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

@article {pmid42575254,
year = {2026},
author = {Di, J and Hu, J and Zhao, F and Qi, J and Wu, Y},
title = {Bifid triple viable tablets are associated with renal biochemical improvement and qualitative gastrointestinal changes in 5/6-nephrectomized rats: An exploratory microbiome-metabolome study.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {},
number = {},
pages = {130987},
doi = {10.1016/j.bbagen.2026.130987},
pmid = {42575254},
issn = {1872-8006},
abstract = {BACKGROUND: Chronic kidney disease (CKD) is accompanied by renal injury, gut-barrier disruption, dysbiosis, inflammation, and disordered iron regulation. We examined whether a clinical multi-strain probiotic produces coordinated renal, intestinal, and metabolic effects in experimental CKD.

METHODS: Male Sprague-Dawley rats underwent 5/6 nephrectomy (5/6 Nx). Dose-response phenotyping compared sham, untreated 5/6 Nx, three Bifid Triple Viable Tablets (BTV) doses, and valsartan (n = 3/group). Independent cohorts provided targeted validation (untreated versus high-dose BTV; n = 6/group) and paired fecal 16S rRNA/serum metabolomics (n = 4/group). Technical replicates were averaged within animals.

RESULTS: High-dose BTV was associated with lower blood urea nitrogen (BUN), serum creatinine (Scr), inflammatory cytokines, and hepcidin, plus qualitatively less renal and gastrointestinal injury. Occludin and zonula occludens-1 (ZO-1) integrated fluorescence did not differ from untreated 5/6 Nx rats (all adjusted P > 0.05; n = 3/group). Validation confirmed lower BUN (27.87 ± 2.09 vs 16.64 ± 3.82 mmol/L; P = 0.000264), Scr (235.75 ± 27.41 vs 132.05 ± 19.50 μmol/L; P = 0.0000343), and interleukin-6 (IL-6; 188.11 ± 8.67 vs 92.21 ± 14.51 pg/mL; P = 5.72 × 10-7) with high-dose BTV. Omics detected 1966 metabolites, 393 differential metabolites, and 160 nominal genus-metabolite associations.

CONCLUSIONS: BTV was associated with reproducible renal biochemical and inflammatory improvement, qualitative gastrointestinal differences, and exploratory microbial-metabolic changes. Barrier-protein findings were nonsignificant, and small, separate cohorts preclude causal inference.},
}

@article {pmid42575421,
year = {2026},
author = {Daşdemir, FO and Sari, MF and Aktaş, B and Kocazeybek, B},
title = {The Exposome-Autoimmunity Axis: Environmental Xenobiotics, Gut Dysbiosis, and Potential Pathways to Immunosenescence.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {116331},
doi = {10.1016/j.fct.2026.116331},
pmid = {42575421},
issn = {1873-6351},
abstract = {The escalating incidence of autoimmune diseases cannot be fully explained by genetics alone. It is increasingly linked to the exposome-the cumulative burden of lifelong environmental exposures. This review examines how pollutants (particulate matter, microplastics, agrochemicals, heavy metals) reshape the gut microbiota-immune axis and disrupt intestinal homeostasis. This triggers profound dysbiosis, characterized by reduced commensal diversity and expanded pathobionts. We highlight three mechanisms driving pollution-induced immune reprogramming: (i) barrier compromise facilitating metabolic endotoxemia; (ii) toxic Aryl Hydrocarbon Receptor (AhR) overactivation skewing the Th17/Treg balance; and (iii) epigenetic modifications like aberrant DNA methylation. Chronic environmental exposure accelerates telomere attrition, inducing premature immunosenescence and inflammaging. This promotes the pathological accumulation of senescent T cells and Age-associated B Cells (ABCs), linking environmental stress to tissue damage and autoantibody generation. However, a major limitation of the current literature is that many in vivo and in vitro models employ supraphysiological concentrations of pollutants that do not reflect actual human exposure scenarios. Without evaluating these specific exposure scenarios against realistic human gut concentrations, it is difficult to determine under which exact conditions the postulated dysbiotic effects occur. Ultimately, mitigating environmental risks and employing microbiota-targeted therapeutics are vital to restore barrier integrity.},
}

@article {pmid42575494,
year = {2026},
author = {Kim, JH and Choi, YJ and Yoo, JH},
title = {Gut microbiome: a key driver and therapeutic target of intestinal fibrosis in Crohn's disease.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2026.00013},
pmid = {42575494},
issn = {1598-9100},
abstract = {Intestinal fibrosis is a debilitating complication of Crohn's disease that often leads to stricture formation, requiring surgical intervention. Despite its clinical significance, effective anti-fibrotic therapies remain an unmet need. Emerging evidence highlights the gut microbiome as a central orchestrator of fibrogenesis, beyond its role in inflammation. This review provides a comprehensive overview of how microbial dysbiosis, which is marked by the expansion of pathobionts such as adherent-invasive Escherichia coli and Clostridium innocuum, drives intestinal fibrosis through multifaceted pathways. We delineate the direct activation of fibroblasts via pattern recognition receptors and indirect mechanisms involving macrophage polarization, T helper 17 cell responses, and the emerging role of the "creeping fat" axis. Furthermore, we discuss how microbial translocation into the mesenteric adipose tissue triggers a profibrotic environment. By synthesizing these mechanistic insights, we suggest that targeting the microbiome-fibrosis axis, through precision modulation of the microbiome or metabolite-based interventions, represents a promising frontier for preventing and reversing fibrostenotic Crohn's disease.},
}

@article {pmid42575708,
year = {2026},
author = {de Oliveira, AFB and Carneiro, BS and de Carvalho, JB and de Oliveira, AR and da Costa da Silva, AL and de Oliveira Veras, AA and Baraúna, RA and das Graças, DA},
title = {Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70396},
doi = {10.1111/1758-2229.70396},
pmid = {42575708},
issn = {1758-2229},
support = {445350/2024-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Metagenomics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism/drug effects ; *Xenobiotics/metabolism ; Brazil ; *Bathing Beaches ; *Drug Resistance, Bacterial ; Biodiversity ; *Drug Resistance, Microbial ; Phylogeny ; Biodegradation, Environmental ; Cities ; },
abstract = {Coastal ecosystems are vital for biodiversity but are increasingly threatened by urbanisation and pollution, which significantly alter local microbial communities. This study assessed bacterial diversity and functional profiles in urban and island beaches in Belém, Brazil. Urban beaches showed significantly higher microbial diversity and evenness, alongside functional plasticity due to pollutant input, while island beaches hosted more specialised and stable communities. Taxonomic analysis revealed the significant enrichment of opportunistic genera such as Comamonas, Clostridium and Paenibacillus in urban areas, and the massive dominance of Prochlorococcus and Candidatus Pelagibacter in island sites. Furthermore, shotgun metagenomics identified a robust genomic potential for xenobiotic degradation and antibiotic resistance in urban microbiomes, whereas island microbiomes were significantly enriched in genes for energy production and biosynthesis. These results underscore the ecological divergence between anthropogenically impacted and natural coastal environments, highlighting the importance of microbiome monitoring for sustainable coastal management.},
}

*Metagenomics
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism/drug effects
*Xenobiotics/metabolism
Brazil
*Bathing Beaches
*Drug Resistance, Bacterial
Biodiversity
*Drug Resistance, Microbial
Phylogeny
Biodegradation, Environmental
Cities

@article {pmid42575748,
year = {2026},
author = {Lourenço, M},
title = {Review: Trends in feed technology and feed additives for a sustainable and resilient livestock production.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {101909},
doi = {10.1016/j.animal.2026.101909},
pmid = {42575748},
issn = {1751-732X},
abstract = {Achieving sustainable and resilient livestock production depends on continued innovation in feed technology and feed additives. Automation, robotics, predictive modelling of effects, machine learning, encapsulation of nutrients and feed additives, precision nutrition, synbiotics, postbiotics and precision biotics are trending in the feed industry, although many are still in early stages of development. A deeper understanding is needed on how the nutritional composition of the feed influences the complex metabolic interactions, digestibility and performance of the host. These insights will allow a more precise feed formulation, improving feed efficiency, animal health and welfare, while reducing emissions and environmental impact of livestock production. This manuscript compiles trends and future perspectives in feed technology and feed additives that will contribute to more sustainable and resilient livestock production systems. Furthermore, the aim of this review article was to identify gaps in research in both areas in order to accelerate the introduction of promising innovations.},
}

@article {pmid42575931,
year = {2026},
author = {Schüßler, C and Chung, N and Léonard, R and Sprenger, H and Rödel, T and Mahoney, KE and Thomsen, S and Ocket, E and Matthaeus, C and Denis, J and Ebert, F and Wolf, M and Morelle, W and Foulquier, F and Braeuning, A and Masselot, CR and Malaker, SA and Maares, M},
title = {Transcriptome, glycome, and mucinome analysis reveal zinc is essential for the composition of mucus in the human goblet cell model HT-29-MTX.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42575931},
issn = {2045-2322},
mesh = {Humans ; *Zinc/metabolism/deficiency ; *Goblet Cells/metabolism ; *Mucins/metabolism/genetics ; Glycosylation ; *Mucus/metabolism ; *Transcriptome ; HT29 Cells ; Intestinal Mucosa/metabolism ; Glycomics ; },
abstract = {Zinc (Zn) deficiency affects approximately 1 billion people worldwide with severe consequences for their health, including increased intestinal infections, inflammation, and diarrhea. Accordingly, the intestinal defense barrier is compromised, leading to epithelial destruction and alteration of mucus. However, the processes and the extent to which Zn deficiency affects mucin synthesis in intestinal goblet cells (GCs) remain poorly understood. To this end, we investigated the impact of Zn deficiency on mucin expression and glycosylation in the human GC model HT-29-MTX. Zn deprivation altered the GC transcriptome, affecting genes involved in Zn transport, mucin synthesis and glycosylation. Accordingly, mucus composition was changed in Zn-deficient GCs, significantly increasing MUC2 and MUC17 on the mRNA and protein level. Several Zn transporters, mostly those associated with the early secretory pathway (ESP), were dysregulated, indicating an adaptive response of cellular Zn homeostasis. Additionally, free Zn was markedly reduced in the ESP, a critical location for glycosylation. Zn deficit substantially changed mucin glycosylation, characterized by an increase in sialylation and a strong decrease in complex N-glycans. All these changes involved widespread dysregulation of glycosyltransferase expression, including an increase in COSMC, a Zn-binding chaperone essential for the core 1 O-glycan formation. Collectively, our in vitro findings demonstrate that Zn is a critical regulator of mucin production and glycosylation in GCs. Zn deficiency might weaken the protective and functional qualities of intestinal mucus, increasing the risk of infections and potentially disrupting host-microbiome interactions.},
}

Humans
*Zinc/metabolism/deficiency
*Goblet Cells/metabolism
*Mucins/metabolism/genetics
Glycosylation
*Mucus/metabolism
*Transcriptome
HT29 Cells
Intestinal Mucosa/metabolism
Glycomics

@article {pmid42575975,
year = {2026},
author = {Pust, MM and Mohamed, AMT and Stražar, M and Arias-Rojas, A and Cunningham-Oakes, E and Brown, EM and Bumber, A and Pishchany, G and Li, C and Ananthakrishnan, AN and Darby, AC and Vlamakis, H and Plichta, DR and Xavier, RJ},
title = {Antisense transcription reveals disease-associated adaptations in the human gut microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42575975},
issn = {2058-5276},
support = {P30 DK043351//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 DK127171//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI172147//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 530694780//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {The gut microbiome is a dynamic ecosystem in which microorganisms constantly adjust their transcriptional programmes. Here we developed metastrand, a framework that integrates strand-aware metatranscriptomics and metagenomics to quantify mRNAs and antisense RNAs (asRNAs) in complex microbial communities at gene-level resolution. In inflammatory bowel disease (IBD), microbial asRNA programmes converged across patients during active disease, correlated with faecal metabolites and calprotectin levels and remained stable during persistent inflammation, highlighting their potential as biomarkers of inflammatory activity in the gut. These programmes involved antisense-to-sense transcriptional shifts at insertion sequence elements with functionally diverse passenger genes and preceded their detection at new genomic locations, linking asRNA dynamics to structural genome rearrangements and redistribution of adaptive functions under selective pressure. Similar dynamics were observed in a mouse model of colitis, oxidative stress in vitro and in patients with pathogen-confirmed gastroenteritis, establishing asRNAs as an important dimension of microbial adaptation in health and disease.},
}

@article {pmid42576026,
year = {2026},
author = {Shiba, S and Yachida, S and Mizutani, S and Totoki, Y and Nakamura, H and Hama, N and Miyoshi, N and Arai, Y and Saito-Adachi, M and Kimura, H and Hayashi, Y and Takamaru, H and Tanaka, K and Hayashi, R and Rokutan, H and Ikuta, S and Kanemitsu, Y and Doki, Y and Eguchi, H and Hattori, S and Saito, Y and Yamada, T and Shibata, T},
title = {Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {42576026},
issn = {1546-1718},
support = {JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP16H06279, 22K16336//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H03662, 23H02892, 25K21771//MEXT | Japan Science and Technology Agency (JST)/ ; },
abstract = {The incidence of colorectal cancer (CRC) has risen in recent decades, with a disproportionate increase observed among younger individuals in Japan and other countries. The etiological contribution of the gut microbiota to CRC pathogenesis is recognized, yet the mechanisms involved remain to be fully clarified. Here we integrated whole-genome sequencing (WGS) and transcriptome profiling of CRC with whole-genome metagenomic sequencing of fecal samples to interrogate host-microbiome interactions at high resolution. Application of interpretable artificial intelligence enabled the stratification of CRC into four distinct microbiome-informed subtypes. WGS analysis identified mutational signatures SBS88 and ID18, linked to colibactin exposure, as early clonal events detected in 44.8% of non-hypermutated patients. Notably, these signatures were significantly more frequent among patients born after the 1960s. Microbiome-based subclassification revealed subtype-specific clinical and molecular features. Collectively, our findings indicate that colibactin exposure constitutes a prevalent and potentially modifiable risk factor for CRC in the Japanese population.},
}

@article {pmid42576221,
year = {2026},
author = {Steele, S and Mazengenya, P and Chambuso, R},
title = {Correction: Pathology-derived clinical micro-architectural diagnostics of tumour-microbiome interactions in colorectal cancer.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
doi = {10.1186/s12967-026-08715-9},
pmid = {42576221},
issn = {1479-5876},
}

@article {pmid42576226,
year = {2026},
author = {Zhu, C and Hu, P and Yuan, P and Yu, J and Zhu, M and Ogamune, KJ and Huang, H and Kim, IH and Manyelo, TG and Ahmed, AA and Cai, D and Liu, H},
title = {Antibiotic exposure during weaning disrupts oral microbiota assembly in piglets.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42576226},
issn = {1674-9782},
support = {SJCX25_2359.//the Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; 32202717//Natural Science Foundation of China/ ; 2023YFD1301200//National Key R&D Program of China/ ; 2023YFD1801100//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: The use of antibiotics in swine production during the stressful weaning period is widespread. While their impact on the gut microbiome is documented, their effect on the developing oral microbiota, a critical gateway to systemic health, remains poorly understood. This study investigated how chronic exposure to tylosin (TYL) or a chlortetracycline-sulfadiazine-penicillin combination (CSP) shapes oral microbiota assembly in piglets from 21 to 60 days of age.

RESULTS: Healthy piglets exhibited a defined ecological succession, transitioning from an early, Pseudomonadota-dominated types of oral microbiota, or referred to as orotypes (driven by Moraxellaceae) at weaning to a stable, mature Bacillota-dominated state (driven by Lachnospiraceae) by 40 days of age. Antibiotic exposure disrupted this developmental program. CSP treatment locked the microbiota in an immature, Pseudomonadota-dominated state, while TYL promoted a dispersed and unstable Bacillota community. Dysbiosis was marked by enrichment of pathobionts (e.g., Moraxella, Bergeyella) and depletion of beneficial commensals like Veillonella and Phocaeicola, with the latter reduced in both the oral and gut microbiota. These structural shifts were linked to dysregulated microbial energy and lipid metabolism. Crucially, antibiotics compromised mucosal immunity, reducing salivary secretory IgA (SIgA), and provoked inflammation, evidenced by elevated salivary extracellular ATP (eATP), histological damage and transcriptome alteration in oral tissue, and changed serum metabolites.

CONCLUSIONS: Our findings demonstrate that early-life antibiotic exposure disrupts the developmental programming of the oral ecosystem. The oral microbiota serves as a sensitive indicator of antibiotic impact and a key mediator of systemic health, highlighting the need for strategies that safeguard microbial succession to promote sustainable swine health.},
}

@article {pmid42576411,
year = {2026},
author = {Botto, E and Lipman, ZM and Temiz, LA and Corea-Selm, L and Grichnik, JM},
title = {Antimicrobial Peptides of the Skin: Roles in Skin Cancer and Clinical Applications.},
journal = {Experimental dermatology},
volume = {35},
number = {8},
pages = {e70341},
doi = {10.1111/exd.70341},
pmid = {42576411},
issn = {1600-0625},
mesh = {Humans ; *Skin Neoplasms/metabolism/drug therapy ; Cathelicidins ; *Antimicrobial Peptides/therapeutic use/metabolism ; *Skin/metabolism ; *Antimicrobial Cationic Peptides/therapeutic use/metabolism ; S100 Calcium Binding Protein A7 ; Ribonucleases/metabolism ; Animals ; Skin Microbiome ; beta-Defensins/metabolism ; Peptides/metabolism ; Immunity, Innate ; S100 Proteins/metabolism ; },
abstract = {Cutaneous antimicrobial peptides (AMPs) are increasingly recognized for their multifaceted roles in skin disease and cancer, and thus application for therapeutic potential. Beyond their contributions to innate defence and the skin's microbiome, AMPs have been implicated in inflammatory skin conditions and cutaneous malignancies. Comprehensive summaries of AMPs' roles in skin cancer and related current clinical developments remain scarce, despite abundant emerging evidence of pro- and anti-tumour properties in other fields. This review provides a comprehensive discussion of AMPs, including dermcidin, psoriasin (S100A7), human cathelicidin (LL-37), RNase-7 and the human β-defensins, in the context of skin cancer research and clinical developments. These AMPs influence skin tumorigenesis through microbiome regulation, innate immune pathways and chronic inflammation, and although the mechanistic details are subject to scrutiny, several AMP-derived therapies, including LL-37 and LTX-315, have been developed for their potential in cutaneous oncology.},
}

Humans
*Skin Neoplasms/metabolism/drug therapy
Cathelicidins
*Antimicrobial Peptides/therapeutic use/metabolism
*Skin/metabolism
*Antimicrobial Cationic Peptides/therapeutic use/metabolism
S100 Calcium Binding Protein A7
Ribonucleases/metabolism
Animals
Skin Microbiome
beta-Defensins/metabolism
Peptides/metabolism
Immunity, Innate
S100 Proteins/metabolism

@article {pmid42576426,
year = {2026},
author = {},
title = {Correction to: Rapid resolution of colon inflammation and microbiome remodeling with vancomycin therapy in a patient with primary sclerosing cholangitis.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {8},
pages = {},
doi = {10.1093/ecco-jcc/jjag123},
pmid = {42576426},
issn = {1876-4479},
}

@article {pmid42576510,
year = {2026},
author = {Nio, SA and Mantilen Ludong, DP},
title = {Water Deficit During the Vegetative Stage Alters the Structure of Root-Associated Microbial Communities in Local North Sulawesi Rice.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {29},
number = {5},
pages = {243-250},
doi = {10.3923/pjbs.2026.243.250},
pmid = {42576510},
issn = {1812-5735},
mesh = {*Oryza/microbiology/growth & development/metabolism ; *Plant Roots/microbiology ; Droughts ; Water/metabolism ; *Microbiota/physiology ; Indonesia ; Rhizosphere ; },
abstract = {Background and Objective: Changes in rhizosphere microbial populations have been reported in response to drought, temperature fluctuations, CO2 levels and other environmental factors. However, the structure of the root-associated microbes in local North Sulawesi rice using a metagenomic approach has not yet been investigated. This study examined the microbial community structure in local North Sulawesi rice (cv. Superwin) under drought (water deficit) conditions compared to well-watered conditions at the vegetative phase. Materials and Methods: Rice plants were grown in polybags filled with a 5:1:1 mixture of garden soil, compost and rice husks and were allowed to grow until the four-fully-expanded leaf stage. They were then subjected to two treatments for 14 days: well-watered conditions (irrigated to 100% field capacity) and water deficit conditions (0% field capacity). Root samples were collected for next-generation sequencing analysis to assess molecular response of Superwin rice to water deficit. Results: During drought, several root-associated microbes were more prevalent, including Nitrospirota at the phylum level, Rubrobacteria at the class level, Micrococcales at the order level, Gaiellaceae at the family level, Gaiella at the genus level and Gaiella occulta at the species level. Conclusion: Root-associated microbes, including taxa Nitrospirota, Rubrobacteria, Micrococcales, Gaiellaceae, Gaiella and Gaiella occulta, have a higher relative abundance in rice plants under water deficit. Gaiella occulta serves as sensitive indicator of water deficit in North Sulawesi local rice, i.e. Superwin.},
}

*Oryza/microbiology/growth & development/metabolism
*Plant Roots/microbiology
Droughts
Water/metabolism
*Microbiota/physiology
Indonesia
Rhizosphere

@article {pmid42576522,
year = {2026},
author = {Hoque, MM and Akter, S and Mahir, JUK and Afrin, N and Shimu, SJ and Auny, FM and Sharker, SM and Mohib, MM and Uddin, MB and Mohiuddin, MS and Choubey, M},
title = {Diabetes and the Nervous System: Linking Peripheral Neuropathy to Central Neurodegeneration.},
journal = {Current diabetes reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115733998440886260306085847},
pmid = {42576522},
issn = {1875-6417},
abstract = {Diabetes mellitus affects both the peripheral and central nervous systems, giving rise to a spectrum of neurological complications that extend far beyond the traditional focus on diabetic peripheral neuropathy (DPN). Chronic hyperglycemia disrupts cellular homeostasis through increased formation of advanced glycation end-products, activation of inflammatory pathways, mitochondrial dysfunction, oxidative stress, and impaired neurovascular regulation. These disturbances converge to drive axonal degeneration, demyelination, synaptic injury, and progressive cognitive decline. Emerging evidence also highlights a critical role for gut dysbiosis and intestinal barrier dysfunction, which facilitate microbial translocation and systemic inflammation, ultimately disrupting the blood-brain barrier and amplifying neuroimmune injury. This narrative review synthesizes current mechanistic, clinical, and translational insights into how metabolic, inflammatory, vascular, and microbial pathways interact to produce diabetes-associated neurodegeneration. We summarize key molecular drivers-including mitochondrial ROS overproduction, microglial and astrocytic activation, endothelial dysfunction, and insulin resistance-while also describing their contributions to DPN, autonomic neuropathy, and diabetes-related cognitive impairment. We further integrate evidence from emerging therapeutic domains, including mitochondrial stabilizers, anti-inflammatory strategies, gut-microbiome modulation, and neurovascular-targeted interventions. Despite advances in understanding, disease-modifying therapies remain limited, and diagnostic tools for early detection are underutilized. Bridging these gaps will require longitudinal human studies, improved biomarkers, and integrative therapeutic approaches that target multiple convergent pathways. A deeper understanding of cross-talk among metabolic, immune, vascular, and microbial systems may enable earlier intervention and more effective strategies to mitigate the neurological burden of diabetes.},
}

@article {pmid42576570,
year = {2026},
author = {Mizutani, Y and Fujii, T and Maeda, Y and Funasaka, K and Ohno, E and Hirooka, Y and Watanabe, H and Tochio, T},
title = {A qPCR-based approach targeting the microbial gene marker nanA of mucin-degrading Akkermansia in Parkinson's disease.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X261462342},
doi = {10.1177/1877718X261462342},
pmid = {42576570},
issn = {1877-718X},
abstract = {BackgroundParkinson's disease (PD) is a multifactorial neurodegenerative disorder increasingly linked to gut microbiota alterations. However, despite advances in fecal microbiota profiling as a non-invasive approach to disease risk assessment, its clinical utility remains limited by a lack of functionally relevant microbial biomarkers.ObjectiveThis cross-sectional study aimed to identify a microbial gene marker reflecting metabolic potential associated with both the presence and severity of PD.MethodsFecal samples from patients with PD (n = 59) and healthy controls (n = 65) were analyzed by 16S rRNA sequencing to characterize taxonomic profiles. Quantitative PCR (qPCR) targeted the consensus sequence of the mucin-degrading nanA gene (nanAkk), a highly conserved within Akkermansia nan gene clusters. Differences in taxonomic composition and nanAkk abundance were examined, and correlations with clinical severity scores evaluated in the PD group.ResultsPatients with PD showed reduced abundance of short-chain fatty acid-producing taxa (Faecalibacterium, Blautia, and Anaerostipes) and increased levels of Akkermansia. Akkermansia abundance correlated positively with motor severity, including Hoehn-Yahr stage. Moreover, nanAkk levels also correlated positively with Hoehn-Yahr stage and were significantly elevated in PD patients compared with controls. Levels in the stage 4-5 group exceeded those in the stage 1-3 group (P = 0.0202), indicating a stage-related increase in mucin-degrading nanAkk abundance.ConclusionsWe have identified nanAkk as a microbial gene marker associated with both the presence and severity of PD. Our qPCR-based quantification shows potential as a non-invasive biomarker for disease stratification.},
}

@article {pmid42576645,
year = {2026},
author = {Lin, X and Chen, Z and Lu, B and Huang, G},
title = {[The role of the nasal microbiome in regulating upper airway immune homeostasis].},
journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery},
volume = {40},
number = {8},
pages = {777-782},
doi = {10.13201/j.issn.2096-7993.2026.08.014},
pmid = {42576645},
issn = {2096-7993},
mesh = {Humans ; *Homeostasis ; *Microbiota ; *Rhinosinusitis/microbiology/immunology ; Rhinitis, Allergic ; Dysbiosis ; *Nasal Mucosa/microbiology ; Chronic Disease ; Immunity, Innate ; },
abstract = {The nasal microbiome serves as a pivotal regulator of immune homeostasis in the upper airway. Under physiological conditions, it maintains immune equilibrium through mechanisms such as reinforcing the epithelial barrier and modulating innate and adaptive immune responses. Microbial dysbiosis, however, is recognized as a key trigger in the pathogenesis of chronic rhinosinusitis （CRS） and allergic rhinitis （AR）. This review summarizes how the nasal microbiome regulates immune homeostasis by influencing epithelial barrier function and immune responses in both health and disease states, with a focus on CRS and AR. It focuses on the characteristics of microbial dysbiosis and immunopathological mechanisms in CRS and AR, and provides perspectives on microbiome-based diagnostic biomarkers and microecological interventional therapeutic strategies.},
}

Humans
*Homeostasis
*Microbiota
*Rhinosinusitis/microbiology/immunology
Rhinitis, Allergic
Dysbiosis
*Nasal Mucosa/microbiology
Chronic Disease
Immunity, Innate

@article {pmid42576658,
year = {2026},
author = {Wali, AF and Talath, S and Rangraze, IR and El-Tanani, M and Khan, S},
title = {Microbiome-Driven Mechanisms in Breast Cancer: Emerging Evidence From Gut Microbial Signatures to Therapeutic Response.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e8376859},
pmid = {42576658},
issn = {2314-6141},
mesh = {Humans ; *Breast Neoplasms/microbiology/therapy ; Female ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; },
abstract = {Breast cancer remains the most frequently diagnosed malignancy among women worldwide, and increasing evidence indicates that the gut microbiome plays a significant role in tumor initiation, progression, and therapeutic response. Microbial dysbiosis and altered metabolite production have been associated with systemic inflammation, estrogen metabolism, immune regulation, and metabolic reprogramming, all of which contribute to breast cancer biology. This review summarizes current preclinical and clinical evidence describing the gut-breast cancer axis and its mechanistic and translational relevance. The review focuses on four major pathways through which gut microbiota may influence breast cancer development and treatment outcomes: immune modulation, estrobolome-mediated estrogen recycling, chronic inflammatory signaling, and microbial metabolite-driven epigenetic and metabolic regulation. Evidence from experimental models and human studies demonstrates that alterations in microbial diversity and enrichment of proinflammatory taxa are associated with tumor progression, subtype-specific biology, and variability in therapeutic response. Emerging findings further indicate that microbiome composition can influence the efficacy and toxicity of chemotherapy, endocrine therapy, radiotherapy, and immunotherapy, highlighting the potential of microbiome-informed precision oncology strategies. In addition, this review discusses current advances in microbiome-targeted interventions including probiotics, dietary modulation, postbiotics, and fecal microbiota transplantation. Despite promising translational potential, significant challenges remain regarding mechanistic validation, standardization of microbiome profiling, reproducibility across cohorts, and clinical implementation. Future research integrating longitudinal multiomics approaches, functional validation studies, and personalized microbiome-based therapeutic strategies may facilitate the development of clinically actionable microbiome interventions for breast cancer management.},
}

Humans
*Breast Neoplasms/microbiology/therapy
Female
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
Animals
Probiotics/therapeutic use

@article {pmid42576686,
year = {2026},
author = {Jeong, DY and Daily, JW and Yang, HJ and Ryu, MS and Ha, GS and Seo, JW and Park, S},
title = {Postbiotic mechanisms of long-term fermented soybean foods in host immunometabolic regulation: a critical appraisal of evidence, contradictions, and precision nutrition perspectives.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/10408398.2026.2715172},
pmid = {42576686},
issn = {1549-7852},
abstract = {Traditionally made long-term fermented soybean (LTFS) foods, including doenjang, miso, ganjang, and douchi, are produced through months to years of fermentation under high-salinity conditions (12-20% NaCl), generating convergent postbiotic profiles comprising free amino acids, isoflavone aglycones, bioactive peptides, indole derivatives, and gamma-aminobutyric acid. These postbiotics engage host immune, metabolic, and redox signaling through AMPK-SIRT1 activation, NF-kB and RAAS suppression, Nrf2-Keap1 induction, and aryl hydrocarbon receptor signaling. Epidemiological evidence from Korean, Japanese, and Chinese cohorts consistently associates LTFS consumption with improved metabolic outcomes despite high concomitant sodium exposure, suggesting that fermentation-derived bioactive compounds suppress the adverse metabolic consequences of sodium. However, most mechanistic evidence derives from cell and animal models, and human intervention data directly measuring signaling endpoints remain sparse. Gut microbiota biotransformation of LTFS-derived bioactive compounds generates secondary metabolites with distinct biological activities, contributing to substantial inter-individual variability in physiological responses and underscoring the need for precision nutrition approaches that account for individual microbiota composition, metabolic phenotype, and genetic background. This review critically evaluates evidence within a postbiotic-to-signaling framework, distinguishes associative observational findings from preclinical mechanistic evidence, identifies contradictions and null findings, and highlights research priorities including standardized metabolite profiling and human intervention studies with mechanistic biomarker endpoints.},
}

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

@article {pmid42576818,
year = {2025},
author = {Pearce, DA and Crown, M and Nelson, A and Jabeen, K and Thompson, JR and Argyraki, A and Hursthouse, AS and Bashton, M and Entwistle, JA},
title = {House dust-a Pandora's box of antimicrobial resistance (AMR) activity?.},
journal = {Sustainable microbiology},
volume = {2},
number = {4},
pages = {qvaf022},
pmid = {42576818},
issn = {2755-1970},
abstract = {The presence and spread of Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistant Genes (ARGs) in the environment is now recognised as one of the top ten global public health threats to humanity. In a previous study, we used citizen science and MiSeq to target 16S rRNA gene amplicons to investigate house dust microbiomes across diverse households and found a core microbiome. In this study, we used shotgun metagenomics to target antimicrobial resistance (AMR) genes in order to investigate the potential for functional differences and to test the hypothesis that there was a core resistome associated with this core microbiome, including any patterns in a core resistome in terms of likely origin and mechanisms of action. In this study we did not find a core resistome, but found that the predominant and most diverse mechanisms of Anti-Microbial Resistance (AMR) in the dust samples were antibiotic target alteration and antibiotic efflux, accounting for ∼70% of cumulative RPKMs detected, potentially representing a compromise between the certainty of working and energy investment required. Despite the core home microbiome previously detected in diverse house dust samples, there was only limited evidence for a core resistome, with only two AMR genes present in all samples.},
}

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

@article {pmid42576846,
year = {2024},
author = {Danchin, A},
title = {Exploring overlooked growth-promoting mechanisms by plant-associated bacteria.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae011},
pmid = {42576846},
issn = {2755-1970},
abstract = {Agriculture-oriented microbiome studies try to develop microbiota beneficial to their plant hosts. This positive goal extends to the soil quality driving plant growth and disease resistance. In research aimed at identifying the causes of this beneficial action, a common interpretation is that microbes will synthesize metabolites useful to their hosts. This view assumes that important microbial metabolites are exported for use by their hosts. Yet, this seems unlikely for essential metabolites, without a counterpart imported from the plants, as the corresponding syntheses would often involve the consumption of resources without explicit benefit to the microbes. Illustrating this function with the example of Bacilli of the Subtilis clade, we emphasize here that the most direct access to the contents of microbial cells is through cell lysis, a phenomenon often linked to the process of sporulation. This process also releases macromolecules that are digested in the environment, releasing key metabolites such as queuine, an important base analog present in the anticodon of some transfer RNAs. This overlooked importance of cell lysis could also be a major cause of the ubiquitous presence of bacteriophages in microbiota.},
}

@article {pmid42576847,
year = {2026},
author = {Wicaksono, WA and Bickel, S and Peissl, J and Marzban, N and Hoefle, D and Abdelfattah, A and Antonietti, M and Berg, G},
title = {Microbiome interventions combined with artificial humic acid treatments for restoring soil bacterial diversity.},
journal = {Sustainable microbiology},
volume = {3},
number = {2},
pages = {qvag012},
pmid = {42576847},
issn = {2755-1970},
abstract = {Soil health is under threat worldwide and technologies for soil restoration are urgently needed. Here we study the effect of artificial humic acids (A-HA) and soil transplants fo one restoration of depleted soil microbiomes. We used a controlled microcosm experiment with gradients of microbial diversity, with and without A-HA, across three soil types. Microbial abundance, diversity, and composition were assessed using qPCR and 16S rRNA gene amplicon sequencing, complemented by metabolomic profiling of water-extractable compounds and the growth characterization of bacterial isolates. A-HA treatment had a stronger effect on bacterial richness and community structure in degraded than in the original soil. Soil microbiome transplants could partially regenerate microbial abundances and increased bacterial richness and diversity in the degraded soils. Interestingly, the combination of A-HAs with addition of 10% soil transplants yielded the best restoration effect. The effect of individual as well as combined treatments strongly depended on the composition of the native soil microbiome. From a mechanistic point of view, A-HA treatment inhibited fast-growing bacteria, which allowed slow-growing bacteria to recover. By combined treatment, depending on the soil type and its native soil microbiome, we can synergistically restore the soil microbiome to resemble its original composition.},
}

@article {pmid42576849,
year = {2026},
author = {Chi, F and Chen, K and Yin, Y and Hakovirta, JR and Saris, PEJ},
title = {From dysbiosis to dysfunction: specific gut microbes and metabolites in the pathogenesis of Parkinson's disease.},
journal = {Sustainable microbiology},
volume = {3},
number = {1},
pages = {qvag002},
pmid = {42576849},
issn = {2755-1970},
abstract = {Parkinson's disease (PD) involves a complex interplay between the gut microbiota, their metabolites, and host neurophysiology. Studies across independent cohorts have begun to reveal reproducible microbial signatures, with taxa such as Desulfovibrio spp., Akkermansia, and Bifidobacterium repeatedly enriched, whereas Prevotellaceae and Faecalibacterium are consistently reduced. Beyond these broad compositional patterns, several species and strains-including Helicobacter pylori, curli-producing Escherichia coli, and Desulfovibrio spp.-have been linked to processes such as α-synuclein aggregation, immune activation, and dopaminergic vulnerability. Microbial metabolites including short-chain fatty acids, hydrogen sulfide, lipopolysaccharides, bile acids, and iron-related compounds provide additional mechanistic connections, influencing gut barrier function, inflammatory responses, and neuronal homeostasis. In this review, we bring together findings from taxonomic, metabolic, and mechanistic studies, evaluate the therapeutic potential of microbiota-targeted interventions. Future research should pivot from descriptive microbiome profiling toward mechanistic studies that delineate causal relationships between defined microbes, their metabolites, and PD pathology. Such efforts are essential for identifying early diagnostic biomarkers and developing targeted microbiota-based therapies that could alter the clinical course of PD.},
}

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

@article {pmid42576857,
year = {2024},
author = {Lang, JC and Shahata, M and Melican, K},
title = {Towards sustainable antimicrobial therapies for Staphylococcus aureus skin infections.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae023},
pmid = {42576857},
issn = {2755-1970},
abstract = {Skin and soft tissue infections (SSTIs) are a major economic and clinical burden. With the emergence of increasing antimicrobial resistance, novel treatment options, as well as advanced drug delivery systems will be essential to fight these infections and meet the UN Sustainability Development Goals (SDGs). SSTIs are commonly caused by Staphylococcus aureus, including the infamous MRSA (methicillin-resistant S. aureus). In this short review, we discuss new antimicrobial therapies with potential to combat skin infections caused by S. aureus. This includes discussion of antimicrobial strategies originating from both the host and microbiota. Adapting immunotherapy-type approaches to infection is also discussed, giving examples of cellular targets of interest. We examine the difficulties of therapeutic delivery into a barrier tissue such as skin and discuss exciting new developments in interdisciplinary approaches that may help overcome these challenges.},
}

@article {pmid42576865,
year = {2024},
author = {Lynch, J},
title = {Rhizomicrobiomics.},
journal = {Sustainable microbiology},
volume = {1},
number = {1},
pages = {qvae016},
pmid = {42576865},
issn = {2755-1970},
abstract = {Rhizomicrobiomics is the study of plant-associated microbes as a strategy for achieving sustainable development goals. With the development of the concept of microbiomes of soil/plant systems, the history leading to this concept over more than a century is reviewed. Microbial growth and community dynamics are discussed from both laboratory and field perspectives. The first use of the term microbiome applied to biological control of plant diseases, but it now seems appropriate to use the specific term rhizomicrobiome to describe the myriads of microbial functions that influence soil health, food production, bioremediation, and climate change. The advance and implications of molecular biology and modern imaging, along with functional analysis of ecosystems from space, coupled with artificial intelligence and machine learning, are indicated as ways to investigate the application of rhizomicrobiomics in achieving the UN Sustainable Development Goals to generate a cleaner planet and secure the future supply of food.},
}

@article {pmid42576872,
year = {2026},
author = {Madakaripura Rangaswamy, GG and Pasupuleti, S and Umfuyisoni, J and Chapman, TA and Plett, JM and Nielsen, UN},
title = {Harnessing indigenous bacterial defenders to improve disease resistance and plant health in vegetable Brassica crops.},
journal = {Sustainable microbiology},
volume = {3},
number = {3},
pages = {qvag025},
pmid = {42576872},
issn = {2755-1970},
abstract = {Vegetable crops in the Brassicaceae family have significant economic and nutritional value, supporting livelihoods worldwide. Despite ongoing efforts to control pathogens, infections continue to degrade crop quality and yield. Rising disease incidence, coupled with restrictions on chemical treatments and limited alternatives, has heightened the need for new, sustainable disease management approaches. The plant microbiome plays a crucial role in sustaining plant health and resilience under stress. Harnessing the microbiome provides an environmentally friendly means to enhance crop production by improving disease resistance. This review summarizes knowledge on how beneficial bacteria could be used to enhance plant health and disease resistance in Brassica crops, highlighting a preference for indigenous bacteria adapted to local growing conditions. We explore the composition and dynamics of the Brassica bacterial microbiome, detailing functional characteristics, biocontrol mechanisms, and potential approaches to optimize the balance between Brassica growth and defence under stress. We discuss methodologies for identifying and characterizing beneficial bacteria, their applications and management, and emphasize challenges hindering broad implementation. This synthesis shows that utilizing indigenous Brassica-associated bacteria through careful isolation, multitraits assessment, and the development of region-specific consortia offers the most reliable path to sustainable disease management. This approach links ecological adaptation with practical agricultural applications.},
}

@article {pmid42576877,
year = {2025},
author = {Page, LD and Strauss, J and Jacobs, K},
title = {The effect of crop-rotation systems in regenerative agricultural environments on the rhizosphere microbiome of dry-land winter wheat.},
journal = {Sustainable microbiology},
volume = {2},
number = {4},
pages = {qvaf020},
pmid = {42576877},
issn = {2755-1970},
abstract = {Regenerative agriculture is a multifaceted approach that aims at transitioning farmers from conventional to sustainable management practices, by increasing biodiversity, functional redundancy, and nutrient cycling efficiency in the soil. This study investigated the effects of three crop rotation systems, wheat after wheat, wheat after medicago, and wheat after canola on the soil fungal and bacterial communities, in a regenerative agriculture system, in the Western Cape, South Africa, following a record-breaking drought (2015-19). Utilizing 16S rRNA and ITS (Internal transcribed spacer region) targeted amplicon sequences, soil-geochemical properties, and qPCR (Quantitative Polymerase Chain Reaction) analyses, it was found that crop rotations had little significant effect on the alpha-diversity between different crop-rotation systems . Medicago and wheat had the most similar communities, with canola diverging from the other rotation systems. Host driven selection was prevalent in the rhizosphere microbiome during the wheat growth period, across treatments and farms. After senescence, the microbiome composition transitioned from the wheat-selected communities towards communities consisting of saprotrophs and yeasts. qPCR analyses of nitrogen-associated genes revealed that genes for nitrification (amoA) and denitrification (nirK) increased during fertilizer application events, whereas genes associated with nitrogen fixation (nifH), denitrification (nirS), and nitrification (nxrB) increased throughout the season. Genera associated with drought and halotolerance were enriched in all samples.},
}

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

@article {pmid42576908,
year = {2026},
author = {Tarnowski, MJ and Stawowy, A and Sonnenschein, EC},
title = {Plastic additives enrich diverse bacterial communities which show the hallmarks of plastic degradation.},
journal = {Sustainable microbiology},
volume = {3},
number = {1},
pages = {qvag003},
pmid = {42576908},
issn = {2755-1970},
abstract = {Plastics contain a variety of chemical additives that enhance their performance but often pose environmental risks due to their persistence and leaching. Microbial degradation offers a promising strategy to mitigate these pollutants, yet efficient methods to identify active degraders remain limited. This project aims to combine biochemical assays with 16S rRNA amplicon sequencing to screen microbial communities for plastic additive biodegradation. Inocula from natural (Chessel Bay, Swansea Bay) and anthropogenic (Wastewater Plant, Recycling Plant) environments were enriched for 22 days, using di(2-ethylhexyl) terephthalate (DEHT) and tetradecane and compared to negative controls. We adapted high-throughput assays to measure community-level growth, death, redox, and esterase activity. DEHT yielded the highest growth, while tetradecane enhanced redox activity. 16S rRNA amplicon sequence analysis identified 957 amplicon sequence variants across 36 cultures. PERMANOVA showed that the substrate explained 39%-63% of the variance in community structure. Both additives enriched bacterial families known to degrade plastics (e.g. Nocardiaceae, which correlated with esterase activity). Other bacterial families not previously associated with plastic degradation (e.g. Vermiphiliaceae) highlight potential for plastic and additive biodegradation. These results demonstrate that diverse environmental microbiomes can metabolize ester- and alkane-based plastic additives. Our methods enable scalable screening of biodegradative communities for bioremediation applications.},
}

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

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

@article {pmid42577073,
year = {2026},
author = {Gomes, MP and Maranho, LT and Espindola, LEC and Yamamoto, FY},
title = {Plant stress physiology under environmental emerging contaminant exposure: from molecular responses to phytoremediation applications.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1877141},
pmid = {42577073},
issn = {1664-462X},
abstract = {The increasing occurrence of emerging environmental contaminants (EECs) in terrestrial and aquatic ecosystems is reshaping plant physiological performance, with implications extending from cellular metabolism to ecosystem function and phytoremediation performance. Pharmaceuticals, pesticides, PFAS, nanomaterials, and plastic-derived particles differ substantially in their physicochemical properties, uptake behavior, intracellular mobility, and biological targets, resulting in highly variable physiological outcomes. Here, we synthesize recent advances in plant stress physiology under EEC exposure through an integrated mechanistic framework linking contaminant uptake and translocation, detoxification pathways, oxidative stress dynamics, phytohormonal signaling, microbiome interactions, and translational phytoremediation strategies. Evidence compiled across contaminant classes demonstrates that plant toxicity is primarily governed by internal exposure dynamics rather than external concentrations alone. Across studies, plant responses frequently exhibit nonlinear physiological patterns, including antioxidant enzyme induction ranging from approximately 1.5- to 4.6-fold, glutathione depletion of 20-50%, nitrate reductase inhibition of 20-60%, and contaminant-specific hormonal responses varying from moderate abscisic acid increases (2-3-fold) to >10-fold jasmonate accumulation under severe stress conditions. Physicochemical properties, vascular transport constraints, and rhizospheric interactions collectively determine the compartmentalization of contaminants, ROS generation, metabolic disruption, and stress signaling outcomes. Oxidative stress emerges as a recurrent integrative regulatory interface linking xenobiotic perception with hormonal reprogramming, detoxification processes, and physiological acclimation, although its magnitude and mechanistic contribution remain dependent on the contaminant and tissue. Importantly, the literature reveals strong nonlinearities in plant responses to contaminant mixtures and co-occurring climate-related stressors, highlighting the limitations of reductionist single-stressor approaches. Recent findings have further demonstrated that plant-associated microbiota substantially influence contaminant fate, redox balance, and phytoremediation efficiency, supporting the concept of holobiont-mediated contaminant tolerance. Finally, advances in omics technologies, microbiome engineering, ecological treatment systems, and predictive modeling are progressively transforming phytoremediation into a physiology-informed and engineerable nature-based solution. Collectively, this review establishes a systems-level framework connecting contaminant transport, redox regulation, hormonal signaling, and microbiome functionality, providing mechanistic insights essential for environmental monitoring, risk assessment, and sustainable remediation under global-change scenarios.},
}

@article {pmid42577254,
year = {2026},
author = {Ouedraogo, FJ and Poulain, AJ and Aris-Brosou, S},
title = {Glacial meltwater is associated with gene-specific diversification of metal resistance genes in high Arctic soil microbiomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1903619},
pmid = {42577254},
issn = {1664-302X},
abstract = {Climate warming accelerates glacial meltwater delivery to Arctic lakes, mobilizing metals from thawing catchments and reshaping the selective landscape experienced by resident microbes. Whether these gradients leave detectable signatures of diversification in environmental resistance genes remains unclear. We investigated four metal resistance genes (merA, arsC, cadA, and chrR) in metagenomic datasets from Lake Hazen (Nunavut, Canada), the largest High Arctic freshwater lake, sampled across a natural hydrological gradient of Control, Low-runoff, and High-runoff regimes. Using a space-for-time substitution design, we combined population-genetic and codon-based approaches to quantify diversity and candidate selection signals, including nucleotide diversity, Tajima's D, non-synonymous-to-synonymous diversity ratios, McDonald-Kreitman tests with outgroup-sensitivity analysis, site-level episodic selection (MEME with false-discovery-rate correction), and gene-wide tests (BUSTED and BUSTED-E) and complemented these with ortholog clustering, within-clade re-analysis, taxonomic profiling, rarefaction, and phylogenetic beta-diversity. Marked heterogeneity emerged among genes: merA showed increasing diversity and patterns consistent with diversification along the runoff gradient, and these signals were preserved within the largest orthologous cluster (90% of haplotypes), supporting an interpretation of within-orthogroup diversification; cadA displayed the strongest McDonald-Kreitman signal under low and high runoff, but its gene-wide BUSTED-E signal collapsed within a single ortholog cluster, suggesting that part of the apparent diversifying signal at the gene-family level reflects inter-subfamily heterogeneity; chrR exhibited the strongest regime structure but its largest orthologous cluster was dominated by Control sequences and 93% of High-regime haplotypes were affiliated with a single bacterial order (Hyphomicrobiales), indicating that the regime contrast for this gene reflects compositional turnover rather than within-lineage evolution; arsC remained largely consistent with neutral or purifying evolution across regimes. Because these inferences derive from metagenomic gene pools sampled across only three hydrological regimes and aggregate variants across taxa, we interpret them as exploratory, hypothesis-generating patterns rather than as demonstrations of population-level adaptation. Our findings highlight environmental resistance genes as candidate indicators of changing biogeochemical conditions in rapidly warming polar ecosystems, while underscoring the importance of orthology and community-composition controls when inferring selection from metagenomic data.},
}

@article {pmid42577386,
year = {2026},
author = {Kumagai, T and Rath, S and Fan, S and Rahman, FZ and Smith, AM},
title = {Environment shapes gut microbiome and determines susceptibility to DSS-colitis in Adamdec1[-/-] mice.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1824007},
pmid = {42577386},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Colitis/chemically induced/microbiology/genetics/immunology ; Mice ; Mice, Knockout ; Dextran Sulfate ; *Gene-Environment Interaction ; Mice, Inbred C57BL ; Disease Susceptibility ; Disease Models, Animal ; *ADAM Proteins/genetics ; Environment ; Male ; Genetic Predisposition to Disease ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is characterized by marked clinical heterogeneity, reflecting complex interactions between host genetics, environmental exposures, and the gut microbiome. Although over 300 genetic risk loci have been identified, these account for only a fraction of disease variance, highlighting the importance of gene-environment interactions. ADAM-like Decysin-1 (ADAMDEC1) is a gastrointestinal-restricted metalloprotease implicated in mucosal repair and immune regulation, with reduced expression reported in IBD. While Adamdec1-deficient mice exhibit increased susceptibility to colitis, the mechanisms underlying phenotypic variability remain poorly understood.

METHODS: To dissect genetic and environmental contributions to colitis severity, C57BL/6J wild-type (WT) and Adamdec1[-/-] mice were co-housed in two distinct environments and subjected to dextran sodium sulfate (DSS)-induced colitis. Disease severity was assessed by weight loss, immune cell infiltration, and transcriptional profiling of inflammatory and epithelial repair markers using flow cytometry and qPCR. Gut microbiome composition was analyzed from fecal samples collected following extended co-housing to evaluate environment-driven microbial differences.

RESULTS: Environmental factors exerted a stronger influence than genotype on gut microbiome composition. WT mice displayed consistent inflammatory and transcriptional responses to DSS across environments, whereas Adamdec1 [-/-] mice exhibited marked cage-dependent variability, ranging from severe colitis to a mild, WT-like phenotype. Severe disease in Adamdec1 [-/-] mice was associated with enhanced neutrophil recruitment, increased CD11b expression, altered monocyte/macrophage activation, impaired epithelial proliferation, and disrupted stem cell-associated gene expression. These phenotypic differences correlated with distinct microbiome profiles indicating genotype-dependent microbial pathogenicity.

CONCLUSION: These findings demonstrate that loss of Adamdec1 creates a state of heightened sensitivity to environmental and microbiome related factors, in which gut microbial composition correlates with differences in inflammatory and epithelial outcomes during colitis. This study identifies a gene-environment-microbiome axis associated with phenotypic variability in intestinal inflammation and provides mechanistic insight into the heterogeneity of IBD. Targeting environmentally driven microbial modifiers may represent a promising strategy for personalized intervention in genetically susceptible individuals.},
}

Animals
*Gastrointestinal Microbiome
*Colitis/chemically induced/microbiology/genetics/immunology
Mice
Mice, Knockout
Dextran Sulfate
*Gene-Environment Interaction
Mice, Inbred C57BL
Disease Susceptibility
Disease Models, Animal
*ADAM Proteins/genetics
Environment
Male
Genetic Predisposition to Disease

@article {pmid42577387,
year = {2026},
author = {Bautista, J and López-Cortés, A},
title = {The microbiome as a systems-level regulator of immune, metabolic, neural, and endocrine signaling in cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1887873},
pmid = {42577387},
issn = {1664-3224},
mesh = {Humans ; *Neoplasms/metabolism/immunology/microbiology ; *Signal Transduction ; *Microbiota/immunology ; Animals ; Endocrine System/metabolism ; Dysbiosis/immunology ; },
abstract = {Cancer progression and therapeutic response remain highly variable across tumor types and are not fully explained by tumor-intrinsic alterations alone. The human microbiome has emerged as a systems-level regulator of cancer biology, integrating signals across immune, metabolic, neural, and endocrine axes. Microbial dysbiosis is associated with sustained inflammatory activation, genomic instability, and epigenetic reprogramming, linking microbial composition with tumor development. Microbiome-derived metabolites, including short-chain fatty acids (SCFAs), bile acids, and tryptophan derivatives, act as intermediates connecting microbial activity with host signaling networks that regulate immune cell function, metabolic pathways, neuroimmune communication, and hormonal balance. Convergence occurs through shared intracellular pathways, including NF-κB, STAT3, and WNT/β-catenin, shaping tumor initiation, progression, and therapeutic response. Microbiome-associated profiles have been proposed as diagnostic, prognostic, and predictive biomarkers, although clinical implementation remains limited by methodological variability, cohort heterogeneity, and lack of causal validation. The review integrates current evidence within a unified systems-level framework, defines mechanistic links between microbial functional outputs and host signaling pathways, and discusses microbiome-targeted strategies with relevance for precision oncology.},
}

Humans
*Neoplasms/metabolism/immunology/microbiology
*Signal Transduction
*Microbiota/immunology
Animals
Endocrine System/metabolism
Dysbiosis/immunology

@article {pmid42577390,
year = {2026},
author = {Krämer, CL and Ly-Sauerbrey, Y and Maier, M and Kadler, L and Rehm, A and Walkenfort, B and Neidhöfer, C and Leuko, S and Schwengers, O and Hasenberg, M and Timofeev, SM and Janssen, S and Beblo-Vranesevic, K and Döscher-Siems, K},
title = {Community matters: stress tolerance and survival of Bacillus subtilis and Staphylococcus capitis in a synthetic space habitat consortium.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1869903},
pmid = {42577390},
issn = {1664-302X},
abstract = {INTRODUCTION: Conventional microbiological methods typically examine isolated bacterial species, which limits the insight into how microorganisms behave in more realistic, complex ecosystems. In contrast, synthetic bacterial consortia offer a practical and ecologically meaningful model for studying species interactions and responses to stress. These interspecies dynamics, both cooperative and competitive, can significantly influence the survival and physiology of individual species, revealing patterns that single-species tests often miss. Exploring microbial resilience under stress is vital for advancing space microbiology and ensuring the functionality of enclosed environments like the International Space Station (ISS) and in the future in spacecraft traveling to the Moon or Mars.

METHODS: To assess the stress tolerance of bacterial species within a consortium, a synthetic bacterial consortium was constructed using species representative of the spacecraft microbiome, including genera such as Bacillus, Pseudomonas, and Staphylococcus. The stress tolerance of Bacillus subtilis and Staphylococcus capitis was evaluated both individually and within the defined consortium under spaceflight-relevant conditions, including desiccation, X-ray irradiation, and hydrogen peroxide exposure. Survival rates were quantified by colony-forming unit (CFU) counts. Co-cultivation approaches were employed to assess biofilm formation and growth within the consortium. Consortium dynamics following stress exposure and cultivation were further investigated using 16S rRNA gene sequencing.

RESULTS: The stress tolerance of B. subtilis and S. capitis differed between individual exposure and consortium conditions. Hereby, the consortium context influenced stress responses in a stressor-specific manner. Co-cultivation experiments demonstrated observable growth in various combinations of consortium members, with differences in early-stage biofilm formation and CFU counts noted. Investigations of consortium dynamics revealed a statistically significant difference before and after incubation indicating that over time the consortium reaches a stabilized relative abundance profile.

DISCUSSION: Our findings underscore the importance of considering community-level interactions when evaluating bacterial stress tolerance. Synthetic bacterial consortia represent a valuable approach to bridging the gap between reductionist and systems-level microbiology, offering critical insights for both terrestrial biotechnology and the advancement of space exploration.},
}

@article {pmid42577410,
year = {2026},
author = {Fan, J and Tan, X and Liu, Y and Liu, Z and Dai, J and Wang, L},
title = {Association of gut microbiome signatures with iron metabolism response to roxadustat in peritoneal dialysis patients with anemia: a cross-sectional study.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1862547},
pmid = {42577410},
issn = {1663-9812},
abstract = {BACKGROUND: Anemia in chronic kidney disease (CKD) is associated with increased cardiovascular risk, impaired quality of life, and reduced survival. Roxadustat, a hypoxia-inducible factor prolyl hydroxylase inhibitor (HIF-PHI), has demonstrated non-inferior efficacy to erythropoiesis-stimulating agents (ESAs) for anemia correction in CKD. Gut microbiota modulate the intestinal HIF-iron metabolism axis, thereby regulating intestinal iron absorption. This cross-sectional study investigated the association between gut microbiome composition and iron-metabolism response to roxadustat, and developed a logistic regression model to identify factors associated with iron metabolism non-response in anemic patients undergoing peritoneal dialysis (PD).

METHODS: Demographic and clinical data were collected at study enrollment, and fecal samples underwent 16S rRNA gene sequencing. Microbial taxa associated with the iron-metabolism response to roxadustat were identified using linear discriminant analysis effect size (LEfSe), differential abundance analysis with DESeq2, and Spearman's rank correlation analysis. Key microbial features were further selected using random forest analysis. Multivariable logistic regression models were constructed using R software (version 4.2.3). Variable selection was performed through stepwise selection based on the Akaike information criterion. Model performance was evaluated with the area under the receiver operating characteristic curve, calibration curves, and decision curve analysis. Internal validation was performed using 10-fold cross-validation and bootstrapping with 1,000 iterations.

RESULTS: The overall iron-metabolism response rate to roxadustat was 39% among the enrolled participants. Random forest analysis identified microbial features associated with the iron-metabolism response to roxadustat. The final multivariable model included Clostridium perfringens, Propionibacterium acnes, Bacilli, Paraeggerthella hongkongensis, compound α-ketoacid tablets, and antihypertensive medication. The final model achieved an AUC exceeding 0.8, with favorable calibration and clinical utility, and showed good discriminative performance for iron metabolism non-response to roxadustat in PD patients.

CONCLUSION: Distinct gut microbiome signatures are associated with the iron metabolism response to roxadustat in anemic PD patients.},
}

@article {pmid42577422,
year = {2026},
author = {Linghu, T and Hu, T and Wu, Z and Wang, Q and Zhao, Y and Wang, Y and Li, K and Qin, X and Tian, J and Zhang, R},
title = {Intestinal microbial remodeling and metabolite regulation may be related to the improvement of social avoidance in depressed mice by Modified Xiaoyaosan.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1774975},
pmid = {42577422},
issn = {1664-302X},
abstract = {BACKGROUND: Increased intestinal permeability is implicated in the pathogenesis of depression. Modified Xiaoyaosan (MXYS) has demonstrated antidepressant-like effects in chronic social defeat stress (CSDS) mice, particularly in improving social avoidance behavior. However, direct evidence that MXYS improves depressive behavior by regulating intestinal permeability remains lacking.

METHODS: Using a CSDS-induced depression mouse model, we investigated the effects of MXYS through an integrated multi-omics approach, combining intestinal histopathology, microbiome, metabolomics, and molecular biology techniques. This strategy allowed systematic assessment of pathological changes, gut microbial composition, metabolite profiles, and protein expression.

RESULTS: MXYS treatment significantly alleviated social avoidance behavior in CSDS mice. It upregulated the expression of tight junction proteins in the colon, jejunum, and hippocampus. MXYS also reduced serum permeability markers of lipopolysaccharide (LPS), D-lactate (D-Lac), and diamine oxidase (DAO), as well as concentrations of pro-inflammatory cytokines TNF-α and IL-1β in both intestinal tissues and the hippocampus. Gut microbiota analysis revealed that MXYS notably decreased the relative abundance of Desulfovibrio in the colon, which was associated with modulation of β-alanine metabolism. In the jejunum, MXYS increased the relative abundance of Clostridium sp. mbf VZ-132 and influenced glycerophospholipid metabolism.

CONCLUSION: MXYS alleviates social avoidance in CSDS-induced depressed mice is associated with the restoration of intestinal barrier function via gut microbiota-mediated pathways. Specifically, it may reduces colon Desulfovibrio abundance to modulate β-alanine/aspartate metabolism and enhance claudin-1 expression, while increasing jejunal Clostridium sp. mbf VZ-132 to regulate glycerophospholipid metabolism and upregulate occludin expression. These findings suggested that MXYS may improves depression-like behavior through segment-specific microbial and metabolic modulation of intestinal permeability.},
}

@article {pmid42577453,
year = {2026},
author = {Rakhmankulova, A and Kozhakhmetov, S and Kovenskiy, A and Mukhanbetzhanov, N and Katkenov, N and Jarmukhanov, Z and Terzic, M and Bapayeva, G and Ukybassova, T and Aimagambetova, G and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Smagulova, B and Vinogradova, E and Kamzayeva, N and Kushugulova, A},
title = {Multi-kingdom cervical microbiome structure in health and dysbiosis: a cross-sectional study from Kazakhstan.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1836889},
pmid = {42577453},
issn = {1664-302X},
abstract = {INTRODUCTION: The cervicovaginal microbiome is a key determinant of reproductive health. Its multi-kingdom structure and ecological interactions remain insufficiently characterized across diverse populations. This study aimed to define the composition and cross-kingdom dynamics of the cervical microbiome in women without HPV infection and with normal cytology in a Kazakhstani population.

METHODS: In this cross-sectional study, cervical samples from 92 reproductive-age women were analyzed using whole-genome metagenomic sequencing to characterize bacterial, viral, fungal, and archaeal communities, together with predicted functional pathways. Microbial communities were stratified into community state types based on dominant bacterial species.

RESULTS: Bacterial composition differed markedly across community states, with Lactobacillus-dominated profiles associated with low diversity and anaerobe-rich communities associated with higher diversity. In contrast, viral, fungal, and archaeal diversity remained relatively stable, although descriptive compositional shifts indicated variation in bacteriophages, methanogenic archaea, and opportunistic fungi in non-Lactobacillus communities. Functional analyses indicated CST-associated pathway differences, suggesting greater metabolic flexibility in dysbiotic states, and exploratory network analysis revealed CST-associated restructuring of bacterial and cross-kingdom co-variation patterns. Notably, more than half of participants exhibited non-Lactobacillus-dominated communities despite the absence of infection or cytological abnormalities, indicating population-specific microbiome configurations.

DISCUSSION: Study demonstrates that the cervical microbiome is accompanied by exploratory cross-kingdom compositional variation and ecological states traditionally considered dysbiotic may represent stable, population-specific configurations, highlighting the need for context-dependent definitions of microbial health.},
}

@article {pmid42577488,
year = {2026},
author = {Prendergast, PJ and Aitchison, A and Ho, SSC and Morris, VK and Göbl, C and Dobson, RCJ and Day, AS and Ogilvie, OJ},
title = {Integrated multiomics reveals stable microbe-metabolite relationships in pediatric celiac disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1866060},
pmid = {42577488},
issn = {1664-302X},
abstract = {Celiac disease is a lifelong immune-mediated disease triggered by dietary gluten and managed exclusively through a strict gluten-free diet. Differences in the gut microbiome are consistently observed in celiac disease, yet the associated metabolic consequences remain insufficiently defined. This study evaluated the stool microbiome-metabolome relationship in children from Canterbury, New Zealand, a region with a notably high prevalence of celiac disease (∼ 1 in 82). Eleven children with untreated celiac disease and 10 controls were assessed, with nine children resampled after 6 months of gluten-free diet adherence. Stool samples were subjected to 16S rRNA sequencing, targeted and untargeted metabolomic profiling, and multi-omics integration using cross-block and machine-learning approaches. Celiac disease was characterized by consistent reproducible changes in a small set of resampled-stable taxa and metabolites, rather than a uniform shift. The most prominent finding was rearrangement within Bacteroides rather than a uniform shift: B. ovatus increased reproducibly in both untreated and treated disease, while integration analyses associated B. fragilis with celiac disease and B. vulgatus with controls. Metabolite changes were observed in two linked axes: a butyrate-led fermentation signature and a redox and organic acid signature, both elevated in untreated disease and shifting toward control levels after 6 months of gluten-free diet. Recovery was partial, and the diet imposed its own signature, notably an increase in the fat-responsive pathobiont Bilophila wadsworthia. Machine learning discrimination was modest (ROC-AUC = 0.66-0.68, PR-AUC = 0.73-0.79), but the microbiome and metabolome aligned along one reproducible cross-omic axis. The results support prioritizing a concise list of reproducible candidate features for mechanistic validation and longitudinal treatment monitoring in more extensive cohorts, rather than for immediate diagnostic application.},
}

@article {pmid42577546,
year = {2026},
author = {Zhan, M and Chen, H and Li, Z and Liu, S and Lu, B and Wang, Z and Wang, H},
title = {Lower Respiratory Microbiome Dysbiosis Is Associated With Poor Prognosis in Acute Severe Lower Respiratory Tract Infection.},
journal = {MedComm},
volume = {7},
number = {8},
pages = {e70907},
pmid = {42577546},
issn = {2688-2663},
abstract = {Acute severe lower respiratory tract infections (asLRTIs) pose a significant clinical challenge, especially in critically ill patients, but the role of the lower respiratory tract microbiome (LRTM) remains unclear. This study aimed to characterize LRTM composition and host immune factors to identify prognostic features of clinical outcomes. The study included 53 asLRTI patients and 35 controls. Metagenomics, metabolomics, proteomics, and RNA sequencing were conducted, while analysis of similarities (ANOSIM) and Cox regression were performed for statistics. Clinical data, including pneumonia severity scores, were collected on BALF sampling, with a 100-day follow-up. LRTM samples were grouped into five clusters (C1-C5). Cluster C5 resembled controls, while others showed significantly lower diversity. LRTM composition correlated with prognosis, with higher pathogenic bacteria abundance linked to poorer outcomes. Cluster C3 was associated with poor prognosis and reduced survival. Metabolite analysis revealed elevated α-ketoisocaproic acid in asLRTIs and higher 10-nitrolinoleate in poor-prognosis patients. Immune responses varied across clusters, with distinct gene and cytokine expression patterns. Cluster C1, associated with Acinetobacter baumannii, exhibited heightened IL17 pathway activation. LRTM composition in asLRTIs is linked to clinical outcomes, with no single gradient of difference but distinct community states characterized by varying pathogens, metabolites, and immune responses.},
}

@article {pmid42577561,
year = {2026},
author = {Soyer, P and Öztürk, AA},
title = {Development and Functional Evaluation of a Pharmabiotic Food Supplement Containing Microencapsulated Lactiplantibacillus pentosus for Oral Microbiome Health.},
journal = {Food science & nutrition},
volume = {14},
number = {8},
pages = {e72243},
pmid = {42577561},
issn = {2048-7177},
abstract = {Oral microbiome dysbiosis is associated with biofilm-related diseases, including dental caries and periodontal infections. This study aimed to develop and evaluate a pharmabiotic oral spray containing microencapsulated Lactiplantibacillus pentosus, sodium hyaluronate, and licorice (Glycyrrhiza glabra) extract to support oral microbial homeostasis. L. pentosus was microencapsulated by freeze-drying using maltodextrin and gum arabic as wall materials. The microencapsulation process resulted in an encapsulation efficiency of 94.74% ± 1.12% and a post-encapsulation viability of 8.17 ± 0.05 log CFU/mL. Four oral spray formulations (F1-F4) were prepared and evaluated for antimicrobial, antibiofilm, antioxidant, physicochemical, microbiological, and stability properties. All formulations exhibited antibacterial activity against Gram-positive oral pathogens, particularly Streptococcus mutans and Staphylococcus aureus, while no inhibitory activity was observed against Pseudomonas aeruginosa or Candida species. Antibiofilm analysis demonstrated substantial inhibition, ranging from 56.17% ± 0.91% to 70.99% ± 1.32% against S. mutans and from 72.42% ± 0.56% to 87.03% ± 1.76% against S. aureus. Antioxidant assays (DPPH, ABTS, and ORAC) confirmed moderate and consistent antioxidant activity across all formulations. During 3 months of storage, probiotic viability remained above 10[8] CFU/mL in most formulations. Viability losses under refrigerated conditions were limited to approximately 0.38-0.50 log CFU/mL, while formulation F2 retained 8.42 ± 0.14 log CFU/mL under accelerated conditions. Among the tested formulations, F1 exhibited the most favorable overall physicochemical characteristics and stability profile. These findings demonstrate that the developed oral spray represents a promising pharmabiotic delivery system combining probiotic viability, antibiofilm activity, and antioxidant potential for supporting oral health and microbial balance.},
}

@article {pmid42577578,
year = {2026},
author = {Song, Y and Zhang, X and Wang, H and Wang, Y and Zhang, S and Li, Y and Cui, X and Li, X and Li, Y and Wang, J and Su, J and Zheng, Y and Gai, W and Liu, W},
title = {Clinical value of radial endobronchial ultrasound combined with metagenomic next-generation sequencing in the malignant tumors patients with pulmonary infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799148},
pmid = {42577578},
issn = {2235-2988},
mesh = {Humans ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Microbiota ; *Endosonography/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; *Neoplasms/complications/drug therapy ; Bacteria/classification/genetics/isolation & purification ; Bronchoscopy ; Aged, 80 and over ; Adult ; Sepsis ; },
abstract = {INTRODUCTION: Patients treated with systemic anti-tumor therapies are more likely to develop pulmonary infections due to weakened immune systems. This study aims to evaluate the clinical application of radial endobronchial ultrasound (R-EBUS) combined with metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of pulmonary infections among patients undergoing systemic anti-tumor therapy.

METHODS: This study is a single-center retrospective analysis that includes 84 patients with pulmonary infections following systemic anti-tumor therapy. Patients were stratified into sepsis (SOFA score ≥2, n=32) and non-sepsis (SOFA score <2, n=52) groups based on Sepsis-3.0 criteria. BALF samples were subjected to both mNGS and conventional microbiological tests (CMT). Pathogen profiles, diagnostic performance, clinical impact on antimicrobial therapy, and microbiome diversity were analyzed.

RESULTS: mNGS demonstrated a significantly higher positive detection rate than CMT (95.24% vs. 30.95%, P < 0.001). mNGS identified a broader spectrum of pathogens, including bacteria, fungi, and viruses, and detected mixed infections more frequently than CMT. The clinical impact of mNGS was positive in 84.52% of cases, primarily by initiating targeted therapy or confirming empirical treatment. Microbiome analysis revealed significantly lower alpha diversity (Shannon, ACE, Chao1 indices) in the severe group compared to the non-severe group.

DISCUSSION: EBUS-guided mNGS of BALF was associated with improved pathogen detection in malignancy patients with pulmonary infections, leading to a high rate of beneficial antimicrobial adjustments. Distinct microbial signatures are associated with infection severity, suggesting potential diagnostic and therapeutic implications.},
}

Humans
Female
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Male
Retrospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Middle Aged
Aged
Microbiota
*Endosonography/methods
*Respiratory Tract Infections/diagnosis/microbiology
*Neoplasms/complications/drug therapy
Bacteria/classification/genetics/isolation & purification
Bronchoscopy
Aged, 80 and over
Adult
Sepsis

@article {pmid42577588,
year = {2026},
author = {Brock, R and Schaupp, L and Schütte, A and Zhou-Suckow, Z and Butz, S and Schatterny, J and Mayer, S and Frank, A and Mengel, JP and Weigel, M and Hain, T and Dalpke, A and Boutin, S and Mall, MA},
title = {Preventive intrapulmonary treatment with Ligilactobacillus murinus reduces airway inflammation and mucus plugging in mice with cystic fibrosis-like lung disease.},
journal = {ERJ open research},
volume = {12},
number = {4},
pages = {},
pmid = {42577588},
issn = {2312-0541},
abstract = {BACKGROUND: Chronic airway dysbiosis plays an important role in the pathogenesis of cystic fibrosis (CF) lung disease and may serve as a therapeutic target. However, studies investigating the effects of direct therapeutic targeting of the airway microbiome are lacking. In this study, we therefore used βENaC-overexpressing (βENaC-Tg) mice and determined the evolution of abnormal lung microbiota and effects of re-balancing bacterial communities on chronic airway inflammation and mucus plugging in this model of CF lung disease.

METHODS: The development of the respiratory microbiome was determined by 16S rRNA gene sequencing and the effects of preventive intranasal instillation of endogenous probiotic bacteria on the lung phenotype were determined in βENaC-Tg mice and wild-type littermates.

RESULTS: Neonatal βENaC-Tg mice developed severe respiratory dysbiosis characterised by an increase in the relative abundance of Streptococcus and a decrease in Ligilactobacillus compared to wild-type littermates. Ligilactobacillus murinus SMH17 was identified as the dominant Ligilactobacillus species in the lungs of neonatal wild-type mice. Preventive treatment by intranasal instillation of L. murinus SMH17 was well tolerated and reduced age-specific markers of airway inflammation including inflammatory cell counts and proinflammatory cytokines in neonatal and juvenile βENaC-Tg mice. In addition, preventive treatment with L. murinus SMH17 reduced airway mucus plugging in βENaC-Tg mice by ∼40%.

CONCLUSION: Preventive intrapulmonary application of the endogenous probiotic L. murinus SMH17 reduces airway inflammation and mucus plugging in mice with CF-like lung disease. These data support further elucidation of inhaled probiotics as a strategy to treat chronic airway dysbiosis in patients with CF.},
}

@article {pmid42577589,
year = {2026},
author = {Curtis-Joseph, N and Laubi, A and Ortiz-Alvarez de la Campa, M and Belenky, P},
title = {Perinatal antibiotics in a db/db mouse model impact obesity and hyperglycemia in a microbiome-dependent manner.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1750320},
pmid = {42577589},
issn = {2813-4338},
abstract = {Obesity affects over one billion people globally; however, the role of the gut microbiome and host genetics in its manifestation is poorly understood. We demonstrate that genetic obesity in leptin-receptor-deficient db/db mice requires a permissive gut microbiome, which is established during early life. Using perinatally-administered antibiotic cocktail treatment until pups were 8-weeks-old, we demonstrate that microbiome perturbation substantially reduces weight gain and significantly reduces hyperglycemia in homozygous, leptin-receptor-deficient db/db (Hom) mice without altering caloric intake or extraction efficiency. 16S rRNA sequencing revealed that antibiotic treatment depletes Muribaculaceae while enriching Akkermansiaceae and Bacteroidaceae. Differential abundance analysis identified Duncaniella muris, a recently characterized Muribaculaceae species, as the most depleted taxon in antibiotic-treated mice. Oral gavage of cultured D. muris into antibiotic-treated db/db mice restored hyperglycemia to pre-treatment levels without affecting body weight, establishing a direct causal link between this specific microbe and glucose increase. These findings reveal that hyperglycemia is not solely genetic, but depends critically on specific microbiota members in a permissive microbial context.},
}

@article {pmid42577720,
year = {2026},
author = {Pakkhesal, S and Pourebrahimian Leilabadi, S and Hamzehzadeh, S and Zare, F and Gholipour-Khalili, E and Malekinejad, F and Fakhkhari, S and Talebi, M and Naseri, A},
title = {Air Pollution and Parkinson's Disease Pathology: Clinical Evidence and the Molecular Mechanisms Linking Airborne Toxicants to Neuroinflammation and Neurodegeneration.},
journal = {Parkinson's disease},
volume = {2026},
number = {},
pages = {6914112},
pmid = {42577720},
issn = {2090-8083},
abstract = {Parkinson's disease (PD) is a neurodegenerative condition, and its rising prevalence necessitates the urgent need to identify modifiable risk factors. Air pollution, a pervasive and also escalating public health problem, has emerged as a potential contributor to the incidence and progression of PD. As urbanization and industrialization continue to exacerbate global air pollution levels, understanding the relationship between airborne toxicants and PD is a pressing scientific and public health priority. In this review, we critically discuss the current epidemiological evidence and the cellular and molecular mechanisms underlying air pollution-induced neurodegeneration in PD. Clinical studies associate long-term interaction with pollutants such as nitrogen oxides, particulate matter, and ozone with increased PD risk. Evidence also suggests that air pollution worsens PD prognosis. Mechanistically, air pollution is hypothesized to contribute to PD pathogenesis through gut microbiome alternations, oxidative stress, and neuroinflammatory pathways, as well as promoting α-synuclein aggregation.},
}

@article {pmid42577828,
year = {2026},
author = {Campbell, MJ and Jorrin, B and Katz, Z and Tkacz, A and Ledermann, R and Poole, PS},
title = {Non-nodulating Paenirhizobium fix nitrogen in association with cereal roots.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag156},
pmid = {42577828},
issn = {2730-6151},
abstract = {Cereal root microbiomes harbour diverse diazotrophic bacteria, yet the taxa capable of sustained nitrogen fixation in association with cereal roots remain poorly characterized. Here, two high-performing nitrogen-fixing strains (B6 and J2) were isolated from barley roots and identified as belonging to the family Rhizobiaceae in the genus Paenirhizobium. Both strains possess plasmid-encoded canonical rhizobial nif and fix genes for nitrogen fixation but lack nodulation genes. Their genomes have a 5.7 Mb chromosome and four repABC plasmids. Unlike most nodulating rhizobia, strains B6 and J2 fixed nitrogen in laboratory culture on a range of carbon sources, achieving maximal activity on organic acids at low ammonium (<0.5 mM) and oxygen concentrations (1-3%). Both strains colonized the total root systems of barley plants, with population densities of 10[6] CFU g[-1] fresh root weight. Strains fixed high levels of nitrogen on barley plants, similar to or greater than other known free-living diazotrophs. These findings expand the ecological context of rhizobial nitrogen fixation and identify cereal-associated Paenirhizobium as a previously unrecognized component of the diazotrophic cereal root microbiome.},
}

@article {pmid42577830,
year = {2026},
author = {Martínez-Cuesta, R and Hoess, R and Geist, J and Schloter, M and Schulz, S},
title = {The larval gut as a mirror: bacterial community composition and functional potential of mayfly larvae reflect site and seasonality differences.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag192},
pmid = {42577830},
issn = {2730-6151},
abstract = {Land use intensification is a major driver of biodiversity loss across ecosystems, yet its consequences for host-associated microbiomes in freshwater food webs remain poorly understood. In this case study, we used the gut microbiome of mayfly larvae (Ephemera danica) as a sensitive biological interface to assess how site-specific adjacent land use types shape microbial community composition and functions in stream ecosystems. Larvae were sampled in summer and autumn from sites adjacent to forest, extensive grassland, and intensive agriculture along the Otterbach stream (Bavarian Forest, Germany). Combining 16S ribosomal RNA (rRNA) amplicon sequencing with long-read metagenomics, we show that site-specific land use, in interaction with seasonality, significantly restructures larval gut bacterial communities without affecting alpha diversity. Rather than introducing distinct agriculturally derived taxa, agricultural land use acted as a selective environmental filter, enriching bacterial groups with specific functional traits. Taxa enriched in the sites adjacent to agricultural sites harboured genes involved in complex carbon and xenobiotic degradation, short-chain fatty acid production, efflux pumps, and stress response. These functional signatures were further supported by 14 metagenome-assembled genomes linked to these enriched taxa. Together, our results reveal that site in combination with seasonality not only reshaped bacterial community composition without affecting alpha diversity but also triggered shifts in the abundance of genes involved in microbial-host interactions and degradation pathways in E. danica larvae. This study also highlights the larval gut microbiome as a sensitive indicator of environmental change, suggesting that environmental microbial shifts may have cascading consequences for freshwater trophic interactions and ecosystem functioning.},
}

@article {pmid42577841,
year = {2026},
author = {Wrigley, SD and Johnson, SA and Gentile, CL and Weir, TL},
title = {Gut microbiome dynamics and cardiometabolic disease progression: evidence from a secondary data analysis of pooled clinical datasets.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1790805},
pmid = {42577841},
issn = {1664-302X},
abstract = {PURPOSE: Individuals with cardiometabolic disease (CMD) often exhibit decreased microbial alpha diversity and/or differences in beta diversity indices than those without CMD. However, it is unclear if these compositional changes in the gut microbiome are a cause or a consequence of CMD. Research suggests individual bacterial species act as drivers of disease, inducing shifts in microbial community and host metabolism. During this process, large-scale compositional changes can develop secondarily, obscuring the original microbial drivers. This study aimed to characterize the gut microbiota of healthy individuals compared to those with early risk factors for CMD to determine whether specific microbial taxa and community associations exist with early stages of hypertension, vascular dysfunction, dyslipidemia, and overweight/obesity.

PROCEDURE: Baseline anthropometric, physiological, and gut microbiome data from three clinical studies previously conducted by our research groups were compiled and re-analyzed.

RESULTS: No differences in alpha and/or beta diversity were observed across CMD parameters. Through a consensus-based differential abundance analysis, we observed that several health-related taxa decreased as CMD levels increased, including Akkermansia, Bacteroides, Bifidobacterium, Blautia, Eubacterium, Lachnospiraceae, Oscillospiraceae, Prevotella, Roseburia, and Ruminococcus. Furthermore, co-occurrence networks of individuals with elevated cardiometabolic parameters showed lower clustering coefficients, higher path lengths, lower degrees, higher modularity, and higher negative cohesion than those with normal parameters.

IMPLICATIONS: The loss of health-associated gut microbiota, along with decreased network connectivity and increased network fragmentation, may play a role in the progression of CMD.},
}

@article {pmid42577916,
year = {2026},
author = {Demmer, RT and Pope, ZC and Avenido, FRR and Mitchell, NR and Richmond Hubbard, PF and Johnson, S and Sharma, S and McDonough, DJ and Rydell, SA and Johnson, A and Pereira, MA},
title = {The Effect of Physical Activity on the Gut Microbiome in Prediabetes: Results from a Randomized Controlled Trial.},
journal = {Diabetes, obesity, and cardiometabolic CARE},
volume = {1},
number = {2},
pages = {219-229},
pmid = {42577916},
issn = {3067-3534},
abstract = {OBJECTIVE: To test the effect of physical activity on the gut microbiome and circulating short chain fatty acids among sedentary adults with prediabetes and overweight/obesity.

RESEARCH DESIGN AND METHODS: In a pilot and feasibility trial, we randomized 77 adults with prediabetes and a sedentary lifestyle into one of two groups: 1) Intervention: Invited to engage in home-based moderate intensity walking 3x/week for 30 minutes/session in weeks 1-4 and for 45 minutes/session during weeks 5-8 of the 8-week intervention; or 2) Control: Maintained habitual physical activity levels. We performed metagenomic sequencing from stool collected at baseline, week 4, and week 8, with short-chain fatty acids (SCFA) measured from serum collected at baseline and week 8. Taxonomic and functional profiling were performed on the metagenomic reads; alpha diversity metrics were subsequently derived. Linear regression assessed the difference in change between the intervention and control groups for alpha-diversity and SCFA levels.

RESULTS: We screened 1,533 participants for eligibility and consented 132. Of these, 87 entered the run-in phase and 77 were randomized. Participants were 51.4±8.9 years old, 87.7% female, and 74% non-Hispanic White. Mean fasting glucose was 103.3±13.2 while mean BMI was 34.4±5.7. In comparison to control, the intervention group experienced decreased alpha diversity as characterized by Shannon, Richness, and Faith's diversity indices by intervention week 8 (P<0.05). Changes in SCFA levels were not statistically significant different in intervention vs. control.

CONCLUSIONS: Randomization to a walking intervention resulted in modest gut microbiome changes among adults with overweight/obesity and prediabetes.},
}

@article {pmid42577959,
year = {2026},
author = {Sun, Z and He, C and Ma, X and Wu, P and Wang, T and Yuan, J and Pu, Y and Zhou, X and Mei, Z and Song, H and Wang, Y and Yue, H and Fu, Y and Zheng, J and Pan, A and Chen, D and Hong, S and Pan, XF and Zheng, Y},
title = {A gut microbiome-lipid axis in early pregnancy is associated with metabolic dysregulation and diabetes risk.},
journal = {iMeta},
volume = {},
number = {},
pages = {e70166},
pmid = {42577959},
issn = {2770-596X},
abstract = {Gestational diabetes mellitus (GDM) reflects metabolic dysregulation that becomes clinically apparent during pregnancy and shares key pathophysiological features with broader forms of diabetes. Gut microbiome-host metabolic interactions may contribute to this process, yet their role in early pregnancy remains incompletely understood. In this prospective nested case-control study within the Tongji-Huaxi-Shuangliu Birth Cohort, 784 pregnant women, including 222 who developed GDM, underwent first-trimester gut metagenomic and plasma lipidomic profiling. Cross-omics analyses were performed to identify microbiome-lipid associations and potential mediation patterns. Women who later developed GDM showed reduced gut microbial diversity and altered microbial profiles in early pregnancy. We identified 26 microbial species associated with GDM risk, with seven species, including Ruminococcus bicirculans (R. bicirculans), showing concordant associations in external type 2 diabetes populations. Microbial pathways related to fatty acid and lipid biosynthesis were enriched in women at higher risk. Plasma lipidomics revealed widespread alterations, particularly among glycosphingolipid-related metabolites. Integrated analyses suggested that lipidomic variation statistically accounted for part of the microbiome-GDM association. A class-level dihexosylceramide feature, DHC 24:1, consistent with lactosylceramide-related metabolites, emerged as a potential mediator and was prioritized for exploratory follow-up. Experimental analyses provided functional support for a microbiome-lipid-host interaction axis. R. bicirculans promoted lactosylceramide 24:1 production in vitro, bacterial colonization and metabolite administration improved insulin tolerance in vivo, and lactosylceramide 24:1 modulated insulin-stimulated AKT signaling dynamics in hepatocytes. These findings identify a gut microbiome-lipid axis associated with metabolic dysregulation in pregnancy and suggest a potential mechanism linking microbial metabolism to host insulin signaling.},
}

@article {pmid42577996,
year = {2026},
author = {Le, J and Bradley, JS and Ramchandar, N},
title = {Pharmacology of Bacteriophage Therapy in Children: A Re-Emerging Paradigm in Antibacterial Therapy.},
journal = {The journal of pediatric pharmacology and therapeutics : JPPT : the official journal of PPAG},
volume = {31},
number = {4},
pages = {483-492},
pmid = {42577996},
issn = {1551-6776},
abstract = {The rise of antibiotic-resistant bacteria has reignited global interest in bacteriophages as potential therapeutic agents. Bacteriophage (phage) therapy provides an alternative to conventional antibiotics to treat serious infections caused by multidrug-resistant pathogens. In this narrative review, we explore the pharmacokinetics (PK), pharmacodynamics (PD), and clinical use of phage therapy in pediatric populations. We conducted PubMed searches for relevant publications from 1959 to September 2025. In contrast to most drugs, phages are self-replicating in the presence of target bacteria, necessitating the use of non-linear, dynamic pharmacology models to integrate phage-bacteria interaction (which can fluctuate over time, based on the presence of susceptible bacteria), as well as host factors such as immune clearance of phages and traditional host mechanisms of clearance of invasive bacterial pathogens. Phages are primarily cleared through the reticuloendothelial system, particularly in the liver and spleen. Advantages of phage therapy over antibiotics include a promising safety profile, preservation of the child's own microbiome, and, compared with some antibiotics, enhanced penetration into biofilms. Our knowledge of the benefits and risks of phage therapy is limited largely to current pediatric case reports and case series. The clinical use spans a wide breadth of clinical infections, mostly involving poorly responsive infections caused by multidrug-resistant bacteria. Until robust, prospective PK-PD and clinical trial data become available to guide therapy, phage therapy should be administered under protocols with individualized dosing and rigorous safety monitoring. Clinical applications using standardized, evidence-based dosing regimens and outcome assessments require further evaluation.},
}

@article {pmid42578434,
year = {2026},
author = {Chaffee, BW and Lieuw, K and Zhang, H and Couch, ET and Jiang, YJ and Momen-Heravi, F},
title = {Oral Nicotine Pouch Use and Associations with Periodontal Status and Salivary Microbiome Dysbiosis.},
journal = {JDR clinical and translational research},
volume = {},
number = {},
pages = {23800844261469532},
doi = {10.1177/23800844261469532},
pmid = {42578434},
issn = {2380-0852},
abstract = {OBJECTIVES: Oral nicotine pouches (ONPs) are increasing in use, yet data on potential oral health effects are scarce. We evaluated whether ONP use is associated with clinical periodontal measures and salivary microbiome dysbiosis in a field-based regional sample. We recruited firefighters, as this population has historically featured an elevated prevalence of oral tobacco use.

METHODS: In this preliminary, cross-sectional study, 26 eligible participants (100% male; ages 26-53 y) were enrolled from fire stations near Sacramento, California (USA), in April-May 2025. Clinical measures from full-mouth periodontal examinations (probing depth, gingival margin position, clinical attachment loss, bleeding on probing) were compared between ONP use (≥15 in the past 30 d, no more than minimal use of other tobacco, n = 12) and tobacco nonuse (n = 14) groups. We conducted 16S rRNA gene amplicon sequencing of saliva samples to determine genus-level profiles using differential abundance testing and Bray-Curtis beta diversity analyses.

RESULTS: Clinical periodontal measures were numerically worse with ONP use, including a higher percentage of sites with ≥3 mm clinical attachment loss (P = 0.009). Across all samples, approximately 130 genera were detected (Streptococcus most abundant). ONP use (vs. tobacco nonuse) was associated with higher abundance of Comamonas, Alloscardovia, F0058, and Dialister and lower abundance of the [Eubacterium] sulci group, Aminipila, Mannheimia, and Peptostreptococcus. Principal coordinates analysis showed substantial overlap between groups, whereas beta dispersion was lower in the ONP group (P = 0.035).

CONCLUSIONS: In this hypothesis-generating study, ONP use was associated with worse periodontal status and salivary microbiome shifts. While these results await confirmation in future studies and additional populations, they suggest plausible oral health risks that should be incorporated into any comprehensive assessment of potential ONP harms.Knowledge Transfer Statement:Although preliminary, these findings provide some of the first evidence that use of oral nicotine pouches is associated with indicators of worse periodontal health. These results should encourage further research to confirm these signals and clarify potential mechanisms. Patients, providers, and product regulators should include oral health when evaluating the risk profile of this product.},
}

@article {pmid42578670,
year = {2026},
author = {Li, Z and Sun, J and Yang, J and Han, P and Min, L and Cheng, Y and Zou, Y and Liu, Z},
title = {Exploring the hypothetical role of Bacteroides species in depression progression: insights from metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0315324},
doi = {10.1128/spectrum.03153-24},
pmid = {42578670},
issn = {2165-0497},
abstract = {Depression, a psychiatric disorder with significant morbidity and mortality, has a complex etiology. Recent advances in microbiome research have highlighted the potential role of fecal microbiota in depression pathogenesis. This study utilized shotgun metagenomic sequencing to compare the fecal microbiota of 28 depression patients and 26 healthy individuals. Significant differences in fecal microbiota composition were observed between the two groups. We generated 350 non-redundant high-quality metagenome-assembled genomes (MAGs) by binning and conducted comparisons between the depression and control groups. Notably, we found that the MAGs enriched in people with depression mostly belonged to Bacteroides, indicating a close link between Bacteroides abundance and the development of depression, suggesting that Bacteroides might be a potential culprit for depression. In the depression group, we found that the module of nitric oxide synthesis was remarkably enriched, and all Bacteroides MAGs contained genes annotated as nitric oxide synthase, suggesting that increased levels of Bacteroides may contribute to elevated nitric oxide synthesis. A distinct microbial signature consisting of Arthrobacter sp._U41, Bacillus cereus, Campylobacter rectus, and Pasteurella dagmatis accurately discriminates between depressed individuals and healthy controls, achieving an average area under the receiver operating characteristic curve of 0.950. This research sheds light on the potential role of fecal microbiota in depression and highlights specific metabolic pathways and microbial markers for further investigation.IMPORTANCEThis research highlighted significant differences in the composition and function of fecal microbiota between individuals with depression and healthy individuals, particularly the enrichment of Bacteroides metagenome-assembled genomes (MAGs) in depression patients. The upregulation of the nitric oxide synthesis pathway associated with these MAGs belonging to Bacteroides in the gut of depression patients had also been observed. The selected bacterial biomarkers reliably differentiate depression cases from healthy controls with high diagnostic accuracy (mean area under the receiver operating characteristic curve = 0.950). Our results suggest the importance of exploring microbial markers as potential diagnostic and therapeutic targets in managing depression.},
}

@article {pmid42578673,
year = {2026},
author = {Mirăuță, B and Riza, A-L and Streata, I and Pirvu, A and Dorobantu, S and Dragos, A and Surleac, M and Netea, MG},
title = {Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0052826},
doi = {10.1128/spectrum.00528-26},
pmid = {42578673},
issn = {2165-0497},
abstract = {The gut microbiome influences host health, affecting gastrointestinal, metabolic, immune, cardiovascular, and neurological functions. A balanced microbiome is associated with favorable health outcomes. However, excessive antibiotic use and dietary habits can disrupt this ecosystem, leading to dysbiosis and affecting body homeostasis. This first comprehensive metagenomic analysis of the gut microbiome in a healthy Romanian cohort, a population underrepresented in microbiome studies and characterized by high antibiotic consumption, addresses a gap in current microbiome research. We report an enrichment of Enterobacteriaceae although overall composition is more comparable to other European than non-European cohorts. Community configurations align with established enterotype patterns, and our analysis provides insight into their relationship with within-phylum diversity. The analysis of antimicrobial resistance provides insight into the prevalence of resistance genes within this reservoir. We specifically report the presence of cfr(E), a Clostridioides difficile gene, and tet(X5), a variant from the ubiquitous tet family, genes not previously reported in healthy European populations. Integration with data from the European Centre for Disease Prevention and Control links the overall prevalence of resistance genes in this reservoir to antibiotic classes with higher community consumption in this population, notably beta-lactams and quinolones, highlighting potential targets for antibiotic stewardship programs. Finally, we investigate the relationship between the microbial profile and the systemic immune responses, inferred from correlations with in vitro cytokine production. Notably, we identify potential immune-priming roles for Collinsella, Flavonifractor, and Bifidobacterium species.IMPORTANCEThis first comprehensive study of the healthy gut microbiome in a Romanian cohort addresses a gap in current microbiome research, dominated by data sets from a limited number of regions. It sets a baseline for the microbiome and resistome composition of this population, and, while definitions of "healthy" microbiomes, or baseline resistomes, remain lacking, such study helps contextualize future studies and support the monitoring of dynamics. The Enterobacteriaceae abundance suggests a microbiome composition potentially influenced by antimicrobial consumption, a relevant pattern in a region with a high burden of nosocomial infections. In addition, the prevalence of antimicrobial resistance genes and the concordance with commonly used antibiotics in the community reinforce the need to address antibiotic use in public health strategies. Although gut microbiome-immunity relationships remain incompletely understood, our findings support a role for microbiome composition in immune-related traits and provide a valuable resource for future studies.},
}

@article {pmid42578693,
year = {2026},
author = {Montgomery, TL and Nelson, EA and Downs, LA and Heney, ER and Lee, MFJ and Martino, C and McDonald, D and Rahman, G and Knight, R and Krementsov, DN},
title = {Integrated multi-omics analysis identifies microbial and metabolic signatures and drivers of CNS autoimmunity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0000226},
doi = {10.1128/msystems.00002-26},
pmid = {42578693},
issn = {2379-5077},
abstract = {Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS), driven by genetic and environmental determinants. The gut microbiome of people with MS (pwMS) is distinct and influences disease through immunomodulatory metabolite production. Circulating metabolites are altered in pwMS, but identifying microbial-metabolic drivers remains challenging. We previously showed that colonization by the gut commensal Limosilactobacillus reuteri exacerbates disease in the experimental autoimmune encephalomyelitis (EAE) model of MS in a tryptophan-dependent manner. Here, we integrated microbiomic and metabolomic data sets from a longitudinal EAE study utilizing high- and low-tryptophan diets in mice colonized with or without L. reuteri. Gut microbiome dynamics, under short- and long-term alterations in tryptophan bioavailability, were affected by diet, microbiome context, or disease. During short-term dietary intervention, L. reuteri colonization exerted a greater impact on microbiome composition than tryptophan bioavailability. With longer dietary exposure and EAE progression, high dietary tryptophan and L. reuteri colonization synergized to elicit profound microbiota changes, including alterations in Lachnospiraceae, Blautia, and Akkermansia. Integration of metabolomic and microbiomic data sets using joint Robust Aitchison PCA revealed clusters of associated metabolites and microbiota enriched for functional pathways, including bile acid and tryptophan metabolism. Metabolites outperformed microbiota in predicting EAE severity, identifying p-cresols and indoles as top disease-associated metabolites. Treatment with p-cresol or 3-indoleglyoxylic acid exacerbated EAE, enhanced proinflammatory T-cell responses, and increased cerebellar pathology. These data demonstrate that dietary responses are shaped by gut microbiome composition and that integrated microbiomic-metabolomic analyses can identify the drivers of disease worsening in MS.IMPORTANCEMultiple sclerosis (MS) is a multifactorial disease influenced not only by genetics but also by environmental factors, potentially including diet and the composition of the gut microbiome. We show that interactions between diet and commensal gut microbiota profoundly impact the levels of immunomodulatory systemic metabolites, including several that are associated with disease in people with MS (pwMS). Importantly, we demonstrate that individual gut microbiota-produced metabolites are sufficient to worsen disease in a mouse model of MS. Integration of gut microbiome and blood metabolite data sets, combined with subsequent predictive modeling, may bolster biomarker identification and the capacity to predict disease severity in pwMS, as compared to the performance of individual data sets alone. These findings highlight metabolites as key mediators linking diet and the gut microbiota to neuroinflammation. Importantly, this work suggests that targeting microbial metabolites or modifying diet-microbiome interactions may represent new strategies to reduce disease activity in MS and related autoimmune disorders.},
}

@article {pmid42578699,
year = {2026},
author = {Choi, BI and Appleberry, H and Fontes Noronha, M and Putonti, C and Wolfe, AJ},
title = {Complete genome sequence of Streptococcus vaginalis strain UMB8616 isolated from the bladder of a female with urge urinary incontinence.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0066126},
doi = {10.1128/mra.00661-26},
pmid = {42578699},
issn = {2576-098X},
abstract = {Streptococcus vaginalis is a recently identified bacterial species closely related to Streptococcus anginosus. It has been isolated from the human urogenital tract. We report the complete genome sequence of S. vaginalis UMB8616 (=ATCC TSD-371 = CCUG 77169 = DSM 115471) isolated from the bladder of a human female with urge urinary incontinence.},
}

@article {pmid42578812,
year = {2026},
author = {Zhu, M and Mtshali, A and Mzobe, G and Magini, N and Mitchev, N and Khan, A and Demidkina, BC and Murthy, M and Lewis, L and Xu, J and Shih, J and Elsherbini, J and Kama, A and Mafunda, NA and Chetty, C and Vermeren, L and Passmore, JS and Happel, AU and Kwon, DS and Symul, L and Potloane, D and Ngcapu, S and Mitchell, CM},
title = {Geographic Variation in Diagnostic Performance of Amsel Criteria and Nugent Score for Vaginal Dysbiosis Defined by 16S rRNA Gene Sequencing.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag399},
pmid = {42578812},
issn = {1537-6613},
abstract = {BACKGROUND: Vaginal dysbiosis characterized by low abundance of vaginal lactobacilli and increased bacterial community diversity, is implicated in multiple adverse health outcomes and is an emerging target for preventive interventions, including live biotherapeutic products (LBPs). The most common clinical presentation of vaginal dysbiosis is bacterial vaginosis (BV), but at least half of people are asymptomatic.

METHODS: We compared identification of BV by Nugent score and Amsel criteria for screening specimens from a Phase 1b randomized trial of a live biotherapeutic product conducted at two sites (CAPRISA, South Africa; MGH, USA), as well as a single follow-up visit from enrolled participants. Using 16S rRNA gene sequencing-based categorization of community state type (CST) as the reference and multinomial mixed-effects logistic models, we evaluated the association of Amsel BV and Nugent BV with CST IV (including subtypes IV-A and IV-B) and tested for site-specific effects.

RESULTS: Amsel BV was significantly associated with CST IV-A, and IV-B; however, the strength of association was significantly diminished at CAPRISA compared to MGH, pointing to site-specific assessment differences or underlying biological variation. Nugent BV yielded stronger associations with CST IV-A, and IV-B and showed no evidence of a site-specific interaction, indicating consistent performance across sites.

CONCLUSION: These findings indicate that diagnostic performance for vaginal dysbiosis varies by framework: Amsel criteria are more susceptible to geographical site effects, whereas Nugent score demonstrates stronger and more site-agnostic associations. For clinical studies targeting vaginal dysbiosis, Nugent scoring and/or sequencing-based approaches should be prioritized for vaginal dysbiosis endpoint definition and stratification.},
}

@article {pmid42579018,
year = {2026},
author = {Vishwas, G and Kakkar, AK and Mehta, S and Pattanaik, S and Bhattacharyya, S and Sharma, V and Modi, M},
title = {Helicobacter pylori eradication therapy and clinical outcomes in Parkinson's disease: a double-blind randomized placebo-controlled trial.},
journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology},
volume = {47},
number = {9},
pages = {},
pmid = {42579018},
issn = {1590-3478},
support = {This work was partially supported by a grant from the Department of Science & Technology & Renewable Energy, Chandigarh//This work was partially supported by a grant from the Department of Science & Technology & Renewable Energy, Chandigarh/ ; },
mesh = {Humans ; Double-Blind Method ; *Parkinson Disease/drug therapy/complications ; *Helicobacter Infections/drug therapy/complications ; Female ; Male ; Treatment Outcome ; Middle Aged ; Aged ; *Helicobacter pylori/drug effects ; Clarithromycin/therapeutic use/administration & dosage ; *Anti-Bacterial Agents/therapeutic use ; Amoxicillin/therapeutic use/administration & dosage ; Drug Therapy, Combination ; Omeprazole/therapeutic use/administration & dosage ; Quality of Life ; Severity of Illness Index ; },
abstract = {BACKGROUND: Helicobacter pylori (HP) infection has been implicated in modifying treatment response and clinical outcomes in Parkinson's disease(PD). This study aimed to evaluate the effect of HP eradication therapy on motor symptoms, non-motor symptom burden, and quality of life in patients with PD.

METHODS: We conducted a double-blind, randomised, placebo-controlled trial in which HP-positive adults with PD were randomised (1:1) to standard triple eradication therapy (omeprazole 20 mg, amoxicillin 1000 mg, and clarithromycin 500 mg, each twice-daily for 14 days) or matched placebo. The primary outcome was the MDS-Unified Parkinson's Disease Rating Scale(MDS-UPDRS) Part III motor score in the ON medication state at 12 weeks. Secondary outcomes included total MDS-UPDRS score, Non-Motor Symptoms Scale (NMSS) score, and Parkinson's Disease Questionnaire-39 (PDQ-39) summary index score.

RESULTS: Out of eighty participants who underwent urea-breath testing, 34 tested positive. Of them, 30 participants were randomised to the two treatment groups. The primary outcome did not differ significantly between groups at 12 weeks (mean difference -3.9; 95% CI -15.5 to 7.6; p=0.49), which was unchanged after adjustment for baseline scores (p=0.13). No significant between-group differences were observed in total MDS-UPDRS score(mean difference -0.13; 95% CI -22.1 to 21.8; p=0.99), NMSS score(mean difference 23.3; 95% CI-8.8 to 55.4; p=0.15), or PDQ-39 scores(mean difference -7.1; 95% CI -35.4 to 21.1; p=0.61).

CONCLUSIONS: HP eradication therapy did not improve motor symptoms, non-motor symptom burden, or quality of life in PD patients over 12 weeks. These findings do not support routine HP eradication as an adjunctive strategy for improving PD symptom control.

TRIAL REGISTRATION: CTRI/2019/04/018524.},
}

Humans
Double-Blind Method
*Parkinson Disease/drug therapy/complications
*Helicobacter Infections/drug therapy/complications
Female
Male
Treatment Outcome
Middle Aged
Aged
*Helicobacter pylori/drug effects
Clarithromycin/therapeutic use/administration & dosage
*Anti-Bacterial Agents/therapeutic use
Amoxicillin/therapeutic use/administration & dosage
Drug Therapy, Combination
Omeprazole/therapeutic use/administration & dosage
Quality of Life
Severity of Illness Index

@article {pmid42579029,
year = {2026},
author = {Holden, A and Hutsell, H and Palchak, L and Luo, L and Ramsey, JD and Kabanov, AV},
title = {Poly(2-oxazoline) micelles for co-delivery of paclitaxel and metronidazole benzoate for dual chemotherapeutic and antibacterial targeting in the tumor microenvironment.},
journal = {Biomedical microdevices},
volume = {28},
number = {3},
pages = {},
pmid = {42579029},
issn = {1572-8781},
support = {R21CA305031/NH/NIH HHS/United States ; R01CA264488/NH/NIH HHS/United States ; },
mesh = {*Paclitaxel/pharmacology/chemistry ; *Micelles ; *Metronidazole/pharmacology/chemistry ; Animals ; *Anti-Bacterial Agents/pharmacology/chemistry ; *Oxazoles/chemistry ; Cell Line, Tumor ; *Tumor Microenvironment/drug effects ; Humans ; Fusobacterium nucleatum/drug effects ; Mice ; *Antineoplastic Agents/pharmacology/chemistry ; Female ; *Drug Delivery Systems ; *Drug Carriers/chemistry ; },
abstract = {Tumor-resident pathogenic bacteria can promote cancer progression and reduce chemotherapy efficacy, yet strategies to simultaneously target both tumor cells and intratumoral microbes remain limited. Here, we report a poly(2-oxazoline) micelle (POx) platform co-encapsulating paclitaxel (PTX) and metronidazole benzoate (MB) to achieve concurrent delivery of anticancer and antibacterial agents. The POx/PTX/MB micelles produced monodisperse populations with high drug loading efficiency and capacity and remained stable in physiological conditions. In vitro, the co-loaded formulation retained cytotoxic activity against two triple-negative breast cancer (TNBC) cell lines and bactericidal activity against Fusobacterium nucleatum. POx/PTX/MB micelles were well-tolerated at pharmacologically relevant doses in a murine model. This work provides a feasible strategy to integrate antimicrobial therapy with chemotherapy, highlighting the potential of POx micelles as a versatile platform for targeting both cancer cells and tumor-associated pathogens. These findings support further development of combination chemotherapeutic-antimicrobial strategies for tumors harboring pathogenic bacteria.},
}

*Paclitaxel/pharmacology/chemistry
*Micelles
*Metronidazole/pharmacology/chemistry
Animals
*Anti-Bacterial Agents/pharmacology/chemistry
*Oxazoles/chemistry
Cell Line, Tumor
*Tumor Microenvironment/drug effects
Humans
Fusobacterium nucleatum/drug effects
Mice
*Antineoplastic Agents/pharmacology/chemistry
Female
*Drug Delivery Systems
*Drug Carriers/chemistry

@article {pmid42579050,
year = {2026},
author = {Tuzcu, M and Ozmen, R and Ali, S and Sahin, K},
title = {Boron as a Context-Dependent System-Level Modulator: Mechanisms and Implications in Chronic Diseases.},
journal = {Biological trace element research},
volume = {},
number = {},
pages = {},
pmid = {42579050},
issn = {1559-0720},
support = {IIRPIG-2024-01-00891//Indian Council of Medical Research/ ; FUBAP-VF.25.39//Firat University Scientific Research Projects Management Unit/ ; },
abstract = {Boron is a biologically active trace element essential to plants and is increasingly recognized as a potentially important modulator of human physiology. This critical narrative review evaluates evidence concerning mineral metabolism, endocrine-related pathways, redox balance, immune signaling, neurological function, cardiometabolic health, osteoarticular disorders, host-microbiome interactions, and boron-containing pharmaceuticals. Boron's Lewis acid properties and its ability to form reversible complexes with cis-diol-containing biomolecules provide a plausible basis for its broad biological effects, including interactions with NAD[+]- and S-adenosylmethionine-related pathways, membrane-associated glycoconjugates, and inflammatory signaling networks. Experimental and limited clinical studies suggest that boron intake at the doses evaluated may influence bone mineralization, vitamin D metabolism, selected endocrine-related biomarkers, antioxidant defense, and inflammatory homeostasis. In parallel, boron-containing compounds have emerged as valuable pharmacological scaffolds, as illustrated by boron-based agents used in oncology, dermatology, infectious disease, and boron neutron capture therapy. However, despite promising mechanistic and translational findings, evidence for boron's strict essentiality in humans remains limited, and no indispensable boron-dependent human pathway has yet been established. Recent concepts, such as conditional essentiality, suggest that boron may become biologically relevant in specific nutritional, metabolic, inflammatory, skeletal, or microbiome-related contexts. Nevertheless, small sample sizes, short intervention periods, heterogeneous formulations, and reliance on surrogate endpoints continue to constrain clinical interpretation. Future studies require speciation-resolved dosing, pharmacokinetic monitoring, adequately powered randomized designs, long-term safety assessment, and clinically meaningful outcomes. Overall, boron represents a promising but incompletely defined trace element at the intersection of nutrition, immunometabolism, host-microbiome biology, and therapeutic drug design.},
}

@article {pmid42579135,
year = {2026},
author = {Wu, B and Fu, K and Gong, J and Qian, W and Sun, Y},
title = {Microbial community restoration in abandoned coal mine lands: ecological assembly, functional mechanisms, and restoration strategies.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42579135},
issn = {1432-072X},
support = {No. 202002AE320005//Major Science and Technology Special Program of Yunnan Province, China/ ; },
mesh = {*Soil Microbiology ; *Coal Mining ; Bacteria/genetics/classification/metabolism/isolation & purification ; *Environmental Restoration and Remediation/methods ; Ecosystem ; Rhizosphere ; *Microbiota ; Soil/chemistry ; Fungi/genetics/classification/metabolism ; Coal ; },
abstract = {Coal mining creates coupled physicochemical stresses, including extreme pH, nutrient depletion, metal enrichment, compaction, and loss of plant-derived carbon, that reduce microbial biomass, simplify interaction networks, and suppress biogeochemical functions. This review synthesizes recent evidence on microbial community restoration in abandoned coal mine lands, with emphasis on community assembly, stress adaptation, functional genes, and the interpretive value of high-throughput sequencing and meta-omics. During natural recovery, microbial propagule dispersal interacts with strong habitat filtering and rhizosphere selection. Pioneer plants and biological soil crusts progressively add carbon and nitrogen, stabilize surfaces, and recruit bacterial, fungal, and phototrophic guilds. Active interventions accelerate these processes by correcting substrate constraints and by inoculating soils, planting holes, seeds, or carriers with locally adapted microorganisms. However, field performance is often limited by competition with resident communities, host mismatch, environmental heterogeneity, and declining inoculant persistence. Restoration assessment should therefore combine taxonomic composition with functional-gene abundance, gene expression, enzyme activity, microbial biomass, and ecosystem-level indicators. Across sites, no single strategy is consistently superior: amendments act rapidly but may require repeated inputs, vegetation-based approaches are slower but potentially self-sustaining, and inoculation is most effective after major physicochemical barriers have been removed. Future research should prioritize replicated field trials, standardized and activity-resolved measurements, locally adapted consortia, and early-stage interventions that influence microbiome composition and function without assuming complete control. These priorities provide a practical basis for precision restoration of mine-affected soils.},
}

*Soil Microbiology
*Coal Mining
Bacteria/genetics/classification/metabolism/isolation & purification
*Environmental Restoration and Remediation/methods
Ecosystem
Rhizosphere
*Microbiota
Soil/chemistry
Fungi/genetics/classification/metabolism
Coal

@article {pmid42579328,
year = {2026},
author = {Pittaccio, L and Knowles, J and Wheatley, RM},
title = {Microbial interactions as key players shaping the emergence and spread of de novo resistance mutations.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {8},
pages = {},
doi = {10.1099/mic.0.001749},
pmid = {42579328},
issn = {1465-2080},
mesh = {*Mutation ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Microbial Interactions/genetics ; *Microbiota/genetics/drug effects ; Humans ; Evolution, Molecular ; },
abstract = {Antibiotic resistance and the microbiome are two of the most prominent and highly active research areas currently in microbiology. However, these studies are commonly siloed. Research into antibiotic resistance often takes a highly pathogenic-centric view, and microbiome studies typically assess changes in community composition at the genus or species level, rather than at the level of small changes in bacterial genotype that often underpin rapid and significant changes in antibiotic resistance. One of the major mechanisms of antibiotic resistance evolution is via the acquisition of de novo resistance mutations, spontaneous mutations that occur randomly and provide a selective advantage in the presence of antibiotics. In this perspective, we address how interactions within the microbiome can shape the emergence and spread of de novo resistance mutations. We outline existing theoretical and empirical support for how microbial interactions have the potential to influence (i) the probability of de novo resistance mutations emerging, (ii) the fitness costs associated with new resistance mutations and (iii) the long-term selection against resistance and the ability of resistant mutants to transmit to new sites. Existing evolutionary theory may help us predict how microbial interactions will impact the probability of resistance mutations emerging, through understanding how microbial communities will impact pathogen population size, mutation rates and the supply of genetic variation. While a number of these links are simple and intuitive, there is a need for empirical data to understand how the complexity of interactions that exist within a microbial community at any one time come together to shape the evolution of antibiotic resistance. Future research in this field has the potential to inform the development of novel strategies to combat antibiotic resistance based on manipulating microbial interactions.},
}

*Mutation
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Microbial Interactions/genetics
*Microbiota/genetics/drug effects
Humans
Evolution, Molecular

@article {pmid42579351,
year = {2026},
author = {Liu, S and Han, D and Bai, T and Chen, H and Li, JP},
title = {Interpreting Divergent Short-Chain Fatty Acid Effects in Alzheimer's Disease: A Seven-Axis Framework.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0777},
pmid = {42579351},
issn = {2152-5250},
abstract = {Studies of short-chain fatty acids (SCFAs) in Alzheimer's disease (AD) report protective, neutral, and adverse findings, but the same class label often conceals non-equivalent exposures and endpoints. We propose an AD-specific interpretive framework that organizes this heterogeneity as a causal sequence: source or intervention → SCFA species, dose, and route → absorption and metabolic filtering → target-compartment exposure → host and disease state → responding cell type → endpoint. Seven interdependent axes-SCFA species, dose, route, compartment, exposure context, disease stage, and responding cell type-identify the coordinates needed to compare studies. This organization separates administered dose from achieved exposure, direct entry into the central nervous system from blood-brain barrier or peripheral gut-brain signaling, and stage-related disease biology from evidence of stage-specific treatment efficacy. It also requires symmetric interpretation of null findings according to exposure verification, target engagement, power, cellular resolution, and endpoint specificity. The framework integrates rather than replaces established microbiome, pharmacological, and neuroimmune principles and has not been validated as a predictor of effect direction. Its explanatory value can be tested by prespecified meta-regression, variance partitioning, interaction analysis, matched-exposure replication, and causal mediation. Persistent opposite effects under matched coordinates would indicate missing dimensions or failure of the framework. This Perspective therefore supports mechanism-linked, biomarker-informed research rather than nonspecific SCFA supplementation in unselected patients.},
}

@article {pmid42579494,
year = {2026},
author = {Lynch, LE and Soni, KG and Spinler, JK and Ambati, CSR and Putluri, N and Fowler, SW and Conner, ME and Nguyen-Phuc, H and Zeng, XL and Blutt, SE and Estes, MK and Preidis, GA},
title = {Microbiota-derived isovalerate ameliorates sex-specific gut barrier dysfunction in malnutrition.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {33},
pages = {e2611392123},
doi = {10.1073/pnas.2611392123},
pmid = {42579494},
issn = {1091-6490},
support = {R01DK133301//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; P30DK056338//HHS | U.S. Public Health Service (PHS)/ ; T32GM136554//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; RP210227//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; P30CA125123//HHS | NIH | National Cancer Institute (NCI)/ ; 2024//The Research Vision at Texas Children's Hospital/ ; },
mesh = {Animals ; Male ; Female ; Intestinal Barrier Function/drug effects ; Mice ; *Malnutrition/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; Intestinal Mucosa/metabolism/drug effects/microbiology ; *Pentanoic Acids/metabolism/pharmacology ; Permeability ; Colon/metabolism/microbiology ; Mice, Inbred C57BL ; Bacterial Translocation/drug effects ; },
abstract = {Malnutrition increases intestinal permeability and the risk of sepsis, yet mechanisms underlying malnutrition-induced gut barrier dysfunction are poorly defined. Here, we aimed to determine how the gut microbiome and microbiota-derived metabolites influence intestinal barrier function in the malnourished host. We induced malnutrition in specific pathogen-free (SPF) and germ-free (GF) mice using a low-protein, low-fat diet. Colonic permeability was quantified in Ussing chambers and invasive bacteria were cultured from liver and spleen. Targeted metabolomics identified microbial metabolites depleted in malnutrition. Candidate metabolites were screened in human-derived colonoid monolayers and administered to malnourished mice to determine whether gut barrier dysfunction can be rescued. Malnutrition thinned the colonic mucus layer, increased gut barrier permeability, and facilitated bacterial translocation in male, but not female, SPF mice. Malnourished GF mice exhibited normal barrier function. In the malnourished intestine, a subset of microbial short-chain fatty acids, the branched-chain fatty acids (BCFAs), was depleted in SPF mice of both sexes. Treating human-derived colonoid monolayers with BCFAs, especially isovalerate, increased transepithelial electrical resistance and altered the expression of genes associated with epithelial junction complexes. In malnourished male SPF mice, either enemas with isovalerate or gavages with its branched-chain amino acid fermentation substrate, leucine, restored the localization of the integral membrane protein claudin-8 within the colonic crypt and reduced barrier permeability. Together, these findings identify BCFAs, including isovalerate, as microbiota-derived regulators of intestinal junction complexes and barrier integrity. We propose the branched-chain amino acid leucine as a microbiota-directed precision nutrition therapy that could target intestinal barrier dysfunction in malnutrition.},
}

Animals
Male
Female
Intestinal Barrier Function/drug effects
Mice
*Malnutrition/microbiology/metabolism
Humans
*Gastrointestinal Microbiome/physiology
Intestinal Mucosa/metabolism/drug effects/microbiology
*Pentanoic Acids/metabolism/pharmacology
Permeability
Colon/metabolism/microbiology
Mice, Inbred C57BL
Bacterial Translocation/drug effects

@article {pmid42579664,
year = {2026},
author = {Lei, P and Tong, S and Xi, W and Liu, Y and Yu, J and Yu, L and Zhao, B and Jia, M and Li, Y and Ma, X and Wang, Y and Guo, Y},
title = {Dysbiosis of the oral-gut microbiome axis in a mouse model of depression.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0355302},
doi = {10.1371/journal.pone.0355302},
pmid = {42579664},
issn = {1932-6203},
mesh = {Animals ; Male ; Mice ; Disease Models, Animal ; *Dysbiosis/microbiology ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Depression/microbiology ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Behavior, Animal ; *Major Depressive Disorder/microbiology ; Microbiota ; },
abstract = {This study aimed to characterize the alterations in both oral and gut microbiota in a mouse model of depression and to explore their potential role in the pathogenesis of major depressive disorder (MDD) through the oral-gut-brain axis. A depression model was established in male C57BL/6J mice using chronic social defeat stress (CSDS) paradigm. Depressive phenotypes were confirmed through social interaction, sucrose preference, open field, tail suspension, and forced swim tests. The microbial composition of oral and gut samples was analyzed using 16S rRNA sequencing, with Linear Discriminant Analysis Effect Size (LEfSe) employed to identify differentially abundant taxa and Spearman correlation analysis to examine microbiota-behavior relationships. CSDS successfully induced robust depression-like behaviors, including social avoidance, anhedonia, and behavioral despair. Beta-diversity analysis revealed significant separation in oral microbiota between CSDS and control groups. LEfSe analysis identified distinct microbial signatures: control mice were enriched in oral Streptococcus and gut commensals including Lachnospiraceae, Bacteroides and Oscillospiraceae, whereas CSDS mice showed expansion of oral Muribacter and Rodentibacter and gut Alloprevotella, Helicobacter and Colidextribacter. Correlation analyses demonstrated significant associations between specific microbial patterns and depression-like behaviors, with control-enriched taxa negatively correlating with behavioral deficits. Furthermore, significant cross-habitat microbial correlations were observed between oral and gut differential taxa. Our findings demonstrate that CSDS induces divergent microbial alterations in both oral and gut ecosystems, which are systematically associated with depression-like behaviors. These results provide compelling evidence for the involvement of the oral-gut-brain axis in depression pathophysiology and suggest that modulating these microbial ecosystems may represent a potential therapeutic strategy for MDD.},
}

Animals
Male
Mice
Disease Models, Animal
*Dysbiosis/microbiology
Mice, Inbred C57BL
*Gastrointestinal Microbiome
*Depression/microbiology
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Behavior, Animal
*Major Depressive Disorder/microbiology
Microbiota

@article {pmid42570966,
year = {2026},
author = {Prendergast, PJ and Bishop, HV and Herbold, CW and Verdu, EF and Dobson, RCJ and Day, AS and Ogilvie, OJ},
title = {Author Correction: Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.},
journal = {Communications medicine},
volume = {6},
number = {1},
pages = {},
doi = {10.1038/s43856-026-01832-y},
pmid = {42570966},
issn = {2730-664X},
}

@article {pmid42571013,
year = {2026},
author = {Pilkowski, AE and Schaal, P and Leibold, L and Seybold, B and Schenz, J and Dalpke, AH and Weigand, MA and Cheaib, BA and Boutin, S and Fiedler-Kalenka, MO},
title = {Airway microbial compartmentalization under mechanical ventilation: a randomized pilot study comparing an endotracheal tube with suction and continuous cuff pressure control (Venner PneuX[®]) to standard intubation.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {},
pmid = {42571013},
issn = {1465-993X},
mesh = {Humans ; Pilot Projects ; *Intubation, Intratracheal/instrumentation/methods/adverse effects/standards ; Male ; Female ; Suction/methods/instrumentation ; Prospective Studies ; Middle Aged ; Aged ; *Respiration, Artificial/adverse effects/methods/instrumentation ; *Pneumonia, Ventilator-Associated/microbiology/prevention & control/diagnosis ; *Microbiota/physiology ; },
abstract = {OBJECTIVES: Ventilator-associated pneumonia (VAP) is driven in part by microaspiration along the endotracheal tube cuff, a process difficult to measure directly in ventilated patients. Because microbial communities differ between airway compartments, changes in their similarity over time may serve as an indirect readout of microaspiration. We assessed whether the Venner PneuX[®] Tube (VT) system, combining cuff-pressure monitoring, subglottic suction, and a biofilm-resistant coating, reduces microbial exchange between airway compartments compared with a standard endotracheal tube (ST).

METHODS: In a prospective, randomized, single-center pilot study, 50 adults with acute respiratory failure received an ST or VT intubation. Microbial communities from five airway niches (throat, tracheal secretions, right upper, right lower, and left lower lung lobes) were sampled by 16 S rRNA sequencing at intubation (T1), after four days of ventilation (T2) and, for the tube tip, at extubation (T3). The primary outcome was the change in beta diversity (Morisita-Horn distances) between tube-associated, upper-airway, and lower-airway communities from T1 to T2.

RESULTS: Twenty-one of 50 randomized patients had complete microbiota data sets (9 ST, 12 VT) and were comparable in demographics, comorbidities, severity, and ventilation duration. In the ST group, tube-associated communities became more similar to tracheal and lower-airway communities from T1 to T2 (e.g. TS-Tube Morisita-Horn 0.55 → 0.30, p = 0.001), while lung regions diverged from each other and from the throat (LLL-LRL 0.08 → 0.31, p = 0.003; LLL-Throat 0.30 → 0.61, p < 0.001). None of these distances changed significantly in the VT group. Lower-airway Shannon diversity declined in both groups, more in the VT group.

CONCLUSIONS: Standard intubation produced progressive microbial convergence between airway compartments, while the VT system did not. The findings provide biological plausibility for previously reported VAP reductions with the VT system and show that microbiota sampling can detect device-related differences in airway community structure, warranting further investigation as an endpoint for evaluating airway devices.

TRIAL REGISTRATION: The study is registered in the German Clinical Trials Register (DRKS- Deutsches Register für klinische Studien) under the clinical trial number: DRKS00029176. The Date of Trial Registration was 07.07.2022.},
}

Humans
Pilot Projects
*Intubation, Intratracheal/instrumentation/methods/adverse effects/standards
Male
Female
Suction/methods/instrumentation
Prospective Studies
Middle Aged
Aged
*Respiration, Artificial/adverse effects/methods/instrumentation
*Pneumonia, Ventilator-Associated/microbiology/prevention & control/diagnosis
*Microbiota/physiology

@article {pmid42571124,
year = {2026},
author = {Ardinata, D and Alferraly, TI and Yosi, A and Pase, MA},
title = {Insulin Resistance and Cutaneous Squamous Cell Carcinoma: A Narrative Review of Molecular Mechanisms.},
journal = {Iranian journal of medical sciences},
volume = {51},
number = {7},
pages = {467-480},
pmid = {42571124},
issn = {1735-3688},
mesh = {Humans ; *Insulin Resistance/physiology ; *Skin Neoplasms/etiology/physiopathology/metabolism ; Cutaneous Squamous Cell Carcinoma ; *Carcinoma, Squamous Cell/etiology/physiopathology ; Oxidative Stress ; Signal Transduction ; Reactive Oxygen Species/metabolism ; },
abstract = {Although the association between diabetes and cutaneous squamous cell carcinoma (cSCC) is well recognized, the specific role of insulin resistance (IR) as an independent driver of cSCC pathogenesis remains underexplored. This review synthesized emerging evidence on the ultraviolet (UV)-independent molecular mechanisms by which IR promotes cSCC initiation and progression. Hyperinsulinemia activates the insulin-like growth factor-1 receptor (IGF-1R), which triggers both the mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) and phosphoinositide 3-kinase/protein kinase B (PI3K/Akt) pathways, stimulating keratinocyte proliferation and suppressing apoptosis. In parallel, hyperglycemia-driven formation of advanced glycation end products (AGEs) and oxidative stress cause deoxyribonucleic acid (DNA) damage and impair tumor suppressor functions, notably that of tumor protein p53 (TP53). The resulting reactive oxygen species (ROS) activate nuclear factor-kappa B (NF-κB), establishing a chronic inflammatory milieu that remodels the tumor microenvironment through cytokines, including interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α), and by upregulating matrix metalloproteinases (MMPs). These processes collectively facilitate the malignant transformation of actinic keratosis (AK) to invasive cSCC. The analysis in the present study identified novel therapeutic targets and reaffirmed the importance of further studies on microbiome interactions and lifestyle interventions for IR-associated cSCC.},
}

Humans
*Insulin Resistance/physiology
*Skin Neoplasms/etiology/physiopathology/metabolism
Cutaneous Squamous Cell Carcinoma
*Carcinoma, Squamous Cell/etiology/physiopathology
Oxidative Stress
Signal Transduction
Reactive Oxygen Species/metabolism

@article {pmid42571126,
year = {2026},
author = {Fulcher, MR},
title = {Differentiation of the Foliar Microbiomes From Co-Occurring Grass Species Reflects Their Recency of Invasion.},
journal = {Ecology and evolution},
volume = {16},
number = {8},
pages = {e74128},
pmid = {42571126},
issn = {2045-7758},
abstract = {Above-ground microbial communities associated with non-native invasive plants are infrequently characterized, particularly during the early stages of an invasion event. This study compared the foliar fungal and bacterial microbiomes of two co-occurring invasive grasses found in the Mid-Atlantic United States, recently introduced Oplismenus undulatifolius and long-established Microstegium vimineum. Amplicon sequencing was used to characterize endophytic communities collected from replicate plots within two field sites, and microbial community diversity, composition, and structure were contrasted between hosts. Despite occupying the same niche space, these invasive grasses carried significantly different microbial communities. Oplismenus supported lower within-sample fungal diversity and greater among-sample heterogeneity than Microstegium, while differences in bacterial communities were weaker and depended on the diversity metric examined. Null model analyses suggested that assembly processes were host- and microbial kingdom-specific. The differences observed between hosts may have resulted from several non-exclusive mechanisms but were generally consistent with an incomplete establishment of stable host-associated symbioses by the more recent invader. Differential abundance analyses also identified multiple host-associated fungal and bacterial lineages, including increased representation of Glomerellales, Pleosporales, and Rhizobiales in Oplismenus. The results of this study contribute to our understanding of co-occurring invasive weed communities and provide insight into the formation of an emerging, invasive Oplismenus microbiome.},
}

@article {pmid42571245,
year = {2026},
author = {Bisschop, K and Wortel, MT and Kraaijeveld, K and Mariën, J and Rathmann, I and Bonte, D and Declerck, S and de Vos, M and Etienne, RS and Goossens, S and Kammenga, J and Mortier, F and Riksen, J and van der Zee, M and Verhoeven, K and Wiezer, S and Zandbergen, L and Egas, M and Ellers, J and Groot, AT and Visser, ME and Blankers, T},
title = {Additive effects of environmental and demographic variation shape the repeatability of evolution across replicated experiments.},
journal = {Evolution letters},
volume = {10},
number = {4},
pages = {382-395},
pmid = {42571245},
issn = {2056-3744},
abstract = {The repeatability of evolution is fundamentally important for understanding the origin and diversification of life as well as for developing evolutionary forecasting tools. Repeatability is limited by stochasticity, here defined as changes that are independent of genotypic fitness effects. Over short timescales, the two main sources of stochasticity of evolutionary change are environmental stochasticity and demographic (life-history) stochasticity. Quantifying the effect of these two sources of stochasticity and how they interact in driving fitness outcomes is crucially important for predicting contemporary evolutionary responses. To gain insights in the effects of stochasticity, five institutes replicated an evolutionary experiment exposing Caenorhabditis elegans to novel rearing conditions. Replication across the institutes led to variation in selective environments, including through divergent microbiomes among institutes. Replication within institutes was done across demographic treatments that influence the potential for population-size dependent fluctuations in allele frequencies (drift) and genetic hitchhiking (draft). We found high among-institute variation in fitness outcomes, which was partially explained by variation in microbiota. Whereas lab-specific effects explained most of the variance in mean fitness, the repeatability of fitness outcomes depended more on demographic heterogeneity. Specifically, population bottlenecks resulted in high among-replicate variation in fitness. When combined, environmental and demographic stochasticity additively reduced repeatability, underlining their additive importance in developing evolutionary forecasting tools. These results further highlight the importance of statistically integrating heterogeneity in experimental evolution to identify factors constraining outcome repeatability and study replicability.},
}

@article {pmid42571430,
year = {2026},
author = {Sa, R and Zhang, F and Zhang, X and Zhang, Y and Hou, S and Gui, L},
title = {Guanidinoacetic acid enhances Tibetan sheep-meat quality through the gut-muscle axis: insights from metabolome-microbiome integration.},
journal = {Food chemistry. Molecular sciences},
volume = {13},
number = {},
pages = {100440},
pmid = {42571430},
issn = {2666-5662},
abstract = {This study evaluated whether dietary guanidinoacetic acid (GAA) was associated with meat quality, jejunal microbiota and muscle metabolomic profiles in Tibetan sheep. A total of 120 healthy, 2-month-old, weaned male Tibetan sheep (17.33 ± 0.21 kg) were allocated to four groups: CON, basal diet (control group); LG, basal diet supplemented with 0.08% GAA; MG, basal diet supplemented with 0.10% GAA; HG, basal diet supplemented with 0.12% GAA. The feeding trial lasted 90 days after a 10-day adaptation. Compared with CON, 0.12% GAA was associated with higher relative abundances of selected jejunal taxa (Eubacterium_nodatum_group, Family_XIII_AD3011_group and Bacillus) and increased acetate and propionate concentrations. Untargeted metabolomics identified significantly altered muscle metabolites associated with glycerophospholipid metabolism, including PC 37:5, PC 38:4 and LPA 14:0. The HG group also showed higher glutathione peroxidase activity and total antioxidant capacity, a higher a* value and lower shear force. Correlation analyses indicated associations among jejunal microbiota, muscle metabolites and meat-quality traits. These findings provide further evidence supporting the potential use of dietary GAA as a feed additive for improving selected meat-quality traits in Tibetan sheep.},
}

@article {pmid42571478,
year = {2026},
author = {Abdah-Bortnyak, R and Brand, H and Finkelshtein, R and Perry, G and Shwartz, D and Brandwein, M and Katz, A and Nuriel-Ohayon, M and Shental, N and Ben-Simon, M and Billan, S and Luder, S},
title = {Characterization of skin microbiome profile before and during radiation therapy and its correlation to the occurrence and severity of radiation dermatitis.},
journal = {Clinical and translational radiation oncology},
volume = {60},
number = {},
pages = {101233},
pmid = {42571478},
issn = {2405-6308},
abstract = {PURPOSE/OBJECTIVES: The purpose of study is to characterize the skin microbiome profile of breast cancer patients before and during radiation therapy, and evaluate the relationship between the microbiome profile and the severity of acute radiation dermatitis (aRD).

MATERIALS/METHODS: In this observational, single-center, single-arm study, breast cancer patients received RT at Rambam Health Care Campus from November 2020 to July 2021. Skin assessments and skin microbiome samples were collected from all patients before, weekly during RT, after completion of the treatment. The outcome measures were: aRD grade, skin microbiome composition at baseline and during RT.

RESULTS: 640 skin samples were collected from 86 patients, bacterial DNA was extracted, and 16S rDNA was amplified and sequenced.At mid-treatment, the bacterial family Clostridiaceae was unique to patients later diagnosed with moderate/severe acute dermatitis, and present in 30% of the samples (p-value = 0.002038). An unknown species of Anaerococcus, designated Anaerococcus US436, was unique to patients in the moderate/severe aRD group at mid-treatment (21.67% in this group, p-value = 0.002038).To increase sample size and reduce noise, we collected all treated samples from all time points and compared the microbiome composition between the groups of dermatitis severity. The Clostridiaceae family and Clostridium genus remained significantly enriched in the moderate/severe group (p-value = 0.002095 and 0.004269, respectively), as well as the Anaerococcus genus and its unknown species (p-value = 0.001825 and 0.007104, respectively).The treated samples for each patient were summed up, and each bacterium was examined for at least one appearance per patient during the treatment. Granulicatella elegans was enriched in the moderate/severe group (p-value = 0.000512), and Bacillus thuringiensis was enriched in the mild group (p-value = 0.000595).

CONCLUSION: A bacterial composition associated with moderate/severe aRD was identified: Clostridium, Anaerococcus US436, and Granulicatella elegans.},
}

@article {pmid42571869,
year = {2026},
author = {Manzoor, M and Leskelä, J and Könönen, E and Lahti, L and Putaala, J and Pussinen, PJ and Paju, S},
title = {Shotgun Metagenomic Analysis Reveals Taxonomic and Functional Transitions in the Salivary Microbiome During Periodontal Disease Progression.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70184},
pmid = {42571869},
issn = {1600-051X},
support = {296541//Research Council of Finland/ ; 316777//Research Council of Finland/ ; 355532//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 369310//Research Council of Finland/ ; 286246//Research Council of Finland/ ; 318075//Research Council of Finland/ ; 322656//Research Council of Finland/ ; //Finnish Dental Society Apollonia/ ; //Sigrid Juselius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; },
abstract = {AIM: To characterise multi-kingdom salivary microbiome profiles across clinically defined periodontal states and identify stage-specific taxonomic and functional alterations using shotgun metagenomic sequencing.

MATERIALS AND METHODS: In this cross-sectional study, 204 adults (mean age 40.3 ± 7.6 years) from the SECRETO study (NCT01934725) underwent clinical and radiographic oral examinations and were classified into six periodontal groups: periodontal health, localised gingivitis, generalised gingivitis, gingivitis with pockets, mild periodontitis (Stages I-II) and severe periodontitis (Stages III-IV). Saliva samples were analysed using shotgun metagenomic sequencing to evaluate microbial diversity, taxonomic composition and functional pathways.

RESULTS: Beta diversity differed between periodontal health and the different disease states (Bray-Curtis: p = 0.049; Jaccard: p = 0.043). Gingivitis with pockets and severe periodontitis showed a significant enrichment of disease-associated species Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Porphyromonas endodontalis, Fusobacterium nucleatum and Parvimonas micra. Among non-bacterial taxa, Candida, Moineauvirus, Pyricularia and Roseolovirus were the predominant genera. A composite metagenomic classifier showed high discriminative performance for gingivitis with pockets (AUC = 0.90; 95% CI: 0.770-1.000) and severe periodontitis (AUC = 0.865; 95% CI: 0.762-0.968).

CONCLUSION: Salivary multi-kingdom microbiome transitions closely reflect the progression of periodontal disease and provide promising biomarkers for identifying at-risk individuals.},
}

@article {pmid42572222,
year = {2026},
author = {Kirilina, IV and Roumiantsev, SA and Gaponov, AM and Savchyk, DV and Khusnutdinova, DR and Grigoryeva, TV and Teplyakova, ED and Shestopalov, AV},
title = {[The contribution of the intestinal microbiome to the formation of the general profile of bacterial DNA in the blood of obese children].},
journal = {Voprosy pitaniia},
volume = {95},
number = {3},
pages = {107-116},
doi = {10.33029/0042-8833-2026-95-3-107-116},
pmid = {42572222},
issn = {0042-8833},
support = {//The research was carried out under the contract no. 0373100122119000041 within the project "Creation of a bank of biosamples of blood serum and feces from healthy donors and patients with obesity, metabolic syndrome, type 2 diabetes mellitus, and impaired mucosal barrier of the gastrointestinal tract, in order to identify candidate species nonspecific mediators of the quorum sensing microbiota systems of human, which modulate the endocrine and metabolic function of adipose tissue"/ ; },
mesh = {Humans ; Child ; *DNA, Bacterial/blood ; Cross-Sectional Studies ; Feces/microbiology ; Adolescent ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Pediatric Obesity/microbiology/blood ; Lipid Metabolism ; Carbohydrate Metabolism ; Obesity/microbiology/blood ; *Gastrointestinal Microbiome ; },
abstract = {UNLABELLED: Obesity is a multifactorial disease. The gut microbiome disturbances play a significant role in the development of obesity, but emerging data point to a blood microbiome and its association with obesity and other pathologies. Bacterial DNA in the blood represents a pathogen-associated molecular pattern capable of activating the immune system and thereby triggering a cascade of inflammatory responses. The question remains open as to where the bacterial DNA originates, which biotopes shape it, and what role the gut microbiome plays in forming the pool of bacterial DNA in blood. The aim of the study was to compare the bacterial DNA profiles of feces and blood in obese children, to establish relationships between bacterial DNA in blood and feces, and with carbohydrate and lipid metabolism parameters.

MATERIAL AND METHODS: This single-center, cross-sectional study included children and adolescents aged 10 to 18 years with varying degrees of alimentary-constitutional obesity (n=79) and without obesity (n=84). The taxonomic profile of bacterial DNA in blood and feces was analyzed using metagenomic sequencing. Bacterial DNA was isolated from blood and stool samples, and the v3-v4 variable region of the 16S rRNA gene was sequenced. To identify the relationship between bacterial DNA in blood and feces and lipid and carbohydrate metabolism parameters [glucose, total cholesterol, high-density lipoprotein and low-density lipoprotein (LDL)], Spearman's correlation coefficients were calculated.

RESULTS: When comparing bacterial DNA from blood and feces, obese children more often isolated DNA from the families Lactobacillaceae (p=0.043), Porphyromonadaceae (p=0.022), Ruminococcaceae (p=0.065) and less often from Prevotellaceae (p=0.028) and Coriobacteriaceae (p=0.085) compared to children and adolescents without obesity. In obese children, the contribution of intestinal taxa (Lachnospiraceae, Ruminococcaceae, Bacteroidaceae) to the formation of the bacterial DNA profile of the blood was significantly reduced, but the contribution of extraintestinal biotopes (skin, soil and water) was more diverse. Positive associations were found between bacterial DNA of fecal Ruminococcaceae taxa and the level of total cholesterol (ρ=0.347, p=0.002) and LDL (ρ=0.313, p=0.005) and of fecal Coriobacteriaceae and these lipid metabolism parameters (ρ=0.304, p=0.007 and ρ=0.317, p=0.005) in obese children. No positive associations were found between fecal and blood taxa and glucose level.

CONCLUSION: In obese and non-obese children and adolescents, the general profile of bacterial blood DNA is formed by both intestinal and extra-intestinal biotopes. However, in obese children, taxa from extra-intestinal biotopes predominate in the formation of the blood microbiome, which is confirmed by analyzing the proximity of the taxonomic composition of bacterial DNA in blood and feces based on beta diversity indices. The relationship of taxa with blood cholesterol and LDL levels can be considered as a target for microbiota modification and thus reducing the risks of metabolic complications in obesity.},
}

Humans
Child
*DNA, Bacterial/blood
Cross-Sectional Studies
Feces/microbiology
Adolescent
Female
Male
RNA, Ribosomal, 16S/genetics
*Pediatric Obesity/microbiology/blood
Lipid Metabolism
Carbohydrate Metabolism
Obesity/microbiology/blood
*Gastrointestinal Microbiome

@article {pmid42572237,
year = {2026},
author = {Cho, H and Park, G and Yun, HJ and Lee, S and Song, B and Shin, M and Lee, YS and Kang, J},
title = {Lacticaseibacillus paracasei ATG-E1 Alleviates Particulate Matter-Induced Airway Inflammation in Association with Altered Inflammatory Signaling, Gut Microbiota, and Fecal Metabolites.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604029},
doi = {10.4014/jmb.2604.04029},
pmid = {42572237},
issn = {1738-8872},
mesh = {Animals ; *Particulate Matter/adverse effects/toxicity ; Mice, Inbred BALB C ; Mice ; Signal Transduction/drug effects ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Lacticaseibacillus paracasei/physiology ; Lung/pathology ; Bronchoalveolar Lavage Fluid ; *Inflammation/chemically induced ; *Probiotics/administration & dosage ; Male ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Particulate matter (PM) acts as an environmental trigger for inflammatory airway diseases. This study investigated whether oral administration of Lacticaseibacillus paracasei ATG-E1 could therapeutically attenuate PM10 diesel exhaust particle (PM10D)-induced airway inflammation, and explored associated changes in inflammatory signaling, gut microbiota, and fecal metabolites. BALB/c mice were intranasally challenged with PM10D on days 0, 3, 6, and 8, and treated with ATG-E1 or dexamethasone after airway inflammation had been induced. Airway inflammation was evaluated using bronchoalveolar lavage fluid (BALF) cytology, flow cytometry, histopathology, enzyme-linked immunosorbent assay, reverse transcription quantitative polymerase chain reaction, and immunoblotting. Lung transcriptomics, cecal 16S rRNA profiling, and fecal metabolomics were performed, and antitussive and expectorant activities were assessed using ammonia-induced cough and phenol red secretion assays. ATG-E1 reduced inflammatory cell infiltration and neutrophilia in BALF, decreased collagen deposition, and lowered levels of pro-inflammatory mediators in BALF and lung tissue. ATG-E1 attenuated PM10D-activated IκBα and ERK phosphorylation, whereas JNK and p38 phosphorylation were not significantly altered by PM10D under the present experimental conditions. ATG-E1 also reduced caspase-1 and interleukin-1α expression. RNA sequencing revealed a broad downregulation of cytokine-cytokine receptor interaction signaling. ATG-E1 treatment was associated with gut microbiome remodeling, including enrichment of Enterorhabdus and Butyricicoccus, and altered fecal metabolite profiles were characterized by increased branched-chain fatty acids and decreased branched-chain amino acids. Functionally, ATG-E1 reduced cough frequency and increased tracheal phenol red output. Overall, L. paracasei ATG-E1 alleviated PM10D-induced airway inflammation and respiratory symptoms, in association with pulmonary immunomodulation and microbiome-associated fecal metabolite remodeling.},
}

Animals
*Particulate Matter/adverse effects/toxicity
Mice, Inbred BALB C
Mice
Signal Transduction/drug effects
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome/drug effects
*Lacticaseibacillus paracasei/physiology
Lung/pathology
Bronchoalveolar Lavage Fluid
*Inflammation/chemically induced
*Probiotics/administration & dosage
Male
RNA, Ribosomal, 16S/genetics

@article {pmid42572585,
year = {2026},
author = {Marrero, KM and Castillo, JS and Lucas-Barbosa, D and Bellantuono, AJ and Marrero, MA and Cid, D and Costa-da-Silva, AL and Verhulst, NO and DeGennaro, M},
title = {Individual humans are more attractive to certain mosquito species.},
journal = {iScience},
volume = {29},
number = {8},
pages = {117006},
pmid = {42572585},
issn = {2589-0042},
abstract = {Humans are not equally attractive to mosquitoes, leaving some more vulnerable to mosquito-borne illnesses than others. Body odor differences likely allow mosquitoes to discriminate between humans. Using a uniport olfactometer, we measured the attraction of Aedes aegypti, Ae des albopictus, and Culex quinquefasciatus mosquitoes for each of our 119 participants. Ae. aegypti, but not other species tested, were slightly more attracted to male than female participants. Each of our three species ranked our participants differently, favoring a distinct subset of our cohort. For each species, mosquito attraction rates were used to define high- and low-attraction human odors and bacterial taxa. For example, Ae. aegypti and Cx. quinquefasciatus attraction was associated with the absence of odors like cyclic alcohols and monoterpenes, while Ae. albopictus attraction was associated with the presence of ketones. Each mosquito species exhibited distinct responses to individual humans, emphasizing both unique and shared cues for targeting their hosts.},
}

@article {pmid42572807,
year = {2026},
author = {Zavos, C},
title = {Letter: Beyond the Last Sachet-Unanswered Questions in a Probiotic Trial for Bile Acid Malabsorption.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70922},
pmid = {42572807},
issn = {1365-2036},
}

@article {pmid42572835,
year = {2026},
author = {Cao, L and Ma, W and Wen, H and Tang, X and Tang, Z and Qiang, B and Zhang, Y},
title = {Melatonin Seed Coating Improves Soybean Growth in Association With Rhizosphere Physiological and Bacterial Community Shifts: Melatonin Alters Soybean Rhizosphere Responses.},
journal = {Journal of pineal research},
volume = {78},
number = {5},
pages = {e70178},
doi = {10.1111/jpi.70178},
pmid = {42572835},
issn = {1600-079X},
support = {2023DXZD0002//Science and Technology Plan Project of Inner Mongolia Autonomous Region/ ; 2025ZX03A01//Key Research and Development Program of Heilongjiang Province/ ; 072603010//Government Procurement Contract of the Ministry of Agriculture and Rural Affairs/ ; CARS-04-PS19//China Agriculture Research System of MOF and MARA/ ; },
mesh = {*Melatonin/pharmacology ; *Glycine max/growth & development/microbiology/drug effects/metabolism ; *Rhizosphere ; *Seeds/growth & development/metabolism ; Soil Microbiology ; Plant Roots/growth & development/microbiology/drug effects ; Bacteria ; *Microbiota/drug effects ; },
abstract = {Melatonin (MT), a potent bioactive molecule, regulates plant development and stress resistance. However, in complex field environments, how MT seed coating recruits soil microbes via root development modulation and exudate release to boost yield remains unclear. In this 2-year field study, five seed coating treatments with or without MT were used to investigate how MT-associated seed coating coordinates soybean growth with root architecture remodeling, exudate profile changes, rhizosphere microenvironment succession, and plant-microbe associations. Results indicated that MT seed coating treatment significantly increased IAA and GA content in roots by 66.3% and 38.2% compared to CK treatment, while inhibiting ABA content. This hormonal synergistic effect markedly enhanced root vitality by 18.4%, synchronously increased total root length and surface area by 54.5% and 62.6%, induced a significant increase in root tip number, and increased malic acid and citric acid contents in root exudates by 37.2% and 29.8% compared to CK. As a result, soybean yield increased by 10.8% under MT treatment. Rhizosphere analyses showed that MT-containing treatments were associated with higher nitrogen-related enzyme activities and improved inorganic nitrogen availability. Microbiome analyses indicated that stochastic processes remained dominant in bacterial community assembly, but MT reduced the relative contribution of stochasticity and promoted relatively stronger deterministic filtering. Correlation analyses showed that Sphingomonas- and Lysobacter-affiliated taxa were positively associated with growth-promoting hormones, tryptophan, root traits, and nitrogen-turnover indicators. Functional prediction suggested that MT-associated bacterial communities had enhanced potential for amino acid metabolism, membrane transport, and energy metabolism. These findings suggest that MT seed coating may promote soybean growth through coordinated changes in root hormonal balance, root architecture, exudate profiles, rhizosphere nitrogen availability, and microbial community structure.},
}

*Melatonin/pharmacology
*Glycine max/growth & development/microbiology/drug effects/metabolism
*Rhizosphere
*Seeds/growth & development/metabolism
Soil Microbiology
Plant Roots/growth & development/microbiology/drug effects
Bacteria
*Microbiota/drug effects

@article {pmid42572877,
year = {2026},
author = {Richardson, E},
title = {What Does the "Immunological Body" Eat? Metchnikoff and Digestion as Warfare.},
journal = {Perspectives in biology and medicine},
volume = {69},
number = {2},
pages = {229-243},
pmid = {42572877},
issn = {1529-8795},
mesh = {Humans ; *Digestion/immunology ; History, 20th Century ; History, 19th Century ; *Gastrointestinal Microbiome/immunology ; *Immune System ; Phagocytosis ; Animals ; *Allergy and Immunology/history ; },
abstract = {Today we are accustomed to the idea that eating certain foods can help to support the immune system. Over the last two decades, this familiar narrative has been bolstered by the rise of microbial science and the growing popularity of biome-led nutrition, which encourages eaters to nourish the flora and fauna of their guts for the sake of better overall health. While our current preoccupation with the microbiome can be dated to the launch of the Human Microbiome Project in 2007, its origin story can be traced much further back. It begins with work undertaken by scientists and physicians around the turn of the 20th century aimed at understanding the significance of microbes in the digestive system. One of those, the Russian zoologist Élie Metchnikoff (1845-1916), is perhaps best remembered as the founder of modern immunology, and his work on phagocytosis-the capacity of certain specialized cells to engulf and eliminate intruders-earned him the Nobel Prize in 1908. According to Metchnikoff, the gut was the "engine of senility," where pathogenic bacteria multiplied and threatened to overwhelm the body's defenses. Transforming the belly into a battleground where good bacteria went to war with bad, Metchnikoff's influential work extended his theorization of organic immunity as a form of intercellular defense to the vexed question of what to eat and created the foundation for Emily Martin's "immunological body," an understanding of the body that likens it to a nation state, defined through the careful maintenance of the boundary between self and non-self, at this intersection of dietetics and immunology.},
}

Humans
*Digestion/immunology
History, 20th Century
History, 19th Century
*Gastrointestinal Microbiome/immunology
*Immune System
Phagocytosis
Animals
*Allergy and Immunology/history

@article {pmid42573234,
year = {2026},
author = {Hsieh, DC-C and Jiang, L and Xue, M and Antonovsky, N and Brady, SF},
title = {Profiling the aromatic amino acid metabolome in the human gut microbiota reveals Clostridioides difficile-specific N-acyl amino acids.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0077926},
doi = {10.1128/msystems.00779-26},
pmid = {42573234},
issn = {2379-5077},
abstract = {Owing to its compositional and chemical complexity, much of the gut microbiota metabolome remains poorly characterized. Aromatic amino acids (AAAs) have a history of being privileged substrates for the biosynthesis of diverse bioactive metabolites and thus represent a potentially rich source of bioactive molecules within the microbiota metabolome. In this study, we leveraged [13]C- and [2]H-labeled aromatic amino acids and untargeted liquid chromatography-mass spectrometry (LC-MS) to profile AAA-derived metabolites produced by 80 phylogenetically diverse human gut bacterial isolates. Collectively, we found 93 unique LC-MS features, majority of which, predominantly produced by Clostridioides difficile, were identified as N-acyl amino acids. C. difficile produced the highest levels of the AAA-derived phenylacetic acid and phenylpropionic acid, exceeding all Bacteroidetes and Proteobacteria strains in our panel. C. difficile's uniquely diverse N-acyl amino acids have the potential to serve as biomarkers for C. difficile colonization and mediators of C. difficile-specific host interaction.IMPORTANCEThe bacterial metabolome is a key component of the microbiota's effect on host physiology, but identifying small molecules that potentially drive this interaction has remained a challenge. This study uses high-throughput and quantitative mass spectrometry metabolomics to show that Clostridioides difficile uniquely converts amino acids into at least 28 N-acyl amino acids, a metabolite family historically linked to diverse bioactivities. Additionally, in C. difficile cultures, high levels of phenylacetic acid, the precursor of 6 N-acyl amino acids, are of interest because previous studies have mechanistically linked microbially produced phenylacetic acid to cardiovascular disease via β2-adrenergic receptor (β2AR) signaling. The identification of species-specific metabolites produced by commensal bacteria provides not only compounds that could serve as sensitive biomarkers of colonization but also helps support the formulation of mechanistic hypotheses regarding how individual species influence their host.},
}

@article {pmid42573237,
year = {2026},
author = {Nematzadeh Somehsaraei, N and Lemuel Hadi, J and Khan Mirzaei, M and Deng, L and Gigl, M and Dawid, C and Schmitt-Kopplin, P and Geydirici, I and Schloter, M and Gschwendtner, S},
title = {In vitro metabolic signaling in two intestinal bacterial isolates: glutamate-driven transcriptional and functional reprogramming in Clostridium butyricum and Bacteroides thetaiotaomicron.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0019026},
doi = {10.1128/msphere.00190-26},
pmid = {42573237},
issn = {2379-5042},
abstract = {UNLABELLED: Monosodium glutamate (MSG; L-glutamate monosodium salt) is among the most widely used flavor enhancers, yet its molecular effects on gut microbial physiology remain poorly understood. Here, we examined the strain-specific transcriptomic and metabolic responses of Clostridium butyricum and Bacteroides thetaiotaomicron grown in pure anaerobic culture with 0.1% (wt/vol) MSG. Although MSG exposure was not associated with major changes in total bacterial biomass dynamics, both species showed a temporal functional reprogramming. In C. butyricum, MSG rapidly intensified metabolic activity to capitalize on exogenous glutamate by activating central carbon metabolism, redox-balancing pathways, and the GABA shunt, thereby collectively enhancing butyrate synthesis, a metabolite associated with gut barrier integrity, energy regulation, and anti-inflammatory signaling. On the other hand, B. thetaiotaomicron adopted a conservative, homeostatic response, suppressing glycan utilization and central carbon and energy metabolism, and maintaining stable SCFA production through controlled regulation that buffered against abrupt dietary perturbations. Overall, MSG functioned as a potent metabolic signal, triggering distinct adaptive strategies in two dominant gut bacteria.

IMPORTANCE: The impact of monosodium glutamate (MSG) as a highly consumed food additive on the gut microbiome is often overlooked, and community-level analyses reveal little change, masking distinct phenotypic responses of individual strains. By combining gene expression and metabolite profiling using two key human gut bacteria, we show that MSG is sensed as a metabolic signal. A butyrate-producing gut bacterium increases energy metabolism and butyrate production, and a fiber-degrading gut bacterium transiently moderates metabolism to maintain stable fermentation products. These differences suggest that MSG's physiological effects may depend on which bacterial groups dominate an individual's microbiome.},
}

@article {pmid42573241,
year = {2026},
author = {Shagam, LI and Elizarova, A and Momozawa, Y and Dmitrieva, J and Mariman, R and Rahmouni, S and Louis, E and Georges, M and Tyakht, AV and Klimenko, N},
title = {Multi-level aggregation analysis of microbiome composition and host gene expression reveals associations with systemic and local immunity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0359325},
doi = {10.1128/spectrum.03593-25},
pmid = {42573241},
issn = {2165-0497},
abstract = {The human gut microbiome plays a critical role in immune regulation, yet the molecular links between microbiome composition and host gene expression remain incompletely understood. We analyzed associations between host gene expression and microbiome composition in a cohort of 315 healthy individuals, integrating microarray-based gene expression data from three intestinal sites (ileum, transverse colon, and rectum) and six immune cell types with microbiome sequencing data. Using a hierarchical feature aggregation strategy combining principal component analysis, clustering, and covariate correction, we discovered significant associations primarily related to immunity. While microbial profiles were similar across the three intestinal sites, the transverse colon yielded the most "microbiome-host gene expression" associations. Among the immune cell types, CD8+ cells showed the highest number of associations. The first principal component of microbiome composition, reflecting a gradient from commensals (e.g., Ruminococcaceae and Christensenellaceae) to proinflammatory taxa ([Ruminococcus] gnavus and Lachnoclostridium), correlated with the expression of TNF-α-linked genes (HMOX1, CPI17, HSD3B2, and SLC5A1). Among individual genera, Catenibacterium abundance was associated with gene expression in both intestinal and immune cells, including negative associations with MRPS21 (related to mitochondrial function) in the transverse colon and with CD8+ gene programs related to T cell differentiation. These findings align with emerging evidence implicating mitochondrial dysfunction in intestinal inflammation. Our results identify multi-level associations between the gut microbiome and host gene expression, suggesting potential mechanisms by which microbiota shape local and systemic immunity and vice versa. The implicated genes and taxa represent candidates for experimental validation to improve understanding of host-microbiome homeostasis and its disruption in disease.IMPORTANCEThe gut microbiome and immune system are engaged in a complex interplay throughout human life. While most associative studies focus on case-control comparisons-typically examining patients with conditions such as inflammatory bowel disease or metabolic diseases-less is known about the molecular links between the microbiome and immune system in healthy individuals. In this study of a large cohort of healthy individuals, we addressed this gap by applying multiscale modeling to tackle the high dimensionality of host-microbiome data. We identified multi-level associations between microbiome composition and host gene expression in both intestinal tissues and immune cells. These findings offer a valuable reference for understanding baseline host-microbiome communication and highlight molecular candidates-such as TNF-α-related genes and mitochondrial pathways-for future experimental validation.},
}

@article {pmid42573244,
year = {2026},
author = {Qiu, L and Huang, J and Li, G and He, Y and Wei, Z and Yang, S},
title = {Differences in rhizosphere microbial communities between Fusarium wilt-resistant and susceptible watermelon cultivars.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0414925},
doi = {10.1128/spectrum.04149-25},
pmid = {42573244},
issn = {2165-0497},
abstract = {To elucidate genotype-associated differences in rhizosphere microbial community assembly, this study compared the microbiomes of three Fusarium wilt-resistant and three susceptible watermelon cultivars using amplicon sequencing. Results revealed distinct bacterial and fungal community structures between the two groups. Notably, resistant cultivars harbored a higher number of unique operational taxonomic units and displayed greater fungal richness compared to their susceptible counterparts. Beyond taxonomic composition, co-occurrence network analysis demonstrated that the fungal community within the resistant group exhibited a more highly connected network topology. Additionally, functional prediction highlighted significant divergence in potential functional profiles, including variations in Forms_Biofilms and Contains_Mobile_Elements. Collectively, these findings demonstrate that rhizosphere microbial composition, diversity, and network complexity are closely linked to watermelon resistance phenotypes. This comprehensive characterization of genotype-driven microbiome variation offers a critical basis for understanding plant-microbe interactions and their potential to enhance plant health.IMPORTANCEFusarium wilt is one of the most destructive diseases affecting watermelon production worldwide, yet the role of soil microbes in helping plants resist this disease has remained unclear. This study shows that disease-related;resistant watermelon plants naturally recruit a richer and more cooperative community of beneficial microbes around their roots. These microbes may help protect the plant by improving nutrient use, forming biofilms that enhance microbial stability, and competing with or inhibiting harmful pathogens. In contrast, susceptible plants rely on only a few protective microbes, making their root environment less stable and more vulnerable to infection. By revealing how plant genetics shape the assembly and function of root-associated microbial communities, this work provides a scientific foundation for developing microbiome-based strategies-such as microbial inoculants or breeding for microbiome‑friendly cultivars-to improve crop resilience and reduce reliance on chemical pesticides.},
}

@article {pmid42573248,
year = {2026},
author = {Narayan, K and Indugu, N and Challa, K and Webb, T and Pitta, D},
title = {Draft genome sequence of Faecalibacterium prausnitzii FP-BI isolated from bovine feces.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0061126},
doi = {10.1128/mra.00611-26},
pmid = {42573248},
issn = {2576-098X},
abstract = {Faecalibacterium prausnitzii was isolated from Holstein calf feces. Species identity was confirmed by partial 16S rRNA gene sequencing and whole-genome sequencing. The draft genome consisted of 48 contigs totaling 3.01 Mb, with an N50 of 138,331 bp and a GC content of 56.53%.},
}

@article {pmid42573252,
year = {2026},
author = {Adami, GR and Fine, M and Schwartz, JL and Wojtowicz, P and Moreira, J},
title = {State of oral innate immunity and salivary microbiome with allogeneic hematopoietic stem cell transplant.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0011826},
doi = {10.1128/spectrum.00118-26},
pmid = {42573252},
issn = {2165-0497},
abstract = {Allogeneic hematopoietic stem cell transplantation (allo-HSCT) and the use of chemotherapy and antibiotics cause large changes in the gut and oral microbiomes. In patients, these differences in the oral microbiome may be related to the re-establishment of the innate immunity in the oral cavity. Saliva samples were collected from a pilot group of allo-HSCT patients before transplant and at the time of engraftment, when blood neutrophil count had rebounded. As expected, alpha diversity measures of the salivary bacterial community (bacteriome) were low prior to the beginning of the treatment and even lower at the time of engraftment. To examine the local innate immunity, a DNA epigenetic/methylation-based identification of salivary granulocytes was performed post-HSCT on harvested oral DNA samples. At the time of engraftment, salivary granulocyte levels were elevated in allo-HSCT patients vs the level in healthy controls. Salivary and blood neutrophil concentrations both trended to correlate with the Chao1 alpha diversity of the salivary microbiome in patients at the time of engraftment.There was correlation or trends toward correlation between levels of both hematocrit and platelets in blood and the Chao1 and Shannon alpha diversity of the saliva microbiome. In conclusion, the data analysis suggested that during the time of engraftment of the donor stem cells those patients with lowerst diversity of oral bacteria also had the lowest numbers of oral and blood neutrophils. This may contribute to the known higher risk of health complications in patients with dysbiotic microbiomes post-HSCT.IMPORTANCELike the gut microbiome, the oral microbiome includes a large variety of bacteria. We analyzed changes in oral microbiota after allogeneic hematopoietic stem cell transplantation. We found that patients with abnormally low numbers of different bacterial types after the transplant procedure may have had the most abnormal innate immune cell systems both orally and in the blood. This highlights a possible link between the oral microbiome and the innate immune system during the crucial period of immune reconstitution.},
}

@article {pmid42573259,
year = {2026},
author = {Cao, KY and Serrador, D and Campbell, JR and Kaul, R and Navarre, WW},
title = {Utilizing natural competence to genetically manipulate Lactobacillus iners.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0044126},
doi = {10.1128/aem.00441-26},
pmid = {42573259},
issn = {1098-5336},
abstract = {UNLABELLED: The healthy human vaginal microbiota is typically dominated by one species of Lactobacillus: L. iners, L. crispatus, L. jensenii, or L. gasseri. L. iners, the most prevalent vaginal microbe globally, is the most fastidious of the vaginal lactobacilli, has the smallest genome, and produces less lactic acid (only the L-isoform). L. iners is also less protective against bacterial vaginosis and uniquely encodes a cholesterol-dependent cytolysin, inerolysin, suggesting it may be a pathobiont. Despite its central role in the health of over one billion females, L. iners biology remains poorly understood, in part, due to a lack of genetic editing tools. Here, we present findings that L. iners is naturally competent and can be transformed easily by exogenous DNA. Natural competence was leveraged to disrupt the iny gene encoding inerolysin, and comGA, encoding the ATPase component of the competence pilus. Both gene disruptions were accomplished using PCR-assembled DNA fragments comprising a drug resistance gene cassette (tetM or ermB) flanked by ~2 kb regions of homology to the L. iners chromosome. We further demonstrate that comGA is essential for L. iners transformation. The ability to rapidly perform targeted deletions in L. iners with in vitro generated DNA templates provides a straightforward and much-needed method to probe the genetics and physiology of these important vaginal bacteria.

IMPORTANCE: This study describes, to our knowledge, the first method for genetically manipulating L. iners, the most prevalent bacteria of the human vaginal microbiota. This work paves the way for the rapid development of genetic tools to explore the physiology of L. iners in the context of the vaginal microbiome and potentially alter its properties as a probiotic.},
}

@article {pmid42573458,
year = {2026},
author = {Baker, JL and Dahle, UR and Petersen, FC},
title = {mGem: Dentistry is strategically positioned yet underleveraged in the battle against antimicrobial resistance.},
journal = {mBio},
volume = {},
number = {},
pages = {e0064726},
doi = {10.1128/mbio.00647-26},
pmid = {42573458},
issn = {2150-7511},
abstract = {Dentists account for roughly 10% of global antibiotic prescriptions and maintain a substantial patient contact footprint. As a result, dentistry is strategically positioned in the global response to the antimicrobial resistance (AMR) crisis, offering unique opportunities to impact antibiotic stewardship, AMR surveillance, and infection prevention. However, these opportunities are underleveraged because antibiotic stewardship is insufficiently emphasized in dental education curricula and competencies, and because dentistry is inconsistently integrated into AMR policy and national action plans. This disconnect perpetuates fragmentation in prescribing practices and weakens the alignment of dentistry with global One Health efforts. Furthermore, it leaves dentistry alienated from broader AMR research, funding, and educational frameworks. Specific integration of dentistry into AMR National Action Plans and implementation of unified, research-supported prescribing guidelines, targeted clinician education, and oral resistome surveillance could help transform dentistry from a blind spot to a fulcrum in the global AMR response.},
}

@article {pmid42573523,
year = {2026},
author = {Das, P and Dey, T and Peterson, CB and Chakraborty, S},
title = {B-MASTER: Scalable Bayesian Multivariate Regression for Master Predictor Discovery in Colorectal Cancer Microbiome-Metabolite Profiles.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag500},
pmid = {42573523},
issn = {1367-4811},
abstract = {MOTIVATION: The gut microbiome shapes cancer therapy response through its influence on host metabolism. While prior studies examine pairwise associations between individual genera and metabolites, there is limited methodology for identifying microbial genera that systematically regulate the overall metabolome. Scalable statistical tools are needed to uncover such system-level "master predictors" in high-dimensional microbiome-metabolome data.

RESULTS: We introduce B-MASTER, a scalable Bayesian multivariate regression framework combining ℓ1 sparsity and ℓ2 group shrinkage to identify essential cross-metabolite regulators. A Gibbs sampler enables near-linear computational scaling, supporting models with millions of parameters. The method is supported by theoretical guarantees, including posterior contraction and selection consistency. Analysis of colorectal cancer microbiome-metabolome data reveals key microbial genera that govern global and cancer-associated metabolite patterns, highlighting system-level regulatory structure.

AVAILABILITY: The B-MASTER code, including demonstration scripts, is available at https://github.com/priyamdas2/B-MASTER. An archived snapshot of the code corresponding to this manuscript is available on Zenodo with DOI: 10.5281/zenodo.20484958.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42573661,
year = {2026},
author = {Hamid, PH and Dewi, DAPR and Nashrulloh, MM and Caro, TM and Insyari'ati, T and Rahma, NN and Mujiyanto, M and Wibowo, MH and Wardhana, AH},
title = {Feeding-state is associated with shifts in the Haemaphysalis bispinosa microbiome and its potential as a sentinel for circulating livestock pathogens.},
journal = {Veterinary research communications},
volume = {50},
number = {5},
pages = {},
pmid = {42573661},
issn = {1573-7446},
mesh = {Animals ; *Ixodidae/microbiology/physiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Cattle/parasitology ; RNA, Ribosomal, 16S/genetics ; Indonesia ; Feeding Behavior ; Female ; *Cattle Diseases/parasitology/microbiology ; *Tick Infestations/veterinary/parasitology ; },
abstract = {Ticks harbour microbial communities that shape their capacity to acquire and transmit host-associated bacteria. Haemaphysalis (H.) bispinosa is a tick that widely infests variety of hosts across Asia, yet how its bacterial communities are reconfigured across the transition from free-living to blood-feeding states in the field remains poorly understood. Herein, we characterise the microbiome of H. bispinosa using full-length 16 S rRNA gene sequencing. A total of 225 ticks were collected from cattle and the surrounding environment in Central Java, Indonesia. The analysis revealed a diverse array of bacterial taxa spanning 21 phyla and 443 genera. A Coxiella lineage was dominant (46.94%), was present in all samples, and constituted the sole universal core taxon. Environmental ticks exhibited near-monocultural profiles (95-99% Coxiella), whereas host-associated ticks showed increased diversity and the incorporation of additional taxa, including Staphylococcus, Mammaliicoccus, Corynebacterium, and Romboutsia. Within-sample diversity was governed by evenness rather than richness: richness (Chao1) did not differ among states (Kruskal-Wallis, p = 0.543). In contrast, the Shannon index increased significantly from environmental ticks (H = 0.23 ± 0.10) to host-associated ticks (HB, 1.62 ± 0.93; HC, 0.95 ± 0.51; p = 0.0155), a pattern mirrored by Pielou's evenness (p = 0.0155; η[2] = 0.60), with environmental ticks differing significantly from both host-associated states. Beta-diversity analysis confirmed significant community separation across feeding states (PERMANOVA: Bray-Curtis p = 0.0071, R[2] = 0.38; Aitchison p = 5 × 10[-4], R[2] = 0.25; Jaccard p = 0.039, R[2] = 0.16). The environmental-to-host-attached transition represented the largest compositional shift, and engorged ticks exhibited partial convergence toward a structured microbiome characterised by co-dominance of Coxiella and Mammaliicoccus. These findings indicate that feeding state is a major factor associated with microbiome variation in H. bispinosa. The detection of Anaplasma-associated ASVs suggests that H. bispinosa has potential utility for monitoring circulating livestock-associated bacteria. Future work integrating functional approaches will be essential to resolve the pathogenic status of the dominant Coxiella lineage and clarify microbiome-mediated effects on pathogen transmission.},
}

Animals
*Ixodidae/microbiology/physiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Cattle/parasitology
RNA, Ribosomal, 16S/genetics
Indonesia
Feeding Behavior
Female
*Cattle Diseases/parasitology/microbiology
*Tick Infestations/veterinary/parasitology

@article {pmid42573704,
year = {2026},
author = {Alrashdan, A},
title = {Toward microbiota-friendly design and evaluation of antimicrobial peptides: a mini-review.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42573704},
issn = {1874-9356},
abstract = {The rise of multidrug-resistant (MDR) bacteria driven by the prolonged use and misuse of conventional antibiotics poses a severe threat to global healthcare systems. To combat this risk, considerable research efforts have focused on the discovery of new antibacterial agents. Over the last decade, antimicrobial peptides (AMPs) have emerged as a highly promising alternative therapy due to their broad-spectrum activity and low propensity for inducing resistance. While numerous therapeutic AMPs have been introduced in the literature and examined for safety and antimicrobial efficacy, their impact on the human microbiota has remained relatively underexplored. Owing to the structural similarities between pathogenic and beneficial bacteria, some of these peptides may adversely affect commensal bacteria, especially at higher doses or following certain routes of administration. Given the importance of preserving ecological homeostasis, this review emphasizes the integration of microbiota safety evaluations at all stages of AMP design and development. It proposes a structured framework for microbiota-inclusive assessment and strategies for the design and delivery of microbiota-friendly variants. This work offers a comprehensive perspective that has received limited systematic attention, providing valuable insights for future research in microbiology and pharmacology.},
}

@article {pmid42573711,
year = {2026},
author = {Haneesh, M and Amalraj, S and Anusha, G and Karthick, V and Poongavanam, SS and Thamarai, R},
title = {Microbiome-Driven Therapeutic Strategies for Type 2 Diabetes: A Systematic Review of Microbiota Modulation, Glycaemic Outcomes, and Transplantation.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42573711},
issn = {1559-0291},
abstract = {Type 2 diabetes mellitus (T2DM) arises from the body's ineffective use or production of insulin. Recent research highlights the significant role of the gut microbiome in metabolism and immunity, indicating that microbial dysbiosis may be associated with T2DM development. This systematic review will explore the link between gut dysbiosis and Type 2 Diabetes Mellitus (T2DM), assess the impact of microbially-targeted therapies such as probiotics, prebiotics, dietary changes, and fecal microbiota transplantation (FMT) on glycaemic and metabolic outcomes in adults with T2DM, and determine if clinical trials validate the application of these therapies for T2DM treatment. An extensive literature search was conducted using PubMed up to January 2024, adhering to PRISMA 2020 guidelines, to identify eligible studies. The studies included were randomized controlled trials or observational studies reporting measurable outcomes related to metabolic health in adults aged 18 and older. A total of 25 studies show that individuals with Type 2 Diabetes Mellitus (T2DM) have lower gut microbial diversity, featuring fewer butyrate-producing bacteria and more inflammation-related bacteria. Probiotic supplementation and dietary fiber intake significantly improve hemoglobin A1c (HbA1c) levels and insulin sensitivity in T2DM patients. Gut microbiota dysbiosis is linked to Type 2 Diabetes Mellitus (T2DM), suggesting that the gut microbiome could be a therapeutic focus. However, while interventions like dietary changes, probiotics, and fecal microbiota transplantation show potential, current evidence does not support their routine clinical application. Recommendations for microbiome interventions should rely on strong evidence from effective longitudinal clinical trials verifying both efficacy and safety.},
}

@article {pmid42573755,
year = {2026},
author = {Ayana, GU and Abdullateef, MM and Yadata, GW and Manzoor, R and Sumana, SL and Gelata, AM and Islam, MM},
title = {Pathogenic mechanisms of Aeromonas hydrophila and the protective role of probiotics in sustainable aquaculture.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42573755},
issn = {1432-072X},
mesh = {*Aeromonas hydrophila/pathogenicity/drug effects ; *Probiotics/pharmacology/administration & dosage ; Animals ; *Aquaculture ; *Gram-Negative Bacterial Infections/veterinary/microbiology/prevention & control ; *Fish Diseases/microbiology/prevention & control ; Fishes/microbiology ; },
abstract = {Aeromonas hydrophila (A. hydrophila) is a pervasive opportunistic fish pathogen responsible for hemorrhagic septicemia and gastrointestinal disease and, together with other motile aeromonads (e.g., A. veronii, A. caviae, and A. dhakensis), for motile aeromonad septicemia (MAS), which cause significant economic losses in the global freshwater aquaculture industry. The widespread use of antibiotics to control A. hydrophila has led to increased antimicrobial resistance and environmental concerns, necessitating the urgent need for sustainable alternative treatments. We systematically retrieved, screened, and selected relevant studies from three databases: Scopus, Web of Science, and PubMed. Articles published between January 1, 2016, and June 1, 2026, were included. Two reviewers independently assessed the eligibility and data quality and extracted information from the identified articles. We performed a bibliometric analysis using VOSviewer and RStudio for visualization. We identified 339 experimental research publications from 2016 to 2026 and selected 39 articles that met the selection criteria for full-text evaluation. For VOSviewer keyword co-occurrence networking, we used the 277 Scopus publications (research articles, reviews, and book chapters) retrieved with the same search string. For the country trend analysis, we used the 464 deduplicated records (research articles, reviews, and book chapters) screened after duplicate removal. The most current keywords used were A. hydrophila, probiotic agents, microbiology, and probiotics. The country trend analysis revealed a remarkable increase in publications over the past 10 years, with key contributions from China, India, Iran, Brazil, and Egypt. The year 2025 recorded the highest publication output over the past 10 years. A diverse repertoire of virulence factors, including act, aerA, fla, ahyI, ahyR, and type III secretion systems, mediates A. hydrophila pathogenicity. Probiotics exert consistent multimodal protection via competitive pathogen exclusion, production of antimicrobial compounds, intestinal barrier enhancement, and host immunomodulation. Probiotics improve growth performance, digestive enzyme production, nutritional composition, immune response, hematology and histopathology, gut microbiome, and survival. This review highlights that probiotics are a viable, evidence-based component of integrated health management programs for A. hydrophila control, complementing rather than universally replacing antibiotics. This review highlights that probiotics are viable, evidence-based, and sustainable alternatives to antibiotics for A. hydrophila control.},
}

*Aeromonas hydrophila/pathogenicity/drug effects
*Probiotics/pharmacology/administration & dosage
Animals
*Aquaculture
*Gram-Negative Bacterial Infections/veterinary/microbiology/prevention & control
*Fish Diseases/microbiology/prevention & control
Fishes/microbiology

@article {pmid42573766,
year = {2026},
author = {Shah, AH and Ravandi, A},
title = {Beyond Passive Congestion: The Inflammatory Gut-Liver Axis in Fontan Circulation.},
journal = {Pediatric cardiology},
volume = {},
number = {},
pages = {},
pmid = {42573766},
issn = {1432-1971},
abstract = {Fontan circulation has traditionally been viewed as passive venous congestion caused by absence of a subpulmonary ventricle. Emerging multi-omic data suggest a broader inflammatory gut-liver-heart syndrome. This viewpoint integrates findings from metabolomics, lipidomics, microbiome-derived metabolites, cytokine-chemokine profiling, and tryptophan-kynurenine pathway analysis to propose that hepatic congestion is biologically active. Bile acid dysregulation, short-chain fatty acid perturbation, mitochondrial stress, interferon-γ/IP-10 signaling, SDF-1α elevation, and kynurenine pathway activation may interact in a feed-forward loop contributing to frailty, impaired exercise capacity, Fontan-associated liver disease, and multiorgan dysfunction. Longitudinal and interventional studies are needed to define reversibility.},
}

@article {pmid42573887,
year = {2026},
author = {Yang, L and Zhao, J and Han, T and Qi, H and Zhao, F and Sun, Z},
title = {Modulating the gut-joint axis: Bifidobacterium longum subsp. infantis B8762 is associated with selective gut microbial and metabolic alterations in knee osteoarthritis.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42573887},
issn = {1573-0972},
support = {U25A20733//National Natural Science Foundation of China/ ; 2022YFD2100702//National Key Research and Development Program of China/ ; YLXKZX-NND-006//Inner Mongolia Agricultural University First-Class Discipline Scientific Research Special Program/ ; CARS36//Earmarked Fund for China Agriculture Research System/ ; },
mesh = {Humans ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Osteoarthritis, Knee/microbiology/metabolism/therapy ; *Probiotics/administration & dosage ; Metabolome ; *Bifidobacterium/physiology ; Metabolomics ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics ; Female ; Knee Joint/microbiology/metabolism ; *Bifidobacterium longum ; },
abstract = {Knee osteoarthritis (KOA) is a debilitating degenerative joint disorder characterized by chronic low-grade inflammation and metabolic dysregulation. The gut microbiota has emerged as an important regulator of systemic inflammatory responses. Building upon our previous clinical findings that Bifidobacterium longum subsp. infantis B8762 (B8762) improved clinical symptoms and inflammatory markers in patients with KOA, the present study investigated the associated alterations in the gut microbiome and fecal metabolome. Fecal samples were collected from probiotic (n = 20) and placebo (n = 20) groups at baseline (0 M) and after a 1-month intervention (1 M). Integrated metagenomic and untargeted metabolomic analyses were performed to characterize changes in gut microbial composition, functional potential, and metabolic profiles. Metagenomic reads mapped to the B8762 reference genome showed a greater increase in B8762-associated mapping rates in the probiotic group than in the placebo group, supporting an association between B8762 supplementation and longitudinal changes in the gut microbiome. Longitudinal analysis further demonstrated greater increases in microbial alpha diversity in the probiotic group. Species-level analyses suggested selective alterations in gut microbial composition, with nominally higher relative abundances of Bifidobacterium pseudocatenulatum and Anaerostipes caccae and lower relative abundances of Holdemania filiformis and Lachnospira SGB5077 (nominal P < 0.05). HUMAnN3-based functional profiling identified enrichment of microbial pathways related to carbon utilization and amino acid biosynthesis, including the bifidobacterial shunt and branched-chain amino acid biosynthesis pathways. Untargeted metabolomics identified nominal between-group differences in metabolites primarily related to lipid metabolism, including lower relative abundances of aldosterone and 7α-hydroxy-4-cholesten-3-one in the probiotic group (nominal P < 0.05). Correlation analysis further revealed associations between differential taxa and selected metabolites, suggesting potential links between gut microbial alterations and steroid-related metabolic pathways. Overall, B8762 supplementation was associated with longitudinal changes in B8762-associated genomic signals, gut microbial diversity and composition, microbial functional potential, and fecal metabolic profiles. These findings provide exploratory multi-omics evidence supporting an association between B8762 supplementation and gut microbial-metabolic remodeling in KOA and generate hypotheses for future mechanistic studies of the gut-joint axis.},
}

Humans
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/drug effects
*Osteoarthritis, Knee/microbiology/metabolism/therapy
*Probiotics/administration & dosage
Metabolome
*Bifidobacterium/physiology
Metabolomics
Male
Bacteria/classification/genetics/isolation & purification/metabolism
Metagenomics
Female
Knee Joint/microbiology/metabolism
*Bifidobacterium longum

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

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

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

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

@article {pmid42574005,
year = {2026},
author = {Bao, Z and Yang, Z and Sun, R and Meng, R and Wu, W and Li, MD},
title = {Associations of smoking, aging, and their interplay with the gut microbiome and chronic disease risk profiles.},
journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco},
volume = {},
number = {},
pages = {},
doi = {10.1093/ntr/ntag174},
pmid = {42574005},
issn = {1469-994X},
abstract = {INTRODUCTION: Smoking and aging are both linked to chronic disease and gut microbiome, but their joint relationship with microbiome composition remains uncharacterized. This study examined the overlap between smoking- and age-associated gut microbial signals and their associations with cardiovascular diseases.

METHODS: We analyzed 6676 participants from a filtered project-specific metadata subset from the Guangdong Gut Microbiome Project together with the public GGMP OTU table. Associations of smoking phenotypes and aging with gut microbiota were examined using multivariable linear models. Additional sensitivity analyses were performed in males only, and robustness analyses were repeated at the family and genus levels.

RESULTS: We identified 222 OTUs associated with first-hand smoking and 117 OTUs associated with second-hand smoke exposure. Among never smokers, age was associated with 330 OTUs. Eighty-five OTUs overlapped between smoking- and age-associated signals. Differences in the abundance of these OTU groups between never smokers and daily smokers were more pronounced in younger than older age strata. The smoking- and age-related OTU groups were associated with several cardiometabolic markers, and mediation analysis suggested that systolic blood pressure may partly account for the association between this overlapping microbial signal and ASCVD risk score. In a male-only sensitivity analysis, the central smoking-aging microbial signal remained directionally consistent. Family- and genus-level robustness analyses also supported persistence of selected associations.

CONCLUSIONS: In this cross-sectional secondary analysis, smoking and aging were associated with overlapping gut microbiome patterns, with stronger smoking-related deviations in younger adults. These findings support future longitudinal studies of microbiome-linked cardiovascular risk in smoking-exposed populations.},
}