@article {pmid42555106,
year = {2026},
author = {Luo, Z and Liu, Y and Wu, H and Xiao, Y and Li, Y and Liu, M and Li, C and Zhu, D and Jin, LN and Dong, T and Yan, W},
title = {Zoo gut plastispheres enable pathogen escape and adaptation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag207},
pmid = {42555106},
issn = {1751-7370},
abstract = {In zoos, intensive human contact and artificial feeding may create pathways for microplastic (MP) ingestion and gut colonization. We hypothesized that ingested MPs form intestinal plastispheres with elevated pathogenic potential and enhanced environmental persistence. To test this, we surveyed feces from 15 zoo-dwelling species and coupled particle characterization, feces-derived intestinal simulations, metagenomic sequencing, and a subsequent water-exposure experiment. Zoo feces contained more abundant MPs than reported for wild counterparts, with fragments predominating and polyethylene terephthalate (PET)/polystyrene (PS) dominating polymer profiles. MP burdens tracked human-animal interaction patterns, with human-fed species (e.g., Tiger, Elephant) carrying the highest loads (88-212 items/g). MPs supported dense biofilms whose composition diverged from bulk gut communities, exhibiting greater compositional variability and substrate-specific assembly. Metagenomic analyses revealed coordinated enrichment of potentially pathogenic taxa, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs), with ARG profiles dominated by efflux- and inactivation-related mechanisms and tightly associated with mobile genetic elements. Elevated Type II/III/IV/VI secretion systems and effector delivery-related VFGs occurred within extracellular polymeric substance-rich biofilms, suggesting enhanced potential for ARG retention and horizontal gene transfer. During the 35-day aquatic exposure, MP-associated communities persisted longer than non-plastic particle-associated communities and free gut microbiota, suggesting that plastic-specific properties promote microbial persistence. PET/PS plastispheres showed the slowest declines in bacterial activity and favored the persistence of Enterococcus, Enterobacter, and Clostridium. Overall, intestinal MPs in zoo animals may select, enrich, and export high-risk microbiomes, highlighting the need for MP mitigation and evidence-based management of zoos and adjacent ecosystems.},
}

@article {pmid42555112,
year = {2026},
author = {Timotej, TD and Ion, GA and Tinkara, R and Tinkara, T},
title = {Viral lysis accelerates microbial succession patterns resembling diatom senescence.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag206},
pmid = {42555112},
issn = {1751-7370},
abstract = {Diatom blooms influence carbon cycling through organic matter production and its deposition or remineralization - processes mediated by the microbial community. Viruses can influence diatom bloom dynamics and even terminate blooms, yet interactions between diatoms, their viruses, and associated bacteria remain poorly resolved. Here, we examined how infection of the toxigenic diatom Pseudo-nitzschia galaxiae by its ssRNA virus PnGalRNAV reshapes host physiology, microbiome structure, and organic-matter processing in non-axenic batch cultures. Using epi-fluorescence microscopy, 16S rRNA amplicon sequencing, and metatranscriptomics, we linked microbial composition, localisation, and functional activity during viral lysis. Infection rapidly collapsed diatom growth and induced a senescence-like host state, with broad repression of photosynthesis, silicon metabolism, and core biosynthetic pathways, alongside induction of heat-shock and other stress-related genes. Concurrently, phycosphere-associated bacteria declined, detritosphere-associated bacteria increased, and community composition shifted from Marinobacter (Gammaproteobacteria) dominated, towards Flavobacteriaceae (Bacteroidetes) dominated, especially by Polaribacter. In non-infected controls Alphaproteobacteria proved to benefit from the stable healthy phycospheres with a distinct DOM pool. Bacterial metatranscriptomes showed significant upregulation of polysaccharide-degradation-associated genes in infected cultures, indicating active utilisation of lysis-derived diatom glycans. Similar compositional and metabolic profiles in infected cultures and later-stage senescent controls suggest infection accelerated senescence-associated microbial processes. Overall, viral lysis converted a productive diatom culture into a detrital, DOM-rich environment that selects for specialised polysaccharide degraders, redirects carbon through the viral shunt and may accelerate nutrient recycling in coastal systems. Extending this approach to natural microbial communities and diverse diatom-virus systems will help determine whether these mechanisms are broadly conserved.},
}

@article {pmid42555374,
year = {2026},
author = {Palagiano, C and Potestio, L and Brescia, C and Napolitano, M},
title = {Pharmacotherapeutic strategies for the treatment of severe juvenile acne.},
journal = {Expert opinion on pharmacotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14656566.2026.2715706},
pmid = {42555374},
issn = {1744-7666},
abstract = {INTRODUCTION: Severe juvenile acne vulgaris represents a highly prevalent chronic inflammatory disorder that may significantly impair quality of life and lead to permanent scarring during adolescence. Increasing understanding of acne pathophysiology has progressively modified therapeutic approaches, with growing emphasis on early intervention, antimicrobial stewardship, and individualized systemic treatment strategies.

AREAS COVERED: This narrative review summarizes current evidence regarding pharmacotherapeutic strategies for severe juvenile acne, with particular focus on systemic therapies. A literature search was conducted in PubMed, Embase, Google Scholar, Cochrane Library, and ClinicalTrials.gov from database inception to March 2026. The pathogenic mechanisms underlying juvenile acne, including sebaceous hyperactivity, follicular hyperkeratinization, Cutibacterium acnes, dysbiosis, immune-inflammatory activation, and hormonal influences, are discussed.

EXPERT OPINION: Severe juvenile acne should not be underestimated as a physiologic condition of adolescence, as delayed or inadequate treatment may result in substantial physical and psychological sequelae. Oral isotretinoin remains the gold-standard therapy for severe nodulocystic, scarring, or treatment-resistant acne. Timely specialist assessment is essential in high-risk adolescents to avoid unnecessary delay when the licensed criteria for isotretinoin treatment are fulfilled; however, its use must remain consistent with applicable product information, regulatory requirements, and risk-minimization measures. Simultaneously, prolonged systemic antibiotic exposure should be minimized through stewardship-oriented approaches integrating benzoyl peroxide combinations and shorter treatment durations. Future therapeutic strategies will likely move toward increasingly individualized, microbiome-conscious, and inflammation-targeted approaches aimed not only at lesion clearance but also at prevention of long-term scarring and psychosocial burden.},
}

@article {pmid42555388,
year = {2026},
author = {Sun, W and Xiao, M and Ali, SL and Jin, C and Khan, A and Shakirullah, and Ni, R and An, Y and Zhang, M and Tian, Y and Kaushik, S and Zhang, Y and Gong, W},
title = {Harnessing the gut microbiome to combat tuberculosis: a technological and clinical review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1847443},
pmid = {42555388},
issn = {2235-2988},
mesh = {Humans ; *Tuberculosis/therapy/diagnosis/microbiology/prevention & control ; *Gastrointestinal Microbiome ; Artificial Intelligence ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Biomarkers ; Multiomics ; },
abstract = {Tuberculosis (TB), especially multidrug-resistant and extensively drug-resistant strains, remains a severe global health threat. Advances in high-throughput sequencing, omics technologies and artificial intelligence have revealed the critical involvement of the gut microbiome (GM) in TB pathogenesis, diagnosis and treatment via the gut-lung axis. The GM modulates host immunity and metabolism; TB patients typically show reduced microbial diversity and enriched pro-inflammatory taxa closely linked to disease severity and treatment responses. Omics research has identified promising biomarkers and pathways for early diagnosis and personalized management, while artificial intelligence improves diagnostic accuracy and treatment outcome prediction. GM-targeted interventions, including probiotics, dietary adjustment and fecal microbiota transplantation, can enhance therapeutic efficacy and relieve adverse drug reactions. Current limitations include insufficient validation of the gut-lung axis' causal mechanisms, lagged clinical translation of biomarkers, biases and errors in diagnosis and prediction, data privacy and security concerns, gaps in intervention research, and poor accessibility of related technologies in resource-scarce medical regions. Future studies need rigorous causal analyses, real-time monitoring tools and large-scale multicenter trials to validate microbiome-based strategies. This review highlights the translational potential of GM interventions to optimize personalized TB prevention, diagnosis and treatment and improve clinical outcomes.},
}

Humans
*Tuberculosis/therapy/diagnosis/microbiology/prevention & control
*Gastrointestinal Microbiome
Artificial Intelligence
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Biomarkers
Multiomics

@article {pmid42555404,
year = {2026},
author = {Hosen, MA and Rahman, T and Rahatuzzaman, and Kabir, RB and Ahsan, CR and Rahman, M and Yasmin, M and Jubair, M},
title = {Uncovering the Hidden Diversity and Antimicrobial Resistance of Uropathogens in a Tertiary-Care Hospital in Bangladesh.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {8327078},
pmid = {42555404},
issn = {1687-918X},
abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections worldwide; however, their diagnosis in low- and middle-income countries often relies on conventional culture and biochemical methods with limited sensitivity. This study evaluated the limitations of routine diagnostic approaches and explored the microbial diversity and antimicrobial resistance (AMR) profiles of uropathogens in a tertiary-care hospital in Bangladesh using integrated culture-based and molecular methods. Among 30 patient urine samples collected in 2025, 10 were selected for detailed analysis due to funding and resource limitations; therefore, the findings should be interpreted as exploratory and may be subject to selection bias. Of these 10 samples, routine hospital diagnostics identified only eight isolates, whereas extended biochemical analysis detected 29 isolates, indicating substantial underestimation of microbial diversity in standard practice. Antibiotic susceptibility testing revealed a high prevalence of multidrug resistance, with 83% and 80% of isolates resistant to ampicillin and clindamycin, respectively. In contrast, nitrofurantoin and fosfomycin retained effectiveness against most isolates, supporting their continued clinical utility. 16S rRNA gene sequencing further revealed complex and heterogeneous microbial communities, with several samples dominated by Escherichia-Shigella, whereas others exhibited polymicrobial profiles including commensal and opportunistic genera. Despite taxonomic variability, microbial diversity did not differ significantly between inpatient and outpatient groups. Functional pathway prediction demonstrated a largely conserved metabolic profile across samples, including pathways associated with virulence, iron acquisition, and AMR. Overall, this study demonstrates that conventional diagnostic methods substantially underestimate uropathogen diversity and may contribute to misdiagnosis and inappropriate antibiotic use. Integrating molecular approaches into routine clinical workflows could improve pathogen detection, enhance AMR surveillance, and support more effective management of UTIs in Bangladesh and similar resource-limited settings.},
}

@article {pmid42555417,
year = {2026},
author = {Kamaljeet, and Vijukumar, A and Shahi, A and Kumar, A and Bhatia, R},
title = {AUTO-brewery syndrome and the human microbiome: Insights into endogenous ethanol production and human diseases.},
journal = {Food science and biotechnology},
volume = {35},
number = {9},
pages = {2415-2436},
pmid = {42555417},
issn = {2092-6456},
abstract = {Auto-Brewery Syndrome (ABS) is a metabolic condition where microbiota dysbiosis undergoes ethanolic fermentation within the gastrointestinal tract. Because the microbial ethanolic fermentation of dietary carbohydrates occurs entirely within the host's gastrointestinal tract, resulting ethanol is referred as "endogenous" while the gut dysbiosis in ABS can rise from multiple fungal or bacterial species. The pathophysiology of ABS is frequently linked to shifts in gut microbiota composition often arising from antibiotics use, high carbohydrate diets, or an underlying immunological or metabolic condition. In this review, the mechanisms behind microbial endogenous ethanol production, the connection between gut, liver, brain, and microbial ethanol-producing routes are examined. Treatments for ABS have been evaluated including antifungals, low-carbohydrate diets, probiotics, and faecal-microbiota transplantation. Lastly, the social, legal, and mental impacts of ABS have been discussed. It would be wise for future studies to develop customized microbiome approaches for detection and treatment guided by omics and AI technologies.},
}

@article {pmid42555451,
year = {2026},
author = {Singh, G and Lavika, and Nandini, and Abhay, and Deepika, and Thakur, N and Kaura, R and Kaur, S and Saini, HS and Khulape, S and Puniya, AK and Dhillon, HS},
title = {Rumen mycobiome dynamics and dairy productivity: functional contributions of fungi to milk yield in bovine ruminants.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1878257},
pmid = {42555451},
issn = {2673-6128},
abstract = {The rumen microbiome is a key factor influencing feed efficiency and milk production in ruminants. However, most studies have focused on the bacterial and archaeal components, with the fungal fraction of the rumen being relatively understudied. The unique ability of anaerobic rumen fungi of the phylum Neocallimastigomycota to colonize and degrade lignocellulosic biomass in the rumen through mechanical disruption of plant cell walls has now made them well known as important functional members of the rumen ecosystem. These fungi are armed with a plethora of carbohydrate-active enzymes degrading fiber and increase the availability of substrates for microbial fermentation. This leads to increased production of volatile fatty acids, especially acetate, which is a major precursor for milk fat production. Recent research evidence has indicated that rumen fungal communities are associated with feed efficiency, fermentation dynamics, and milk composition traits such as fat and protein content in bovine ruminants such as cattle and buffalo. However, most of the studies available are correlative, and the direct causal relationships between fungal activity and milk productivity are poorly delineated. High-throughput sequencing and multi-omics approaches have broadened our knowledge of fungal diversity and function; however, there are still limitations in reference databases and methodological biases. This review summarizes the current knowledge of the diversity, ecological roles, and functional contributions of anaerobic rumen fungi, with special reference to their association with milk production. It also highlights significant methodological and conceptual gaps and proposes future avenues for the integration of fungal ecology into microbiome-based approaches to improve dairy productivity. We need a holistic multi-kingdom view of the rumen microbiome to design efficient and sustainable dairy production systems.},
}

@article {pmid42555752,
year = {2026},
author = {Rachid, R and Martinez-Blanco, M and Kuziel, GA and Stephen-Victor, E and Groussin, M and Orakov, A and Russell, G and Nguyen, LTT and Poyet, M and Mukhatayev, Z and Yee, CSK and Albuhairi, S and Kteish, R and Rahman, EA and Farraj, FA and Wang, Z and Dahlberg, S and Ryan, M and Fitzgerald, M and Elverson, W and Lee, JJ and Schneider, L and MacGinnitie, A and Crestani, E and Queheillalt, D and Burke-Roberts, E and Watson, J and Elliott, RJ and Wong, WF and Osman, M and Voyksner, R and Hohmann, E and Huttenhower, C and Alm, E and Rakoff-Nahoum, S and Chatila, TA},
title = {Fecal microbiome transplant in food allergy in humans and mice identifies a role for bile acid metabolites in oral tolerance.},
journal = {Science translational medicine},
volume = {18},
number = {861},
pages = {eaee3263},
doi = {10.1126/scitranslmed.aee3263},
pmid = {42555752},
issn = {1946-6242},
mesh = {Animals ; Humans ; *Bile Acids and Salts/metabolism ; *Food Hypersensitivity/immunology/therapy/microbiology ; *Fecal Microbiota Transplantation ; Mice ; Adult ; T-Lymphocytes, Regulatory/immunology ; Administration, Oral ; Female ; *Immune Tolerance ; Male ; },
abstract = {The gut microbiome has been implicated in the pathogenesis of food allergy (FA), prompting microbiome-focused interventions. We evaluated, in a phase 1 open-label trial (NCT02960074), the safety and efficacy of oral encapsulated fecal microbiome transplantation (FMT) in 15 adults with peanut allergies. An increase in the peanut reactivity threshold was noted in 3 of 10 participants not pretreated with antibiotics and 3 of 5 participants pretreated with antibiotics, without safety issues. In responders, FMT increased tolerogenic RORγt[+] regulatory T cells (Treg cells) and decreased T helper 2 cells (TH2 cells). Mice transplanted with the microbiomes of post-FMT responders were protected from FA in association with increased RORγt[+] Treg cell percentages and increased colonization with members of the gut Bacteroides. In both humans and mice, protection by FMT was associated with increased bile acid metabolites. Deletion of a bile salt hydrolase in a candidate protective Bacteroides abrogated FA suppression in mice. These results suggest that FMT is a safe and potentially promising therapeutic modality for treating FA.},
}

Animals
Humans
*Bile Acids and Salts/metabolism
*Food Hypersensitivity/immunology/therapy/microbiology
*Fecal Microbiota Transplantation
Mice
Adult
T-Lymphocytes, Regulatory/immunology
Administration, Oral
Female
*Immune Tolerance
Male

@article {pmid42556070,
year = {2026},
author = {Wespiser, M and Rochefort, P and Gauduchon, T and Coste, C and Caux, C and Ray-Coquard, I and Perol, M and Blay, JY and Heudel, PE},
title = {Pharmacological prevention of second primary cancers: From chemoprevention to precision cancer interception.},
journal = {Cancer treatment reviews},
volume = {149},
number = {},
pages = {103200},
doi = {10.1016/j.ctrv.2026.103200},
pmid = {42556070},
issn = {1532-1967},
abstract = {BACKGROUND: The growing population of cancer survivors is increasingly exposed to the long-term risk of second primary cancers (SPCs), which represents a major source of morbidity and mortality. While current prevention mainly relies on surveillance and screening, pharmacological and immunological strategies may offer opportunities to reduce SPC incidence in selected high-risk populations.

METHODS: This narrative review synthesises current evidence on pharmacological prevention strategies for SPCs, including endocrine therapy, aspirin and non-steroidal anti-inflammatory drugs, PARP inhibitors, metformin, GLP-1 receptor agonists, statins, nicotinamide, immune checkpoint inhibitors, cancer vaccines, and microbiome modulation. Evidence from randomised trials, observational studies, translational research, and ongoing clinical trials was reviewed, with particular attention to SPC-specific endpoints, biological rationale, safety, and clinical applicability.

RESULTS: The strongest evidence currently supports endocrine therapy for reducing contralateral breast cancer in patients with hormone receptor-positive breast cancer, and aspirin in selected populations such as Lynch syndrome carriers or patients with molecularly defined colorectal cancer. Other repurposed agents, including metformin, statins, GLP-1 receptor agonists, and nicotinamide, remain investigational, with most available data addressing incident cancer, recurrence, or surrogate endpoints rather than SPC prevention specifically. Immunological approaches are emerging as particularly promising strategies. Retrospective studies and exploratory analyses of randomised trials suggest that immune checkpoint inhibitors may reduce the occurrence of new malignancies, while neoantigen-based vaccines, especially in Lynch syndrome, provide an early proof of concept for cancer immunoprevention.

CONCLUSIONS: Pharmacological prevention of SPCs is an expanding but remains a heterogeneous field. Current evidence supports a shift from broad chemoprevention toward biologically informed, risk-adapted prevention strategies. Future progress will depend on dedicated SPC-focused trials, biomarker-driven patient selection, long-term safety evaluation, and integration of pharmacological prevention into broader cancer interception programmes.},
}

@article {pmid42556158,
year = {2026},
author = {Sharmin, A and Zalbegi, S and Bhatia, M and Siddiquee, M and Thomas, AB and Yun, TS and Bishop, WM and Kang, DW and Seo, Y},
title = {Integrated management of cyanobacterial harmful algal blooms: Coupling algaecide treatment with bioaugmentation of toxin degraders.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {142970},
doi = {10.1016/j.jhazmat.2026.142970},
pmid = {42556158},
issn = {1873-3336},
abstract = {Cyanobacterial harmful algal blooms (CHABs) are a growing global concern, threatening drinking water safety and complicating water treatment through cyanotoxin release, operational disruptions and increased costs. Although chemical algaecides are widely applied for rapid bloom suppression, they frequently induce cyanobacterial lysis, releasing intracellular toxins that further challenge treatment and increase risks for smaller utilities lacking advanced infrastructure. Bioaugmentation with toxin-degrading bacteria has emerged as a complementary and sustainable strategy, however, the effects of algaecides on bioaugmented bacteria remain poorly understood. This study evaluated an integrated strategy combining algaecide application with bioaugmentation for simultaneous CHAB and cyanotoxin control. Two copper-based (SeClear® and Algimycin® PWF) and two hydrogen peroxide-based (PAK®27 and Oximycin®P5) algaecides were tested in combination with a microcystin (MC)-degrading bacterium, Sphingopyxis sp. IM1 under laboratory and mesocosm conditions. Among the four algaecides and tested concentrations, PAK®27 exhibited the highest compatibility with IM1, with substantial toxin removal observed only under low-dose conditions and after sufficient oxidant decay when IM1 was introduced 24 h post-treatment. Laboratory experiments showed that medium-dose PAK®27 followed by IM1 bioaugmentation reduced chlorophyll-a by 76.7% and dissolved MC-LR by 96.6%. In lake mesocosms, maximum-dose PAK®27 with IM1 achieved 77.6% chl-a reduction and 96% cyanobacterial suppression, lowering MC concentrations below 1 µg/L within 3 days. Microbiome profiling confirmed cyanobacterial collapse accompanied by the proliferation of green algae, diatoms, and heterotrophs, with IM1 abundance negatively correlated with toxin concentrations. These findings demonstrate that hydrogen peroxide-based algaecides combined with targeted bacterial bioaugmentation can provide an effective strategy for rapid toxin mitigation and microbial community recovery in CHAB-impacted waters.},
}

@article {pmid42556226,
year = {2026},
author = {Zhang, H and Shen, J and Bai, G and Ma, Y and Chu, R and Zhang, N and Zhang, G and Zuo, L and Li, L},
title = {Niche-driven microbial assembly across the soil-root continuum of Casuarina equisetifolia under a heavy metal pollution gradient.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120615},
doi = {10.1016/j.ecoenv.2026.120615},
pmid = {42556226},
issn = {1090-2414},
abstract = {Heavy metal pollution (HMP) threatens soil ecosystems and plant health. This study integrated 16S rRNA sequencing, network analysis, environmental mapping, and bacterial isolation to investigate how distinct ecological niches of Casuarina equisetifolia modulate microbial communities under metal stress. Results revealed a spatial pollution gradient, with Pb[2+], Zn[2+], and Cd[2+] decreasing with distance from the mine, while As[5+], Cr[3] [+], and Ni[2+] remained near background levels but displayed significant niche-dependent enrichment, especially for Cr[3] [+], and Ni[2+] in rhizosphere soil under medium and high pollution. Niche was the primary driver of microbial divergence, with only 0.56% of OTUs shared between the soil and root compartments. Rhizosphere soils harbored more unique OTUs and higher α-diversity than non-rhizosphere soils. Root endosphere and rhizosphere soil communities were consistently dominated by Actinobacteria across all pollution levels, whereas non-rhizosphere soil communities shifted from Proteobacteria (low pollution) to Actinobacteria (medium) and Chloroflexi (high). LEfSe identified niche-specific biomarkers from the phylum to genus levels, with high-pollution roots harboring the most diverse indicators. Heavy metals and soil properties (pH, CEC, and SOM) collectively shaped community assembly, with distinct drivers per niche: CEC and Enterobacter in non-rhizosphere soil, pH and Acidobacteriales in rhizosphere soil, and Zn as the central hub in the root endosphere network. Isolation yielded 63 metal-tolerant strains across eight genera, predominantly Bacillus cereus sensu lato group, whose niche origin shifted from the rhizosphere (low pollution) to the non-rhizosphere (medium) to the roots (high pollution), suggesting pollution-associated enrichment. These findings reveal niche-specific community assembly and pollution-driven enrichment of metal-tolerant Bacillus cereus s.l. in the root endosphere.},
}

@article {pmid42556260,
year = {2026},
author = {Dhilipkannah, P and Jiang, F},
title = {Coordinated microbial-inflammatory associations in never-smoking lung cancer.},
journal = {Lung cancer (Amsterdam, Netherlands)},
volume = {219},
number = {},
pages = {109561},
doi = {10.1016/j.lungcan.2026.109561},
pmid = {42556260},
issn = {1872-8332},
abstract = {BACKGROUND: While smoking is the leading cause of lung cancer, the increasing incidence among never-smokers is a growing concern, highlighting non-tobacco-related mechanisms of carcinogenesis. Emerging evidence suggests that respiratory microbial dysbiosis and associated inflammatory responses may contribute to lung tumorigenesis. We previously showed that elevated abundances of Selenomonas, Streptococcus, and Veillonella are correlated with lung cancer independent of smoking history. Here, we examine whether circulating microbial and inflammatory profiles are linked to lung cancer in never-smokers.

METHODS: Circulating bacterial DNA representing the three genera was quantified by droplet digital PCR, and seven systemic inflammatory cytokines were measured by ELISA in plasma of 56 ever-smoker lung cancer patients, 56 never-smoker lung cancer patients, and 78 healthy controls. Integrative statistical modeling was performed to evaluate relationships among bacterial DNA burden, inflammatory activation, smoking history, and cancer status.

RESULTS: Plasma DNA levels of Selenomonas, Streptococcus, and Veillonella, together with IL-6, TNF-α, IL-1β, IL-8, and IL-17A, were elevated in lung cancer patients compared with controls (all p < 0.05). No significant differences were observed between smoking and never-smoking lung cancer patients for bacterial DNA levels, IL-6, TNF-α, or IL-17A (all > 0.05), whereas modest but statistically significant differences were observed for IL-8 (P = 0.036) and IL-1β (P = 0.048). Bacterial DNA burden was correlated with systemic inflammatory cytokine activation independent of smoking history (all p < 0.05).

CONCLUSIONS: A smoking-independent microbial-inflammatory signature is associated with lung cancer and provides a foundation for future studies evaluating its biological significance and clinical utility for diagnosis and management.},
}

@article {pmid42556262,
year = {2026},
author = {Dai, W and Yang, F and Chen, W and Liu, C and Henawy, AR and Liu, X and Huang, F and Cai, M and Zheng, L and Yu, Z and Gong, Y and van Huis, A and Zhang, J and Cheng, W},
title = {Paenibacillus polymyxa drives root fatty acyl metabolites-rhizosphere Pseudomonas abundance interaction to suppress root-knot nematode disease in tomato.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128662},
doi = {10.1016/j.micres.2026.128662},
pmid = {42556262},
issn = {1618-0623},
abstract = {Root-knot nematodes (RKNs) pose a severe threat to global agricultural production, highlighting the urgent need for effective biocontrol agents. However, the mechanisms by which biocontrol agents suppress RKNs in complex soil environments remain poorly understood, which hinders the development and practical application of these agents. In the present study, the application of Paenibacillus polymyxa KM2501-1 significantly reduced RKN disease, with a control efficacy of 69.89%. Metabolomics analysis revealed that the biocontrol agent P. polymyxa altered the composition of tomato root exudates, leading to the identification of a key fatty acyl metabolite 8-methylnon-6-enoic acid. Specifically, P. polymyxa increased the abundance of 8-methylnon-6-enoic acid, which exhibited repellent activity against RKNs in vitro and suppressed RKN infection in situ. Metagenomic analysis further demonstrated that P. polymyxa reshaped the tomato rhizosphere microbial community and promoted the enrichment of Pseudomonas putida, particularly its representative strains PR035 and PR036. Both strains exhibited significant biocontrol efficacy against Meloidogyne incognita. A significant positive correlation was observed between the levels of key metabolite 8-methylnon-6-enoic acid and the abundance of P. putida, and their combined application exhibited effective control against M. incognita. Overall, this study demonstrates that the suppression of RKNs by P. polymyxa is associated with triggering the exudation of fatty acyl metabolites from tomato roots and enriching rhizosphere Pseudomonas populations. These findings provide valuable insights into the interplay between root metabolites and the rhizosphere microbiome in mediating synergistic plant disease control, offering a theoretical basis for the development of next-generation microbial nematicides.},
}

@article {pmid42556364,
year = {2026},
author = {Raes, J},
title = {Translating the gut microbiome: where are we?.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {11},
number = {9},
pages = {750-752},
doi = {10.1016/S2468-1253(26)00181-0},
pmid = {42556364},
issn = {2468-1253},
}

@article {pmid42556662,
year = {2026},
author = {Fan, Y and Xu, Z and Zheng, H and Han, J and Hu, S and Pan, X and Ma, R and Liu, C and Tian, Y},
title = {Dietary carboxymethyl starch improves glycemic control and enhances barrier function via Bifidobacterium-mediated galactose metabolism in vivo and in organoids.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153925},
doi = {10.1016/j.ijbiomac.2026.153925},
pmid = {42556662},
issn = {1879-0003},
abstract = {Etherified resistant starches (ERS), including hydroxypropyl starch (HPS), carboxymethyl starch (CMS), and hydroxyethyl starch (HES), are emerging as functional food ingredients with potential to modulate glycemic responses and gut health. However, their comparative efficacy and underlying gut-mediated mechanisms remain poorly defined. This study systematically evaluated their digestive properties and effects on gut microbiota. In vitro digestion demonstrated that etherification substantially increased resistant starch content, with CMS exhibiting approximately 70% resistant starch content and the lowest estimated glycemic index (GI = 53) among the tested starches. In vivo evaluation further showed that CMS significantly attenuated the peak postprandial glucose level (9.6 mmol/L) compared with native starch (17.4 mmol/L). Microbiome analysis revealed that CMS intervention was associated with specific remodeling of the gut microbiota, notably enriching beneficial Bifidobacterium pseudocatenulatum and Bifidobacterium adolescentis. Functionally, integrated KEGG pathway analysis and metabolomics consistently indicated that CMS markedly downregulated galactose metabolism, evidenced by reduced concentrations of galactose-related metabolites such as galactonic acid and galactitol. Furthermore, Spearman correlation analysis highlighted a strong mechanistic link between B. adolescentis abundance and galactose metabolic shifts. Crucially, utilizing, CMS-derived microbiota enhanced intestinal barrier function and galactose metabolism via co-culture model of gut microbiota and colonic organoids. Overall, CMS as a promising functional food ingredient that not only mitigates postprandial glycemia but also improves gut health by regulating microbiota-dependent galactose metabolism.},
}

@article {pmid42556710,
year = {2026},
author = {Simón-Vicente, L and Lafont, MO and Franch, MA and Menéndez-Trillo, P and Rivadeneyra-Posadas, J and Miguel-Pérez, I and Aguado, L and Siscart, IM and Piñeiro, DD and Mariscal, N and Megías-Lobón, G and Calvo, S and Cubo, E and Saiz-Rodríguez, M},
title = {Gut microbiome composition in Huntington's disease: Stage-dependent differences between premanifest and manifest patients.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124617},
doi = {10.1016/j.lfs.2026.124617},
pmid = {42556710},
issn = {1879-0631},
abstract = {BACKGROUND: Huntington's disease (HD) is a progressive neurodegenerative disorder with substantial clinical heterogeneity. The gut microbiome has been proposed as a potential modulator of neurodegeneration, but its role in HD and across disease stages remains unclear.

METHODS: This cross-sectional case-control study included 50 individuals with HD (35 manifest, 15 pre-manifest) and 36 age- and sex-matched cohabiting controls. Stool samples were analysed using 16S rRNA sequencing. Clinical, lifestyle, and dietary variables were recorded. Microbial diversity and differential taxonomic abundance were assessed, accounting for relevant covariates.

RESULTS: No significant differences in global microbial diversity were observed between HD and controls. Age was the main factor associated with both alpha and beta diversity. However, HD was associated with discrete taxonomic differences. More pronounced alterations were identified between manifest and pre-manifest stages, with exploratory genus-level compositional differences identified between disease stages. Antibiotic exposure significantly reduced microbial richness and influenced community structure.

CONCLUSIONS: Gut microbiome alterations in HD may differ across clinical stages rather than reflecting global dysbiosis. These exploratory findings suggest that microbiome composition may contribute to disease heterogeneity, although confirmation in larger longitudinal and independent cohorts is required before considering its potential as a biomarker or therapeutic target.},
}

@article {pmid42556887,
year = {2026},
author = {Mitrea, L and Martău, GA and Călinoiu, LF and Vodnar, DC},
title = {Microbiota, fermentation, and metabolite biotransformation: Pathways to functional foods and personalised nutrition.},
journal = {Advances in food and nutrition research},
volume = {121},
number = {},
pages = {79-130},
doi = {10.1016/bs.afnr.2026.02.001},
pmid = {42556887},
issn = {1043-4526},
mesh = {*Fermentation ; Humans ; *Functional Food ; *Biotransformation ; *Gastrointestinal Microbiome/physiology ; *Precision Medicine ; },
abstract = {Fermentation is among the oldest biotechnological processes and a modern platform for precision metabolic engineering, enabling the targeted production of health-promoting metabolites. The human gut microbiota, with its complex enzymatic potential, converts dietary substrates into a wide range of bioactive molecules, including short-chain fatty acids, vitamins, neuroactive compounds, and polyphenol-derived metabolites that influence host metabolism, immunity, and neurological functions. Advances in microbial genomics, systems biology, and synthetic biology now allow the design of fermentation processes and engineered microbial strains capable of producing specific metabolites with improved bioavailability and tailored health effects. Precision fermentation integrates traditional microbial fermentation with genome editing, metabolic flux optimisation, and AI-assisted pathway design to achieve predictable yields of vitamins, polyphenols, bioactive peptides, and long-chain polyunsaturated fatty acids. These innovations create opportunities to develop functional foods, nutraceuticals, and personalized nutrition strategies that match metabolite profiles to an individual's microbiome composition. This chapter explores the mechanistic links between microbial metabolism and host health, reviews emerging fermentation technologies for targeted metabolite production, and highlights industrial case studies demonstrating the transition of precision fermentation from research to commercial applications.},
}

*Fermentation
Humans
*Functional Food
*Biotransformation
*Gastrointestinal Microbiome/physiology
*Precision Medicine

@article {pmid42557497,
year = {2026},
author = {Chen, E},
title = {First poo transplant to treat food allergy in people has 'exciting' results.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42557497},
issn = {1476-4687},
}

@article {pmid42557505,
year = {2026},
author = {Dos Santos, RAC and Hidalgo-Martinez, K and Muñoz-Perez, JM and Laspisa, DJ and Li, C and Mendes, LW and Riaño-Pachón, DM and Wallace, JG},
title = {Diurnal dynamics of maize gene expression is associated with phyllosphere microbiome composition.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42557505},
issn = {1618-1905},
abstract = {Bacterial communities play important roles in the plant phyllosphere. Both microbial communities and their hosts exhibit endogenous circadian rhythms while simultaneously responding to environmental changes across the diurnal cycle. However, the interaction between the host and microbiome is still poorly understood. Here, we exploit paired sequencing data of host transcriptome and microbiome derived from diverse maize genotypes in field conditions and under two contrasting diurnal periods. Expression patterns of known maize circadian clock genes were consistent with the expected sampling phases. Groups of co-expressed genes that responded to diurnal periods were associated with nucleic acid-binding, heat stress responses, and photosynthesis. Microbiome analysis revealed only modest differences in alpha diversity between midday and midnight samples. However, beta diversity indicated a significant shift in community composition. Co-occurrence network analysis identified keystone taxa specific to each time point, suggesting time-dependent ecological roles within the phyllosphere microbiome. Cross-correlation analyses between host gene expression and bacterial taxon abundance revealed a greater number of host-microbe associations during the night. Several canonical circadian clock genes significantly correlated with microbial taxa. Our findings provide initial evidence for diurnal associations between host gene expression and leaf-associated bacteriome, suggesting that maize diurnal transcriptional dynamics, including the activity of circadian clock genes, may contribute to shaping the composition and functional potential of the phyllosphere microbiome.},
}

@article {pmid42557545,
year = {2026},
author = {Rodríguez Del Río, Á and Cui, Y and Mansour, I and Rillig, MC},
title = {Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42557545},
issn = {1471-2164},
mesh = {*Soil Microbiology ; Metagenomics ; Metagenome ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Genomics ; Phylogeography ; Phylogeny ; *Prokaryotic Cells ; *Archaea/genetics/classification ; },
abstract = {Most soil prokaryotic species remain uncultivated, limiting our understanding of the terrestrial microbiome. Metagenomic sequencing, and particularly the study of metagenome-assembled genomes (MAGs), represents an unprecedented opportunity to characterize the genomic features and biogeography of uncultivated prokaryotic taxa at the large scale. Here, we analyze 40,039 genomic bins from cultivated and uncultivated soil taxa within the SMAG catalog, and examine the occurrence of uncultivated prokaryotes in 9,012 metagenomic samples from the Sandpiper resource. Compared to genera with cultivated representatives, uncultivated soil prokaryotes show smaller genomes, lower G + C content, tendency to acidophilic, non-alkaline, thermophilic and host-associated lifestyles, and slower growth rates, with the latter having the highest predictive power for cultivation status. Uncultivated soil microbes also show unique gene repertoires, characterized by a depletion of biosynthetic and motility genes. We also show that completely uncultivated genera are more abundant in tropical and arctic soils, indicating substantial hidden diversity in these regions. Our work emphasizes that current cultivation efforts systematically fail to capture a particular fraction of soil prokaryotic diversity, and provides guidelines for future cultivation strategies.},
}

*Soil Microbiology
Metagenomics
Metagenome
*Bacteria/genetics/classification
*Genome, Bacterial
*Genomics
Phylogeography
Phylogeny
*Prokaryotic Cells
*Archaea/genetics/classification

@article {pmid42557733,
year = {2026},
author = {Murillo-Herrera, AI and Eguiarte, LE and Acuña Gómez, EP and Castro, C and Acevedo, J and Castrillon, J and Oyarzún-Galaz, L and Valenzuela, P and Aguayo-Lobo, A and Pastene, LA and Souza, V},
title = {Temperature and Ultraviolet Radiation Influence the Skin Microbiome of Humpback Whales.},
journal = {Molecular ecology},
volume = {35},
number = {15},
pages = {e70500},
doi = {10.1111/mec.70500},
pmid = {42557733},
issn = {1365-294X},
support = {R20F0009//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {Animals ; *Ultraviolet Rays ; RNA, Ribosomal, 16S/genetics ; Female ; *Humpback Whale/microbiology ; *Skin Microbiome ; Male ; *Temperature ; *Bacteria/classification/genetics ; *Skin/microbiology ; Ecuador ; Ecosystem ; *Microbiota ; Seawater ; Sequence Analysis, DNA ; Seasons ; DNA, Bacterial/genetics ; },
abstract = {The skin microbiome of humpback whales harbours diverse microbial communities that play a crucial role in host skin protection and environmental interaction. However, studies on cetacean skin microbiomes in the Southern Hemisphere focus on feeding grounds, with limited information on microbiome dynamics at breeding grounds and during migration across contrasting habitats. We characterised the skin microbiome of 46 humpback whales from two seasonal habitats: the Magellan Strait feeding ground and the Ecuadorian coast breeding ground, comparing age, sex, environmental conditions, and seawater. Amplicon sequencing of the 16S rRNA gene revealed no differences in alpha diversity, but habitat-specific compositional shifts were found. Psychrobacter was detected in both regions, with higher abundance in the feeding ground, while Tenacibaculum remained abundant across sites. Additional taxa exhibited habitat-specific patterns, including bacteria associated with thermal sensitivity and ultraviolet radiation-tolerance in the Magellan Strait, and lactic acid bacteria in Ecuador. Skin microbiomes were similar between age classes and sexes, but distinct from seawater. Our findings show that geographic and environmental factors, such as superficial seawater temperature and maximum ultraviolet B radiation, shape the skin microbiome of humpback whales, with certain taxa reflecting migratory behaviour across seasonal habitats.},
}

Animals
*Ultraviolet Rays
RNA, Ribosomal, 16S/genetics
Female
*Humpback Whale/microbiology
*Skin Microbiome
Male
*Temperature
*Bacteria/classification/genetics
*Skin/microbiology
Ecuador
Ecosystem
*Microbiota
Seawater
Sequence Analysis, DNA
Seasons
DNA, Bacterial/genetics

@article {pmid42557796,
year = {2026},
author = {Griffin, CD and Schreiber, J and Bierwert, A and Olaso, CM and Medeiros, MCI},
title = {Microbial mediation of invasion: Effects of environmental microbiota on the development and physiology of Aedes albopictus.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70106},
pmid = {42557796},
issn = {1365-2915},
support = {/NH/NIH HHS/United States ; //University of Hawai'i at Mānoa Undergraduate Research Opportunities Program/ ; },
abstract = {Global invasions by the mosquito Aedes albopictus pose serious threats to biodiversity and public health due to its capacity to vector multiple emerging infectious diseases. As a highly invasive species, its success is closely linked to environmental conditions during its complex life cycle. In this study, we investigated how compositionally distinct environmental microbiomes influence A. albopictus development, physiology and starvation resistance. Larvae were reared in mesocosms containing water from three sources-laboratory, plastic buckets and bromeliad tanks-each filtered at three levels (30-50 μm, 10 μm and 0.1 μm) to manipulate microbial diversity. We found that microbial community composition significantly affected larval development time and pupation success. Larvae reared in water with reduced microbial diversity developed faster and had higher pupation success than those exposed to more complex communities. Although lipid concentrations and time to adult eclosion were unaffected across habitat types, adult survival under starvation conditions varied significantly by microbial exposure and sex. Females from low-diversity habitat types exhibited the highest survival, suggesting early-life microbial environments influence adult fitness traits critical to invasion success. These results highlight the ecological importance of environmental microbiomes in shaping mosquito life history and suggest that microbial diversity in larval habitat types may influence the establishment and spread of A. albopictus in novel environments.},
}

@article {pmid42557889,
year = {2026},
author = {Super, C and Asif, M and Compher, C and Schurr, TG and Hoke, MK},
title = {Work-Influenced Circadian Disruption Connected to Disease Risk but Not Microbiomes in a Cohort of Philadelphia Nurses.},
journal = {American journal of human biology : the official journal of the Human Biology Council},
volume = {38},
number = {8},
pages = {e70314},
doi = {10.1002/ajhb.70314},
pmid = {42557889},
issn = {1520-6300},
support = {BCS-2147647//National Science Foundation/ ; DFG 584233//Wenner-Gren Foundation/ ; },
mesh = {Humans ; *Nurses/statistics & numerical data ; *Circadian Rhythm ; Philadelphia/epidemiology ; Adult ; Working Conditions ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Risk Factors ; Cohort Studies ; *Chronobiology Disorders/epidemiology ; *Cardiometabolic Risk Factors ; },
abstract = {OBJECTIVES: Circadian rhythms influence activity cycles in humans, and circadian rhythm disruption (CRD) can negatively impact cardiometabolic disease risk and microbiome composition. This study documented CRD in a sample of nurses in Philadelphia, examining connections between CRD, disease risk, and work environment factors, proposing the concept of work-influenced circadian disruption (WICD).

MATERIALS AND METHODS: A total of 75 nurses were recruited for the study. Disease risk indicators included triglycerides (TRG), C-reactive protein (hs-CRP), blood pressure (BP), and fecal gut microbiome composition. Surveys recorded CRD via sleep/exhaustion levels, weekly exercise, mealtime timing/length, shift diet, and night shift work. Work environment variables included staff/resources, physician-nurse relations, break times, and patient care assignments. Mixed multiple regression models assessed CRD's associations with cardiometabolic disease risk indicators (H1) and work environment variables (H2). Microbiome similarity by CRD variables was tested using PERMANOVAs.

RESULTS: Lower exercise levels were associated with higher hs-CRP (β = -4.2, p = 0.05), TRG (β = -9.8, p = 0.03), BP (β = -3.6, p = 0.01), and less break time (β = 0.1, p = 0.01). Higher exhaustion was linked to elevated hs-CRP (β = 6.0, p = 0.02) and fewer staff/resources (β = -0.7, p = 0.01). Less mealtime was associated with higher BP (β = -0.2, p = 0.05) and shorter breaks (β = 0.2, p = 0.04). Night shifts were linked to higher BP (β = 6.3, p = 0.01). CRD variables were not significantly associated with microbiome profiles.

CONCLUSIONS: CRD is associated with disease risk indicators and with work environment variables but not with microbiome profiles, suggesting these relationships may operate through other pathways. Further studies should explore biobehavioral networks in WICD.},
}

Humans
*Nurses/statistics & numerical data
*Circadian Rhythm
Philadelphia/epidemiology
Adult
Working Conditions
Female
Male
Middle Aged
*Gastrointestinal Microbiome
Risk Factors
Cohort Studies
*Chronobiology Disorders/epidemiology
*Cardiometabolic Risk Factors

@article {pmid42557943,
year = {2026},
author = {Lockwood, MB and Gallon, L and Kortan, E and Tussing-Humphreys, L},
title = {Pain syndromes in transplantation: the role of the gut microbiome.},
journal = {Current opinion in organ transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOT.0000000000001308},
pmid = {42557943},
issn = {1531-7013},
abstract = {PURPOSE OF REVIEW: The purpose of this review is to discuss common pain phenotypes in transplantation, summarize known gut microbiome features associated with chronic pain, and to map known gut microbiome features in transplantation with diagnosis-independent pain features.

RECENT FINDINGS: Persistent pain is common across solid organ and hematopoietic stem cell transplantation, arises from diverse mechanisms, and often extends well beyond the perioperative period. Growing evidence supports the gut microbiome as a biologically plausible modulator of chronic pain across disease states, including transplantation. Alterations in microbial diversity, microbial metabolites, intestinal barrier integrity, and neuroimmune signaling have been linked to pain amplification and central sensitization across multiple chronic pain conditions. In transplant populations, exposure to immunosuppressive therapies, antibiotics, metabolic comorbidities, and other transplant-related stressors creates a unique environment for sustained microbiome disruption that may contribute to persistent symptom burden.

SUMMARY: Collectively, these data highlight the importance to systematically assess and manage pain as a core transplant outcome rather than a secondary concern, and to highlight the potential role of the gut microbiome as a risk screening tool or a therapeutic target for pain interventions. Although mechanistic and observational data support biologic plausibility, transplant-specific microbiome-pain evidence remains preliminary and warrants longitudinal investigation.},
}

@article {pmid42558207,
year = {2026},
author = {Yang, Y and Ren, L and Zhang, Y and Wang, X and Shang, J and Zhang, L},
title = {Microbiota in cholestatic diseases: crosstalk among bile composition, the biliary microbiome, and host immunity.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1884030},
pmid = {42558207},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Microbiota/immunology ; Bile Acids and Salts/metabolism ; *Cholestasis/microbiology/immunology/metabolism ; *Bile/metabolism/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; },
abstract = {Cholestatic liver diseases are a heterogeneous group of hepatobiliary disorders caused by impaired bile formation, secretion, or excretion, leading to hepatocyte injury, biliary inflammation, fibrosis, and eventually cirrhosis. Traditional studies have largely focused on isolated mechanisms, including bile acid toxicity, immune dysregulation, and genetic susceptibility. However, recent advances in metagenomics, metabolomics, and immunology have highlighted the critical role of the gut and biliary microbiota in disease pathogenesis. This review proposes the core concept of a "tripartite interplay among bile composition, biliary microbiome, and host immunity," integrating the dynamic crosstalk among these three axes in cholestatic liver diseases. Bile composition shapes microbial communities and modulates immune responses through receptors such as FXR and TGR5. In turn, the biliary microbiome regulates bile acid metabolism and immune activity through microbial metabolites. Meanwhile, the host immune system senses microbial signals via pattern-recognition receptors, triggering inflammatory pathways and influencing microbial colonization and metabolism. These reciprocal interactions form complex feedback loops that drive disease progression from early inflammation to chronic fibrosis and cirrhosis. Based on this framework, emerging diagnostic approaches combine microbial signatures, bile acid profiles, and immune markers into multidimensional biomarker systems. Therapeutically, integrated strategies targeting the microbiome, bile acid metabolism, and immune pathways may offer synergistic benefits. Despite challenges including sampling difficulty, interindividual variability, and limitations of current models, future technologies such as single-cell sequencing, spatial transcriptomics, and multi-omics integration may enable precision diagnosis and targeted therapy.},
}

Humans
Animals
*Microbiota/immunology
Bile Acids and Salts/metabolism
*Cholestasis/microbiology/immunology/metabolism
*Bile/metabolism/immunology/microbiology
*Gastrointestinal Microbiome/immunology

@article {pmid42558256,
year = {2026},
author = {Chen, Z and Wu, W and Chen, Y and Li, F and Xie, X and Lin, Y and Zhang, X and Ye, Q},
title = {Targeting the gut microbiota: emerging strategies to enhance healing of diabetic foot ulcers.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1865273},
pmid = {42558256},
issn = {1664-2392},
mesh = {Humans ; *Diabetic Foot/microbiology/therapy ; *Wound Healing/physiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Diabetes Mellitus, Type 2/complications/microbiology ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; },
abstract = {Diabetic foot ulcer (DFU) affects up to 34% of diabetic patients, with a 1-year recurrence rate of approximately 40%. This review primarily focuses on type 2 diabetes mellitus (T2DM), the most common form of diabetes associated with DFUs. Emerging evidence shows that gut microbiota critically influences DFUs healing through immune modulation (e.g., Treg/Th17 balance), regulation of inflammatory responses via short-chain fatty acids (SCFAs) that inhibit NF-κB, the gut-immune-skin axis, and systemic effects of microbial metabolites. Microbiota-targeted interventions-probiotics, prebiotics, fecal microbiota transplantation, and dietary strategies-can restore microbial balance and reduce inflammation, thereby promoting DFUs healing. These findings provide a mechanistic foundation for microbiome-based therapies and guide future clinical research.},
}

Humans
*Diabetic Foot/microbiology/therapy
*Wound Healing/physiology
*Gastrointestinal Microbiome/physiology
Animals
*Diabetes Mellitus, Type 2/complications/microbiology
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Prebiotics/administration & dosage

@article {pmid42558262,
year = {2026},
author = {Guan, Y and Chang, D},
title = {Dietary index for gut microbiota score is inversely associated with carotid calcified plaque score in ischemic stroke patients.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1811243},
pmid = {42558262},
issn = {2296-861X},
abstract = {BACKGROUND: Diet influences gut microbiota-derived metabolites, which may affect vascular inflammation and calcification. The Dietary Index for Gut Microbiota (DI-GM) captures dietary patterns hypothesized to support favorable microbial metabolite profiles. In this study, we examined whether higher DI-GM scores are associated with lower carotid calcification burden in ischemic stroke patients and whether trimethylamine N-oxide (TMAO) is statistically associated with this relationship, without implying causality.

METHOD: In this cross-sectional study of 788 ischemic stroke patients from Central Hospital Affiliated to Shandong First Medical University, we calculated DI-GM scores from validated food frequency questionnaires and quantified carotid calcification using the Agatston method via computed tomography angiography. Plasma TMAO levels were measured by enzyme-linked immunosorbent assay (ELISA) ELISA.

RESULTS: Our findings revealed that participants in the highest DI-GM tertile had significantly lower calcification scores (76.07 ± 14.55) compared to the lowest tertile (316.00 ± 75.33, p < 0.001). Higher DI-GM scores correlated with lower TMAO, and decreased inflammatory markers (all p < 0.001). Each one-unit increase in DI-GM was independently associated with lower calcification odds (adjusted OR = 0.60, p = 0.02). Mediation analysis confirmed that TMAO significantly mediated these associations, accounting for substantial proportions of the total effects of DI-GM score on inflammatory markers, plaque thickness, and calcification score.

CONCLUSION: Higher DI-GM score is cross-sectionally associated with lower carotid calcification and TMAO-mediated pathways, but causality remains unproven without longitudinal and microbiome-sequencing data.},
}

@article {pmid42558303,
year = {2026},
author = {Li, Z and Duan, Z and Liu, R and Yu, S and Wang, N and Chen, H and Xu, Q},
title = {Morphology-defined bacterial vaginosis and HPV-related cervical screening abnormalities: a two-year real-world study with histopathologic correlation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1890650},
pmid = {42558303},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vaginosis, Bacterial/microbiology/pathology/diagnosis ; *Papillomavirus Infections/pathology/diagnosis/virology/complications ; Retrospective Studies ; Adult ; *Human Papillomavirus Viruses/genetics ; *Cervix Uteri/pathology/virology/microbiology ; *Papillomaviridae/genetics/classification ; Middle Aged ; China ; Genotype ; Vagina/microbiology/pathology/virology ; Uterine Cervical Neoplasms/virology/pathology ; Early Detection of Cancer ; },
abstract = {BACKGROUND: Bacterial vaginosis (BV) is characterized by reduced Lactobacillus dominance and enrichment of anaerobic bacteria. Although BV has been associated with human papillomavirus (HPV) infection, its relationship with cytologic abnormalities and biopsy-confirmed cervical lesions remains incompletely defined in real-world laboratory settings.

METHODS: We conducted a retrospective real-world study integrating vaginal fluorescence microscopy, 21-genotype HPV genotyping, thin-prep cytology (TCT), and cervical histopathology records from January 2024 through December 2025 at a tertiary hospital in China. Morphology-defined BV was defined by clue cells or Gardnerella-like anaerobic bacteria on vaginal fluorescence microscopy and was not equivalent to Nugent scoring, Amsel criteria, culture-based diagnosis, or molecular microbiome profiling. HPV and TCT records were matched within a prespecified 30-day window after patient-level deduplication. Multivariable logistic regression adjusted for year, age, and vaginal microecological covariates. A 90-day sensitivity analysis was performed. The histopathology cohort was clinically selected and was analyzed as a correlation subgroup rather than as a random sample of the screening cohort.

RESULTS: The main 30-day analysis included 4,492 unique patients, of whom 587 (13.07%) had morphology-defined BV. After multivariable adjustment, morphology-defined BV remained associated with overall HPV positivity (adjusted odds ratio [aOR] 1.560; 95% confidence interval [CI] 1.293-1.883), high-risk HPV positivity (aOR 1.611; 95% CI 1.327-1.957), HPV multiple infection (aOR 1.976; 95% CI 1.526-2.559), TCT abnormality (aOR 1.465; 95% CI 1.125-1.907), and concurrent high-risk HPV positivity plus TCT abnormality (aOR 1.558; 95% CI 1.174-2.066). After additional adjustment for high-risk HPV, the BV-TCT association was attenuated and non-significant. Among 825 patients with cervical histopathology records, BV was not independently associated with any histologic lesion grade, whereas high-risk HPV, HPV16/18, and TCT abnormality were the principal predictors of histopathologic disease.

CONCLUSION: Morphology-defined BV was associated with HPV infection and HPV-related cytologic abnormalities, but not with histologic cervical lesions in the clinically selected biopsy subgroup. These findings suggest that routine morphologic evidence of BV marks an HPV-related screening-positive phenotype rather than an independent histopathologic lesion predictor.},
}

Humans
Female
*Vaginosis, Bacterial/microbiology/pathology/diagnosis
*Papillomavirus Infections/pathology/diagnosis/virology/complications
Retrospective Studies
Adult
*Human Papillomavirus Viruses/genetics
*Cervix Uteri/pathology/virology/microbiology
*Papillomaviridae/genetics/classification
Middle Aged
China
Genotype
Vagina/microbiology/pathology/virology
Uterine Cervical Neoplasms/virology/pathology
Early Detection of Cancer

@article {pmid42558343,
year = {2026},
author = {Liu, L and Lin, J and Sang, K and Lai, J and Huang, N and Zhong, P and Liu, Y and Chen, S},
title = {Bile acid signaling at the gut-vascular interface: a novel modulator of hantavirus endothelial barrier dysfunction.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1883162},
pmid = {42558343},
issn = {2235-2988},
mesh = {Animals ; Humans ; *Orthohantavirus/pathogenicity/physiology ; *Bile Acids and Salts/metabolism ; *Signal Transduction ; Receptor, Farnesoid X-Activated ; Rats ; *Endothelial Cells/virology/metabolism ; Gastrointestinal Microbiome ; *Hantavirus Infections/virology/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; NF-kappa B/metabolism ; Lung/virology/microbiology ; Vascular Cell Adhesion Molecule-1/metabolism/genetics ; },
abstract = {Hantavirus infection triggers life-threatening hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), driven by severe endothelial barrier breakdown and systemic capillary leakage. Clinical severity varies widely with undefined host regulators, and no targeted endothelial-protective treatments exist. Recent data link hantaviruses to gut microbiome remodeling, while bile acid (BA) receptors FXR and TGR5 potently inhibit NF-κB-mediated endothelial inflammation. We synthesize four core lines of evidence. First, metagenomic reports confirm hantavirus reshapes gut/lung microbiota in rodent reservoirs. Second, we re-analyzed three public GEO datasets via standardized RNA-seq/microarray pipelines: (i) GSE245916: SEOV-infected human/rat lung ECs show conserved VCAM1/ICAM1 upregulation (human VCAM1 log2FC=+1.17, P = 0.023; rat Icam1 log2FC=+0.32, padj=0.016) with unaltered FXR; (ii) GSE7271: SEOV-infected rat lung displays sustained Nfkb1 suppression (all timepoints, P<0.05) and day-15 Slc10a2 downregulation (P = 0.028); (iii) GSE270172: PUUV 3D vessel chips feature robust IL6 elevation (log2FC=+1.22, P = 3.1×10[-8]) and disrupted BA transporters (ABCC3 log2FC=-1.44, P = 7.4×10[-][12]). TGR5 (GPBAR1) was undetectable in endothelial cells across all datasets. Third, FXR/TGR5 agonists repress NF-κB inflammation and mitigate lung vascular injury. Fourth, HTNV upregulates CH25H to block HMGCR-dependent cholesterol synthesis, depleting BA precursor substrates. We propose a unified pathogenic model: hantavirus-triggered gut dysbiosis plus virus-impaired cholesterol metabolism deplete circulating FXR/TGR5 agonistic BAs, relieving constitutive inhibition of endothelial NF-κB and monocyte NLRP3 inflammasomes to exacerbate capillary leakage. We define tiered testable predictions covering clinical multi-omics cohorts, in vitro receptor modulation assays and in vivo pharmacological interventions. This gut microbiota-BA-FXR/TGR5 axis represents a repurposable therapeutic target for hantavirus diseases, though direct causal evidence connecting BA signaling to viral vascular damage remains absent; our framework offers a rigorous testable roadmap for subsequent validation.},
}

Animals
Humans
*Orthohantavirus/pathogenicity/physiology
*Bile Acids and Salts/metabolism
*Signal Transduction
Receptor, Farnesoid X-Activated
Rats
*Endothelial Cells/virology/metabolism
Gastrointestinal Microbiome
*Hantavirus Infections/virology/metabolism
Receptors, G-Protein-Coupled/metabolism
Receptors, Cytoplasmic and Nuclear/metabolism
NF-kappa B/metabolism
Lung/virology/microbiology
Vascular Cell Adhesion Molecule-1/metabolism/genetics

@article {pmid42558395,
year = {2026},
author = {Schandl, M and Ertl, T and Vass, RA},
title = {Hyperglycemia during the first 1000 days as a driver of metabolic programming.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1899593},
pmid = {42558395},
issn = {1664-2392},
mesh = {Humans ; Pregnancy ; Female ; *Hyperglycemia/metabolism/complications ; Developmental Origins of Health and Disease ; Animals ; *Prenatal Exposure Delayed Effects/metabolism ; Infant, Newborn ; *Fetal Development ; Epigenesis, Genetic ; Metabolic Reprogramming ; },
abstract = {The first 1000 days of life, spanning from conception to the end of the second postnatal year, represent a critical developmental window during which environmental and metabolic exposures exert long-lasting effects on offspring health. Among these exposures, maternal and early-life hyperglycemia have emerged as major determinants of metabolic programming and future cardiometabolic disease risk. Increasing evidence suggests that hyperglycemic exposure during this vulnerable period induces complex alterations in placental function, fetal endocrine adaptation, epigenetic regulation, and postnatal metabolic homeostasis, thereby predisposing offspring to obesity, insulin resistance, type 2 diabetes mellitus, and neurodevelopmental disturbances later in life. This review summarizes current evidence regarding the mechanistic pathways linking hyperglycemia during the first 1000 days to adverse metabolic outcomes. We discuss the role of maternal hyperglycemia in placental dysfunction, oxidative stress, inflammation, and altered nutrient transport, as well as its effects on fetal pancreatic development, adipogenesis, and insulin signaling. Particular emphasis is placed on emerging evidence implicating epigenetic modifications, mitochondrial dysfunction, microbiome alterations, and endocrine dysregulation in developmental programming. We further examine the impact of neonatal and early infant metabolic exposures on growth trajectories, adiposity, neurodevelopment, and long-term cardiometabolic health. Finally, we highlight current knowledge gaps and potential opportunities for early intervention, including optimized glycemic control during pregnancy, nutritional modulation, breastfeeding promotion, and precision prevention strategies targeting high-risk mother-infant dyads. A deeper understanding of the biological mechanisms underlying hyperglycemia-induced metabolic programming may facilitate the development of preventive approaches aimed at reducing the intergenerational transmission of metabolic disease.},
}

Humans
Pregnancy
Female
*Hyperglycemia/metabolism/complications
Developmental Origins of Health and Disease
Animals
*Prenatal Exposure Delayed Effects/metabolism
Infant, Newborn
*Fetal Development
Epigenesis, Genetic
Metabolic Reprogramming

@article {pmid42558510,
year = {2026},
author = {Xiong, Z and Liu, X and Deng, X and Zhang, C and Yang, K and Zhao, Z and Ding, T and Liu, S and Zhou, Z},
title = {Recombinant Bacillus subtilis spores expressing cholera toxin B and ovalbumin prevent ovalbumin-specific food allergy in mice by upregulating regulatory T cells and modulating gut microbiome flora.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1872151},
pmid = {42558510},
issn = {1664-3224},
mesh = {Animals ; *Bacillus subtilis/genetics/immunology ; *Ovalbumin/immunology/genetics ; *Food Hypersensitivity/immunology/prevention & control/microbiology ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Cholera Toxin/genetics/immunology ; Mice ; Female ; Mice, Inbred BALB C ; *Gastrointestinal Microbiome/immunology ; *Spores, Bacterial/genetics/immunology ; Immunoglobulin E/blood ; Disease Models, Animal ; Cytokines/metabolism ; Allergens/immunology ; Immune Tolerance ; },
abstract = {BACKGROUND: Although oral immunotherapy has shown clinical efficacy in treating food allergies, its broader implementation is constrained by the occurrence of adverse effects. Consequently, inducing allergen-specific immune tolerance during early life can be a preventive strategy to reduce the development of food allergy.

OBJECTIVE: Here, we developed a novel fusion protein cholera toxin B (CTB)-ovalbumin (OVA) expressed on Bacillus subtilis (B.s-CotC-CTB-OVA) spore surface and investigated whether B.s-CotC-CTB-OVA spores prevent OVA-induced food allergy in a mouse model and explored the potential underlying mechanisms.

METHOD: Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot were used to confirm that CTB-OVA was expressed on B. subtilis spores. Female BALB/c mice were orally administered with B.s-CotC-CTB-OVA spores and B. subtilis spore control (B.s-CotC and B.s-CotC-CTB) for 4 weeks. Then, sensitization and challenge with OVA were performed on mice. Fecal OVA-secretory IgA (sIgA) and serum OVA-IgE, IgG1, and IgG2a levels were measured by enzyme-linked immunosorbent assay (ELISA). The gut microbiome was analyzed by 16S rDNA sequencing. After challenge, diarrhea score, anaphylactic reactions score, splenocyte interleukin (IL)-10, IL-4, and interferon-γ (IFN-γ), and Treg levels were measured. mRNA of IL-10, IL-4, IFN-γ, and Foxp3 were measured. Fecal microbiota transplant (FMT) was used to explore the mechanisms of microbiome in B. subtilis on food allergy.

RESULTS: Recombinant CTB-OVA was successfully expressed on the surface of B. subtilis. Oral administration of B.s-CotC-CTB-OVA can increase fecal OVA-sIgA, alleviate food allergy symptoms, and decrease serum OVA-IgE in mice with significance (p < 0.05). Moreover, oral administration of B.s-CotC-CTB-OVA can significantly reduce serum OVA-IgG1, OVA-IgG2, IL-4, spleen mast cells, and eosinophil levels and significantly increase serum IL-10 and Treg levels (p < 0.05). Additionally, microbiome analysis shows that oral administration of B.s-CotC-CTB-OVA can significantly increase the relative abundance of Muribaculaceae and significantly decrease the relative abundance of Alistipes. FMT partially reproduced the reduction in serum OVA-specific IgE, but did not significantly improve allergic symptom or diarrhea scores, suggesting that gut microbiota alterations may partially contribute to the immunological effects of B.s-CotC-CTB-OVA.

CONCLUSION: These findings suggest that B.s-CotC-CTB-OVA spores may serve as a preventive oral antigen-delivery strategy to promote antigen-specific immune regulation and partially modulate microbiota-associated immune responses in OVA-induced food allergy.},
}

Animals
*Bacillus subtilis/genetics/immunology
*Ovalbumin/immunology/genetics
*Food Hypersensitivity/immunology/prevention & control/microbiology
*T-Lymphocytes, Regulatory/immunology/metabolism
*Cholera Toxin/genetics/immunology
Mice
Female
Mice, Inbred BALB C
*Gastrointestinal Microbiome/immunology
*Spores, Bacterial/genetics/immunology
Immunoglobulin E/blood
Disease Models, Animal
Cytokines/metabolism
Allergens/immunology
Immune Tolerance

@article {pmid42558570,
year = {2026},
author = {Shittu, A},
title = {Inflammation, infection, and immune dysregulation in chronic kidney disease: translational and epidemiological perspectives.},
journal = {Frontiers in nephrology},
volume = {6},
number = {},
pages = {1919658},
pmid = {42558570},
issn = {2813-0626},
abstract = {Chronic kidney disease (CKD) represents a growing global health challenge associated with substantial morbidity, mortality, and healthcare burden. Although metabolic and haemodynamic factors, particularly diabetes mellitus and hypertension, remain major contributors, increasing evidence demonstrates that persistent inflammation and immune dysregulation are central mechanisms influencing CKD initiation, progression, and complications. The renal immune microenvironment consists of complex interactions among resident kidney cells, infiltrating immune cells, inflammatory mediators, and molecular signalling networks that regulate tissue repair, fibrosis, and disease outcomes. Persistent activation of innate and adaptive immune responses promotes cytokine release, oxidative stress, endothelial dysfunction, and maladaptive tissue remodelling, contributing to progressive loss of kidney function. Infectious diseases and altered host-microbiome interactions may further amplify systemic inflammation and immune imbalance, particularly in vulnerable populations. Advances in immunology and molecular medicine have identified inflammatory biomarkers and immune-related pathways with potential applications in early detection, risk stratification, and targeted interventions. This Mini Review synthesizes current evidence linking inflammation, infection, and immune dysregulation with CKD progression, highlighting translational opportunities and epidemiological perspectives. Integrating mechanistic insights with population-level evidence may accelerate precision approaches for improving CKD prevention, monitoring, and therapeutic outcomes.},
}

@article {pmid42558572,
year = {2026},
author = {Wang, H and Tin, F and Chen, H and Jiao, F and Wu, M and Sun, S and Lin, L and Li, D and Zheng, H and Niu, Z and Lan, M and Yilmaz, B and Eriksson, JG and Wang, M and Macpherson, A and Clemente, JC and Xu, J and Xie, RH and Zheng, X and Zhou, T and Wang, J and Shen, W and Huang, B and Chen, X and Li, H and He, Y},
title = {Maternal and infant gut microbiome.},
journal = {iMeta},
volume = {},
number = {},
pages = {e70151},
pmid = {42558572},
issn = {2770-596X},
abstract = {Early-life gut microbiome assembly is a pivotal determinant of lifelong health; however, the integrated frameworks governing this process across developmental milestones remain insufficiently defined. This review establishes a multidimensional framework by delineating the crosstalk between the gut microbiome and the host throughout the preconception, prenatal, postpartum, and early childhood stages. We first highlight the emerging paradigm of biparental microbial contributions during the preconception period, detailing how paternal and maternal niches jointly prime offspring development. Moving into pregnancy, we examine the maternal reservoir, integrating the role of gut microbiota-derived metabolites across multiple trimesters in prenatal priming and vertical transmission. For the postpartum period, we discuss the development of the multikingdom gut microbiome and address the impacts of delivery modes and clinical interventions. Here, we articulate a critical knowledge gap: the discrepancy between taxonomic "catch-up" and true functional restoration, particularly in vulnerable cohorts such as preterm infants. Furthermore, we propose a "developmental synchronization" model within the maternal-infant-microbiome continuum. This model posits that early-life "windows of opportunity" are defined by the obligate temporal coupling of host physiological maturation with stage-specific microbial metabolic signals. From a translational perspective, we discuss how this framework informs the development of precision interventions, such as stage-specific probiotics, prebiotics, or metabolic modulators. These therapies aim to restore not only the microbial composition but also the synchronized functional dialog between the microbiome and host development. By mapping the "microbiota-metabolite-host target-physiological phenotype" network, we provide a systematic roadmap for precision-targeted interventions during the first 1000 days of life.},
}

@article {pmid42558585,
year = {2026},
author = {Kuang, G and Qiu, Z and Li, L and Bai, J and Ji, H and Liu, Y},
title = {Bacteria-related signals in brain metastases: evidence boundaries, tumor-microenvironment remodeling, and translational prospects.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1893882},
pmid = {42558585},
issn = {2296-634X},
abstract = {Brain metastases (BrM) develop within a highly specialized central nervous system niche shaped by the blood-brain barrier/blood-tumor barrier, brain-resident stromal cells, myeloid populations, and distinct metabolic constraints. Emerging studies suggest that bacteria-related signals can be detected in primary and metastatic brain tumors; however, their biological meaning remains incompletely defined. In particular, low-biomass brain tissues are highly vulnerable to reagent contamination, environmental carry-over, batch effects, and bioinformatic misclassification, making it essential to distinguish molecular bacterial traces from viable intratumoral bacteria or a bona fide tumor microbiome. In this review, we propose a graded conceptual framework that separates bacterial signals/elements, intratumoral bacteria, and intratumoral microbiota/microbiome according to evidentiary strength. We summarize current evidence for the spatial and cellular localization of bacteria-related signals in BrM and discuss potential source models, including primary-tumor carry-over, hematogenous dissemination, gut microbiota-derived metabolites, oral microbial input, and bacterial extracellular vesicles. We further examine how these signals may interact with the BrM tumor microenvironment by influencing tumor-cell stress adaptation, myeloid inflammatory niches, antigen-presentation pathways, vascular-barrier remodeling, and metabolic reprogramming. Particular attention is given to the emerging gut-brain-metastasis axis and to cancer-type-specific contexts in breast cancer, lung cancer, and melanoma brain metastases. From a translational perspective, bacteria-related signals in BrM may eventually contribute to biomarker development, patient stratification, and therapeutic modulation of the microbe-host axis. Nevertheless, current evidence remains insufficient to conclude that BrM broadly harbor stable, active, and clinically actionable microbial communities. Future progress will require multi-source matched cohorts, longitudinal sampling, stringent low-biomass contamination control, absolute quantification, spatial validation, functional models, and explicit separation of microbial presence, viability, and causality. A rigorous evidence-based approach will be essential for moving this field from intriguing associations toward biologically interpretable and clinically meaningful applications.},
}

@article {pmid42558610,
year = {2026},
author = {Li, Z and Li, X and Sun, B and Wu, H and Zhang, J and Wan, X and Zhao, B and Xiao, N and Qi, Z and Li, Q and Liu, H},
title = {Dose-dependent supplementation of Schizochytrium in the biofloc system modulates dual microbiomes to enhance growth and survival in Pacific white shrimp (Litopenaeus vannamei).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1867320},
pmid = {42558610},
issn = {1664-302X},
abstract = {Integrating microalgae into biofloc system is a promising yet debated strategy in Pacific white shrimp (Litopenaeus vannamei) aquaculture, due to its inconsistent efficacy even for the same microalgal species. Such inconsistent performances are likely dose-dependent and the underlying microbial mechanisms remain elusive. Here, we investigated the impacts of supplementing microalga strain, Schizochytrium sp. ATCC 20888, at low (10[3] cells/mL, M1) and high (10[6] cells/mL, M2) levels compared with a clear water (CLW) system. Schizochytrium supplementation improved growth performance and feed efficiency and the M2 treatment further increased shrimp survival. Transcriptional profiling revealed the M2 treatment upregulated the expression of genes relevant to hepatopancreatic lipid and protein digestion (trypsin and lipase) and intestinal amino acid transportation (peptide transporter 1). Concurrently, M2 fortified the intestinal defense against pathogenic microbes by enhancing antimicrobial genes (lysozyme and penaeidin 3a). Redundancy analysis further supported the growth promotion was closely associated with improved lipid and a corresponding protein-sparing effect. Notably, Schizochytrium persisted at an extremely low abundance, whilst 16S rRNA sequencing revealed its disproportionate impact as a rare taxon on the microbiota in both biofloc and gut. High-dose supplementation enriched beneficial genera such as Aureispira, Marivita, Neptuniibacter, and Phaeodactylibacter in bioflocs, which are vital for nutrient recycling. Meanwhile, the intestinal microbiota was characterized by enrichment of the probiotic Fusibacter and the suppression of the opportunistic pathogen Shewanella. Overall, Schizochytrium orchestrates a dose-dependent reshaping of biofloc and gut microbiomes, effectively boosting the growth, feed efficiency, and specifically reinforcing antimicrobial activity of L. vannamei.},
}

@article {pmid42558660,
year = {2026},
author = {Zeng, L and Ren, Y and Huang, H and Wang, Q and Li, H and Song, J and He, F and Li, J},
title = {Gut metabolites: key factors in the cross-talk between the gut microbiota and tumor immunotherapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1882542},
pmid = {42558660},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/metabolism ; Animals ; *Immunotherapy/methods ; Tumor Microenvironment/immunology ; },
abstract = {This review synthesizes recent research findings and proposes an integrated "microbiota-metabolite-immune-oncology" framework, highlighting how gut-derived metabolites regulate the dynamics of tumor immunity and informing the development of next-generation immunotherapies. Key metabolites-including short-chain fatty acids (SCFAs), bile acids (BAs), trimethylamine N-oxide (TMAO), indole-3-propionic acid (IPA), and urolithin A-exert bidirectional effects on antitumor immunity through multiple mechanisms. These include histone acetylation-driven epigenetic reprogramming, aryl hydrocarbon receptor (AhR)- and farnesoid X receptor (FXR)-mediated metabolic reprogramming, and direct regulation of immune effectors such as CD8[+] T cells and myeloid-derived suppressor cells. Emerging evidence highlights specific roles of these metabolites within the tumor microenvironment (TME): microbial dysbiosis can amplify immunosuppressive circuits, whereas targeted enrichment of certain metabolites may enhance the efficacy of immune checkpoint blockade. Integrative multi-omics analyses have revealed the vascular remodeling effect of TMAO and the spatiotemporal heterogeneity of BAs, thereby connecting the gut-liver-tumor axis and achieving overall immune regulation. By mapping a precision-oriented metabolic roadmap, this review identifies underexplored therapeutic avenues-such as metabolite-targeted interventions and engineered probiotics-that, when combined with immune checkpoint inhibitors, may enable personalized, microbiome-based strategies with the potential to improve outcomes in cancer immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Neoplasms/therapy/immunology/metabolism
Animals
*Immunotherapy/methods
Tumor Microenvironment/immunology

@article {pmid42558675,
year = {2026},
author = {Mo, W and Cai, F and Li, L and Liang, J and Zhang, J and Yao, L and Mo, S and Liao, Y and Tang, S and Liu, Z and Chen, Z and Qin, M and Liu, S and Zou, J and Huang, J},
title = {Mapping research trends in irritable bowel syndrome and the gut microbiome: a cross-database bibliometric analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1900159},
pmid = {42558675},
issn = {1664-302X},
abstract = {BACKGROUND/OBJECTIVES: Research on irritable bowel syndrome (IBS) and the gut microbiome has expanded rapidly. However, the structural evolution of this literature has not been systematically characterized across major indexing platforms.

METHODS: We performed a parallel bibliometric analysis of the Web of Science Core Collection (WoSCC, n = 1,502), Scopus (n = 1,163), and PubMed (n = 975). The analysis included English-language articles and reviews published from January 2000 to December 2025. WoSCC served as the primary dataset, and Scopus and PubMed were analyzed in parallel for cross-database comparison. Bibliometric mapping and visualization were performed using VOSviewer, CiteSpace, and bibliometrix.

RESULTS: Annual output increased from fewer than 10 articles per year before 2010 to 162 in 2025. This acceleration became marked after 2014 and was reproduced across all three databases. The United States and China led publication volume, whereas the UK output was concentrated in a small number of flagship centers. Our analysis suggests three developmental phases: compositional profiling and culture-dependent benchmarks (2000-2012), community-level characterization and interventional consolidation (2012-2017), and neuroendocrine and short-chain fatty acid mechanisms (2017-2025). Visceral hyperalgesia and hypothalamic-pituitary-adrenal axis dysregulation showed the strongest currently active keyword bursts. Diet-related and precision-oriented approaches also gained visibility.

CONCLUSION: IBS-gut microbiome research has shifted from descriptive profiling toward mechanistic, diet-related, and precision-medicine themes. These findings provide a structured overview of the field and help clarify priorities for its next phase.},
}

@article {pmid42558707,
year = {2026},
author = {Khan, I},
title = {Editorial: Natural products: a microecological perspective for treating diabetes and its complications.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1896973},
pmid = {42558707},
issn = {2296-861X},
}

@article {pmid42558754,
year = {2026},
author = {Fan, C and Zhang, Y and Zhang, J and Xu, C and Wang, X and Fan, Y},
title = {Relationship Between Vaginal Microbiome and Preterm Birth During Pregnancy: In Different Ethnic Populations.},
journal = {Women's health reports (New Rochelle, N.Y.)},
volume = {7},
number = {},
pages = {26884844261471777},
pmid = {42558754},
issn = {2688-4844},
abstract = {The incidence of preterm birth (PTB) varies and remains stubbornly high across different countries and regions. Besides, PTB can lead to a wide range of maternal and infant complications and even death in severe cases. Despite the severity of the consequences of PTB, the exact causes of morbidity remain unclear. In the past few years, with the development of the microbiome, a growing body of research focuses on the impact of vaginal microbiome (VMB) on PTB. Moreover, accumulating studies have suggested that the VMB plays a crucial role in the development of PTB. In addition, the VMB varies greatly in different populations. Therefore, in this review, we describe the normal VMB in women with or without pregnancy. Subsequently, we highlight differences in the VMB among ethnically diverse PTB populations. Overall, understanding the relationship between the VMB and PTB in different populations is essential for developing targeted interventions and personalized approaches to reduce the risk of PTB. Further research is needed to fully elucidate the specific microbial patterns and mechanisms underlying this association.},
}

@article {pmid42558801,
year = {2026},
author = {Zhou, T and Li, G and Ye, W and Wu, L and Liu, H and Guo, J and Wen, Y and Li, J and Wu, M and Li, W and Wu, H},
title = {The interplay of the microbiome, host genetics, and epigenetic modifications in gastric cancer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1834439},
pmid = {42558801},
issn = {1664-302X},
abstract = {Gastric cancer is one of the most prevalent gastrointestinal malignancies worldwide, with Helicobacter pylori infection, host genetic susceptibility and environmental exposure serving as major driving risk factors. Accumulating studies have demonstrated that host genetics, the microbiome and epigenetic modifications collectively govern gastric cancer initiation and progression. These three components form a bidirectional regulatory axis: host genetic profiles and epigenetic remodeling shape the composition of endogenous microbial communities, while the microbiome and its metabolites trigger epigenetic reprogramming to modulate transcription of oncogenes and tumor suppressors. Deciphering this intricate tripartite regulatory network holds great potential to facilitate the development of precise therapeutic interventions for gastric cancer. This review delineates the respective roles of host genetics, the microbiome and epigenetic modifications throughout gastric cancer evolution and summarizes corresponding prospective intervention strategies. We elaborate on the reciprocal interplay between the microbiome and host genetic/epigenetic factors, and highlight the vital clinical significance of this crosstalk for gastric cancer prevention and treatment.},
}

@article {pmid42558826,
year = {2026},
author = {Battaglia, EG and Leonardi, G and Banfi, PI and Volpato, E},
title = {Neurocognitive and neurophysiological consequences of sleep-disordered breathing in bronchiectasis: the role of respiratory rehabilitation.},
journal = {Frontiers in rehabilitation sciences},
volume = {7},
number = {},
pages = {1846233},
pmid = {42558826},
issn = {2673-6861},
abstract = {Bronchiectasis (BE) is a chronic respiratory disease characterized by a vicious cycle of irreversible bronchial dilatation and persistent respiratory infections which results in progressive functional impairment and reduced quality of life. Increasing attention has been directed toward comorbidities that may aggravate disease burden, including sleep-disordered breathing (SDB), which remains underrecognized in this population. Emerging evidence suggests that SDB, particularly obstructive sleep apnea (OSA), is highly prevalent in BE and may contribute to adverse outcomes through mechanisms such as intermittent hypoxia, systemic inflammation, microbiome alterations, and ventilatory instability. This narrative review synthesizes current evidence on the relationship between BE and SDB, with a focus on the underlying pathophysiological mechanisms, the neurophysiological and cognitive consequences and the implications for rehabilitation. A comprehensive literature search was conducted using PubMed, Embase, and the Cochrane Library, supplemented by evidence from related chronic respiratory diseases. Available data indicate that sleep disturbances are common in BE and are associated with impaired daytime functioning, reduced quality of life as well as increased symptom burden, independent of disease severity. Rehabilitation interventions, in particular pulmonary rehabilitation, positive airway pressure (PAP), and non-invasive ventilation (NIV), may offer clinically meaningful benefits by enhancing gas exchange, improving sleep quality and patient-reported outcomes. However, high-quality evidence specific to BE populations remains limited. In conclusion, we consider that recognizing SDB as a potentially modifiable trait in bronchiectasis highlights the need for integrated, multidisciplinary management strategies. Future research should prioritize prospective studies to clarify the role of targeted rehabilitation interventions and to support evidence-based clinical practice.},
}

@article {pmid42558902,
year = {2026},
author = {Liu, E and Jia, J and Liu, Q and Li, C and Li, S and Cai, T},
title = {The Microbiome-Mitochondria Axis in aging: a self-reinforcing vicious cycle linking metabolic dysregulation, mitochondrial quality control failure, and inflammaging.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1874222},
pmid = {42558902},
issn = {1664-302X},
abstract = {Aging is a progressive degenerative process of cellular and systemic homeostasis in organisms, with mitochondrial dysfunction and altered intercellular communication as core hallmarks of this process. During aging, the gut microbiome and mitochondria exhibit a highly synchronized degenerative trajectory: this is characterized by decreased microbial diversity, reduced abundance of beneficial short-chain fatty acid (SCFA)-producing bacteria, and expansion of pro-inflammatory pathobionts in the gut, alongside impaired oxidative phosphorylation efficiency, excessive reactive oxygen species (ROS) production, and compromised quality control in mitochondria. Built on the evolutionary cornerstone of endosymbiotic theory, this review establishes a theoretical framework for the Microbiome-Mitochondria Axis (MMA) and proposes that the ancient molecular homology between mitochondria and modern gut bacteria has preserved a sensitive cross-species signal crosstalk mechanism. This review systematically dissects the bidirectional communication mechanisms of the MMA. First, microbial metabolites-including SCFAs, tryptophan-derived indole metabolites, and secondary bile acids-regulate mitochondrial energy metabolism, oxidative stress responses, and dynamic homeostasis via key signaling pathways such as AMPK-PGC-1α, AhR-Nrf2, and FXR/TGR5. Conversely, dysfunctional mitochondria actively reshape the gut microenvironment and propagate sterile inflammation through multiple pathways: mitochondrial ROS (mtROS)-mediated intestinal barrier disruption, metabolic reprogramming of immune cells toward a pro-inflammatory phenotype, and activation of the cGAS-STING innate immune pathway triggered by mitochondrial DNA (mtDNA) release. Here, we propose a unified theoretical framework centered on the MMA as a self-reinforcing pathological loop. In this model, gut dysbiosis drives depletion of beneficial microbial metabolites, which triggers mitochondrial quality control failure, mtDNA leakage, and inflammaging; in turn, inflammaging exacerbates gut dysbiosis by remodeling the intestinal microenvironment, thus forming a closed, self-amplifying vicious cycle. The MMA links multiple hallmarks of aging, including epigenetic alterations, immunosenescence, and stem cell exhaustion, providing a unifying pathological basis for age-related disorders such as neurodegenerative diseases, cardiovascular diseases, sarcopenia, and osteoarthritis. It also offers a systematic entry point for anti-aging interventions targeting the bidirectional metabolic-immune crosstalk between the microbiome and mitochondria.},
}

@article {pmid42559032,
year = {2026},
author = {Sun, Y and Li, X and Zheng, X and Sun, X and Liu, J and Zhang, S and Zhang, G and He, W and Huo, W and Zuo, J},
title = {Habitat environment is associated with the microbiota of the human terminal airway.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1887778},
pmid = {42559032},
issn = {1664-302X},
abstract = {While environmental exposures are closely associated with the human microbiome, the microbial landscape of the terminal airways remains largely uncharacterized due to the ethical challenges of tissue sampling. To address this gap, we analyzed surgically resected idiopathic lung bullae (localized developmental anomalies surrounded by otherwise normal tissue) to establish a baseline microbiome atlas. We performed ultra-deep metagenomic sequencing on terminal airway tissues from 60 subjects residing in two climatically distinct Chinese cities: Zhuhai (a subtropical coastal region) and Yinchuan (an arid, high-altitude industrial area on the Qinghai-Tibet Plateau). Our analysis revealed that the high-altitude Yinchuan cohort exhibited significantly higher microbial loads and alpha diversity compared to the coastal Zhuhai cohort. Functionally, the Yinchuan microbiome was enriched in taxa associated with fatty acid beta-oxidation, alongside a markedly higher burden of virulence factors and antibiotic resistance genes. These compositional and functional differences may be associated with regional variation in climate, altitude, and local antibiotic usage patterns, whereas the Zhuhai cohort exhibited greater fungal diversity. Ultimately, this study provides the tissue-resolved microbial atlas of the human terminal respiratory tract and reveals substantial differences in microbial composition and function across distinct habitat environments. Furthermore, these findings suggest a potential association between environmental conditions and variation in resident microbiota, providing a basis for future investigations into how environmental change may influence respiratory microecology and human health.},
}

@article {pmid42559081,
year = {2026},
author = {Zhang, Y and Wang, Q and Zhai, Y and Wang, Q and Li, Z and Liu, Y and Liu, S},
title = {Filtration-enriched metabolites and their association with salivary microbiota: a combined two-cohort analysis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2711156},
pmid = {42559081},
issn = {2000-2297},
abstract = {OBJECTIVE: We aimed to identify significantly reduced metabolites (SRMs) in saliva by filtration and to analyze their associations with oral microorganisms.

METHODS: A total of 423 volunteers were assigned into two cohorts. Paired saliva samples were collected from cohort 1 (n = 60) and underwent metabolomics analysis before and after filtration. SRMs were identified based on the following thresholds: variable importance in projection ≥1, false discovery rate <0.05, and fold change ≥10. The pre-filtration samples from Cohort 1 were subjected to microbiome analysis. Saliva samples collected from cohort 2 (n = 334) underwent metabolomic and microbiome analyses, but were not filtered.

RESULTS: Principal coordinates analysis revealed a clear separation between pre- and post-filtration samples. The filtered saliva samples had approximately 5.8% fewer detectable metabolites. Notably, over half of the SRMs had an unknown origin, indicating significant knowledge gaps in oral metabolites. Prevotella melaninogenica and Veillonella parvula were core species associated with the SRMs (hypoxanthine and phosphatidylcholine), with purine metabolism identified as enriched pathway for Prevotella melaninogenica.

CONCLUSIONS: Filtration can reshape saliva metabolite profiles. This study combined key metabolite filtration with integrated multi-omics and functional analyses, providing new insights into saliva metabolism and microbe-metabolite interactions.},
}

@article {pmid42559590,
year = {2026},
author = {Zhu, L and Jiang, S and Yan, Q and Zhou, Y and Zhang, Y and Peng, H and Zhou, L},
title = {Exploring the Role of Microbiota-Mediated Gut-Kidney Axis in Acute Kidney Injury: Immunomodulation and Therapy.},
journal = {Kidney diseases (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {722-733},
pmid = {42559590},
issn = {2296-9381},
abstract = {BACKGROUND: Acute kidney injury (AKI) remains a major clinical problem characterized by high morbidity and an increased risk of progression to chronic kidney disease (CKD). Immune cell infiltration and activation are important features of AKI; however, the upstream mechanisms that shape this inflammatory response are not fully understood. Emerging evidence suggests that gut microbiota dysbiosis and systemic immune activation may contribute to renal injury, but the functional significance of the gut-kidney axis in AKI pathogenesis remains to be further clarified.

SUMMARY: This review synthesizes current evidence regarding gut-kidney crosstalk in AKI, with a focus on the immunometabolic impact of microbiota-derived metabolites. We discuss the potential roles of short-chain fatty acids, indole derivatives, indoxyl sulfate (IS), p-cresol sulfate (PCS), and trimethylamine-N-oxide (TMAO) in regulating T and B lymphocytes, macrophages, neutrophils, and other immune cell populations. Importantly, we distinguish direct AKI-related evidence from findings extrapolated from CKD, uremic conditions, or broader microbiome-immunity studies. Potential therapeutic interventions, including pharmacological modulation and probiotic strategies aimed at restoring gut-kidney homeostasis, are also highlighted.

KEY MESSAGES: The gut-kidney axis is increasingly recognized as a potential contributor to immune-mediated injury and repair in AKI. However, the causal roles and temporal dynamics of several gut-derived uremic toxins, including IS, PCS, and TMAO, remain incompletely defined in AKI. By integrating direct AKI evidence with indirect evidence from CKD and broader microbiome-immunity studies, this review provides a more balanced conceptual framework for understanding renal immunopathology and identifying potential microbiome-targeted strategies to mitigate AKI and its progression to CKD.},
}

@article {pmid42560044,
year = {2026},
author = {Slack, J and Wilcher, E and Hua, X and Wan, Y and Liu, J and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Shi, J and Abnet, CC and Vogtmann, E},
title = {Long-term stability at -80°C of oral wash and saliva samples for microbiome analyses.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057326},
doi = {10.1128/spectrum.00573-26},
pmid = {42560044},
issn = {2165-0497},
abstract = {Large-scale prospective biological studies necessitate the storage of oral samples for numerous years to accrue adequate sample sizes. However, there is minimal research on the impact of long-term storage of oral samples on the oral microbiome. We investigated the freezer stability over 5 years of the oral microbiome measured from oral wash and saliva samples to provide insight for future microbiome analyses of stored oral samples. Healthy participants provided oral wash and saliva samples using Scope mouthwash and the OMNIgene ORAL collection device, respectively. DNA was extracted from an aliquot of each sample type at baseline, the V4 region of the 16S rRNA gene sequenced, and additional aliquots were then similarly extracted and sequenced after being stored for approximately 1 month, 12 months, and 5 years after collection. Intraclass correlation coefficients (ICC) and 95% confidence intervals (CI) were calculated for 4 alpha-diversity metrics, the first 2 principal coordinates of four beta-diversity matrices, and the 14 most abundant genera. The alpha diversity and beta diversity ICCs for both sample types remained stable over 5 years. For example, the 5-year Shannon index ICCs were 0.94 (95% CI: 0.88, 0.98) and 0.90 (95% CI: 0.72, 0.95) for oral wash and saliva samples, respectively. The ICCs for the relative abundances of the examined genera during the 5 years of freezer storage were also generally stable. Both oral wash and saliva samples were relatively stable for diversity metrics and relative abundance after 5 years when stored at -80°C.IMPORTANCELarge, prospective studies will likely need to store biospecimens for many years in the freezer prior to DNA extraction and sequencing for analyses considering the association between the microbiome and specific health conditions. In this study, we demonstrated that oral wash using Scope mouthwash and saliva specimens in the OMNIgene ORAL kit have generally stable microbiome communities for up to 5 years at -80°C.},
}

@article {pmid42560056,
year = {2026},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0246825},
doi = {10.1128/aem.02468-25},
pmid = {42560056},
issn = {1098-5336},
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug-resistant gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document the potential sources of the corresponding resistance genes. This study searched for potential emerging colistin resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments that all contained eptA genes. We confirmed their ability to confer significant colistin resistance in Escherichia coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter genomes, marking them as potential mcr genes or their precursors. This study highlights the potential for functional metagenomic selections for colistin resistance to capture genes from unexpected environmental sources such as the goose fecal microbiome.IMPORTANCEColistin is an important antibiotic of last resort, and increasing resistance to this drug via mobile phosphoethanolamine transferase genes, such as mcr-1, threatens its clinical utility. Given the discovery of mcr-1 in pigs, the ability of animals to act as vectors in the spread of colistin resistance is alarming. We show here that functionally selected Acinetobacter phosphoethanolamine transferase genes from the goose microbiome have the ability to confer clinical levels of colistin resistance when transferred into E. coli. While the genes are annotated as eptA homologs, closer study of these genes suggests that they may be mobilized within the Acinetobacter genus, suggesting that they may be mcr genes of concern instead.},
}

@article {pmid42560063,
year = {2026},
author = {Peng, L and Dai, L-l and Tao, L and Li, G and Zhu, J-q and Zhang, H},
title = {Rice-crayfish farming mode drives distinct soil properties and ecological assembly of soil microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0383225},
doi = {10.1128/spectrum.03832-25},
pmid = {42560063},
issn = {2165-0497},
abstract = {UNLABELLED: Rice-crayfish farming (RCF) system represents an effective ecological agricultural model characterized by the cyclical spatiotemporal integration of rice farming and crayfish aquaculture. However, the effects of farming mode and stage on soil microbial community structure over time remain insufficiently explored. In this study, we investigated taxonomic and functional changes in soil microbiomes and their associations with soil nutrient fertility in both RCF and rice monoculture (RM) systems. Our findings demonstrated that RCF significantly increased soil pH, total nitrogen (TN), and soil organic carbon (SOC) compared to RM across multiple growth stages (P < 0.05). Two-way analysis of variance showed that both mode and stage affected the Chao1 index, while the Shannon index was only affected by stage. Microbial community analysis revealed clear structural differences between the two systems (P < 0.001). Functional prediction indicated lower chemoheterotrophy but higher photoheterotrophy, aromatic degradation, and sulfur cycling in RCF, along with reduced nitrogen cycling function. Co-occurrence network analysis further showed a longer average path length and higher modularity in RCF than in RM. Modules 3 and 6 in RCF were positively correlated with pH, TN, and SOC. Overall, RCF stabilizes the soil environment and selects for specific functionally sensitive taxa, thereby promoting the formation of a highly modular microbial network, which ultimately maintains the synergistic stability of soil nutrients and the microbial community.

IMPORTANCE: The present study comprehensively compared two different farming modes in terms of their soil microbiome structures and the associations between the microbiomes and soil nutrient fertility. Rice-crayfish farming (RCF) model-specific microbial taxa were identified, and their modularity was found in RCF. These findings provide valuable insights into microbial community responses and regulation in ecological agriculture, establishing a robust microbiological foundation for optimizing rice-aquatic animal integrated farming management and advancing sustainable agricultural practices.},
}

@article {pmid42560133,
year = {2026},
author = {Helliwell, JA and Kirby, A and Chilton, C and Wood, H and Quirke, P and Jayne, DG},
title = {Defunctioning stomas and the effect of oral antibiotic bowel preparation in colorectal surgery: a microbiome-based hypothesis.},
journal = {The British journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjs/znag102},
pmid = {42560133},
issn = {1365-2168},
}

@article {pmid42560299,
year = {2026},
author = {Liang, F and Li, J and Yue, Y and Pan, J and Liu, C and Cheng, D and Zhang, N and Li, K and Chu, F and Wu, H},
title = {Distinct Gut Microbiome and Metabolome Profiles Associate with Differential Responses to Immunotherapy in Colorectal Cancer.},
journal = {Polish journal of microbiology},
volume = {75},
number = {2},
pages = {168-194},
pmid = {42560299},
issn = {2544-4646},
mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/metabolism ; *Metabolome ; *Immunotherapy ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; Male ; Middle Aged ; Aged ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The composition of the intestinal microbiome has been identified as a key factor influencing the efficacy of immune checkpoint inhibitors. This study aimed to systematically evaluate the potential associations among gut microbiota, metabolic profiles, and clinical outcomes in patients with MSI-H advanced colorectal cancer (CRC) treated with immunotherapy. Twenty advanced CRC patients receiving immunotherapy were enrolled and categorized into clinical benefit response (CBR) and non-benefit (NCB) groups based on treatment efficacy. Fecal samples were analyzed using metagenomic sequencing and untargeted metabolomics. The results revealed significant enrichments of s_Clostridium unclassified and metabolites such as guanosine, 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid, and quercetin 3-(6"-malonyl-glucoside) in the CBR group, suggesting their potential positive predictive value for immunotherapy response. Conversely, the NCB group showed significant enrichments of s_Roseburia hominis, s_Marseilla massiliensis, and metabolites including pyrophosphate, riboflavin, and PC(22:5(4Z,7Z,10Z,13Z,16Z)/14:0), indicating a possible association with treatment resistance. By integrating fecal metagenomics and metabolomics, this study reveals distinctive "flora-metabolite" interactions linked to therapeutic response in advanced CRC patients undergoing immunotherapy. Specific microbial and metabolic profiles were positively or negatively correlated with immunotherapy outcomes, highlighting their potential not only as predictive biomarkers but also as a theoretical foundation for developing individualized immunotherapy strategies based on microecological modulation.},
}

Humans
*Colorectal Neoplasms/therapy/microbiology/metabolism
*Metabolome
*Immunotherapy
*Gastrointestinal Microbiome
Female
Feces/microbiology
Male
Middle Aged
Aged
Metabolomics
Bacteria/classification/genetics/isolation & purification

@article {pmid42560302,
year = {2026},
author = {Guo, H and Wang, J and Niu, Y and Liu, F},
title = {Microbial Signatures in Head and Neck versus Gastrointestinal Tumors: Identification and Prognostic Modeling.},
journal = {Polish journal of microbiology},
volume = {75},
number = {2},
pages = {123-138},
pmid = {42560302},
issn = {2544-4646},
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/diagnosis ; *Gastrointestinal Neoplasms/microbiology/diagnosis ; Prognosis ; *Bacteria/classification/isolation & purification/genetics ; Nomograms ; *Microbiota ; },
abstract = {This study identified key intra-tumor microbial signatures distinguishing head and neck cancers from gastrointestinal cancers and explored their diagnostic and prognostic potential. Intra-tumor microbial data of five cancer types were obtained from the Cancer Microbiome Atlas, and corresponding clinical data were retrieved from the Cancer Genome Atlas. The Wilcoxon test was used to analyze differences in microbial populations. Univariate logistic regression, least absolute shrinkage and selection operator, and recursive feature elimination were sequentially applied to screen optimal microbial markers, and a support vector machine classification model was constructed. A nomogram model and Kaplan-Meier curves were used to validate the predictive and prognostic value of the optimal microbes, respectively. Overall, 463 tumor samples and 47 controls were included. Twenty-three microbes showed significant differences in distribution between head and neck and gastrointestinal tumors; among these, eight overlapping microbes were selected as optimal markers. The SVM model based on these eight microbes achieved AUCs of 0.937 and 0.856 in the training and validation datasets, respectively. The nomogram model constructed with these markers showed high predictive accuracy (C-index = 0.8944 in training, 0.8023 in validation). Kaplan-Meier analysis revealed that high abundance of Capnocytophaga, Lachnospiraceae, and Bacteroidales was significantly associated with longer overall survival in both head and neck tumors and gastrointestinal tumors (all P < 0.05). The eight intra-tumor microbial communities serve as a robust signature for distinguishing head and neck tumors from gastrointestinal tumors. Among these, Capnocytophaga, Lachnospiraceae, and Bacteroidales have potential as prognostic biomarkers to improve survival prediction in cancers.},
}

Humans
*Head and Neck Neoplasms/microbiology/diagnosis
*Gastrointestinal Neoplasms/microbiology/diagnosis
Prognosis
*Bacteria/classification/isolation & purification/genetics
Nomograms
*Microbiota

@article {pmid42560303,
year = {2026},
author = {Shih, MY and Yang, YC and Liu, YR},
title = {A Pilot Longitudinal 16S rRNA Gene Sequencing Study Exploring the Relationship Between Gut Microbiota and Body Composition in Healthy Adults.},
journal = {Polish journal of microbiology},
volume = {75},
number = {2},
pages = {157-167},
pmid = {42560303},
issn = {2544-4646},
mesh = {Humans ; *Body Composition ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Pilot Projects ; Feces/microbiology ; Adult ; *Gastrointestinal Microbiome ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; },
abstract = {The gut microbiome is linked to body composition, yet most studies involve probiotic or dietary interventions. This study explored relationships between changes in body composition and the fecal microbiota under natural lifestyle conditions. A repeated-measures design involved 15 adults completing four body composition assessments at 3-month intervals. Fecal samples from each time point underwent 16S rRNA gene sequencing. Participants were stratified by body composition parameters, and microbial profiles from initial and final measurements were compared to assess longitudinal patterns. Overweight participants showed lower alpha diversity. Linear mixed models revealed fecal microbiota remained stable across all four time points, with no statistically significant continuous trends observed longitudinally. Exploratory baseline-to-endpoint comparisons across stratified groups and Spearman correlation analyses suggested potential microbiota shifts, though these associations remained statistically non-significant. Preliminary observations exhibited that the OTU identified as Parasutterella excrementihominis tended to associate with higher body fat, whereas the putative species Akkermansia muciniphila showed a potential inverse association. Representative taxa, such as Dialister invisus, appeared enriched in individuals with higher skeletal muscle percentages, whereas the OTU assigned to Bifidobacterium pseudocatenulatum showed the opposite trend. Several associations differed by sex, suggesting modulation by host factors. These preliminary findings suggest possible fecal microbiota patterns associated with body composition, even without targeted interventions. While lacking robust linear associations in this small pilot cohort, the observed directional consistency across statistical approaches highlights the potential of fecal microbes as candidate indicators of metabolic health. These exploratory results require further validation in larger, longitudinal studies with sufficient statistical power.},
}

Humans
*Body Composition
*RNA, Ribosomal, 16S/genetics
Male
Female
Pilot Projects
Feces/microbiology
Adult
*Gastrointestinal Microbiome
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification
Middle Aged

@article {pmid42560340,
year = {2026},
author = {Zheng, B},
title = {Toward Meta-Omics Governance of the Urban Microbiome Commons.},
journal = {Annals of the New York Academy of Sciences},
volume = {1562},
number = {1},
pages = {e70361},
pmid = {42560340},
issn = {1749-6632},
support = {JAT220336//Fujian Provincial Young and Middle-aged Teachers' Education and Research Project/ ; 2024I0043//Fujian International Cooperation Project/ ; 3502Z202372040//Xiamen Natural Science Foundation Youth Project/ ; },
mesh = {Humans ; *Microbiota/physiology ; Animals ; Cities ; Multiomics ; Probiotics ; },
abstract = {Urban microbial communities are undergoing directional homogenization across soils, wildlife gut microbiota, and human exposure pathways, yet no monitoring framework exists to track this loss or govern the probiotic city interventions now scaling without ecological oversight. I argue that the urban microbiome constitutes an "invisible commons": a shared, depletable resource whose depletion goes unaccounted for because it has never been made measurable. The meta-omics community has the tools to change this. I propose five monitoring priorities and six immediately deployable indicators and show that the governance architecture required to convert these measurements into decisions already exists in conservation biology. What is missing is not new science but the decision to apply existing methods to this domain. With antibiotic resistance causing over one million deaths annually and probiotic city interventions advancing without resistance gene screening, that decision is overdue.},
}

Humans
*Microbiota/physiology
Animals
Cities
Multiomics
Probiotics

@article {pmid42560743,
year = {2026},
author = {Meyer, MB and Pike, JW},
title = {The Vitamin D Receptor Story: Discovery, Control, and Genomic Reach.},
journal = {The Journal of endocrinology},
volume = {},
number = {},
pages = {},
doi = {10.1530/JOE-26-0204},
pmid = {42560743},
issn = {1479-6805},
abstract = {The vitamin D receptor (VDR) is a ligand-activated nuclear receptor that mediates the biological actions of vitamin D and is a critical regulator of mineral homeostasis, cellular differentiation, immune function, and metabolism. VDR is a high-affinity intracellular binding protein for the most active vitamin D metabolite, 1,25-dihydroxyvitamin D3 (1,25D). Early biochemical and molecular studies established VDR as a member of the nuclear receptor superfamily, functioning as a transcription factor that heterodimerizes with the retinoid X receptor and binds vitamin D response elements to regulate gene expression. Since the cloning of the VDR gene in the 1980s, characterization of its structural domains, and identification of co-regulators significantly advanced understanding of its genomic mechanisms of action. Over the past several decades, research has expanded the scope of VDR biology beyond classical calcium and phosphate metabolism. Genome-wide binding analyses and transcriptomic studies have revealed extensive VDR cistromes and context-dependent gene networks across diverse tissues. These advances have positioned VDR as a key factor linking vitamin D availability to tissue-specific outcomes. Despite substantial progress, fundamental questions remain including mechanisms governing tissue-specific VDR actions, integration of genomic signaling pathways, and role of VDR in complex diseases such as cancer, autoimmune disorders, and aging. Additionally, how VDR function is modulated by chromatin context, metabolic state, and the microbiome remains incompletely understood. Here, we summarize what is known about these actions of VDR and its history of discovery. Addressing these questions will be essential for translating mechanistic insights into improved therapeutic strategies targeting the vitamin D axis.},
}

@article {pmid42561489,
year = {2026},
author = {Khobragade, R and Chaudhary, A and Gautam, Y and Ali, MAM and Patil, H and Kaushalye, P and Deshmukh, I and Umekar, M and Trivedi, R},
title = {Neuroimmune mechanisms of the gut-brain axis in treatment-resistant depression: Implications for microbiome-based therapeutic strategies.},
journal = {Journal of neuroimmunology},
volume = {421},
number = {},
pages = {579050},
doi = {10.1016/j.jneuroim.2026.579050},
pmid = {42561489},
issn = {1872-8421},
abstract = {Treatment-resistant depression (TRD) represents a major clinical challenge characterised by inadequate response to conventional antidepressant therapies and high relapse rates. Emerging evidence suggests that TRD may extend beyond monoaminergic dysfunction and may involve dysregulation of the HPA axis, neuroinflammation, impaired neuroplasticity, and disruption of the gut-brain axis (GBA). Gut dysbiosis has been associated with treatment resistance through alterations in monoamine turnover, immune signalling, intestinal barrier integrity, and drug-microbiome interactions affecting antidepressant bioavailability. This review integrates emerging evidence supporting targeted modulation of the GBA as a mechanistically informed strategy for TRD. Specific microbial strains (e.g., Christensenella minuta, Akkermansia muciniphila, Bifidobacterium breve CCFM1025), microbial metabolites (e.g., indole-3-propionic acid, indole-3-lactic acid, anserine), and phytochemicals (e.g., curcumin, matrine, salidroside) are discussed for their proposed roles in modulating neuroendocrine signalling, neuroinflammation, and synaptic plasticity. The review also highlights emerging peripheral biomarkers, including the kynurenine/tryptophan ratio, serum metabolomics, and lymphocyte serotonin transporter clustering, as candidate tools for stratified psychiatry. Most of the evidence discussed in this review comes from animal studies, in vitro systems, and computational analyses, while direct evidence in patients with treatment-resistant depression remains limited. These findings provide important mechanistic insights into gut-brain axis dysfunction but require further validation in human TRD populations. Biomarker-guided and endotype-based approaches targeting the gut-brain axis may offer a useful framework for future research, although their clinical utility has yet to be established.},
}

@article {pmid42561662,
year = {2026},
author = {Tan, J and Huang, S and Yin, G and Wang, L and Wang, J and Yuan, P and Liu, J and Yao, K},
title = {Astragalus polysaccharides prevent kidney stone formation in an ethylene glycol-induced rat model via modulation of gut microbiota and short-chain fatty acid production.},
journal = {International immunopharmacology},
volume = {187},
number = {},
pages = {117209},
doi = {10.1016/j.intimp.2026.117209},
pmid = {42561662},
issn = {1878-1705},
abstract = {Kidney stones are a common urological disorder associated with significant pain and renal complications. Astragalus polysaccharides (APS) are a bioactive component of Traditional Chinese Medicine that has shown therapeutic potential in renal disorders, potentially through the modulation of the gut microbiota and its metabolites. Based on its properties, it was hypothesized that APS could prevent kidney stone formation by modulating gut microbiota and altering short-chain fatty acid (SCFA) production. In this study, an ethylene glycol-induced rat model was used to investigate APS's effects on kidney stone formation, renal injury, gut microbiome composition, and targeted SCFAs metabolomics. APS treatment significantly reduced calcium oxalate crystal deposition and urinary oxalate levels, alleviated renal tissue damage, and regulated key bacterial taxa involved in oxalate metabolism and SCFA production, particularly restoring serum butyric acid levels. Sodium butyrate supplements further enhanced the protective function of APS in kidney stones. Fecal microbiota transplantation (FMT) results revealed that antibiotic-depleted recipients of microbiota from healthy mice donors or APS-treated mice donors exhibited improved renal function compared with recipients of stone microbiota. These findings support that APS prevents kidney stone formation by modulating the gut-kidney axis through microbiota and metabolite changes, with FMT demonstrating the functional contribution of gut microbial communities to disease outcomes. Therefore, APS represents a promising natural therapeutic approach for kidney stone prevention and highlights the relevance of microbiota-based strategies in managing kidney stones.},
}

@article {pmid42561700,
year = {2026},
author = {Odoh, CK and Liu, Y and Arachchige, CSV and Naidu, R},
title = {Perfluorohexane sulfonate (PFHxS) restructures the rhizosphere microbiome of Lupinus polyphyllus.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143219},
doi = {10.1016/j.jhazmat.2026.143219},
pmid = {42561700},
issn = {1873-3336},
abstract = {Perfluorohexane sulfonate (PFHxS) is persistent and highly mobile that is increasingly detected in agricultural soils, raising concerns about its long-term ecological impacts on plant-soil systems. Despite its widespread, little is known about how PFHxS restructures rhizosphere microbial communities, modifies microbial ecological interactions, or affects soil biochemical functioning that underpins ecosystem resilience. Using Lupinus polyphyllus as a model legume, this study investigated the effects of PFHxS (5, 25, and 125 mg/kg) on plant performance, soil biochemical functions, and rhizosphere microbial communities, with the latter characterized using high-throughput sequencing and microbial network analyses. PFHxS exposure at 5 mg/kg stimulated plant growth, whereas higher PFHxS concentrations attenuated this growth-promoting effect. Bacterial communities remained comparatively resilient and continued to be dominated by Actinobacteria, Proteobacteria, and Firmicutes, whereas fungal communities exhibited pronounced sensitivity, with Chao1 richness and unique operational taxonomic units (OTU) declining by 50.6% and 69.2%, respectively. Despite the compositional resilience of bacterial communities, Bray-Curtis ordination, heatmap clustering, and microbial network analyses revealed concentration-dependent restructuring of rhizosphere microbial interactions under PFHxS exposure. Collectively, these findings identify fungal communities as the most sensitive component of the rhizosphere microbiome to PFHxS stress and provide new insight into PFHxS-driven rhizosphere responses with implications for ecological risk assessment.},
}

@article {pmid42561728,
year = {2026},
author = {Roncero-Ramos, B and Romero, M and Plaza-Álvarez, PA and Zema, DA and Lucas-Borja, ME and Muñoz-Rojas, M},
title = {Soil bacterial and fungal communities respond differently to post-fire restoration treatments.},
journal = {Journal of environmental management},
volume = {415},
number = {},
pages = {130623},
doi = {10.1016/j.jenvman.2026.130623},
pmid = {42561728},
issn = {1095-8630},
abstract = {Wildfires are increasing in frequency and severity in Mediterranean forests, intensifying the need for effective post-fire management strategies that support long-term ecosystem recovery. While the effects of wildfire and post-fire interventions on soil physicochemical properties are relatively well documented, their long-term impacts on soil microbial communities, key drivers of ecosystem functioning, remain poorly understood. In this study, we assessed long-term differences in soil bacterial and fungal communities associated with wildfire and post-fire management in a Mediterranean pine forest six years after a high-severity fire. We evaluated bacterial and fungal communities under salvage logging and straw mulching, applied individually and in combination, using high-throughput DNA metabarcoding of soil samples. Our results showed persistent differences between burnt soils and nearby unburnt reference soils six years after the fire, with contrasting responses between bacteria and fungi, i.e., bacterial communities under the combined mulching and salvage logging treatment were more similar to those in unburnt reference soils, whereas fungal communities remained structurally distinct across all burnt treatments. The combined mulching and salvage logging treatment was also associated with lower fungal alpha diversity than that observed in unburnt reference soils, while salvage logging alone showed no comparable patterns. These findings highlight contrasting long-term trajectories of soil microbial communities following wildfire and post-fire management and emphasize the need to consider belowground biodiversity when designing restoration strategies in fire-prone Mediterranean ecosystems.},
}

@article {pmid42561959,
year = {2026},
author = {Li, M and Li, S and Zheng, D and Liao, B and Niu, H and Wang, Y and Liu, X and Pan, H and Yu, Y and Zhou, P and Li, R},
title = {Lactobacillus gasseri postbiotics ameliorate age-related decline in endometrial receptivity.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.06.018},
pmid = {42561959},
issn = {1934-6069},
abstract = {Endometrial senescence contributes to a decline in fertility in women of advanced reproductive age, with emerging evidence linking it to remodeling of the uterine microbiome, particularly a reduced Lactobacillus abundance. Here, using a cross-sectional human cohort with clinical follow-up, we identify an age-related shift in the endometrial microbiome, characterized by the loss of beneficial Lactobacillus-enriched states and increased Lactobacillus iners. This shift is associated with impaired endometrial receptivity and less favorable embryo transfer outcomes. Functional screening of reproductive tract isolates highlights Lactobacillus gasseri as a candidate strain with strong antioxidant, anti-inflammatory, and adhesion-related activities. In cells and mouse models, L. gasseri and its exopolysaccharides (EPSs) attenuate endometrial senescence and improve implantation in aged mice. Mechanistically, these effects are mediated, at least partly, through the modulation of Hippo-YAP signaling. These findings suggest that restoring beneficial Lactobacillus and applying EPSs may represent complementary strategies to improve endometrial function and fertility outcomes in women of advanced reproductive age.},
}

@article {pmid42562139,
year = {2026},
author = {Domi, E and Hoxha, M and Zappacosta, B and Cakoni, R and Abbasciano, M and Tricarico, D},
title = {Early Mycotoxins Exposure: A Hidden Driver Of Cardiometabolic Risk.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {109260},
doi = {10.1016/j.toxicon.2026.109260},
pmid = {42562139},
issn = {1879-3150},
abstract = {Mycotoxins are fungal contaminants frequently detected in staple foods worldwide. While their toxic effects on growth and organ function are well recognized, their contribution to cardiometabolic disease programming during early life has received less attention. This review highlights the role of developmental exposure to major mycotoxins, including aflatoxins, ochratoxins, fumonisins, zearalenone, and deoxynivalenol, as a hidden driver of long-term cardiometabolic risk. Evidence indicates that exposure occurs during fetal life through placental transfer and after birth through breast milk, infant formula, and contaminated complementary foods. Because detoxification pathways and physiological systems are still developing, fetuses, infants, and young children are particularly vulnerable to mycotoxin-induced damage. Experimental and epidemiological studies show that early exposure can impair endocrine signaling, promote oxidative stress and chronic inflammation, alter lipid and glucose metabolism, induce gut microbiome dysbiosis, promote vascular injury, and trigger epigenetic changes. These interconnected mechanisms contribute to metabolic dysregulation and increase susceptibility to obesity, insulin resistance, hypertension, and cardiovascular disease later in life. Overall, current evidence supports the concept that mycotoxins represent an underrecognized environmental factor in the onset of cardiometabolic disease. Greater attention to exposure monitoring, risk assessment, and preventive interventions, especially during critical developmental periods may help reduce the long-term burden of metabolic disorders.},
}

@article {pmid42562459,
year = {2026},
author = {Mazumder, S and Bhattacharya, D and Lahiri, D and Nag, M and Maity, S and Saha, D and Kumar, N and Singh, V and Sharma, S and Dwivedi, SP and Rajeev, M and Raj, S and Rustagi, S and Nargiza, A and Mamarakhimov, O and Sanayeva, L},
title = {Food-derived dietary alkaloids: structure-biofunctionality relationships in modulating gut microbial biofilms for downregulation of colorectal carcinogenesis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119629},
doi = {10.1016/j.foodres.2026.119629},
pmid = {42562459},
issn = {1873-7145},
mesh = {*Biofilms/drug effects ; Humans ; *Colorectal Neoplasms/prevention & control/microbiology ; *Alkaloids/pharmacology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Structure-Activity Relationship ; *Carcinogenesis/drug effects ; *Diet ; Down-Regulation ; Animals ; },
abstract = {Colorectal cancer (CRC) is the second most common cancer across the globe, accounting for 10% cancer-related deaths annually. CRC has been recognized as a consequence of microbial (such as F. nucleatum, E. coli (pks[+] strains) biofilms, inflammatory signaling, and redox imbalance in the human gut. Hence, natural bioactive substances as a part of the daily diet are crucial for the downregulation of biofilm-mediated CRC. Dietary alkaloids, nitrogen-containing secondary metabolites, have been identified as potential chemotherapeutic agents that can inhibit biofilm formation through quorum-sensing inhibition, modulating the tumor microenvironment, including redox and inflammatory pathway regulation. The present review primarily focuses on the alkaloids' structure-function relationships, microbial biotransformation, and inhibition of pathogenic biofilms, through downregulation of NF-κB, IL-6, STAT3-mediated inflammatory cascades, apoptosis, induction of autophagy, and balancing the redox-oxidative homeostasis. Further, the synergistic effect of alkaloids with dietary fiber, short-chain fatty acid (SCFA)-mediated synergy, and polyphenol compounds is essential for microbial-epithelial barrier activity and metabolic homeostasis regulation. However, the integration of dose windows, dietary patterns, and regulatory landscapes is essential to establish dietary alkaloids as a functional food in biofilm-mediated CRC prevention. Moreover, bioavailability of dietary alkaloids is a potential challenge, and nano-enabled delivery, specifically lipid and polymeric nano carriers, is considered for the controlled delivery, mucosal bioactivity, and reduced systemic exposure of alkaloid carriers for colon mucosa bioactivity. Overall, the integration of microbiome with dietary alkaloids as bioactive food components, to modulate biofilm and tumor micro-niches, underlines the translational potential of dietary alkaloids for CRC prevention.},
}

*Biofilms/drug effects
Humans
*Colorectal Neoplasms/prevention & control/microbiology
*Alkaloids/pharmacology/chemistry
*Gastrointestinal Microbiome/drug effects
Structure-Activity Relationship
*Carcinogenesis/drug effects
*Diet
Down-Regulation
Animals

@article {pmid42562478,
year = {2026},
author = {Zhang, HY and Huang, TC and Chai, LJ and Shi, W and He, YX and Lu, ZM and Zhang, XJ and Wang, ST and Shen, CH and Shi, JS and Xu, ZH},
title = {Integrating ecological networks and metagenomics to decipher core microbial drivers of organic acid metabolism during heaped fermentation of sauce-flavor Baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119702},
doi = {10.1016/j.foodres.2026.119702},
pmid = {42562478},
issn = {1873-7145},
mesh = {*Fermentation ; *Metagenomics/methods ; *Food Microbiology ; *Bacteria/metabolism/genetics/classification ; Volatile Organic Compounds/metabolism/analysis ; Acetic Acid/metabolism/analysis ; Caproates/analysis ; Taste ; Lactic Acid/metabolism/analysis ; *Fermented Foods/microbiology ; *Microbiota ; Pentanoic Acids ; Hemiterpenes ; },
abstract = {Organic acids play crucial roles in both flavor quality and microbial succession of sauce-flavor Baijiu; however, the core microbial drivers responsible for their metabolism remain poorly understood. This study systematically investigated the microbial drivers of organic acid metabolism across six sequential rounds (R1-R6) of heaped fermentation. A total of 24 organic acids were identified, including nine non-volatile organic acids (NVOAs) and 15 volatile organic acids (VOAs). HPLC analysis revealed that the total content of acetic acid and nine NVOAs increased significantly across rounds, rising from 29.35 g/kg in R1 to 66.40 g/kg in R6. Lactic acid was the most abundant NVOA, while acetic acid, isovaleric acid, and hexanoic acid were the primary volatile contributors. Co-occurrence network analysis identified 488 consistently correlated bacterial pairs that clustered into two distinct guilds. Guild 2, mainly comprising Virgibacillus, Kroppenstedtia, Oceanobacillus, and Bacillus, exhibited high abundance (47%-78%) across all rounds and was defined as the core bacterial guild. Spearman correlation analysis revealed that guild 2 was positively correlated with NVOAs (69.41%) but negatively correlated with VOAs (63.02%). Metagenomic analysis reconstructed seven key pathways involved in organic acid biosynthesis. Kroppenstedtia, Lentibacillus, Desmospora, and Oceanobacillus were identified the taxa harboring the genetic potential most frequently detected across multiple pathways, with Kroppenstedtia and Lentibacillus exhibiting the highest gene abundances. These findings provide a theoretical foundation for targeted regulation of organic acid content in sauce-flavor Baijiu production.},
}

*Fermentation
*Metagenomics/methods
*Food Microbiology
*Bacteria/metabolism/genetics/classification
Volatile Organic Compounds/metabolism/analysis
Acetic Acid/metabolism/analysis
Caproates/analysis
Taste
Lactic Acid/metabolism/analysis
*Fermented Foods/microbiology
*Microbiota
Pentanoic Acids
Hemiterpenes

@article {pmid42182435,
year = {2026},
author = {Wallace, M and Allen, ML and Karasov, TL and Puri, AW},
title = {A Bacterial Natural Product Reshapes Phyllosphere Microbiome Composition by Blocking Carotenoid Biosynthesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.14.725204},
pmid = {42182435},
issn = {2692-8205},
support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; },
abstract = {The microbial communities that inhabit the phyllosphere, the above-ground portion of plants, are important for plant growth and resilience. However, the natural products that mediate interactions among these organisms and with their environment remain understudied, limiting our molecular-level understanding of how phyllosphere microbial communities are structured and maintained. Natural product-mediated microbial competition is typically associated with growth inhibition, but may also occur through other mechanisms in these communities. Many bacteria produce pigments to mitigate oxidative stress, and here we identify listianol, a previously undescribed natural product that inhibits the pigmentation of diverse bacteria. Listianol blocks carotenoid biosynthesis by targeting the desaturases CrtN and CrtI. This activity sensitizes normally pigmented bacteria to UVB radiation in vitro , and a listianol-producing strain reshapes the composition of a model bacterial community on Arabidopsis thaliana under UVB exposure. Together, these findings identify pigmentation inhibition as a potential form of competition in the phyllosphere.},
}

@article {pmid42551625,
year = {2026},
author = {Poboży, T and Poboży, K and Domańska-Poboża, J and Kotela, A and Konarski, W},
title = {Gut microbiome and avascular necrosis: A scoping review of current evidence and knowledge gaps.},
journal = {Bone},
volume = {},
number = {},
pages = {118041},
doi = {10.1016/j.bone.2026.118041},
pmid = {42551625},
issn = {1873-2763},
abstract = {Avascular necrosis (AVN) is a progressive bone disorder characterized by impaired blood supply, osteocyte death, and structural collapse, most commonly affecting the femoral head. In recent years, growing evidence has suggested that gut microbiota may influence skeletal health through immune, metabolic, and vascular pathways. This scoping review aimed to systematically map current evidence on the relationship between gut microbiota and AVN and to identify key knowledge gaps. Following Joanna Briggs Institute methodology and PRISMA-ScR guidelines, a comprehensive search of PubMed, EMBASE, ScienceDirect, Web of Science Core Collection, ClinicalTrials.gov, and Cochrane CENTRAL was conducted. Thirteen eligible studies, including experimental, clinical, multi-omics, and Mendelian randomization analyses, were included. The available evidence indicates that AVN, particularly glucocorticoid- and alcohol-associated forms, is consistently associated with intestinal dysbiosis, reduced production of short-chain fatty acids, immune activation, vascular impairment, and altered bone remodeling. Animal and translational studies demonstrate partial reversal of pathological changes through microbiota-targeted interventions, while human studies reveal etiology-specific microbiota-metabolome signatures. Genetic analyses further support a potential causal contribution of selected microbial taxa and pathways. Overall, current data support the existence of a multidimensional gut-bone axis in AVN. However, most evidence remains indirect - derived from animal models, cross-sectional human studies, and genetic inference rather than from direct interventional testing in patients. Well-designed longitudinal and interventional investigations are needed to clarify causality and therapeutic potential.},
}

@article {pmid42551693,
year = {2026},
author = {Pedersen, AL and Dayon, L and Affolter, M and Seifert, J},
title = {A streamlined workflow for high throughput metaproteomic analysis of the rumen microbiome.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105721},
doi = {10.1016/j.jprot.2026.105721},
pmid = {42551693},
issn = {1876-7737},
abstract = {Metaproteomics can provide direct functional insights into complex microbial communities, yet its application in rumen research remains limited due to labor-intensive and low-throughput sample preparation workflows before the MS analysis. This work aimed to develop and characterize a streamlined, high throughput metaproteomic workflow optimized for rumen samples. Key steps, including microbial cell extraction, cell lysis, protein digestion, and LC-MS/MS acquisition, were systematically assessed and optimized to reduce hands-on time while maintaining deep proteome coverage. The optimized workflow integrates a minimized cell extraction protocol using 0.5 g starting material and in-solution tryptic digestion. Application of the final workflow to 72 samples from in vitro fermentation revealed that biological variability between inocula dominated technical variability, which remained moderate (median CV of 21-24% across batches). Overall, the optimized workflow supports robust taxonomic and functional characterization of the rumen microbiome with improved scalability. These advances provide a foundation for applying metaproteomics to larger experimental designs, including nutritional trials and cohort studies, thereby enabling broader functional interrogation of rumen microbial ecosystems. SIGNIFICANCE: This study addresses current limitations in the application of metaproteomics to rumen microbiome research by developing a streamlined and scalable sample preparation workflow. By optimizing key steps and reducing sample input while maintaining reproducibility and proteome coverage, this work enables more efficient processing of larger sample sets. These advances support the broader use of metaproteomics in rumen studies and facilitate functional investigations relevant to animal nutrition and sustainable livestock production.},
}

@article {pmid42551765,
year = {2026},
author = {Battelli, MG and Bortolotti, M and Bolognesi, A and Polito, L},
title = {XANTHINE OXIDOREDUCTASE IN DIGESTIVE DISEASES: A CONTEXT-DEPENDENT REDOX SWITCH LINKING INFLAMMATION, METABOLISM AND CARCINOGENESIS.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2026.08.007},
pmid = {42551765},
issn = {1873-4596},
abstract = {Xanthine oxidoreductase (XOR) is a molybdenum-containing enzyme that catalyzes the final steps of purine catabolism, generating uric acid and, under specific conditions, reactive oxygen species (ROS) and reactive nitrogen species. Due to its high expression in the liver and gastrointestinal tract, XOR has emerged as an important regulator of redox homeostasis, innate immunity and metabolic adaptation in digestive diseases. This review examines the role of XOR in hepatic disorders, intestinal ischemia-reperfusion (I/R) injury and inflammatory bowel disease (IBD), focusing on oxidative stress, tissue injury, host-microbiome interactions and carcinogenesis. Evidence indicates increased XOR activity in inflammatory and fibrotic liver diseases, where ROS generation contributes to hepatocellular damage, fibrosis and disease progression. In intestinal I/R injury, XOR links ATP depletion and hypoxanthine accumulation to reperfusion-associated oxidative stress, barrier dysfunction, bacterial translocation and systemic inflammation. In IBD, XOR participates in cytokine amplification, redox imbalance, thiopurine metabolism and inflammation-associated colorectal carcinogenesis. Emerging evidence also supports bidirectional interactions between XOR/urate metabolism and the gut microbiota, suggesting a broader role for XOR in regulating intestinal immune homeostasis. However, the biological significance of XOR is strongly context dependent. Whereas increased XOR activity promotes inflammatory tissue injury, advanced gastrointestinal malignancies are frequently characterized by reduced XOR expression, loss of cellular differentiation and enhanced de novo purine synthesis. Overall, XOR emerges as a central, but highly plastic, regulator at the interface between metabolism, inflammation and host-microbiome interactions in digestive diseases. Its clinical exploitation will depend on the ability to understand, rather than oversimplifying, this complexity.},
}

@article {pmid42551774,
year = {2026},
author = {Cheng, Y and Yu, S and Huang, Y and Liu, B},
title = {Engineered microorganisms and nanomaterials in cancer therapy: Emerging hybrid systems and translational challenges.},
journal = {Nanomedicine : nanotechnology, biology, and medicine},
volume = {},
number = {},
pages = {103002},
doi = {10.1016/j.nano.2026.103002},
pmid = {42551774},
issn = {1549-9642},
abstract = {The convergence of synthetic biology and nanotechnology has created new opportunities for cancer diagnosis and therapy. Engineered microorganisms exhibit unique tumor-targeting, colonization, and immunomodulatory capabilities, while nanomaterials provide versatile platforms for drug delivery, imaging, and controlled therapeutic release. This review summarizes recent advances in the application of engineered microorganisms and nanomaterials in oncology, with a focus on their mechanisms of action, therapeutic potential, and translational challenges. We discuss the roles of the tumor microbiome in cancer progression, microbial engineering strategies for tumor targeting and immune regulation, and the development of nanomaterial-based delivery systems and immunotherapies. Particular attention is given to microbe-nanomaterial hybrid platforms, which combine the advantages of both systems to enhance therapeutic efficacy and modulate the tumor microenvironment. Finally, key challenges related to biosafety, biocompatibility, regulatory approval, and clinical translation are highlighted. The integration of engineered microorganisms and nanomaterials represents a promising strategy for next-generation precision oncology and may accelerate the development of more effective and personalized cancer therapies.},
}

@article {pmid42552038,
year = {2026},
author = {Peter L, IR and Chatterjee, D and Chrishone, AF and Francis, D},
title = {Metabolic therapeutic targets in Alzheimer's disease.},
journal = {International review of neurobiology},
volume = {188},
number = {},
pages = {1-32},
doi = {10.1016/bs.irn.2026.05.010},
pmid = {42552038},
issn = {2162-5514},
mesh = {Humans ; *Alzheimer Disease/metabolism/drug therapy ; Animals ; *Energy Metabolism/physiology/drug effects ; *Brain/metabolism ; *Mitochondria/metabolism ; Glucose/metabolism ; },
abstract = {Alzheimer's disease (AD) is increasingly recognized as a disorder marked not only by amyloid-β and tau pathology, but also by profound disturbances in brain energy metabolism that arise early in disease progression. Accumulating evidence indicates that impairments in glucose utilization, insulin signaling, and mitochondrial function precede neurodegeneration and contribute directly to synaptic failure and cognitive decline. This chapter presents a comprehensive overview of Alzheimer's disease through the lens of metabolic dysfunction, highlighting disrupted neuronal bioenergetics as a central and unifying feature of pathogenesis. We examine key metabolic pathways implicated in AD, including cerebral glucose hypometabolism, brain insulin resistance, impaired glycolysis, mitochondrial oxidative phosphorylation deficits, oxidative stress, and altered mitochondrial dynamics. The chapter further discusses therapeutic strategies aimed at restoring metabolic homeostasis, such as insulin sensitization, enhancement of glucose transport, activation of mitochondrial biogenesis, modulation of the electron transport chain, and the use of mitochondria-targeted antioxidants. In parallel, alternative energy approaches-including ketone metabolism, fatty acid oxidation, and pentose phosphate pathway activation-are explored as promising avenues to bypass glucose-dependent energy deficits and reinforce neuronal resilience. Emerging directions in metabolic therapeutics are also highlighted, including combination treatment strategies, NAD[+]-sirtuin and AMPK signaling, and the expanding role of the gut microbiome-brain metabolism axis. By integrating insights from experimental models, neuroimaging studies, and clinical trials, this chapter underscores the potential of metabolic interventions to enable early, disease-modifying strategies for Alzheimer's disease.},
}

Humans
*Alzheimer Disease/metabolism/drug therapy
Animals
*Energy Metabolism/physiology/drug effects
*Brain/metabolism
*Mitochondria/metabolism
Glucose/metabolism

@article {pmid42552151,
year = {2026},
author = {Bai, QX and Luo, KM and Jia, LH and Jia, J and Kantawong, F and Tan, RZ and Wang, L},
title = {The Therapeutic Application of Epigenetic Regulation by Natural Herbal Compounds in Kidney Diseases.},
journal = {Seminars in nephrology},
volume = {},
number = {},
pages = {151711},
doi = {10.1016/j.semnephrol.2026.151711},
pmid = {42552151},
issn = {1558-4488},
abstract = {Kidney diseases, represented by chronic kidney disease (CKD) and acute kidney injury (AKI), pose significant global public health challenges due to their complex pathogenesis and limited therapeutic options. In recent years, epigenetic regulation-including DNA methylation, histone modifications, and non-coding RNAs-has been shown to play a crucial role in the progression of kidney diseases, offering new directions for therapeutic strategies. Natural herbal compounds have emerged as a research focus for modulating epigenetic mechanisms owing to their multi-target effects, low toxicity, and broad bioactivity. This review outlines the regulatory functions of epigenetic mechanisms across various kidney diseases and illustrates how natural herbal compounds can mitigate renal injury via multi-target epigenetic modulation. These compounds have been shown to reverse renal fibrosis, attenuate inflammatory responses, suppress oxidative stress, and protect podocytes and renal tubular epithelial cells by targeting DNA methyltransferases, histone-modifying enzymes, and non-coding RNAs, including microRNAs and long non-coding RNAs. However, challenges such as limited bioavailability and insufficiently elucidated in vivo mechanisms impede clinical translation. Future research should prioritize structural optimization, advanced delivery systems, and investigations into gut microbiome interactions to enhance therapeutic applicability. Overall, this review highlights the promise of epigenetics-based therapeutic strategies using herbal active ingredients for kidney disease intervention, though further validation and optimization are needed for clinical application.},
}

@article {pmid42552215,
year = {2026},
author = {Kamba, S and Kuroki, M and Takemura, I and Tabata, H and Minei, R and Shimamoto, M and Ogura, A and Hasegawa, M and Ishikawa, M},
title = {Enrichment of Lysobacter in a long-term organically managed agricultural field with low soilborne disease incidence.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2026.07.002},
pmid = {42552215},
issn = {1347-4421},
abstract = {Disease-suppressive soils, in which soilborne pathogens are naturally suppressed, offer a promising model for sustainable crop protection, particularly in organic farming systems where chemical disease control options are limited. Although disease suppression in these soils is considered to rely on biological control, the underlying mechanisms remain poorly understood. In this study, we investigated soil from a long-term organically managed field in Shiga Prefecture, Japan, where soilborne disease incidence has remained consistently low, to identify bacterial community features potentially associated with this field. The 16S rRNA gene amplicon sequencing indicated that this soil harbored a bacterial community distinct from those of nearby agricultural soils. Following the application of organic compounds, the genus Lysobacter, a taxon with known antagonistic activity against plant pathogens, was markedly enriched in response to proteinaceous organic inputs. This enrichment was consistent across sampling times and specific to certain proteinaceous organic inputs, whereas minimal effects were observed on chitin, N-acetyl-d-glucosamine, or cysteine. Broader soil surveys indicated that Lysobacter enrichment was not strictly associated with whether soils had been managed under organic or conventional farming practices. Stepwise multiple regression analysis identified 10 co-occurring bacterial genera that were strongly associated with Lysobacter abundance. These findings highlight condition-dependent Lysobacter enrichment as a characteristic microbial response to proteinaceous organic amendments in this low-disease-incidence field and provide microbial insights that may inform microbiome-based strategies for sustainable soil management.},
}

@article {pmid42552305,
year = {2026},
author = {Lu, Y and Shao, D and Xiao, Y and Jiang, YZ and Shao, ZM},
title = {Migration of immune cells in tumors and inflammation: molecular mechanisms and therapeutic targets.},
journal = {Signal transduction and targeted therapy},
volume = {11},
number = {1},
pages = {},
pmid = {42552305},
issn = {2059-3635},
support = {82341003//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Neoplasms/immunology/pathology/therapy/genetics ; *Inflammation/immunology/pathology/therapy/genetics ; *Tumor Microenvironment/immunology/genetics ; *Cell Movement/immunology/genetics ; Animals ; Chemokines/immunology ; },
abstract = {Cancer and inflammatory diseases are critically influenced by dynamic interactions between pathological tissues and the host immune system. The precise migration of immune cells into the local microenvironments of tumors or inflammation is a fundamental prerequisite for them to exert their functions. Immune reservoirs, including tertiary lymphoid structures, secondary lymphoid structures, bone marrow and the intestinal tract, serve as critical mobilization hubs for diverse lymphoid and myeloid populations to infiltrate tumors or inflamed sites. The directional migration of immune cells is orchestrated through complex regulatory networks involving chemokine or cytokine-receptor pairs, adhesion molecule interactions, extracellular vesicle signaling, metabolic reprogramming and microbiota modulation. In both tumors and inflammation, immune cell trafficking shapes the local immune landscape, contributing to either immune protection or pathological progression. Contemporary therapeutic strategies targeting immune cell migration encompass the following axes: precision modulation of chemokine or cytokine networks, architectural reprogramming of lymphatic structures or extracellular matrix, dietary intervention and strategic manipulation of microbiome. Nevertheless, clinical translation remains hindered by microenvironmental heterogeneity, suboptimal migratory efficiency, and technical limitations in longitudinal tracking of cellular dynamics. This review integrates recent findings from oncology and inflammatory diseases to explore the origins, phenotypes and trafficking mechanisms of migratory immune cells, highlighting how advances in understanding immune migration across cancer and inflammation can inform therapeutic innovation and precision immunomodulation.},
}

Humans
*Neoplasms/immunology/pathology/therapy/genetics
*Inflammation/immunology/pathology/therapy/genetics
*Tumor Microenvironment/immunology/genetics
*Cell Movement/immunology/genetics
Animals
Chemokines/immunology

@article {pmid42552537,
year = {2026},
author = {Shi, W and Li, N and Cheng, S and Zhao, Y and Zhang, Y and Ding, H and Li, Y and Bi, R and Lu, X and Li, Z and Wang, Y},
title = {Chemotherapy-driven gut microbiota remodeling in ovarian cancer: a prospective longitudinal study.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42552537},
issn = {1479-5876},
mesh = {Humans ; Female ; *Ovarian Neoplasms/drug therapy/microbiology ; Longitudinal Studies ; Prospective Studies ; *Gastrointestinal Microbiome/drug effects ; Neoplasm Recurrence, Local/microbiology/pathology ; *Antineoplastic Agents/therapeutic use/pharmacology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The gut microbiome shapes chemotherapy efficacy and outcomes in several cancers, but evidence in ovarian cancer (OC) remains limited and largely cross-sectional. Despite high initial response rates, long-term relapse in OC remains frequent, while conventional markers capture only short-term therapeutic sensitivity. Whether longitudinal gut-microbiome trajectories during chemotherapy are associated with long-term recurrence remains unknown.

METHODS: Within the prospective SOCFCP cohort (N = 91; 13 recurrences), 100 serial fecal samples from a 33-patient sub-cohort were analyzed by 16S rRNA sequencing across the early, middle and late chemotherapy phases. Microbial successional trajectories and their association with recurrence were assessed by linear mixed-effects modeling, multivariable MaAsLin3 and repeated-measures correlation (rmcorr) networks, alongside stratified and covariate-adjusted sensitivity analyses and patient-level bootstrap assessment. The cumulative severe-toxicity-recurrence relationship was estimated by Firth penalized-likelihood regression, suited to sparse, separation-prone events.

RESULTS: Microbial α-diversity rose progressively across the chemotherapy course (Shannon time effect p = 0.002), consistent with ecological succession, with higher turnover among peripheral than in core taxa (p = 0.005). Cumulative severe toxicity was not associated with recurrence (Firth OR = 0.99, 95% CI 0.68-1.39). Crucially, recurrent patients exhibited a progressive depletion of Fusicatenibacter (recurrence × time coefficient = -5.35, q < 0.001) that persisted across all sensitivity analyses-stratified, medication-adjusted, antibiotic-depleted and clinically-adjusted models (coefficient -4.60 to -5.66, all q < 0.001). PICRUSt2-based functional inference identified recurrence-associated differences in predicted de novo nucleotide-biosynthesis and cell-wall-assembly pathway abundance (q < 0.05). A bootstrap-supported co-variation network further linked specific taxa, notably Escherichia-Shigella and Roseburia, to these recurrence-associated pathways.

CONCLUSION: Chemotherapy-driven gut-microbiome remodeling, in particular the recurrence-associated depletion of Fusicatenibacter, was associated with long-term OC relapse, whereas cumulative severe toxicity showed no significant association with recurrence. These longitudinal microbial dynamics support a candidate non-invasive marker that warrants external validation, and provide a hypothesis-generating rationale for testing whether targeting specific predicted bacterial functional pathways can modulate the host anti-tumor milieu.},
}

Humans
Female
*Ovarian Neoplasms/drug therapy/microbiology
Longitudinal Studies
Prospective Studies
*Gastrointestinal Microbiome/drug effects
Neoplasm Recurrence, Local/microbiology/pathology
*Antineoplastic Agents/therapeutic use/pharmacology
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid42553012,
year = {2026},
author = {AlRamadneh, TN and S, RJ and Nayak, PP and Nanda, A and Hasnaawei, SA and Bhatt, A and Chauhan, AS and Singla, S and Nourizadeh, M},
title = {Microbiota-Neuroinflammation Crosstalk in Primary Brain Tumors: Focus on Glioblastoma.},
journal = {Brain and behavior},
volume = {16},
number = {8},
pages = {e71648},
doi = {10.1002/brb3.71648},
pmid = {42553012},
issn = {2162-3279},
mesh = {Humans ; *Glioblastoma/microbiology/immunology/metabolism ; *Brain Neoplasms/microbiology/immunology/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology/immunology ; *Neuroinflammatory Diseases/immunology/metabolism/microbiology ; Tumor Microenvironment/immunology ; Blood-Brain Barrier/metabolism ; Inflammation ; },
abstract = {PURPOSE: Glioblastoma (GBM) is the most aggressive primary brain tumor in adults and remains difficult to treat because of diffuse invasion, immunosuppression, metabolic adaptability, and therapy resistance. This review evaluates how gut microbiota and microbiota-associated neuroinflammatory signaling may contribute to GBM biology and therapeutic response.

METHOD: We synthesized mechanistic, preclinical, translational, and emerging clinical evidence on microbiota-neuroinflammation interactions in GBM. The review focused on gut-brain axis pathways, microbial metabolites, blood-brain barrier (BBB) regulation, glial and myeloid immune activity, tumor-associated microbial signatures, microbial peptide-HLA presentation, and microbiome-informed biomarker or therapeutic strategies.

FINDING: Current evidence suggests that microbiota-related signals may influence GBM through systemic immune modulation, short-chain fatty acids, tryptophan-derived metabolites, polyamines, BBB effects, and altered microglial and tumor-associated myeloid cell function. Polyamine metabolism may sustain myeloid-cell-mediated immunosuppression in the acidic GBM tumor microenvironment, whereas microglial GLUT5-dependent fructose metabolism may limit inflammatory antigen presentation and adaptive antitumor immunity. Sequencing-based studies have reported bacterial and fungal nucleic acid signatures in brain tumor specimens, but these findings require careful interpretation because of low biomass, contamination risk, and methodological variability. Preclinical models further indicate that microbiome modulation can alter inflammatory tone, tumor growth, immune-cell infiltration, and response to immune checkpoint blockade.

CONCLUSION: Microbiota-regulated neuroinflammation is a biologically plausible contributor to GBM progression, immune suppression, and treatment resistance. However, most evidence remains preclinical or early translational. Well-controlled, spatially resolved, multi-omic studies are required before microbiome-based biomarkers or interventions can be clinically implemented for patient stratification and future precision clinical neuro-oncology applications.},
}

Humans
*Glioblastoma/microbiology/immunology/metabolism
*Brain Neoplasms/microbiology/immunology/metabolism
Animals
*Gastrointestinal Microbiome/physiology/immunology
*Neuroinflammatory Diseases/immunology/metabolism/microbiology
Tumor Microenvironment/immunology
Blood-Brain Barrier/metabolism
Inflammation

@article {pmid42553056,
year = {2026},
author = {Elias, AE and El-Chami, C and Bagnall, J and McBain, AJ and O'Neill, CA},
title = {Lacticaseibacillus rhamnosus GG lysate inhibits Staphylococcus aureus biofilm formation in human skin explants.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1885754},
pmid = {42553056},
issn = {2235-2988},
mesh = {Humans ; *Biofilms/drug effects/growth & development ; *Staphylococcus aureus/drug effects/physiology/growth & development ; *Skin/microbiology ; *Lacticaseibacillus rhamnosus ; Skin Microbiome ; Bacterial Lysates ; Keratinocytes/microbiology ; Organ Culture Techniques ; *Probiotics/pharmacology ; },
abstract = {Staphylococcus aureus is a leading cause of skin and soft tissue infections and a major nosocomial pathogen, with biofilm formation contributing to significantly higher morbidity and mortality. In atopic dermatitis (AD), where skin barrier dysfunction and microbial dysbiosis are common features, S. aureus abundance and biofilm formation are associated with disease severity and flare recurrence. We previously demonstrated that a lysate of Lacticaseibacillus rhamnosus GG (LGG)- a common human commensal and widely used probiotic strain- can inhibit S. aureus attachment to human keratinocytes by mechanisms including displacement and competitive exclusion. In this study, we extended these findings utilizing organ-cultured human skin to evaluate the protective effects of LGG lysate against S. aureus challenge in a physiologically relevant model. LGG lysate preserved skin integrity by preventing S. aureus penetration, proliferation, eDNA release and biofilm maturation. These effects were dose-dependent and effective when the lysate was applied from 24 hours pre-S. aureus inoculation to up to 3 hours post inoculation. Together, these data provide mechanistic insight into microbiome- pathogen interactions at the skin surface which could be exploited for therapeutic potential, particularly in the prevention of nosocomial S. aureus skin infections and mitigating S. aureus-driven flares in AD.},
}

Humans
*Biofilms/drug effects/growth & development
*Staphylococcus aureus/drug effects/physiology/growth & development
*Skin/microbiology
*Lacticaseibacillus rhamnosus
Skin Microbiome
Bacterial Lysates
Keratinocytes/microbiology
Organ Culture Techniques
*Probiotics/pharmacology

@article {pmid42553057,
year = {2026},
author = {Huang, P and Cai, Z},
title = {Identifying epigenetic and microbial biomarkers for preterm birth using DNA methylation and gut microbiome data.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1743283},
pmid = {42553057},
issn = {2235-2988},
mesh = {Humans ; Female ; *DNA Methylation ; *Premature Birth/diagnosis/genetics/microbiology ; Pregnancy ; *Biomarkers/blood ; Case-Control Studies ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Preterm birth (PTB), defined as delivery before 37 weeks, is a major cause of neonatal morbidity and mortality worldwide. Evidence suggests that both epigenetic dysregulation and gut microbial imbalance contribute to the inflammatory and metabolic disturbances associated with PTB; however, few studies have examined these factors in conjunction to identify integrated predictive biomarkers.

OBJECTIVES: This study aimed to identify epigenetic and microbial signatures associated with PTB by integrating maternal second-trimester genome-wide DNA methylation profiles with gut microbiome composition.

METHODS: A case-control study was conducted with 120 pregnant women, grouped into two categories: preterm (≤37 weeks, n = 60) and full-term (>37 weeks, n = 60). Maternal blood and fecal samples were collected simultaneously. DNA methylation was profiled using the Illumina MethylationEPIC array, and gut microbiota were characterized through 16S rRNA sequencing. Differentially methylated regions (DMRs) and differentially abundant taxa were identified using FDR < 0.05. Sparse canonical correlation analysis and network modeling were applied to integrate the datasets and identify linked epigenetic-microbial features predictive of PTB.

RESULTS: Women with PTB showed distinct methylation changes in immune and inflammation-related genes, including IL6, CXCL10, TNFAIP3, and PPARGC1A. Gut microbiome analysis revealed significantly reduced α-diversity (Shannon index: 2.81 ± 0.31 vs. 3.42 ± 0.36, p = 0.002), enrichment of pro-inflammatory taxa (Prevotella, Sutterella, Veillonella), and depletion of beneficial genera, including Lachnospiraceae, Faecalibacterium, and Bifidobacterium. Integrated analysis showed strong cross-domain associations (r = 0.68, p < 0.001), linking immune-gene hypomethylation with enrichment of inflammatory taxa. The combined biomarker panel achieved high predictive performance (AUC = 0.87; sensitivity = 82%; specificity = 84%), outperforming methylation-only and microbiome-only models. Functional enrichment highlighted convergence on NF-κB signaling, cytokine interactions, and butyrate metabolism.

CONCLUSIONS: The study shows that coordinated epigenetic alterations and gut microbial dysbiosis contribute to PTB. These biomarkers are detectable during the second trimester (18-24 weeks), supporting their potential for mid-pregnancy risk stratification. The integrated methylation-microbiome signature offers strong potential for early, non-invasive prediction and supports development of targeted maternal interventions.},
}

Humans
Female
*DNA Methylation
*Premature Birth/diagnosis/genetics/microbiology
Pregnancy
*Biomarkers/blood
Case-Control Studies
*Epigenesis, Genetic
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Adult
Feces/microbiology

@article {pmid42553064,
year = {2026},
author = {Skupa, SA and Hernandez, JB and Smith, AL and Drengler, EM and Rai, J and Pan, J and Seth, AK and Rai, SN and Clayton, JB and D'Angelo, CR and El-Gamal, D},
title = {Impact of high-fat Western diet on chronic lymphocytic leukemia disease progression and gut microbiome profile in Eµ-TCL1 mice.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1842275},
pmid = {42553064},
issn = {2234-943X},
abstract = {BACKGROUND: The composition and function of the gut microbiome have been shown to contribute to both health and disease. One of the most powerful modulators of microbial composition and function is diet.

MATERIALS AND METHODS: Using the Eµ-TCL1 murine model of B-cell chronic lymphocytic leukemia (CLL), we assigned male and female mice to a high-fat, high-carbohydrate Western diet (HF) or standard chow (CH) diet.

RESULTS: Mice consuming a HF diet had significantly shorter survival than those consuming a CH diet, irrespective of sex. We also observed a significant increase in splenic involvement by CLL in the HF diet-fed mice at time of sacrifice. Mice receiving the HF diet demonstrated immediate and profound effects on the gut microbiome, marked by reduced alpha diversity and significantly different community composition as measured by beta diversity. A larger change in alpha diversity between the pre-CLL engraftment (F1) and 4-weeks post-engraftment (F3) assessment significantly correlated with higher disease burden at week 4 (p = 0.009, r = 0.406) and worse survival (p = 0.001, r = -0.492). Notably, there was a sustained increase in Akkermansia muciniphila and Bacteroidetes thetaiotaomicron in HF diet-fed mice, coupled with a corresponding increase in microbiome functional pathways related to arginine and histidine biosynthesis, chitin degradation, and nucleotide biosynthesis.

DISCUSSION: Collectively our data provides evidence of the profound and sustained impact of a high-fat Western diet on the gut microbiome community and CLL pathogenesis in the Eµ-TCL1 murine model of CLL.},
}

@article {pmid42553088,
year = {2026},
author = {Huang, Y and Zhao, Y and Xin, X and Lin, S},
title = {Molecular insights into lower respiratory tract microbiota reveal disease-specific biomarkers and shared microbial networks in asthma and COPD.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1840378},
pmid = {42553088},
issn = {2235-2988},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Asthma/microbiology ; *Biomarkers/analysis ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; *Respiratory Tract Infections/microbiology ; Female ; Male ; Middle Aged ; Aged ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Adult ; },
abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) exacerbate chronic airway diseases, yet phenotype-specific microbial signatures are poorly defined. We applied broncho-alveolar lavage fluid (BALF) genomic sequencing to identify biomarkers for asthma and chronic obstructive pulmonary disease (COPD).

METHODS: Between December 2023 and February 2025, 1-146 adults with suspected LRTI enrolled from the First Hospital of Jilin University underwent BALF next-generation sequencing. Patients were stratified by lung function, with the impaired pulmonary function group further divided into asthma, COPD-mild-moderate, and COPD-severe subgroups. Disease-specific key biomarkers were identified using machine learning algorithms and analyzed for co-occurrence.

RESULTS: Impaired pulmonary function was not only associated with pathogenic microorganisms and its higher microbial burden, but also associated with a distinct community structure. Random forest models revealed disease-specific biomarkers, with Prevotella intermedia, Finegoldia magna, and Human parvovirus enriched in asthma, Veillonella parvula, Human respiratory syncytial virus, and Haemophilus influenzae enriched in COPD-mild-moderate, and Human respiratory syncytial virus, Human coronavirus, and Human parainfluenza virus enriched in COPD-severe. Co-occurrence network identified hubs linking asthma-centric (Haemophilus parainfluenzae and Schaalia odontolytica) and COPD-centric (Klebsiella pneumoniae, Veillonella parvula, and Streptococcus constellatus) clusters, suggesting potential cross-phenotype microbial crosstalk.

CONCLUSIONS: Genomic sequencing profiling delineates distinct yet overlapping airway microbiota across separate pulmonary dysfunctional diseases - asthma and COPD. Compact biomarker panels classify each condition accurately and reveal shared microbial hubs that may drive chronic inflammation and exacerbations, supporting microbiome-guided precision diagnostics and therapy.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology
*Asthma/microbiology
*Biomarkers/analysis
*Microbiota/genetics
Bronchoalveolar Lavage Fluid/microbiology
*Respiratory Tract Infections/microbiology
Female
Male
Middle Aged
Aged
Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Adult

@article {pmid42553090,
year = {2026},
author = {Yunusbaeva, M and Sabirova, D and Borodina, L and Khasanova, K and Yunusbayeva, A and Altinbaev, R and Ganiev, I and Yunusbayev, B},
title = {Bifidobacterium- and Escherichia-dominant ecological guilds shape altered microbial metabolic capacity of the gut microbiome in tuberculosis patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1751447},
pmid = {42553090},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; *Tuberculosis/microbiology ; *Bifidobacterium/metabolism/isolation & purification ; Adult ; Metabolic Networks and Pathways ; Male ; Middle Aged ; },
abstract = {INTRODUCTION: The gut microbial community plays a key role in maintaining the host immune homeostasis. However, current analytical approaches analyze individual taxa rather than gut communities, thereby missing community-level functions performed by units, such as ecological guilds. Delineating ecological units is a promising approach for summarizing the functional output of microbes and their impact on the host.

METHODS: In this study, we investigated gut bacteria in 33 tuberculosis patients and 47 healthy controls using enterosignatures (ESs), ecological units of co-occurring bacteria related by function. We focused on detecting enterosignatures enriched in the gut communities of tuberculosis (TB) patients. For each patient-enriched enterosignature, we counted the metabolic pathways encoded by its member species. In this manner, we characterized the functional potential of ecological guilds enriched in TB patients. Finally, we tested whether ecological guilds correlate more closely with disease and host biomarkers.

RESULTS AND DISCUSSION: We show that inferred ESs represent reproducible units that facilitate proper comparison of identified ecological guilds to those observed in worldwide donor populations. Namely, dominant enterosignatures in the analyzed healthy donors reproduced the same ecological guilds observed among healthy individuals worldwide. In contrast, most TB patients carried two enterosignatures (ES-Bifi and ES-Esch) that were hallmarks of disturbed gut communities and atypical for healthy adults. We estimated the abundance of metabolic pathways encoded by member species of these patient-enriched ESs. We found that an increase in bacterial species comprising ES-Bifi and ES-Esch harbor an increased number of pathways for fermenting simple sugars, with end products such as acetate and lactate. A greater number of ecological guilds that ferment glucose to lactate might indicate an altered gut environment in patients, including increased acidity and disturbed carbohydrate flux. Taken together, our analyses suggest that ESs represent a biologically meaningful unit for reducing the complexity of the human gut microbiome and a tool for recognizing sharper patterns behind noisy taxonomic and functional diversity.},
}

Humans
*Gastrointestinal Microbiome
Female
*Tuberculosis/microbiology
*Bifidobacterium/metabolism/isolation & purification
Adult
Metabolic Networks and Pathways
Male
Middle Aged

@article {pmid42553157,
year = {2026},
author = {Wang, S and Liu, J and Zheng, J and Hu, M and Tian, C},
title = {Beyond desalinization: root interactions with halophyte Suaeda salsa reshape soybean rhizosphere metabolite-microbiome networks.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1847720},
pmid = {42553157},
issn = {1664-462X},
abstract = {INTRODUCTION: Halophyte-based intercropping may involve root interactions beyond desalinization in alleviating salt stress in glycophytes.

METHODS: To elucidate the mechanisms of root interactions enhancing soybean (Glycine max) salt tolerance intercropping with Suaeda salsa, we analyzed rhizosphere metabolomes and bacterial communities under two salt treatments (no additional NaCl, S1; 3 g kg[-1] NaCl, S3) and three root interaction modes: (1) plastic barrier (no root interactions), (2) nylon mesh barrier (root interactions only), and (3) no barrier (root interactions with potential salt redistribution).

RESULTS: Both NL and NS significantly increased soybean biomass compared with PL under both salt treatments, with no significant difference between NL and NS. Under S3, NL increased soybean biomass by 80% relative to PL without significantly changing soil electrical conductivity, accompanied by increases in rhizosphere carbohydrates, organic acids, betaine, flavonoids, and putative plant growth-promoting bacteria (PGPB). Although soybean rhizosphere Na[+] decreased under NS compared with PL and NL, this was accompanied by reduced putative PGPB abundance and no further biomass increase compared with NL. Coumestrol, trehalose-6-phosphate, and isopentenyl pyrophosphate (IPP) were identified as hub metabolites associated with soybean rhizosphere microbial community structure, with the IPP-related module representing a potential component of the salt-response network. Intercropping also increased available phosphorus (AP) in both species' rhizospheres, with increases in soybean associated with organic acids and those in S. salsa associated with rhizosphere pH shifts and putative PGPB changes.

DISCUSSION: These findings indicate that root interactions enrich salt-tolerance-related metabolites in the soybean rhizosphere and suggest potential metabolic-microbial coupling underlying intercropping-induced salt tolerance.},
}

@article {pmid42553192,
year = {2026},
author = {Huang, M and Jackson, PPJ and Chatzifragkou, A and Rastall, RA},
title = {Exploring the prebiotic potential of commercial cellobiose: a randomized, controlled trial.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e13},
pmid = {42553192},
issn = {2632-2897},
abstract = {Cellobiose, a β-(1 → 4)-linked disaccharide indigestible by humans, is a novel candidate prebiotic. Evidence from controlled human trials on its effects on the gut microbiota and metabolites remains limited. We conducted an exploratory randomised, double-blind, placebo-controlled trial in 37 healthy adults. Participants were allocated to three arms for 4 weeks, received 5 g/day and 10 g/day for cellobiose, oligofructose P95, or maltodextrin placebo. The primary endpoint was change in absolute abundance of Bifidobacterium and Lactobacillus (measured by 16S rRNA gene sequencing). Secondary endpoints included other taxa, diversity, faecal short-chain fatty acids (SCFAs) measured by gas chromatography-mass spectrometry and gastrointestinal (GI) tolerability. Cellobiose did not significantly change Bifidobacterium or Lactobacillus versus baseline or placebo (P > 0.05). Oligofructose P95 induced a borderline increase in Bifidobacterium (P = 0.049). Overall community composition remained unchanged. However, network analyses under cellobiose revealed tighter positive correlations among key genera. Faecal SCFA levels were not altered. GI symptom rates were low and similar across all arms. Cellobiose, at doses up to 10 g/day, is safe and well tolerated but did not enrich classic beneficial taxa. The findings suggest cellobiose drives subtle community shifts towards butyrate-producing bacteria.},
}

@article {pmid42553207,
year = {2026},
author = {Zhao, R and Xiao, Y and Fan, X},
title = {Circadian rhythms in the tumor microenvironment: spatiotemporal immune regulation and chronotherapeutic opportunities.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1878388},
pmid = {42553207},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Circadian Rhythm/immunology ; Animals ; *Neoplasms/immunology/therapy ; *Chronotherapy ; Circadian Clocks ; },
abstract = {The tumor microenvironment (TME) is increasingly recognized as a temporally organized ecosystem rather than a static structural niche. Circadian rhythms, generated by transcriptional-translational feedback loops involving CLOCK, BMAL1, PER, CRY, REV-ERB, and ROR, coordinate systemic physiology and local cellular programs that are directly relevant to tumor initiation, progression, and therapeutic response. In this review, we summarized how circadian regulation shapes tumor rhythmicity across multiple biological scales, from central clock-mediated synchronization to peripheral clocks within epithelial cells, stromal cells, adipocytes, and immune populations. Emphasis is placed on the spatiotemporal regulation of antitumor immunity within the TME. At the same time, dendritic cell migration, antigen presentation, CD8[+] T cell infiltration, and T cell exhaustion display time-dependent features that influence the efficacy of immune surveillance and immunotherapy. These findings supported a four-dimensional view of the TME, in which biological timing is a critical determinant of immune competence. We further discussed emerging therapeutic strategies that exploit circadian biology, including small-molecule clock modulators, rhythm-responsive nanomedicine, chronologically optimized CAR-T cell therapy, and time-of-day-dependent immune checkpoint blockade. Although most mechanistic evidence remains preclinical, and many clinical observations are retrospective, current data suggest that treatment timing may be a modifiable, low-cost parameter for improving anti-tumor efficacy while reducing toxicity. Finally, we highlighted future opportunities in microbiome-informed chronotherapy, multi-omics profiling, and digital twin modeling. Integrating temporal information into oncology may shift precision medicine from a static biomarker-driven framework toward a dynamic, time-resolved therapeutic paradigm.},
}

Humans
*Tumor Microenvironment/immunology
*Circadian Rhythm/immunology
Animals
*Neoplasms/immunology/therapy
*Chronotherapy
Circadian Clocks

@article {pmid42553212,
year = {2026},
author = {Bajguz, A and Żeruń, J},
title = {Brassinosteroids as phytohormonal shields against micro- and nanoplastic stress in plants.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1920456},
pmid = {42553212},
issn = {1664-462X},
abstract = {Microplastics (MPs) and nanoplastics (NPs) are biologically active stressors in agricultural soils, where they alter soil physical structure, disrupt rhizosphere processes, impair water and nutrient acquisition, and provoke oxidative and hormonal disequilibrium in plants. Brassinosteroids (BRs), particularly brassinolide and 24-epibrassinolide, have recently emerged as modulators of plant responses to plastic-particle stress. Current evidence indicates that BRs do not detoxify plastics directly. Instead, they reorganize plant performance across interconnected layers: aquaporin-linked NP transport, antioxidant and ascorbate-glutathione metabolism, photosystem II function, hormone crosstalk, secondary metabolism, and rhizosphere feedbacks. In tomato, BRs reduced polystyrene-NP accumulation in edible tissues by suppressing aquaporin genes. In Pinellia ternata and rice, BRs attenuated MP/NP-induced growth inhibition by restoring photosynthetic efficiency and redox control. This mini review synthesizes these findings and frames BRs as eco-hormonal regulators of the plant-plastic-soil interface, while highlighting priorities for field-realistic validation.},
}

@article {pmid42553649,
year = {2026},
author = {Canonaco, F and Acerbi, E and Stella, F},
title = {Correction: Improving DirectLiNGAM for high-dimensional microbiome data: roots screening and eBIC based model selection.},
journal = {Frontiers in systems biology},
volume = {6},
number = {},
pages = {1929002},
doi = {10.3389/fsysb.2026.1929002},
pmid = {42553649},
issn = {2674-0702},
abstract = {[This corrects the article DOI: 10.3389/fsysb.2026.1835323.].},
}

@article {pmid42553678,
year = {2026},
author = {Hu, R and Wu, J and Chen, N and Ma, W and Hu, Q},
title = {Gut-testis axis: how microbiota influence male reproductive health.},
journal = {Asian biomedicine : research, reviews and news},
volume = {20},
number = {3},
pages = {149-154},
pmid = {42553678},
issn = {1875-855X},
abstract = {The intestinal flora forms a complex ecosystem that interacts with the host, influencing health and fitness through mechanisms that connect with distant organs like the brain, liver, muscles, and testes. The gut microbiota plays a vital role in regulating androgen production and metabolism, and can cross the blood-testis barrier to influence spermatogenesis. This review highlights the significance of the gut-testis axis in male reproductive and sexual health, based on extensive studies exploring how gut microbes impact testicular function. Gaining this understanding deepens our knowledge of the gut-testis axis and its role in male reproductive health.},
}

@article {pmid42553701,
year = {2026},
author = {Balardin, RR and Nora, DD and Figueroa Rosado, YZ and Hardy, ICW and Godoy-Vitorino, F and Verle Rodrigues, JC},
title = {Behavioral and Microbial Profiling of the Bethylid Wasp Cephalonomia stephanoderis for Biocontrol of the Coffee Berry Borer.},
journal = {Biological control : theory and applications in pest management},
volume = {219},
number = {},
pages = {},
pmid = {42553701},
issn = {1049-9644},
abstract = {The coffee berry borer (CBB, Hypothenemus hampei) is the most destructive pest of coffee, causing significant economic consequences in an array of coffee-producing regions, including Puerto Rico. Following the implementation of biological control programs using the parasitoid wasp Cephalonomia stephanoderis, key questions remain regarding how laboratory-reared wasps compare to field wasps in retaining beneficial traits, such as foraging, host attack, and offspring production. It is also of interest whether laboratory and field populations differ in the microbiota they harbor, as microbial communities can directly influence insect performance. Making these comparisons, we find that core natural-enemy functions remain largely intact in laboratory-reared wasps, but that small differences exist between these and field-collected wasps in terms of host-stage preference and oviposition timing. We also find substantial differences in microbial composition between field-collected wasps and those reared in the laboratory. Field-collected parasitoids harbored a simple microbial profile dominated by the Actinomycetota, a diverse phylum of Gram-positive bacteria, particularly in the family Corynebacterium, while laboratory-reared wasps exhibited higher diversity involving a broader range of bacterial phyla. These microbiome differences, confirmed by alpha and beta diversity analyses, suggest that laboratory rearing restructures parasitoid-associated microbial communities. While behavioral performance remained largely comparable, differences in microbial community composition suggest that microbiota should be considered when evaluating laboratory-reared agents for pest management programs. Further studies are needed to better understand microbial shifts and their potential links to parasitoid behavior and performance.},
}

@article {pmid42553733,
year = {2026},
author = {Deng, J and Chen, FH and Wu, WJ and Huang, TY and Cui, GZ and Hong, W},
title = {Pleiotropic roles of the MATE transporter CD20030 in Clostridioides difficile: linking multidrug resistance to oxidative stress defense and virulence regulation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1865850},
pmid = {42553733},
issn = {1664-302X},
abstract = {BACKGROUND: The multidrug-resistant pathogen Clostridioides difficile (C. difficile) presents a persistent clinical threat. While Multidrug and Toxic Compound Extrusion (MATE) transporters are recognized as xenobiotic efflux pumps, their pleiotropic roles in pathogen physiology, particularly in stress adaptation and virulence regulation, remain largely unexplored. Understanding how C. difficile adapts and thrives in the face of host defenses and antimicrobial pressures, potentially influencing gut microbiome dynamics, is crucial for combating C. difficile infection.

METHODS: We functionally characterized the MATE transporter gene CD20030 (mate) in C. difficile 630. A markerless deletion mutant (Δmate) and a complemented strain were constructed using a CRISPR-Cas9 system. Phenotypic assays determining antimicrobial susceptibility, oxidative stress tolerance, autolysis, and cytotoxicity were integrated with comparative proteomic profiling to assess the physiological changes.

RESULTS: The Δmate mutant demonstrated broad-spectrum hypersensitivity to antibiotics and hydrogen peroxide, indicating the involvement of this transporter in intrinsic resistance and oxidative defense. The mutant exhibited reduced autolysis; however, toxin production (tcdA and tcdB) and cytotoxicity were significantly upregulated. In soft agar assays, the mutant showed expanded surface spreading. Proteomic data identified a >10,000-fold downregulation of flagellar structural proteins (FliC, FlgC) and a concurrent upregulation of the surface adhesin CwpV. This molecular evidence indicates a "swimming-to-sliding transition" driven by metabolic stress, rather than active swimming motility. These phenotypic and proteomic shifts present a resource reallocation strategy, where the bacterium sacrifices energy-consuming flagellar assembly to prioritize survival and virulence, potentially altering its interaction with the gut epithelial surface and resident microbiota.

CONCLUSION: The MATE transporter (CD20030) operates as a pleiotropic regulatory hub and metabolic sentinel in C. difficile. Its absence induces metabolic reprogramming that orchestrates a motility-virulence trade-off, linking multidrug resistance directly to bacterial pathogenesis. These physiological adaptations likely dictate the pathogen's colonization and persistence strategies within the gut niche, potentially perturbing the host-microbiome equilibrium during infection.},
}

@article {pmid42553854,
year = {2026},
author = {Ferrini, A and Del Monaco, A and Zampogna, B and Bosso, A and Zampoli, A and Parisi, FR and Capperucci, C and Diaz Balzani, LA and Papalia, R},
title = {Hip Osteoarthritis and the Human Microbiome: Current Concepts, Biological Insights and Future Directions.},
journal = {Orthopedic reviews},
volume = {18},
number = {},
pages = {164467},
pmid = {42553854},
issn = {2035-8164},
abstract = {Osteoarthritis (OA) is among the leading causes of disability worldwide, yet its pathogenesis remains incompletely understood. Once considered a "non-inflammatory" degenerative disorder, OA is now recognized as a condition driven by chronic low-grade inflammation. Emerging evidence implicates gut dysbiosis as a modifiable risk factor, promoting systemic inflammation through impaired gut permeability and translocation of microbial components. These immune-modulating molecules can trigger pro-inflammatory cascades and pathological bone remodeling. This review summarizes current knowledge linking gut dysbiosis and knee osteoarthritis and extends these insights to hip osteoarthritis (HOA). Observational and genetic studies support a causal role for the microbiota, identifying specific taxa associated with either increased or reduced HOA risk. Preclinical and clinical data describe a mechanistic axis linking intestinal dysbiosis, synovial inflammation, and cartilage degeneration. In animal models, particularly under high-fat/high-sucrose diets, visceral adiposity emerges as a major driver of joint damage. While microbial metabolites such as short-chain fatty acids appear protective, the detection of microbial DNA within joint tissues remains controversial, suggesting possible joint-specific microbial ecosystems. Based on these findings, microbiota-targeted strategies are under investigation as potential interventions to influence OA progression and relieve hip pain. However, longitudinal cohorts and randomized clinical trials in HOA are needed to clarify causal mechanisms and therapeutic efficacy in HOA.},
}

@article {pmid42553918,
year = {2026},
author = {Chen, H and Zhang, B and Zhu, B and Zhou, P and Xu, C and Li, Q and Chen, W},
title = {Comparison of the effects of stent-based diversion technique versus prophylactic double-lumen ileostomy on intestinal flora in postoperative patients with rectal cancer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1791364},
pmid = {42553918},
issn = {1664-302X},
abstract = {BACKGROUND: The stent-based diversion technique (SDT), as a novel surgical approach for reducing anastomotic leakage (AL) following low anterior resection (LAR), achieving effective intestinal diversion while avoiding ileostomy and subsequent stoma reversal surgery. Although multicenter randomized controlled trials have demonstrated the safety of SDT, the alterations in postoperative intestinal microbiota following SDT remain inadequately characterized.

METHODS: This study enrolled 40 patients with mid-low rectal cancer (21 SDT, 19 PDI). Rectal swab samples were collected preoperatively and at 3 weeks and 3 months postoperatively (n = 120) for metagenomic sequencing. α- and β-diversity analyses were performed to compare microbial community characteristics. LEfSe was used for differential analysis of species and KEGG functional pathways. Postoperative clinical outcomes including AL and anastomotic stricture (AS) were assessed.

RESULTS: The SDT group showed a significantly lower incidence of AS compared with the PDI group (4.76% vs. 31.58%, p < 0.05). Preoperative α- and β-diversity were comparable between groups. Postoperatively, the SDT group exhibited higher microbial richness at both 3 weeks and 3 months (both p < 0.05). In the PDI group, the α-diversity showed a continuous decline from 3 weeks to 3 months postoperatively compared with the preoperative baseline (p < 0.05). However, the SDT group demonstrated no significant decrease in α-diversity at 3 weeks (p > 0.05), but did at 3 months (p < 0.05). Significant intergroup β-diversity divergence emerged from 3 weeks onward (both p < 0.05). The SDT group showed significant structural changes from 3 weeks to 3 months (p < 0.05), whereas the PDI group remained stable. At 3 weeks, opportunistic pathogens (e.g., Parvimonas micra) were enriched in the PDI group, while the SDT group enriched beneficial taxa (e.g., Akkermansia). By 3 months, the PDI group exhibited enrichment of oral/genitourinary-derived bacteria (Prevotellaceae, Porphyromonas, Fusobacterium), whereas the SDT group showed higher abundance of beneficial Bacteroidota (e.g., Phocaeicola vulgatus). Functionally, the SDT group enriched amino acid and carbohydrate metabolism pathways, while the PDI group enriched translation and energy metabolism pathways.

CONCLUSION: We found that SDT better preserves postoperative gut microbiota diversity, promotes the restoration of beneficial bacteria, and influences microbial functional pathways, thereby establishing a more favorable microbiome environment for patients.},
}

@article {pmid42554126,
year = {2026},
author = {Reggiardo, B and Saad, J and Travers, MA and Labreuche, Y and Goudenège, D and Toulza, E and Broquard, C and Andree, KB and Mougin, J and Argenta, N and Courtay, G and Pouzadoux, J and Romatif, O and Caro, A and Furones, D and Vezzulli, L and Corno, G and Di Cesare, A and Gairin, I and Petton, B and Wegner, KM and Montagnani, C and Boulo, V and Destoumieux-Garzón, D},
title = {Vibrio Community Structure Shapes the Diversity of Carbenicillin-Hydrolysing Class A β-Lactamase Circulating in European Coastal Environments.},
journal = {Environmental microbiology},
volume = {28},
number = {8},
pages = {e70383},
doi = {10.1111/1462-2920.70383},
pmid = {42554126},
issn = {1462-2920},
support = {869178-AquaticPollutants//European Union's Horizon 2020 research and innovation programme/ ; //Institut Français de Recherche pour l'Exploitation de la Mer/ ; ANR-21-EXES-0005//Agence Nationale de la Recherche/ ; ANR-10-LABX-41//Agence Nationale de la Recherche/ ; 88881.987362/2024-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; Sv1064/25//Comité Français d'Evaluation et la Coopération Universitaire et Scientifique avec le Brésil/ ; //Centre National de la Recherche Scientifique/ ; },
mesh = {Animals ; *Vibrio/enzymology/genetics/classification/isolation & purification/drug effects ; Europe ; *beta-Lactamases/genetics/metabolism ; *Carbenicillin/metabolism ; *Seawater/microbiology ; Ostreidae/microbiology ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Coastal environments are increasingly recognised as reservoirs of known antibiotic resistance genes (ARGs), but are less frequently identified as sources of novel ARGs. Here, we investigated class A β-lactamases circulating in European coastal environments used for oyster farming. We examined their diversity, function, and the ecological factors associated with their geographic distribution and environmental dynamics. A high diversity of carbenicillinases was detected in the culturable microbiome of European oysters. The Harveyi and Splendidus clades were key Vibrio lineages structuring the geography of carbenicillinase diversity. The Harveyi clade was primarily associated with the circulation of known carbenicillinases in Mediterranean samples, whereas the Splendidus clade contributed previously uncharacterized carbenicillinase sequences across all Europe. A one-year seasonal monitoring revealed that Vibrio alginolyticus drives the circulation of blaCARB-42 in the Mediterranean Thau lagoon, with dynamics strongly associated with seawater temperature. blaCARB-42 conferred intrinsic resistance to both carboxypenicillins and aminopenicillins in V. alginolyticus, which was found in most other species of the Harveyi clade with additional resistances to aztreonam, third-generation cephalosporins and aminoglycosides. Since the Harveyi clade includes major human pathogens, these findings have direct implication for environmental and One Health surveillance, as rising seawater temperatures may increase coastal exposure to antibiotic-resistant Harveyi clade Vibrio.},
}

Animals
*Vibrio/enzymology/genetics/classification/isolation & purification/drug effects
Europe
*beta-Lactamases/genetics/metabolism
*Carbenicillin/metabolism
*Seawater/microbiology
Ostreidae/microbiology
Phylogeny
Anti-Bacterial Agents/pharmacology

@article {pmid42554132,
year = {2026},
author = {Masum, MHU and Nayem, MR and Mahdeen, AA and Sultana, S and Barua, A},
title = {Characterizing the Milk Microbiome in Subclinical Mastitis: A Pilot 16S rRNA-Based Study in Cattle and Water Buffalo.},
journal = {Veterinary medicine and science},
volume = {12},
number = {5},
pages = {e71154},
doi = {10.1002/vms3.71154},
pmid = {42554132},
issn = {2053-1095},
mesh = {Animals ; *Buffaloes ; *Milk/microbiology ; Cattle ; *Microbiota ; Pilot Projects ; Female ; *Mastitis, Bovine/microbiology ; RNA, Ribosomal, 16S/analysis ; Bangladesh ; *Bacteria/classification/isolation & purification ; RNA, Bacterial/analysis ; },
abstract = {BACKGROUND: In the dairy sector of Bangladesh, subclinical mastitis (SCM) is a substantial and frequently undiagnosed challenge, with reported prevalence rates of 60%-77% in cattle and approximately 52% in buffaloes. Due to its complex characteristics and progressive development, efficient diagnosis and management are essential for enhancing dairy productivity.

OBJECTIVES: This pilot study employed 16S rRNA amplicon sequencing using Oxford Nanopore's MinION to investigate the milk microbiota of healthy and mastitic cattle and buffalo.

RESULTS: A total of 423 clustered nucleotide sequences were identified in the samples, indicating significant taxonomic diversity: 11 phyla, 26 classes, 58 orders, 120 families and 272 genera. Distinct phylum-level patterns were observed, with Firmicutes predominating in healthy milk and a relative increase in Proteobacteria and Actinobacteriota in mastitic samples. At the genus level, Streptococcus and Lactococcus were predominant in mastitic samples, whereas Staphylococcus and Lactococcus were more prevalent in healthy milk. The results indicate that although overall microbial diversity was relatively consistent across groups, mastitis correlated with alterations in bacterial community composition, with notable differences between cattle and buffalo.

CONCLUSION: This study suggests a potential association between SCM and microbial shifts; however, microbiome profiling cannot yet be recommended for diagnostic application. Clinical applicability requires validation in large-scale studies with individual-level sampling.},
}

Animals
*Buffaloes
*Milk/microbiology
Cattle
*Microbiota
Pilot Projects
Female
*Mastitis, Bovine/microbiology
RNA, Ribosomal, 16S/analysis
Bangladesh
*Bacteria/classification/isolation & purification
RNA, Bacterial/analysis

@article {pmid42554290,
year = {2026},
author = {Sulaiman, I and Maher, TM},
title = {The Gut Speaks to the Lung: Fecal Microbiota and Survival in Idiopathic Pulmonary Fibrosis.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag410},
pmid = {42554290},
issn = {1535-4970},
}

@article {pmid42554585,
year = {2026},
author = {Yang, Y and Olah, P and Salava, A and Barker, J and Lauerma, A and Andersson, B and Fyhrquist, N and Homey, B and Alenius, H},
title = {Multi-omics analyses reveal host-microbe interactions in atopic dermatitis and psoriasis.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70654},
pmid = {42554585},
issn = {1468-3083},
support = {261366//FP7 Health/ ; 821511//Innovative Medicines Initiative 2 Joint Undertaking/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) and psoriasis (PSO) are chronic inflammatory skin diseases that impose substantial physical and psychological burdens. Although fungal-bacterial balance is important for skin immune homeostasis, the role of the skin mycobiome and its interaction with bacterial communities and host immunity in these diseases remains poorly understood.

OBJECTIVES: To characterize alterations in the skin mycobiome and its interactions with bacterial communities and host immune responses in AD and PSO.

METHODS: Adult patients with chronic AD, plaque-type PSO and healthy volunteers were included in this study. Skin microbiota samples and biopsies were collected from lesional and non-lesional skin areas, including the posterior thigh for AD and the lower back for PSO. Whole-metagenome shotgun sequencing was used to profile microbial communities. SparCC was used to construct fungal-bacterial co-occurrence networks, and integration of host transcriptomic and microbial features was performed using O2PLS.

RESULTS: Both AD and PSO showed disease-associated restructuring of Malassezia species and reduced fungal-bacterial ecological connectivity in lesional skin. In AD, Malassezia arunalokei was inversely associated with Staphylococcus aureus and linked to antimicrobial peptide-centred host gene modules enriched for IL-17 signalling. Its abundance decreased with increasing disease severity and inversely correlated with inflammatory immune cell signatures. In PSO, altered Malassezia composition was associated with IL-17-driven transcriptional programmes and lipid metabolic pathways, suggesting interactions between fungal imbalance and inflammatory-metabolic processes.

CONCLUSIONS: Our findings expand current models of skin dysbiosis beyond bacteria and suggest that disrupted fungal-bacterial interactions are linked to immune activation in AD and PSO and, in AD, to disease severity. Although further validation is required, skin microbiome features may provide clinically relevant information for disease monitoring, patient stratification and future microbiome-informed therapeutic strategies. Our study lays the groundwork for microbiome modulation as a potential therapeutic strategy for AD and PSO.},
}

@article {pmid42554630,
year = {2026},
author = {Tandon, A and Bais, AK and Shrinet, J and Tripathi, V and Gupta, D},
title = {Effect of alcohol and smoking on methamphetamine users' oral microbiome and metabolome.},
journal = {The American journal of drug and alcohol abuse},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/00952990.2026.2697752},
pmid = {42554630},
issn = {1097-9891},
abstract = {Background: The oral microbiome comprises the microbial communities inhabiting the oral cavity, whereas the oral metabolome reflects the small molecules generated by host and microbial metabolic activity. These systems may provide insight into substance-related physiological disruption, including altered inflammation, immune signaling, and host - microbial interactions. Although the individual effects of methamphetamine, alcohol, and smoking have been explored, their combined impact on these systems remains largely unexplored.Objectives: To investigate the metabolic and microbiome alterations associated with chronic methamphetamine use in individuals with alcohol and tobacco use.Methods: High-throughput metabolomic and microbiome datasets from methamphetamine users (Males:168, Females: 50), stratified by self-reported tobacco smoking and alcohol use, were analyzed using integrative bioinformatics approaches, including multivariate and pathway enrichment analyses, to identify dysregulated metabolic pathways and microbial alterations across defined subgroups.Results: The study revealed significant upregulation in metabolites like prostaglandin E2 (log-2-fold-change: 2.63, Cohen's D: |~0.881|, p-val: 7.1 × 10[-10]) and glutamylisoleucine (log-2-fold-change: 1.42, Cohen's D: |~0.88|, p-val: 2.5 × 10[-2]). Microbes such as Bacteroides (log-2-fold-change: -4.91, Cohen's D: |~1.95|, p-val: 1.3 × 10[-4]) and Brachymonas (log-2-fold-change: -2.47, Cohen's D: |~1.09|, p-val: 5.8 × 10[-3]) were significantly downregulated. This suggests that long-term concurrent methamphetamine use, alcohol consumption, and smoking are associated with alterations in microbial and metabolic pathways related to oxidative stress, glutathione metabolism, and neuroactive signaling.Conclusions: The oral microbiome and metabolomic profiles may serve as accessible indicators of substance-related biological disruption. They may also help identify clinically relevant targets for monitoring risk, guiding personalized interventions, and developing informed strategies to support recovery.},
}

@article {pmid42554875,
year = {2026},
author = {Zhang, H and Zhang, Y and Zhang, C and Yang, Y and Hu, B and He, T and Zhang, J and Song, X and Su, Y},
title = {Microbial architects of cigar fermentation: a critical review of beneficial roles in quality enhancement and detrimental potential for mould spoilage.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42554875},
issn = {1432-072X},
support = {2023530000241002//the Science and Technology Plan Project of the China National Tobacco Corporation, Yunnan Provincial Company/ ; yxyc2023007//General Project of the Science and Technology Program of Yuxi Company, Yunnan Provincial Tobacco Company/ ; },
mesh = {*Fermentation ; *Fungi/metabolism/growth & development ; *Nicotiana/microbiology/metabolism ; *Food Microbiology ; *Bacteria/metabolism/classification/isolation & purification ; },
abstract = {Cigar tobacco fermentation is a microbially driven process that transforms raw tobacco leaves into a product with distinctive sensory attributes, yet the current understanding of the microbial roles in this process remains fragmented between descriptive community surveys and isolated mechanistic studies, with beneficial and detrimental microbial functions rarely integrated into a unified risk-benefit assessment. This review critically examines the microbiology of cigar fermentation through a dual-axis framework organized around beneficial metabolic functions and detrimental spoilage potential, each resolved into microbial identity, biochemical mechanism, and environmental modulation dimensions. We synthesize evidence from culture-dependent and culture-independent studies on microbial community assembly and succession, where Bacillus, Staphylococcus, and Aspergillus emerge as core fermentation genera, and evaluate the complementary three-pathway system - macromolecular enzymatic degradation, targeted biotransformation of tobacco alkaloids and polyphenols, and de novo biosynthesis of aroma-active volatiles - that drives flavor and quality enhancement. We further analyze the contrastive microbial balance governing tobacco-specific nitrosamine (TSNA) formation, where nitrate-reducing bacteria compete with nitrate-assimilating and nitrite-scavenging microorganisms to determine the net TSNA load. In parallel, we critically examine the mould spoilage microbiology of cigar fermentation, identifying the environmental thresholds - humidity above 80% RH, water activity above 0.85, and inadequate aeration - that select for mycotoxigenic Aspergillus and Penicillium species producing aflatoxins and ochratoxin A at levels that persist into the finished product. We survey emerging biotechnological strategies spanning bioaugmentation with defined starter cultures, biostimulation through environmental optimization, and biocontrol of spoilage fungi, and identify five critical research gaps - including the absence of gnotobiotic fermentation models and the predominance of correlative over causal studies - that must be addressed to translate microbial ecology into predictable fermentation biotechnology. By integrating microbial ecology, fermentation biochemistry, spoilage prevention, and applied biotechnology, this review is intended for researchers in tobacco microbiology and fermentation science, as well as cigar manufacturers, quality-control practitioners, and biotechnologists seeking microbiome-based strategies for quality improvement and risk mitigation.},
}

*Fermentation
*Fungi/metabolism/growth & development
*Nicotiana/microbiology/metabolism
*Food Microbiology
*Bacteria/metabolism/classification/isolation & purification

@article {pmid42546842,
year = {2026},
author = {Su, Y and Qin, X and Guo, L and Zhao, H},
title = {Distinguishing true from false idiopathic pulmonary fibrosis: Progress in biomarkers for early identification of rheumatoid arthritis.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {101021},
doi = {10.1016/j.bj.2026.101021},
pmid = {42546842},
issn = {2320-2890},
abstract = {BACKGROUND: Patients initially diagnosed with idiopathic pulmonary fibrosis (IPF) have an underlying risk of being in a preclinical phase of rheumatoid arthritis (RA), but effective biomarkers for early identification of this transition are lacking.

OBJECTIVE: This review aims to comprehensively summarize predictive markers for future RA in patients meeting IPF diagnostic criteria, supporting early risk stratification and pre-arthritic intervention.

METHODS: Using "idiopathic pulmonary fibrosis", "rheumatoid arthritis", "predictive markers", "markers", "clinical research", "in vitro experiments", "mechanism", and their combinations as keywords, a structured literature search was conducted in the PubMed database for relevant literature from 2001 to 2025.

RESULTS: The propensity for RA to develop in patients initially meeting IPF diagnostic criteria has a multi-dimensional basis: genetic susceptibility provides the background; immune dysregulation mediates the dissemination of autoimmunity from a pulmonary origin to systemic involvement; inflammatory markers reflect disease activity; environmental exposure acts as an external trigger. Based on these mechanisms, four predictive marker types were identified: genetic susceptibility, immune activation, inflammatory injury, and environmental exposure. However, current studies are mainly cross-sectional and retrospective, lacking prospective validation of predictive efficacy; combined application strategies, clinical value and microbiome-based indicators all require further clinical verification.

CONCLUSION: This review identified four early-warning markers-genetic susceptibility, immune activation, inflammatory injury, and environmental exposure-that may signal future RA in patients initially presenting with IPF. These findings support shifting from passive diagnosis to active screening for earlier intervention. Future research should focus on multi-dimensional prediction models, prospective cohort studies, and ultimately achieving early identification and intervention for this hidden RA-prone population.},
}

@article {pmid42547019,
year = {2026},
author = {Wu, YZ and Yu, JC and Li, J and Yang, CJ and Mao, SY},
title = {Integrated multi-omics analysis reveals the co-adaptive mechanisms between ruminal microbiota and host epithelium in water buffaloes under chronic heat stress.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28742},
pmid = {42547019},
issn = {1525-3198},
abstract = {Chronic heat stress is a major environmental challenge constraining water buffalo (Bubalus bubalis) production, yet its mechanistic impacts on the ruminal ecosystem remain unclear. This study aims to systematically elucidate the coordinated changes in ruminal microbial structure and function, metabolome, and epithelial transcriptional responses in water buffaloes under chronic heat stress. Ten cannulated buffaloes (Nili-Ravi × Murrah) were used as experimental subjects and randomly assigned to 2 groups: one receiving fan and sprinkler cooling (NHS) and the other exposed to the natural environment (HS). This study aimed to analyze their apparent digestibility, ruminal fermentation parameters, and ruminal microbial community structure and function along with their metabolic characteristics, as well as to dissect the transcriptional responses of the rumen epithelium to chronic heat stress. Results showed that chronic heat stress did not significantly affect feed intake or apparent nutrient digestibility, but markedly altered ruminal fermentation and nitrogen metabolism, manifested as a reduced ammonia nitrogen (NH3-N) concentration (HS vs. NHS, 4.44 vs. 7.86 mg/dL), an increased proportion of acetate (HS vs. NHS, 68.86 vs. 66.74%), and a decreased proportion of propionate(HS vs. NHS, 20.40 vs. 22.14%). Chronic heat stress imposed selective pressure on the ruminal microbial community, driving functional changes at the microbial level. The overall abundance of multiple CAZyme families increased, enhancing the potential for structural carbohydrate degradation; concurrently, the abundance of genes encoding key enzymes for pyruvate-to-acetyl-CoA conversion rose, consistent with elevated acetate synthesis potential; enrichment of nitrogen metabolism-related genes suggested enhanced microbial ammonia assimilation capacity. At the metabolic level, chronic heat stress induced specific metabolite dynamics, including decreased phosphatidylcholine PC(16:0/18:1(9Z)) content and accumulation of the flavonoid metabolite naringenin, indicating co-activation of phospholipid hydrolysis and flavonoid metabolic pathways. At the host level, transcriptional changes in rumen epithelium were primarily reflected in reduced ion transport capacity and enhanced cellular stress protection. In summary, the adaptive response of water buffaloes to chronic heat stress is primarily driven by the functional plasticity of the ruminal microbiome, which maintains energy supply and metabolic homeostasis to some extent by altering carbon and nitrogen metabolic fluxes; meanwhile, transcriptional regulation in the host rumen epithelium contributes to co-adaptation, though certain absorption-related functions may be compromised due to stress. These findings provide a biological basis for maintaining ruminal functional homeostasis and health in water buffaloes under high-temperature conditions through nutritional interventions.},
}

@article {pmid42547063,
year = {2026},
author = {Starr, ME and Taylor, MD and Su, L and Murao, A and Schwulst, SJ and Lederer, JA and Brenner, M},
title = {New Approach Methodologies (NAMs) Complement but Cannot Replace Animal Models in Critical Care Medicine Research.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiag108},
pmid = {42547063},
issn = {1938-3673},
abstract = {Critical care research focuses on life-threatening conditions such as sepsis, trauma, hemorrhage, and burn injury, which account for millions of hospitalizations and hundreds of thousands of deaths annually in the United States alone. Recent policy initiatives by the U.S. Food and Drug Administration (FDA) and the National Institutes of Health (NIH) have promoted New Approach Methodologies (NAMs), including organoids, organ-on-chip platforms, and computational models, as alternatives to animal research. While NAMs offer valuable tools for mechanistic investigation and screening applications, this review examines whether current NAM technologies can adequately replace animal models in critical care research. Critical illness involves the whole organism, including dynamic organ-organ interactions, immune-microbiome crosstalk, and adaptive systemic feedback loops. By examining major domains in critical care research and targeted organ injuries, it becomes clear that while NAMs excel at interrogating isolated subsystems, they cannot currently replicate integrated physiological responses. Animal models remain essential for questions requiring assessment of multi-organ dysfunction, therapeutic safety evaluation, and clinically relevant disease trajectories. Premature policy shifts away from animal research will impede advances in critical care medicine. This review proposes a "methodological pluralism" approach that integrates NAMs with appropriately designed animal studies through harmonized endpoints and reverse-translation frameworks. Recommendations include continued refinement of animal models to better represent the heterogeneity of human populations, adoption of quality standards for preclinical research, and strategic deployment of both NAMs and animal models based on fit-for-purpose criteria. We believe this approach will satisfy ethical considerations, scientific rigor, and public health needs in critical care research.},
}

@article {pmid42547359,
year = {2026},
author = {Binda, C and Gibiino, G and Perini, B and Coluccio, C and Fabbri, S and Giuffrida, P and Cucchetti, A and Casadei, A and Lucchi, G and Cristini, F and Raumer, L and Savarino, E and Cricca, M and Benech, N and Sambri, V and Fabbri, C},
title = {Microbiological assessment of bile in patients after endoscopic retrograde cholangio-pancreatography (ERCP): The "MICROBILE" registry.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2026.06.015},
pmid = {42547359},
issn = {1878-3562},
abstract = {BACKGROUND: Microbial communities were recently revealed in the biliary tract of pancreaticobiliary disorders. However, evidence is limited and comparative data are lacking.

AIMS: We aimed to characterize the biliary microbiota in patients with naïve papilla affected by obstructive jaundice eligible for endoscopic treatment.

METHODS: 222 consecutive patients undergoing ERCP were prospectively enrolled from July 2022 to August 2023. Bile was sampled before and after sphincterotomy,then stored for cultures and resistance profiles.

RESULTS: Pre-sphincterotomy (66,6%) and post-sphincterotomy samples (67,5%) revealed bacterial growth, with similar components. Gram-positive bacteria, as Enterococcus spp, were mainly identified. Age ≥60 years, Charlson Comorbidity Index (CCI) ≥4, fever, ongoing antimicrobial therapy and positive blood cultures were associated with positive bile cultures. Positive C-reactive protein was independently related to positive cultures. Multidrug Resistand (MDR) strains, according to international standardized definition, were detected (18%), with a higher prevalence of ESBL bacteria and E. faecium VRE. Antimicrobial therapy was an independent risk factor for MDR biliary bacteria in the multivariate analysis. Positive cultures, polymicrobial flora, and MDR bacteria were similar in malignant and benign disease.

CONCLUSION: Multiple clusters and MDR bacteria were detected in patients with obstructive jaundice. We identified clinical and biochemical risk factors for bacteriobilia and MDR commensals.},
}

@article {pmid42547409,
year = {2026},
author = {Burow, C and Shenderey, R and Chowdhury, F and Shah, N and Pai, N},
title = {Nutritional and environmental determinants of maturation and disruption of the early life gut microbiome: A narrative review.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.70127},
pmid = {42547409},
issn = {1941-2444},
abstract = {The first 1000 days of life represent a critical window for gut microbiome assembly, with lifelong implications for child growth, immune development, and disease risk. This review synthesizes evidence on maternal, perinatal, and especially nutritional factors that influence early-life intestinal colonization and highlights the consequences of microbial disruptions during this period. In utero exposures and birth-associated factors can profoundly shape microbial development, reducing diversity and beneficial taxa. Nutrition exerts a particularly dominant and modifiable influence: breastfeeding supports Bifidobacterium-rich communities, while formula use and early complementary feeding shape microbiota diversity and metabolic function. Dietary quality, fiber intake, and food diversity are key determinants of microbial maturation and resilience. Undernutrition and inadequate diets contribute to microbial dysbiosis, creating a self-reinforcing cycle of malabsorption, growth failure, and long-term metabolic consequences. Early microbial perturbations are associated with a range of acute and chronic diseases, including necrotizing enterocolitis, obesity, type 1 diabetes, inflammatory bowel disease, and atopic disorders. Strategies to restore microbial balance require further validation, particularly in nutritionally vulnerable populations. The absence of a universal definition for a "healthy" pediatric microbiome limits the development of targeted interventions. Emerging metrics, such as microbiota-for-age z-scores and functional microbiome profiling, may help define microbiota maturity and therapeutic efficacy.},
}

@article {pmid42547464,
year = {2026},
author = {Kim, HB and Park, J and Lim, CS and Um, JY and Chung, BY and Park, CW and Lee, DK and Kim, HO},
title = {Skin Lipid Dysregulation in Atopic Dermatitis and Related Inflammatory Skin Diseases.},
journal = {Allergy, asthma & immunology research},
volume = {18},
number = {4},
pages = {485-506},
doi = {10.4168/aair.2026.18.4.485},
pmid = {42547464},
issn = {2092-7355},
support = {RS-2022-NR070251/NRF/National Research Foundation of Korea/Korea ; RS-2023-KH141546/MOHW/Ministry of Health and Welfare/Korea ; /Hallym/Hallym University/Korea ; },
abstract = {Epidermal lipids are essential for skin barrier function and actively influence cutaneous immune homeostasis. Recent advances have transformed our understanding of skin lipid dysregulation in allergic diseases, revealing complex bidirectional relationships between barrier dysfunction and immune activation. This review provides a comprehensive analysis of the 2020-2025 literature on skin lipid metabolism in allergic and inflammatory diseases, with a particular focus on molecular mechanisms, diagnostic biomarkers, therapeutic advances, and implications for precision medicine. Key discoveries include the finding that sphingomyelin deacylase, long linked to ceramide (CER) deficiency, is actually the β-subunit of acid ceramidase. In atopic dermatitis, this enzyme shifts its substrate specificity to sphingomyelin, depleting the barrier lipid pool. Type 2 cytokines, particularly interleukin (IL)-4 and IL-13, suppress lipid biosynthesis through Janus kinase (JAK)/Signal Transducer and Activator of Transcription 6-mediated downregulation of fatty acid (FA) elongases. This suppression, particularly affecting elongation of very long-chain fatty acid (ELOVL) enzymes, such as ELOVL1, ELOVL3, and ELOVL6, disrupts the synthesis of ultra-long-chain CERs essential for barrier function. JAK inhibitors effectively reverse T helper 2 (Th2)-mediated lipid suppression, while optimized topical lipid ratios (3:1:1 CER: cholesterol: FA) enhance barrier repair. Innovations, such as lipid nanoparticles and microbiome-modulating therapies, further support personalized treatment strategies. The integration of barrier repair with targeted immunomodulation-guided by lipidomic and genomic profiling-marks a paradigm shift toward predictive and preventive approaches in allergic skin diseases. Early intervention strategies that simultaneously address immune dysregulation and lipid metabolism hold promise for preventing the atopic march and sustaining long-term remission.},
}