier, JF and Tardif, S and Kembel, SW and Ziter, C and Laprise, C and Paquette, A and Girard, C and Laforest-Lapointe, I},
title = {Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients.},
journal = {The Science of the total environment},
volume = {1023},
number = {},
pages = {181623},
doi = {10.1016/j.scitotenv.2026.181623},
pmid = {41785576},
issn = {1879-1026},
abstract = {Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosol dynamics. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and plant particles composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and plant particles. Based on beta diversity, sampling period alone explained up to 40% of plant particle, 29% of fungal, and 11% of bacterial bioaerosol composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.},
}

@article {pmid41782409,
year = {2026},
author = {Yang, J and Xiao, Y and Cui, J and Song, R and Ma, W and Liu, J and Miao, C and Sun, X and Kong, X and Zhang, ZS and Zhou, L and Yao, Z and Wang, Q},
title = {A 4-guanidinobutanoic acid-SLC36A1 axis drives a microbiota‒host feedback loop to regulate intestinal homeostasis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2639216},
doi = {10.1080/19490976.2026.2639216},
pmid = {41782409},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Humans ; Mice ; Homeostasis ; *Intestinal Mucosa/metabolism/microbiology/drug effects ; *Guanidines/metabolism/pharmacology ; Colitis, Ulcerative/microbiology/metabolism ; Mice, Inbred C57BL ; Bacteroides/metabolism ; *Butyrates/metabolism ; Disease Models, Animal ; Stem Cells/metabolism ; Feedback, Physiological ; *Amino Acid Transport System y+/metabolism/genetics ; Akkermansia ; },
abstract = {The role of gut microbiota‒derived metabolites in regulating the intestinal mucosal barrier remains poorly defined. Here, we identified 4-guanidinobutanoic acid (4-GBA), produced by Bacteroides stercorirosoris, as a critical regulator of intestinal homeostasis. Using untargeted metabolomics, organoid co-cultures, mouse models, and single-cell RNA sequencing, we demonstrated that 4-GBA enhances intestinal stem cells (ISCs) function and goblet cell differentiation. This promotes Akkermansia muciniphila enrichment through mucus-dependent niche expansion, establishing a microbiota‒host feedback loop. Mechanistically, 4-GBA upregulates the proton-coupled amino acid transporter SLC36A1 and activates the Hedgehog signaling pathway to drive epithelial reprogramming. Clinically, SLC36A1 expression inversely correlates with ulcerative colitis (UC) severity in human samples. Furthermore, the SLC36A1 agonist sarcosine enhances barrier homeostasis and attenuates colitis in mice, highlighting the diagnostic and therapeutic potential of this axis in UC. Our findings reveal a novel microbiome-host axis through which a microbial metabolite modulates epithelial function and microbial ecology, offering a potential therapeutic strategy targeting microbiota-epithelial crosstalk for UC management.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
Humans
Mice
Homeostasis
*Intestinal Mucosa/metabolism/microbiology/drug effects
*Guanidines/metabolism/pharmacology
Colitis, Ulcerative/microbiology/metabolism
Mice, Inbred C57BL
Bacteroides/metabolism
*Butyrates/metabolism
Disease Models, Animal
Stem Cells/metabolism
Feedback, Physiological
*Amino Acid Transport System y+/metabolism/genetics
Akkermansia

@article {pmid41781688,
year = {2026},
author = {Cinek, O and Hubáčková, K and Litošová, K and Hlináková, L},
title = {Heterogeneity Primer Spacers Improve the Performance of Massively Parallel Amplicon Sequencing of the V3-V4 Region of the 16 S rDNA as well as the 18 S Region for Blastocystis Subtyping.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02708-3},
pmid = {41781688},
issn = {1432-184X},
}

@article {pmid41779172,
year = {2026},
author = {Roldán, DM and Carrizo, D and Sánchez-García, L and Menes, RJ},
title = {Temperature Response of Aerobic Methane-Oxidizing Bacteria in Lake Sediments from King George Island, Maritime Antarctica.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02717-2},
pmid = {41779172},
issn = {1432-184X},
}