@article {pmid40754205,
year = {2025},
author = {Bassey, PO and Ilomuanya, MO and Oseni, BA and Ogundemuren, DA and Oyediran, KO and Ekeji, EN and Abia, P},
title = {Advancements in drug delivery systems for women's reproductive health: Vaginal microbiome as a target for innovative drug delivery systems.},
journal = {European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V},
volume = {},
number = {},
pages = {114831},
doi = {10.1016/j.ejpb.2025.114831},
pmid = {40754205},
issn = {1873-3441},
abstract = {The vaginal microbiome, predominantly made up of Lactobacillus spp., plays a pivotal role in women's reproductive health, especially in dysbiosis associated with various gynecological disorders. In this comprehensive review, we discussed the current advancements in drug delivery systems targeting the vaginal microbiome, the limitations of traditional approaches, as well as explored innovative strategies in drug delivery with the vaginal microbiome as the focal point. The composition and functions of the vaginal microbiome were critically evaluated, emphasizing its significance in maintaining reproductive health. Conventional drug delivery methods, including oral, parenteral, and topical routes are faced with pharmacokinetic challenges such as poor bioavailability and limited targeted delivery. The emergence of vaginal drug delivery systems such as gels, films, rings, nanoparticulate formulations and electrospun fibers show the potential to enhance therapeutic efficacy through localized and sustained drug release. We highlighted the findings on crucial formulation considerations including physicochemical properties of drugs, excipient selection, and targeting strategies. Furthermore, we analyzed pre-clinical studies utilizing in vitro models including organ-on-a-chip and 3D cell cultures, as well as in vivo animal models to assess the safety, efficacy, and pharmacokinetics of these innovative systems. Additionally, the review revealed that cutting-edge technologies such as electrospun fibers and 3D bioprinted scaffolds show promises for precise control over drug release kinetics and probiotic delivery. Future directions should focus on personalized approaches, ethical considerations, and patient education to fully leverage these technologies for improving women's reproductive health outcomes globally.},
}

@article {pmid40754036,
year = {2025},
author = {Xiao, J and Severance, EG},
title = {Inflammation manipulation and a complement-centered reboot of the Toxoplasma gondii model of schizophrenia.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106313},
doi = {10.1016/j.neubiorev.2025.106313},
pmid = {40754036},
issn = {1873-7528},
abstract = {The protozoan parasite, Toxoplasma gondii, has evolved a creative skillset to engage and sustain itself within a diversity of warm-blooded hosts. Progression to adulthood requires residence in the definitive host, Felidae, a taxonomic family encompassing the beloved, sometimes maligned, housecat. Humans are intermediate hosts, primarily infected following ingestion of foodstuffs containing T. gondii tissue cysts or T. gondii oocysts shed by cats. Although most human cases are asymptomatic, acute inflammation and deadly encephalopathies can result if the infection is congenital, or the host is immunocompromised. Increasingly, presumably benign asymptomatic infections are being investigated for behavioral outcomes and complex brain disorders such as schizophrenia. While not typically considered an inflammatory disorder, reports of muted idiopathic inflammation-like comorbidities in schizophrenia persist and cannot be discounted by the usual covariants, medications and metabolic factors. T. gondii's survival success may depend on its ability to regulate host inflammation and satisfy its own life-stage requirements for both motility and quiescence. Within the setting of this fluctuating inflammatory environment putatively controlled by T. gondii, other gene and environmental forces are also at work. We consider a model of schizophrenia centered on complement gene variants and the unique capacity for this set of immune pathways to perpetrate and perpetuate neurobiological dysfunction. We examine T. gondii's connections to the gut, to chronic stress, how its relationship with schizophrenia has matured, and how the boundaries between what qualifies as gene and environment have become blurred as we enter a new era of the microbiome and more personalized medicine.},
}

@article {pmid40754005,
year = {2025},
author = {Hegazy, RA},
title = {Unraveling Liver Cirrhosis: Bridging Pathophysiology to Innovative Therapeutics.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70037},
pmid = {40754005},
issn = {1440-1746},
abstract = {Liver cirrhosis is a complex and progressive condition resulting from sustained liver injury and chronic inflammation. Characterized by extensive fibrosis, disrupted liver architecture, and impaired function, cirrhosis represents the end stage of many chronic liver diseases. While traditionally considered irreversible, emerging evidence suggests that targeted interventions may modify disease progression, offering new hope for patients. This review explores the evolving understanding of liver cirrhosis, integrating insights into pathophysiology, systemic implications and innovative therapeutic approaches. At the core of cirrhosis development lies the activation of hepatic stellate cells (HSCs), driven by a cascade of pro-fibrotic signals, including transforming growth factor-beta (TGF-β) and Wnt/β-catenin pathways. Recent studies highlight the pivotal role of epigenetic regulation, mechanotransduction and cellular crosstalk in perpetuating fibrogenesis. Advances in single-cell transcriptomics and spatial biology are revealing unprecedented details of the cellular and molecular heterogeneity within cirrhotic tissue. Beyond the liver, cirrhosis exerts systemic effects, involving the gut-liver axis, vascular remodeling, and multi-organ dysfunction. The gut microbiome has emerged as a critical modulator, with dysbiosis and microbial translocation contributing to inflammation and disease progression. Therapeutic strategies targeting microbiome restoration, such as probiotics and fecal microbiota transplantation (FMT), are showing promise. Diagnostics are undergoing a paradigm shift with the advent of noninvasive tools, including elastography and liquid biopsy technologies. Circulating biomarkers, such as extracellular vesicles and noncoding RNAs, offer real-time insights into disease dynamics. On the therapeutic front, anti-fibrotic agents, senolytics, and regenerative approaches, such as stem cell therapy and liver organoids, are being explored. As artificial intelligence and computational modeling enhance predictive capabilities, a precision medicine approach to cirrhosis management is becoming feasible. This review highlights the need for interdisciplinary research to translate these advances into effective clinical solutions, bridging the gap between pathophysiology and innovative therapeutics.},
}

@article {pmid40753386,
year = {2025},
author = {AlHilli, MM and Sangwan, N and Myers, A and Tewari, S and Lindner, DJ and Cresci, GAM and Reizes, O},
title = {The effects of dietary fat on gut microbial composition and function in a mouse model of ovarian cancer.},
journal = {Journal of ovarian research},
volume = {18},
number = {1},
pages = {174},
doi = {10.1186/s13048-025-01731-1},
pmid = {40753386},
issn = {1757-2215},
support = {K12CA076917//NIH K12CA076917 Clinical Oncology Training Program/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; *Ovarian Neoplasms/microbiology/pathology ; Mice ; Disease Models, Animal ; Humans ; *Dietary Fats/pharmacology ; Diet, Ketogenic ; Cell Line, Tumor ; Mice, Inbred C57BL ; Diet, High-Fat ; },
abstract = {OBJECTIVES: The gut microbiome (GM) is pivotal in regulating inflammation, immune responses, and cancer progression. This study investigates the effects of a ketogenic diet (KD) and a high-fat/low-carbohydrate (HF/LC) diet on GM alterations and tumor growth in a syngeneic mouse model of high-grade serous ovarian cancer (EOC).

METHODS: Thirty female C57BL/6 J mice injected with KPCA cells were randomized into KD, HF/LC, and low-fat/high-carbohydrate (LF/HC) diet groups. Tumor growth was monitored with live, in vivo imaging. Stool samples were collected at the time of euthanasia and analyzed by 16SrRNA sequencing and shotgun metagenomic sequencing was performed to identify differential microbial taxonomic composition and metabolic function.

RESULTS: Our findings revealed that KD and HF/LC diets significantly accelerated EOC tumor growth compared to the LF/HC diet in a xenograft model. GM diversity was markedly reduced in KD and HF/LC-fed mice, correlating with increased tumor growth, whereas LF/HC-fed mice showed higher GM diversity. Metagenomic analyses identified distinct alterations in microbial taxa including Bacteroides, Lachnospiracae bacterium, Bacterium_D16_50, and Enterococcus faecalis predominantly abundant in HF/LC-fed mice, Dubsiella_newyorkensis predominantly abundant in LF/HC-fed, and KD fed mice showing a higher abundance of Akkermansia and Bacteroides. Functional pathways across diet groups indicated polyamine biosynthesis and fatty acid oxidation pathways were enriched in HF/LC-fed mice.

CONCLUSIONS: These results highlight the intricate relationship between diet andthe gut microbiome in promoting EOC growth. The potential role of dietary interventions in cancer prevention and treatment warrants further investigation.},
}

Animals
Female
*Gastrointestinal Microbiome/drug effects
*Ovarian Neoplasms/microbiology/pathology
Mice
Disease Models, Animal
Humans
*Dietary Fats/pharmacology
Diet, Ketogenic
Cell Line, Tumor
Mice, Inbred C57BL
Diet, High-Fat

@article {pmid40753175,
year = {2025},
author = {D'Aloisio, LD and Ballal, M and Ghosh, S and Haskey, N and Abulizi, N and Karimianghadim, R and Liu, C and Sruthi, P and Nagarajan, L and Vasudevan, S and Shetty, V and Purandare, M and Bhaumik, U and Howlader, DR and Pakpour, S and Barnett, J and Gibson, DL},
title = {The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {151},
doi = {10.1038/s41522-025-00778-8},
pmid = {40753175},
issn = {2055-5008},
mesh = {Humans ; *Gastrointestinal Microbiome ; India ; *Emigrants and Immigrants ; Cross-Sectional Studies ; Adult ; RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; Female ; *Acculturation ; Canada ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; *Diet ; *Diet, Western ; Inflammatory Bowel Diseases/microbiology ; Young Adult ; North American People ; },
abstract = {Indian immigration to westernized countries has recently surged, increasing their risk of Inflammatory Bowel Disease (IBD) post-migration. While crucial for understanding IBD risk, the gut microbiome remains understudied in Indians. This cross-sectional study examines the impact of westernization on the gut microbiomes of Indians residing in India, Indo-Immigrants, and Indo-Canadians compared to Euro-Canadian and Euro-Immigrant controls. Stool samples for 16S rRNA and shotgun sequencing assessed microbial taxa and functional profiles, alongside dietary and demographic data to evaluate lifestyle patterns. Indians and Indo-Immigrants had distinct microbiotas from controls, with high abundances of Prevotella spp. and CAZymes reflecting their high complex carbohydrate diet. Indo-Canadians exhibited a transitional microbiome towards westernization, mirroring increasing dietary acculturation. Considering 44% of Canadians are first- and second-generation immigrants and the global adoption of westernized practices, future research should investigate the health implications of such microbiome transitions in immigrant populations and newly industrialized nations.},
}

Humans
*Gastrointestinal Microbiome
India
*Emigrants and Immigrants
Cross-Sectional Studies
Adult
RNA, Ribosomal, 16S/genetics
Male
Feces/microbiology
Female
*Acculturation
Canada
*Bacteria/classification/genetics/isolation & purification
Middle Aged
*Diet
*Diet, Western
Inflammatory Bowel Diseases/microbiology
Young Adult
North American People

@article {pmid40752853,
year = {2025},
author = {Santiwijai, M and Taoka, Y},
title = {Effect of Bacillus subtilis and fungal enzymes on immune responses and gut microbiota of masu salmon (Oncorhynchus masou masou).},
journal = {Developmental and comparative immunology},
volume = {},
number = {},
pages = {105424},
doi = {10.1016/j.dci.2025.105424},
pmid = {40752853},
issn = {1879-0089},
abstract = {The effects of oral administration of probiotics Bacillus subtilis (BS) and Aspergillus sojae-fermented materials (AFM) supplementation on immune responses and the gut microbiome of masu salmon Oncorhynchus masou masou were evaluated. Masu salmon (44.07 ± 7.1 g) were individually raised on a commercial diet without supplementation (control group), with B. subtilis strain DB9011 at 1.0 x 10[6] cfu/g-feed (BS group), and with A. sojae-fermented materials supplementation at 0.2 % (AFM group) for 24 days. Lysozyme activity in fish serum was determined using turbidimetric assays. Immune-related gene expression and gut microbiota were analyzed through real-time PCR and metagenomics analysis with a next-generation sequencer, respectively. Both the BS and AFM groups showed higher lysozyme activity but lower serum protein concentrations compared to the control group without significant different. The gut bacterial composition in the BS and AFM groups was dramatically different compared to that in the control group. The alpha diversity of the BS group showed significantly greater richness in terms of Chao1, faith_pb, and shannon_entropy. Conversely, the alpha diversity of the AFM group showed significantly greater richness only on faith_pb. The expression of immune-related genes such as TNF-α and IFN-γ was upregulated in the treatment group compared to the control group. IL1-β was upregulated in the AFM group. Regarding IL1-β, no differences were observed between the control and BS group. Thus, results indicated that oral administration of the BS and AFM modify gut microbiota and stimulated the expression of immune-gene expression.},
}

@article {pmid40752722,
year = {2025},
author = {Speas, RL and McCloskey, JE and Bressler, NM and Frankot, MA and Gratzol, C and Pechacek, KM and Martens, KM and Haar, CV},
title = {Caloric restriction worsens decision-making impairments and gut dysbiosis after brain injury in male rats.},
journal = {Experimental neurology},
volume = {},
number = {},
pages = {115410},
doi = {10.1016/j.expneurol.2025.115410},
pmid = {40752722},
issn = {1090-2430},
abstract = {Traumatic brain injury (TBI) causes long-term deficits in decision-making and disrupts the gut microbiome. Dysbiosis of the gut microbiome is a potential contributor to the development of multiple psychiatric and neurological disorders and may be a contributor to chronic symptoms from TBI. Caloric restriction is often used to assess psychiatric-related behaviors in animals, but also affects the gut microbiome. Thus, understanding how caloric restriction interacts with the microbiome, injury processes, and behavioral outcomes is critical. In the current study, we evaluated the effects of caloric restriction versus free feeding on a frontal controlled cortical impact TBI. Rats were trained on the rodent gambling task, an analog of the Iowa gambling task, to assess risk-based decision-making. The microbiome was sampled through the acute to subacute period post-injury and lesion size and microglia counts evaluated at 10 weeks post-injury. Caloric restriction did not affect decision-making at baseline, but did affect motivational variables. TBI impaired decision-making and this effect was exacerbated by caloric restriction. Other motivation-related variables followed a similar pattern of impairment with TBI driving impairments that were worsened by caloric restriction. The gut microbiome was initially dysbiotic, but largely recovered within 14 days post-injury. Despite this, acute gut measurements were predictive of chronic decision-making impairment. This finding could indicate a role for the gut microbiome in modifying acute and subacute TBI pathology and suggest that interventions targeting the gut may have a limited window of opportunity to treat long-term deficits.},
}

@article {pmid40752622,
year = {2025},
author = {Choi, HS and Joung, JY and Bae, HJ and Oh, NS},
title = {Fermented casein with Lactobacillus gasseri KML39 alleviates systemic inflammation interacting with the gut-brain-microbiome axis in dextran sulfate sodium-induced colitis mice.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26659},
pmid = {40752622},
issn = {1525-3198},
abstract = {This study investigated the preventive effects of fermented casein with Lactobacillus gasseri KML39 (FSC) on systemic inflammation through modulation of the gut-brain-microbiome axis in a dextran sulfate sodium (DSS)-induced colitis mouse model. Lactobacillus gasseri KML39 was selected based on its superior casein fermentation properties, proteolytic and antioxidant activities, and probiotic potential, including acid and bile tolerance and intestinal adhesion ability. We found that FSC significantly suppressed the expression of proinflammatory cytokines (COX-2, iNOS, TNF-α, IL-1β, and IL-6) and reduced nitric oxide (NO) production in LPS-stimulated RAW 264.7 cells. In DSS-induced colitis mice, body weight loss, shortened colon length, and colonic tissue damage were observed compared with the control group. Dextran sulfate sodium also activated NF-κB signaling, leading to the upregulation of iNOS and COX-2 in both colonic and brain tissues, along with elevated serum TNF-α and corticosterone levels. Furthermore, DSS treatment compromised intestinal and blood-brain barrier integrity, as indicated by the downregulation of tight junction proteins (occludin and claudin-5). Additionally, DSS negatively regulated neurotransmitter receptors (NMDAR, GABAR, and D2DR) and neurodevelopmental markers (BAX and Bcl-2) in the brain, suggesting neuroinflammatory and neurodegenerative effects. The FSC pretreatment effectively restored tight junction integrity, attenuated neuroinflammation, and improved gut microbiota composition. Notably, Proteobacteria and Bacteroides were significantly enriched in the DSS-treated group, whereas their abundance was normalized by FSC pretreatment. These findings highlight systemic inflammation as a key driver of colitis-associated neuroinflammation and demonstrate the potential of FSC as a therapeutic agent for gut-brain-microbiome axis dysfunction in colitis.},
}

@article {pmid40752589,
year = {2025},
author = {Ng, SK and Flaherty, PW and Ancheta, M and Tindbaek, KA and Sekhon, MK and Huang, JJ and Portuguese, AJ and Albittar, A and Kopmar, NE and Cowan, AJ and Shadman, M and Hirayama, AV and Till, BG and Cassaday, RD and Turtle, CJ and Liu, C and Xie, H and Leisenring, WM and Gauthier, J and Liang, EC and Hill, JA},
title = {Opportunities to improve antibiotic stewardship, and identification of blood biomarkers associated with bacteremia following CAR-T cell therapy.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2025.07.022},
pmid = {40752589},
issn = {2666-6367},
abstract = {BACKGROUND: Cytokine release syndrome (CRS) is frequent after chimeric antigen receptor T-cell therapy (CAR-T). CRS and bacteremia share clinical features, making it difficult to distinguish between the two and deliver targeted treatment. As a result, most patients with CRS receive empiric broad-spectrum antibiotics that may adversely impact long-term outcomes.

OBJECTIVES: The objectives of this study were to identify blood biomarkers that distinguish between CRS and bacteremia in the first month after CAR-T. We also describe the utilization of empiric antibiotics to identify opportunities for improved antimicrobial stewardship.

STUDY DESIGN: We identified patients who received CAR-T for hematologic malignancies between July 2013 and April 2024. We calculated the cumulative incidences of CRS and bacteremia within 30 days post-CAR-T. In a matched case control analysis, where three patients with CRS and no bacteremia (controls) were matched to each patient with bacteremia (cases), we described the clinical characteristics of CRS, bacteremia, and antibiotic exposure. We then assessed the levels and kinetics of six biomarkers (C-reactive protein [CRP], interleukin-6, ferritin, fibrinogen, lactate dehydrogenase, and D-dimer) for their ability to discriminate between bacteremia and CRS using Mann-Whitney U tests and generalized estimating equation (GEE) models.

RESULTS: Among 694 CAR-T recipients, 517 (75%; 95% confidence interval [CI], 71-78%) developed CRS. Bacteremia occurred in 19 patients with a cumulative incidence of 2.7% (95% CI, 1.7-4.2%) within 30 days and 1.4% (95% CI, 0.7-2.6%) within 14 days of CAR-T. The median time from blood culture to positive result was one day (interquartile range [IQR], 1-1). Among the 57 matched controls, CRS occurred a median of four days (IQR, 1-5) post-CAR-T, all were hospitalized for fevers, and 92% of CRS events were treated with empiric antibiotics for a median of seven days (IQR, 5-8). As a result, for every patient with bacteremia treated with antibiotics within the first 14 days, an estimated 52 patients with CRS and no serious bacterial infection received empiric antibiotics. The levels and kinetics of biomarkers were similar among cases and controls within 14 days after CAR-T. Beyond day +14, CRP, D-dimer, and ferritin levels were significantly higher among patients with bacteremia and distinguished cases from controls with moderate discrimination (area under the curve of 0.77, 0.77, and 0.81, respectively). In addition, increasing CRP and fibrinogen ≥ 14 days post-CAR-T were significantly associated with bacteremia (odds ratio [OR], 1.46; 95% CI, 1.07-2.01 and OR, 4.32; 95% CI, 1.28-14.61 per 0.25 log10 increase in biomarker level per day, respectively).

CONCLUSION: We demonstrate that most CAR-T recipients who developed CRS received empiric broad-spectrum antibiotics, but bacteremia was rare. Although blood biomarkers were unable to distinguish between CRS and bacteremia early after CAR-T, higher CRP, D-dimer, and ferritin and rising levels of CRP and fibrinogen ≥14 days post-CAR-T were associated with bacteremia and can facilitate earlier targeted interventions. These data highlight opportunities for improved antibiotic stewardship in the context of CRS, which is critical given the association between broad-spectrum antibiotic exposure, gut microbiome dysbiosis, and worse outcomes after CAR-T.},
}

@article {pmid40752380,
year = {2025},
author = {Sendo, S and Vela, AJ and Ro, M and Thiruppathy, D and Wilkinson, EL and Zhao, Z and Hsieh, WC and Yang, S and Coras, R and Bergot, AS and Guma, M and Nguyen, A and McBride, DA and Devkota, S and Thomas, R and Shah, NJ and Svensson, MND and Zengler, K and Stanford, SM and Bottini, N},
title = {Interaction between haploinsufficiency of PTPN2 and patient microbiome promotes autoimmune arthritis in mice.},
journal = {Journal of autoimmunity},
volume = {156},
number = {},
pages = {103452},
doi = {10.1016/j.jaut.2025.103452},
pmid = {40752380},
issn = {1095-9157},
abstract = {Gut dysbiosis is observed in patients with rheumatoid arthritis (RA) and juvenile idiopathic arthritis (JIA), however, how it promotes disease in interaction with other environmental and genetic risk factors remains unclear. Here we assessed interactions between gut dysbiosis and RA/JIA-associated loss of function haplotypes of the RA/JIA-associated PTPN2 gene by inducing mannan-induced arthritis in germ-free PTPN2[+/+] and PTPN2 haploinsufficient (PTPN2[+/-]) SKG mice reconstituted with fecal microbiota from six patients with seropositive RA. Mannan-induced arthritis and lymph node T cell immunophenotypes were identical in germ free PTPN2[+/+] vs PTPN2[+/-] SKG mice. While no difference in arthritis severity was seen among PTPN2[+/+] mice recipient of RA gut microbiota, two microbiomes (RA#02 and RA#86) enhanced arthritis in PTPN2[+/-] mice. The microbiome of RA patient microbiota recipient mice exclusively clustered by patient of origin and the RA#86 microbiome was found to carry a significant expansion of Prevotella genera, which is associated with RA dysbiosis. RA#86 microbiota-recipient PTPN2[+/-] mice selectively displayed increased joint GM-CSF expression and an expansion of CD4[+]RORγt[+]FoxP3[-] T cells in the joints, without evidence of increased intestinal inflammation, gut barrier leakage or expansion of P. copri in post-mannan fecal samples. Monocolonization with P. copri caused enhanced arthritis and CD4[+]RORγt[+]FoxP3[-] T cells expansion in PTPN2[+/-] vs PTPN2[+/+] mice. Our data support current views about P. copri promotion of autoimmune arthritis and suggest that its pathogenicity can be amplified via interaction with a dysbiotic context and risk factors that enhance gut mucosa immune responses.},
}

@article {pmid40752329,
year = {2025},
author = {Kamyab, H and Chelliapan, S and Khalili, E and Mediavilla, DPZ and Khorami, M and Aminabhavi, TM and Vasseghian, Y},
title = {Nanobioremediation of heavy metals using microorganisms.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126736},
doi = {10.1016/j.jenvman.2025.126736},
pmid = {40752329},
issn = {1095-8630},
abstract = {Heavy metals (HMs) in soil are a big threat to environmental and agricultural sustainability. This review discusses the development of the nanobioremediation paradigm (an approach combining nanotechnology and microbiological processes) for the treatment of HM toxicity. Recent advances in nanoparticle (NP)-based approaches to their ability to improve microbial detoxification methods, such as adsorption, redox transformation, and enzyme activation forms of microbial detoxification are discussed. Key findings suggest that many engineered NPs (e.g., zero-valent iron, biogenic metal oxides) can enhance HM immobilization efficiencies and contour microbial performances and functions of the soil microbiome. Still, there are areas of uncertainty regarding NP-microbe-soil interactions, long-term ecotoxicological effects, and applicability at the field level that are critical to be discussed. Future research directions are advised to focus on the eco-designed NPs, optimizing microbial consortia specific to the soil, and interdisciplinary frameworks linking the laboratory methods and materials to the real-world applications.},
}

@article {pmid40752197,
year = {2025},
author = {Soffritti, I and D'Accolti, M and Bini, F and Mazziga, E and Volta, A and Bisi, M and Mazzacane, S and De Cesare, A and Indio, V and Manfreda, G and Caselli, E},
title = {Harnessing probiotics and bacteriophages to fight Salmonella and limit the use of antibiotics in broilers: a study in commercial conditions.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105595},
doi = {10.1016/j.psj.2025.105595},
pmid = {40752197},
issn = {1525-3171},
abstract = {The poultry industry is facing the growing need to decrease the use of antibiotics to prevent increasing antimicrobial resistance (AMR). Toward this aim, probiotics and bacteriophages have been suggested as an alternative to antibiotics to reducing Salmonella in broilers, which poses risks to food safety and public health. Previous results showed that selected Bacillus probiotics can significantly limit broiler contamination, and anti-Salmonella phages are already available in the US and EU. However, a comprehensive evaluation of the impact of probiotics and phages on commercial poultry farms is still lacking. To this aim, a pre-post study was conducted in a poultry farm experiencing recurrent Salmonella outbreaks, to assess the anti-Salmonella effectiveness of a combined probiotic-phage approach. The study included two complete rearing cycles: T1, conducted in standard conditions and used as a control, and T2, when probiotics and phages were applied. Salmonella monitoring was performed in both the environment and broilers throughout the study periods, showing a significant 90 % decrease in Salmonella presence in T2 compared to T1 cycle (P ≤ 0.001). The decrease was observed at both the environmental and animal (caeca) levels. Notably, the whole broiler caecal microbiome was modified in T2 compared to T1 broilers, evidencing a significant increase in biodiversity accompanied by an earlier appearance of Ruminococcus, Clostridium, and Faecalibacterium genera. In parallel, broiler mortality was reduced by 72 % and broiler weight was increased by 6.4 % in T2 vs. T1 broilers (P ≤ 0.01). The findings indicate that a combined probiotic/phage approach could be a promising strategy to combat the Salmonella burden, while reducing the requirement for antibiotics and improving broiler health.},
}

@article {pmid40752193,
year = {2025},
author = {Woo, SH and An, SH and Kim, YB and Gu, BH and Kim, M and Jung, HJ and Shim, SH and Joo, SS and Ji, W and Ban, BC and Lee, KW and Kong, C and Kim, M},
title = {Poncirus trifoliata peel extract supplementation elevates gut CD4+ T cells and microbial diversity in both laying hens and broilers.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105548},
doi = {10.1016/j.psj.2025.105548},
pmid = {40752193},
issn = {1525-3171},
abstract = {Intestinal diseases have long plagued the chicken industry, leading to reduced egg production in laying hens and compromised growth performance in broilers, causing significant economic losses in the farming industry. For that reason, natural products have been widely used as dietary immunomodulators in the chicken industry to prevent infectious diseases while sustaining a healthy gut, regulating immune cells, maintaining the gut barrier, and balancing the microbiome. However, the impact of Poncirus trifoliata, a member of the citrus family, on the health, immunity, and productivity of laying hens and broilers has not yet been clearly elucidated. Therefore, we evaluated the effect of the Poncirus trifoliata peel extract (PE) on the growth performance of broilers and egg production in laying hens. Additionally, we analyzed gut immune-related parameters, including oxidative stress indices, gut barrier functions, and gut microbiome. Approximately 21-week-old laying hens and 1-day-old broilers were randomly divided into two groups: one group was fed a control (CON) diet and the other was fed a diet supplemented with PE. The PE group exhibited increased expression of glutathione peroxidase 2 (Gpx2; P < 0.01) in laying hens and occludin (Ocln; P < 0.01) in broilers. Furthermore, PE treatment increased the CD4+ T cell populations (P < 0.01) and the gut microbial diversity in the intestine of both laying hens and broilers. Our findings suggest that PE administration could be a promising strategy for improving intestinal health in laying hens and broilers by modulating tight junction expression, intestinal immune cells, and the microbial communities.},
}

@article {pmid40752139,
year = {2025},
author = {Jennifer, LG and Larnaudie, A and Béné, MC and Cocherie, T and Perazzi, M and El-Houat, Y and Kammerer, E and Bastit, V and Pointreau, Y},
title = {Relationships between oral microbiome and head and neck squamous cell carcinoma: a systematic review.},
journal = {Oral oncology},
volume = {168},
number = {},
pages = {107571},
doi = {10.1016/j.oraloncology.2025.107571},
pmid = {40752139},
issn = {1879-0593},
abstract = {BACKGROUND: There is growing evidence about oral dysbiosis in patients with head and neck squamous cell carcinoma (HNSCC).

METHODS: A Pubmed literature search was performed on March 2025, with "oral microbiome" and "head and neck cancer" keywords.

RESULTS: Alterations in the oral microbiome have been described in patients with HNSCC, at the salivary and intratumoral level, with enrichment in bacteria associated with periodontal disease, and a relative reduction in commensal bacteria. A strong association between dysregulation of the oral microbiome and hallmarks of cancer has been demonstrated, including deregulation of cellular metabolism, sustained proliferative signaling, induction of hypoxia, immunosuppression, inflammation and genome instability.

CONCLUSIONS: The development of microbial models integrating salivary abundance of selected bacteria might favor non-invasive screening procedures in high-risk populations. Baseline oral microbiome appears as a significant prognosticator of both treatment efficacy and overall survival, highlighting new possibilities for modulation through medical intervention and treatment personalization.},
}

@article {pmid40752126,
year = {2025},
author = {Hong, W and Yang, S and Shu, W and Price, G and Song, L},
title = {Spatiotemporal dynamics of multi-kingdom microbiome interactions drive CNPS cycling in landfills.},
journal = {Waste management (New York, N.Y.)},
volume = {206},
number = {},
pages = {115048},
doi = {10.1016/j.wasman.2025.115048},
pmid = {40752126},
issn = {1879-2456},
abstract = {Landfill ecosystems represent significant terrestrial carbon sinks, where municipal solid waste (MSW) undergoes decomposition and transformation through biochemical reactions mediated by multi-kingdom microbiome. However, the spatial and temporal characterization of microbial interactions and collaboration within these multi-kingdom microbiomes remain largely unknown. In this study, we reveal the hierarchical and collaborative mechanisms by which multi-kingdom microbiomes drive carbon, nitrogen, phosphorus, and sulfur cycling across a 30-meter landfilling depth, corresponding to a landfilling age of 1 to 4 years. Through integration of metagenomics and network analyses, we elucidated vertical succession patterns in microbial community structure and function. The surface layer (1-2 years) was centered on bacterial-dominated primary metabolism, with Enterococcus aquimarinus and Brevundimonas bullata inferred to mediate metabolic coupling through fermentation, nitrogen fixation andphosphorus solubilization. Concurrently, phage-driven host lysis may contribute to the suppression of acidification. In the middle layer (2-3 years), co-occurrence patterns between archaea and fungi suggest mutualistic interaction supporting methanogenesis, wherein fungi such as Anaeromyces robustus would supply key substrates for methanogens such as Methanofollis ethanolicus. In the bottom layer (3-4 years), fungi, bacteria, and viruses collaborate under nutrient-limited conditions, with phages employing a "kill-the-winner" approach to sustain ecosystem function and stability. Collectively, our findings indicate that key microbial connectors across kingdoms contribute to elemental cycling through cross-kingdom interaction, including substrate exchange and nutrient supply. This study advances our understanding of multi-kingdom microbial dynamics during MSW decomposition and offers a conceptual framework for enhancing biogeochemical cycling efficiency within landfill ecosystems.},
}

@article {pmid40752116,
year = {2025},
author = {Kremer, FS and Rodrigues, RDS and Omori, WP and de Oliveira, RR and de Oliveira, GAS and Nero, LA},
title = {Prediction of blown pack in vacuum-packaged beef based on microbiome profiles and supervised machine learning.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111375},
doi = {10.1016/j.ijfoodmicro.2025.111375},
pmid = {40752116},
issn = {1879-3460},
abstract = {The preservation of vacuum-packaged beef products is essential for maintaining shelf life. However, the occurrence of blown pack phenomenon, characterized by the expansion of packaging due to gas production by spoilage microorganisms, is still a challenge. In the present work, we demonstrate that microbiome analysis using next generation sequencing (NGS) and machine learning might be useful in the analysis, modeling and prediction of spoilage and blown pack in vacuum-packaged beef. Beef systems (n = 10) were vacuum-packed, stored at 4 and 15 °C, and their populations were monitored based on NGS at 0 h and 7, 14, 21 and 28 days. Our analysis allowed the prediction of blown pack based on information of the initial microbiome in beef and storage conditions, identification of the relationship of different bacteria genera associated with spoilage along with temperature, which were consistent with differential abundance analysis, and estimate the relationship of temperature and blown pack. Using SHAP (Shapley Additive Explanations) to interpret the XGBoost model, we identified temperature as the most influential factor in blown pack prediction when considering microbiome data from day zero. Additionally, SHAP analysis of Random Forest and XGBoost models based on OTU Spearman correlation and linear regression, computed about time, highlighted Peptoniphilus as the most important bacterial genus, followed by Hafnia and Peptostreptococcus. Additional studies might extend these methods for other types of meat, cuts and including additional storage conditions, allowing a better modeling of the dynamics in the microbiome associated with the blown pack phenomenon.},
}

@article {pmid40751913,
year = {2025},
author = {Santiago-Borges, JM and Rosen, AL and Hernandez-Leyva, A and Tomera, CP and Lint, MA and Paharik, AE and Vanyo, V and Pinkner, JS and Dodson, KW and Chen, SL and Hsieh, CS and Hultgren, SJ and Kau, AL},
title = {Uropathogenic Escherichia coli niche occupancy determines the effects of mucosal vaccine against FimH.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116077},
doi = {10.1016/j.celrep.2025.116077},
pmid = {40751913},
issn = {2211-1247},
abstract = {In people with urinary tract infections (UTIs), uropathogenic Escherichia coli (UPEC) often colonizes the gut, forming a reservoir and contributing to recurrent UTIs. Mucosal immunization targeting UPEC within the gut presents a promising antibiotic-sparing strategy to prevent UTIs by depleting this reservoir. The FimH adhesin that tips type 1 pili is a critical virulence factor in UTI and aids in gut colonization. Here, we assess the potential of a FimH mucosal vaccine to reduce UPEC gut colonization in mice. Our findings show that vaccine-induced depletion of an introduced UPEC strain was influenced by microbial competition from pre-established microbes. This competition partially restricted the incoming UPEC strain to the mucus, where immunization was associated with reduced FimH expression. These results demonstrate that oral FimH vaccine effectiveness relies on intra-niche competition, underscoring the complexity of host-pathogen interactions that must be considered as we refine immune tools to target gut microbes.},
}

@article {pmid40751880,
year = {2025},
author = {Varghese, EM and George, J and Hareendran, A and Anilkumar, A and Narayanan, AAY and James, J and Thykoottathil, V and Prasad, A and Perincherry, L and Cyriac, B and Jisha, MS},
title = {Dynamics of rice microbiome: insights into functional diversity, environmental influences, response to stress, and applications.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {296},
pmid = {40751880},
issn = {1573-0972},
support = {7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; 7134/SC/ST Cell/2023/MGU//Rashtriya Uchchatar Shiksha Abhiyan (RUSA), Govt. of India/ ; },
mesh = {*Oryza/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; Stress, Physiological ; Rhizosphere ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Agriculture ; },
abstract = {Rice is the primary diet for the vast majority of the world's population. Since rice is a mainstay of the diet for most Asians, research must be prioritized to boost rice productivity. Scientific advances have unveiled various techniques for sustainable rice production. One promising strategy is understanding plant-microbe interactions, which significantly affect plant health, growth, and productivity. In addition to its agricultural significance, the rice plant harbors a diverse microbiome within its rhizosphere, phyllosphere, and endosphere, which plays a crucial role in its growth, health, and resilience to stress. This review examines the intricate interactions within the rice microbiome, highlighting its functional diversity and critical roles in nutrient cycling, pathogen control, and stress alleviation. Soil properties, environmental circumstances, and agronomic methods are crucial determinants influencing microbial community composition and functionality. Additionally, the rice microbiome demonstrates dynamic alterations under stress conditions, adapting to biotic and abiotic challenges. The mechanisms involved in the rice microbial community assembly and shifts under various stress situations are also dealt. Lastly, the progress in microbiome research, the prospects for microbiome-based therapies in rice cultivation, and the difficulties in applying these insights into field applications are highlighted. Therefore, a deeper understanding of the microbial shifts during various stress conditions and extensive studies on the functional aspects of rice microbiome, attained through this review, present transformative prospects for improving agricultural resilience, productivity, and sustainability amid global environmental and food security issues.},
}

*Oryza/microbiology/growth & development
*Microbiota
Soil Microbiology
Stress, Physiological
Rhizosphere
Bacteria/classification/genetics/isolation & purification
Biodiversity
Agriculture

@article {pmid40751875,
year = {2025},
author = {Malik, YS and Pathania, A and De, UK and M, M and Panwar, H and Kaur, J and Mishra, A and Kumar, N and Ghosh, S and Sarkar, VK and Sakshi, },
title = {Exploring the Therapeutic Landscape of Probiotics in Enteric and Respiratory Viral Infections.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40751875},
issn = {1867-1314},
abstract = {In recent times, the understanding of the human microbiome and its impact on health and disease has undergone a paradigm shift, leading to ground-breaking discoveries in the field of probiotics. Probiotics, live microorganisms known for conferring health benefits when administered adequately, have garnered significant interest for their potential to modulate the immune system's response to viral infections in both humans and animals. The emergence of enteric and respiratory viruses as significant global health threats has prompted intensive research efforts to identify novel therapeutic strategies. Traditional antiviral therapies often face challenges such as drug resistance, limited efficacy and adverse effects, underscoring the urgent need for alternative approaches. In this context, probiotics have emerged as a promising avenue for the prevention and treatment of viral infections due to their ability to modulate the host immune response, enhance mucosal barrier function and exert direct antiviral effects. This review aims to provide a comprehensive overview of the therapeutic landscape of probiotics against enteric and respiratory viruses. Based on latest findings from preclinical and clinical studies, we have explored the mechanisms underlying the antiviral activity of probiotics and their potential role in mitigating viral infections. Furthermore, promising avenues for harnessing probiotics as adjunctive or standalone interventions against enteric and respiratory viral infections have been discussed here.},
}

@article {pmid40751848,
year = {2025},
author = {Amobonye, A and Pillay, B and Hlope, F and Asong, ST and Pillai, S},
title = {Postbiotics: an insightful review of the latest category in functional biotics.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {293},
pmid = {40751848},
issn = {1573-0972},
support = {CPRR240509218140//This study was supported by grants from the National Research Foundation, Republic of South Africa./ ; },
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome/drug effects ; Prebiotics ; *Functional Food ; Animals ; Synbiotics ; Bacteria/metabolism ; },
abstract = {Postbiotics have recently emerged as one of the latest functional food products due to the ever-evolving landscape for microbiome-targeted health interventions. Postbiotics, along with other functional biotics, viz., probiotics, prebiotics and synbiotics, confer their health benefits mainly via the modulation of the gut microbiota. Postbiotics are considered more promising than probiotics as they elicit similar effects, despite being inactivated, thus relegating concerns of strain activity and stability that have been raised about probiotics. This review attempts to provide critical insights into postbiotics by firstly revising its definition to create a streamlined framework for further discourse on the interplay between postbiotics, nutrition, microbiota, and health. Similarly, this review establishes the nexus between postbiotics and probiotics while highlighting that postbiotics can also be derived from other microbes apart from lactobacilli such as yeasts and fungi. Furthermore, an overview of the extraction and production of postbiotics are presented as well as the biochemistry of short-chain fatty acids, enzymes, peptides, polysaccharides, peptidoglycans and teichoic acids, which have all been identified as postbiotic components. Finally, their bioactivities (antioxidant, anti-inflammatory, antidiabetic, immunomodulatory, anti-hypertensive, antimicrobial) and the patent landscape of postbiotics are evaluated to promote its innovative applications in the food, veterinary, pharmaceutical and cosmetic industries. Having identified major gaps and areas of improvement, it is believed that this critical review will serve as a guide in the increasing effort to advance the industrial potential of postbiotics.},
}

*Probiotics
Humans
*Gastrointestinal Microbiome/drug effects
Prebiotics
*Functional Food
Animals
Synbiotics
Bacteria/metabolism

@article {pmid40751379,
year = {2025},
author = {Dong, L and Xin, Z and Zhang, C and Valverde-Pérez, B and Song, C},
title = {Sea Ice Freezing and Melting Modulate the Estuarine Sediment Nitrogen Removal Process Through Affecting the Microbiome.},
journal = {Global change biology},
volume = {31},
number = {8},
pages = {e70387},
doi = {10.1111/gcb.70387},
pmid = {40751379},
issn = {1365-2486},
support = {2023YFC3208402//National Key Research and Development Program of China/ ; 42293263//National Natural Science Foundation of China/ ; 52422904//National Natural Science Foundation of China/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; *Microbiota ; Estuaries ; *Freezing ; *Nitrogen/metabolism ; Climate Change ; *Ice Cover/microbiology ; Bacteria/metabolism ; Denitrification ; Nitrification ; },
abstract = {Climate change accelerates sea ice dynamics, and its freezing and melting profoundly alter the bottom water environment, affecting microbial ecosystems and biogeochemical processes. However, the holistic effects of sea ice-induced environmental changes on microbial nitrogen removal processes in estuaries remain unclear. This study conducted a sea ice freezing and melting simulation and investigated the response mechanism of microbial nitrogen removal processes in estuarine sediments to sea ice dynamics by combining [15]N labeling and molecular techniques. Results indicated that temperature was the most critical factor influencing nitrifying microorganisms and nitrification rates during sea ice freezing and melting. The increase in nitrate availability at the early stage of freezing enhanced microbial denitrification, followed by decreased denitrification rates due to the inhibitory effects of high salinity and low temperatures on denitrifying bacteria abundance. Anammox rates decreased during the freezing period, primarily due to the inhibitory effects of increased salinity, and recovered during the melting period. It was estimated that approximately 26%-30% of the annual terrestrial inorganic nitrogen input was removed by estuarine sediments, with approximately 87%-89% of this removal occurring via denitrification and 11%-13% via anammox. The inorganic nitrogen flux removed via sediment during sea ice period accounted for about 7% of the annual total removal flux. Overall, this study reveals how sea ice dynamics regulate microbial nitrogen removal in estuarine sediments, providing valuable insights into predicting and managing nitrogen removal in cold-region estuaries under global climate change.},
}

*Geologic Sediments/microbiology/chemistry
*Microbiota
Estuaries
*Freezing
*Nitrogen/metabolism
Climate Change
*Ice Cover/microbiology
Bacteria/metabolism
Denitrification
Nitrification

@article {pmid40751372,
year = {2025},
author = {Bryant, JA and Straub, TJ and Pardi, DS and Litcofsky, KD and Kelly, CR and Chafee, ME and Cohen, SH and Khanna, S and Berenson, CS and Wortman, J and Sims, M and Ford, CB and Lombardo, MJ and McGovern, BH and von Moltke, L and Kraft, CS and Henn, MR and Hasson, BR},
title = {Comparability of gastrointestinal microbiome and bile acid profiles in patients with first or multiply recurrent Clostridioides difficile infection.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf408},
pmid = {40751372},
issn = {1537-6613},
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) treatment guidelines suggest varied approaches for patients with first (frCDI) or multiply recurrent CDI (mrCDI). Low microbial diversity, elevated primary bile acids (BA), and low secondary BA concentrations favor germination of C. difficile spores into toxin-producing bacteria and are believed to increase rCDI risk. Greater understanding of the gastrointestinal (GI) microbiome in rCDI may inform management of the disease. We describe a post hoc comparison of GI microbiome and bile acid profiles between patients with frCDI and mrCDI in a Phase 3 open-label trial, ECOSPOR IV, of fecal microbiota spores, live-brpk (VOWST®; VOS, formerly SER-109), an orally-administered live microbiome therapeutic.

METHODS: Patients received VOS following symptom resolution after standard-of-care antibiotics. Pre-treatment baseline (within 3 days following antibiotic completion) and week 1 post-dosing stool samples were collected for whole metagenomic sequencing and metabolomics. Diversity was calculated from MetaPhlAn2 species profiles. Concentrations of primary and secondary BAs were measured via targeted LC-MS/MS.

RESULTS: rCDI rates through week 8 were similarly low in both frCDI and mrCDI patients (6.5% vs. 9.7%, respectively). Baseline microbial diversity was similarly low between frCDI and mrCDI subgroups (p>0.05). Diversity and secondary BA concentrations increased in both subgroups, whereas primary BA concentrations declined following VOS dosing, leading to few differences between subgroups at Week 1.

CONCLUSIONS: These data suggest commonalities in microbiome disruption in patients with frCDI and mrCDI that contribute to recurrence and suggest that antibiotics followed by a live microbiome therapy may be an optimal treatment strategy for rCDI, regardless of number of prior CDI recurrences.},
}

@article {pmid40751369,
year = {2025},
author = {Hopkins, JR and Vizzari, G and Bennett, AE and Malacrinò, A},
title = {Fire Limits Soil Microbial Dispersal and Differentially Impacts Bacterial and Fungal Communities.},
journal = {Global change biology},
volume = {31},
number = {8},
pages = {e70386},
doi = {10.1111/gcb.70386},
pmid = {40751369},
issn = {1365-2486},
support = {ECS0000009//Ministero dell'Università e della Ricerca/ ; },
mesh = {*Soil Microbiology ; *Fires ; *Fungi/physiology/classification ; *Bacteria/classification ; *Microbiota ; Climate Change ; Ecosystem ; *Mycobiome ; Biodiversity ; },
abstract = {Fire is a globally pervasive force reshaping ecosystems, yet its influence on the ecological processes structuring soil microbiomes remains poorly understood. Using a meta-analysis of > 2600 amplicon sequencing samples across 19 global studies, we tested whether fire alters soil microbiome assembly processes, diversity, and ecological selection for pyrophilic specialists. Contrary to prevailing assumptions, we found that fire did not significantly shift ecological selection processes in bacteria or fungi but instead constrained dispersal, particularly reducing dispersal in bacterial and fungal communities and increasing ecological drift in fungi. Despite limited evidence for ecological selection, fire consistently filtered for specialist taxa, increasing their relative abundance across microbial communities. Fire also reduced fungal diversity and evenness, while bacterial communities exhibited greater dominance and loss of rare taxa. These findings support the idea that fire promotes microbial post-fire niche specialization while disrupting dispersal pathways. Our results indicate that increasing fire frequency and severity under climate change may homogenize soil microbial communities, reduce microbial resilience, and constrain ecosystem recovery.},
}

*Soil Microbiology
*Fires
*Fungi/physiology/classification
*Bacteria/classification
*Microbiota
Climate Change
Ecosystem
*Mycobiome
Biodiversity

@article {pmid40751229,
year = {2025},
author = {Kumar, P and Chandel, RS and Verma, SC and Sharma, N and Saini, S and Bishist, R and Lata, S},
title = {Biostimulation through natural biological inputs on fruiting, nutrient availability and rhizosphere microbiome in legume intercropped 'Sweet Charlie' strawberry (Fragaria × Ananassa Duch.).},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1009},
doi = {10.1186/s12870-025-07017-4},
pmid = {40751229},
issn = {1471-2229},
}

@article {pmid40751224,
year = {2025},
author = {Reinoso-Peláez, EL and Saura, M and González, C and Ramón, M and Calvo, JH and Serrano, M},
title = {The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {177},
pmid = {40751224},
issn = {2049-2618},
support = {RTI-2018-096487-R-C33//Ministerio de Ciencia, Innovación y Universidades/ ; },
mesh = {Female ; Animals ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Sheep/microbiology ; *Fertility ; *Bacteria/classification/genetics/isolation & purification ; Pregnancy ; Genomics ; Metagenome ; },
abstract = {BACKGROUND: Despite advancements in artificial insemination, sheep fertility rates remain suboptimal. Recent studies in other species highlight the critical role of reproductive microbiota in influencing fertility outcomes. This research explores the relationship between ovine vaginal microbiota, associated functional pathways, and fertility using advanced nanopore long-reading metagenomic sequencing on 297 ewes from three Spanish breeds across four herds. The study aimed to describe a core vaginal microbiota, analyse the complex interactions with herd, breed, age, and parity factors, and identify taxa and genes associated with reproductive success by artificial insemination.

RESULTS: The study identified Staphylococcus, Escherichia, and Histophilus as the most abundant genera. Microbial communities varied considerably between breeds and herds, with high predictive accuracy (> 90%) in classification models. Differential abundance analysis revealed that the genera Histophilus, Fusobacterium, Bacteroides, Campylobacter, Streptobacillus, Gemella, Peptoniphilus, Helococcus, Treponema, Tissierella, and Phocaeicola were more abundant in non-pregnant ewes. Some of these taxa were also associated with four COG entries and one KEGG orthologue significantly linked to non-pregnancy, primarily involving carbohydrate metabolism, defence mechanisms, and structural resilience. Age and parity were also associated with microbiota composition, particularly in ewes older than five years or with more than three parturitions, suggesting that cumulative physiological changes may contribute to microbial shifts over time.

CONCLUSIONS: The ewe's vaginal microbiome appears to be mainly influenced by both herd and breed, though distinguishing genetic from environmental factors is challenging within our study design. While the overall microbiota showed a subtle effect on pregnancy, certain genera had a significant negative impact, likely due to pathogenic or inflammatory properties that disrupt reproductive health. The metagenomic approach used here enabled not only comprehensive taxonomic classification but also detailed functional analysis, providing deeper insights into the microbiome's role in reproductive outcomes. Video Abstract.},
}

Female
Animals
*Vagina/microbiology
*Microbiota/genetics
*Metagenomics/methods
Sheep/microbiology
*Fertility
*Bacteria/classification/genetics/isolation & purification
Pregnancy
Genomics
Metagenome

@article {pmid40750967,
year = {2025},
author = {Chen, S and Li, Y and Liu, J and Wu, J and Zhao, H and Cao, R and Zhou, S},
title = {Gut Microbial Metabolite Crosstalk in Crohn's Disease: Network Pharmacology Unveils Dual-Axis Pathogenesis and Therapeutic Targets.},
journal = {BioFactors (Oxford, England)},
volume = {51},
number = {4},
pages = {e70038},
doi = {10.1002/biof.70038},
pmid = {40750967},
issn = {1872-8081},
support = {82460757//National Natural Science Foundation of China/ ; ZDYF2023SHFZ114//Hainan Province Science and Technology Special Fund/ ; },
mesh = {*Crohn Disease/microbiology/drug therapy/metabolism/genetics/pathology ; *Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Network Pharmacology ; Proto-Oncogene Proteins c-akt/genetics/metabolism ; Signal Transduction ; Protein Interaction Maps ; Molecular Dynamics Simulation ; Molecular Docking Simulation ; PPAR gamma/genetics/metabolism ; },
abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, is driven by dysregulated interactions between gut microbiota and host metabolism. Here, we developed a computational framework integrating multiomics profiling, network pharmacology, and molecular dynamics simulations to systematically map microbiota-metabolite-target-signaling (M-M-T-S) networks and identify therapeutic candidates. By analyzing gut microbial metabolomics and CD-associated targets (via SwissTargetPrediction [STP]/SEA), we constructed a protein-protein interaction (PPI) network enriched for 50 intestinal hub targets (IL6, AKT1, PPARG; degree centrality [CD] > 19.4), which orchestrate inflammatory (TNF/IL-17/TLR, FDR = 3.8 × 10[-12]) and metabolic (PPAR, FDR = 1.5 × 10[-10]) pathways. Structure-based screening (AutoDock Vina/AMBER20) revealed 3-indolepropionic acid (IPA) as a high-affinity AKT1 binder (ΔG = -67.4 kJ/mol), while Genipin exhibited robust binding to PTGS2, both validated by 100-ns dynamics simulations (RMSD < 3.8 Å). Mechanistic network analysis uncovered a dual-axis regulatory paradigm: a pro-inflammatory axis (Clostridiumspp.-derived LPS aggravates Th17 polarization via TLR4/IL-17 signaling) and a reparative axis (Faecalibacterium prausnitzii-produced butyrate enhances barrier integrity through PPARγ-mediated NF-κB suppression). Phylogenetic analysis linked microbial functional traits (e.g., LPS/SCFA synthesis) to evolutionary conservation, highlighting clade-specific roles in CD progression. Drug-likeness evaluation (SwissADME/ADMETlab 2.0) prioritized IPA as a lead candidate due to its superior solubility (7.65 mg/mL), nonhepatotoxic profile, and AhR agonism, outperforming Genipin. This study establishes IL6/AKT1/PPARG as central therapeutic hubs and positions IPA for clinical translation. Our framework bridges multiomics integration with precision medicine, offering a scalable strategy to decode microbiome-driven pathologies and accelerate metabolite-based therapeutics.},
}

*Crohn Disease/microbiology/drug therapy/metabolism/genetics/pathology
*Gastrointestinal Microbiome/drug effects/genetics
Humans
Network Pharmacology
Proto-Oncogene Proteins c-akt/genetics/metabolism
Signal Transduction
Protein Interaction Maps
Molecular Dynamics Simulation
Molecular Docking Simulation
PPAR gamma/genetics/metabolism

@article {pmid40750891,
year = {2025},
author = {Tsementzi, D and Meador, R and Eng, T and Shelton, J and Scott, I and Konstantinidis, KT and Modesitt, S and Bruner, DW},
title = {Associations among HPV persistence, the vaginal microbiome, and cervical cancer recurrence.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {858},
pmid = {40750891},
issn = {1479-5876},
support = {Supplement to Winship Cancer Institute//Winship Cancer Institute/ ; Emory University//Winship Cancer Institute/ ; 3 P30 CA138292-13//Winship Cancer Institute/ ; unrestricted fund from Sigma Theta Tau Foundation/Oncology Nursing Foundation.//Oncology Nursing Foundation/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology/virology ; *Microbiota ; *Uterine Cervical Neoplasms/microbiology/virology/pathology ; *Neoplasm Recurrence, Local/microbiology/virology/pathology ; Middle Aged ; *Papillomaviridae/physiology ; Adult ; Aged ; Longitudinal Studies ; *Papillomavirus Infections/complications/virology ; },
abstract = {BACKGROUND: In the US, up to 60% of cervical cancer (CxCa) survivors will have persistent HPV infection, the causative agent of CxCa, and up to 35% will develop recurrent local CxCa within 4 years after chemo-radiation therapy. Preliminary studies suggest healthy vaginal microbiome (VM) could affect the acquisition, persistence, and clearance of HPV. Through longitudinal studies, we investigate associations between the dynamics of VM, HPV persistence, cancer recurrence (CR), and outcomes in gynecologic cancer survivors who completed cancer treatments.

METHODS: We enrolled 49 patients with Stage IB-IIIC CxCa who completed radiation therapy (RT) alone or concurrent chemoradiation (chemoRT). VM sequencing and HPV typing were performed on samples obtained at baseline (T0, pre-treatment), T1, T2, and T3 (3, 6, and 12 months after the completion of cancer treatment). Patients were evaluated for CR up to 4 years following the end of treatment.

RESULTS: Among all patients, 33% (16/49) had CxCa recurrence within 2-3 years post-therapy. The vaginal microbiome exhibited high diversity, Prevotella-dominant communities; only 20% were dominated by lactobacilli at any time. Post-treatment hrHPV was detected in 17 out of 41 women (41.5%) with follow-up samples. We identified key taxa, such as Prevotella species, which were highly associated with CxCa recurrence and post-treatment detection of hrHPV.

CONCLUSIONS: Our findings link Prevotella-dominant, high diversity vaginal microbiome communities with post-therapy hrHPV persistence and cervical cancer recurrence in gynecologic cancer survivors. Such findings warrant further research into the role of the microbiome in modulating cervical cancer progression and response to therapy, suggesting modulation of the microbiome with probiotics or other methods could be considered a novel approach to improve cervical cancer treatment outcomes.},
}

Female
Humans
*Vagina/microbiology/virology
*Microbiota
*Uterine Cervical Neoplasms/microbiology/virology/pathology
*Neoplasm Recurrence, Local/microbiology/virology/pathology
Middle Aged
*Papillomaviridae/physiology
Adult
Aged
Longitudinal Studies
*Papillomavirus Infections/complications/virology

@article {pmid40750823,
year = {2025},
author = {Adebayo, AA and Enagbonma, BJ and Babalola, OO},
title = {Comparative metagenomics on community structure and diversity of rhizomicrobiome associated with monoculture and soybean precedent carrot.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28161},
doi = {10.1038/s41598-025-13605-z},
pmid = {40750823},
issn = {2045-2322},
mesh = {*Daucus carota/microbiology/growth & development ; *Glycine max/microbiology/growth & development ; Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Plant Roots/microbiology ; Biodiversity ; Agriculture/methods ; },
abstract = {Several studies have explored the impact of cropping systems, including monoculture and crop rotation, on the plant rhizosphere - an essential dynamic in designing strategies for optimizing soil health and crop productivity. It remains largely unknown how these agricultural practices drive the diversity and community structure of the microbiome in the carrot rhizosphere. Thus, this study aims to profile the core rhizo-microbiome of carrots grown under a monoculture system and those grown after soybean cultivation. The microbial DNA extracted from 12 soil samples collected from monoculture carrot rhizosphere (MCR), soybean-precedent carrot rhizosphere (SCR), and uncultivated land (bulk soils) (BS) were analyzed via shotgun metagenomics sequencing. Findings show that bacterial phyla were the most dominant taxa across the sampling points. Principal Component Analysis (PCA) revealed that Pseudomonadota, Bacillota, and Actinomycetota are significantly enriched in soybean-precedent carrot rhizosphere, monoculture carrot rhizosphere, and bulk soil, respectively. Furthermore, genera Bradyrhizobium and Agromyces were significantly enriched, and Rhodococcus was exclusively present in soybean-precedent carrot rhizosphere. Alpha and Beta diversity analyses indicated that the microbial community composition was unique within and between the sampling sites (genus level). Redundancy Analysis (RDA) demonstrated that soil properties like silt (contributing 84.2%), total nitrogen (contributing 83.2%), organic carbon (contributing 81.0%), and sand texture (contributing 75.8%) explained the variance in microbiome composition. This study provides fundamental insight into how cropping systems influence carrot rhizo-microbiome. Crop rotation practice with soybeans was found to increase microbial composition and diversity in carrot plantations.},
}

*Daucus carota/microbiology/growth & development
*Glycine max/microbiology/growth & development
Rhizosphere
*Metagenomics/methods
Soil Microbiology
*Microbiota/genetics
*Bacteria/genetics/classification
Plant Roots/microbiology
Biodiversity
Agriculture/methods

@article {pmid40750665,
year = {2025},
author = {Kim, JH and Kim, JS and Eo, H and Yang, S and Lee, CH and Park, SA and Oh, MS},
title = {Streptomyces rimosus-rich soil exposure alleviates depression-like behaviors by modulating neuroinflammation and synaptic plasticity in mice with stress.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28117},
pmid = {40750665},
issn = {2045-2322},
support = {NRF-2022R1A2C1012553//National Research Foundation of Korea/ ; },
mesh = {Animals ; Mice ; *Neuronal Plasticity/drug effects ; *Depression ; *Streptomyces/metabolism ; *Soil Microbiology ; *Stress, Psychological ; Male ; *Neuroinflammatory Diseases ; Cytokines/metabolism ; Behavior, Animal ; Microglia/metabolism ; Disease Models, Animal ; Soil/chemistry ; Mice, Inbred C57BL ; },
abstract = {Soil contains a wide range of microbial communities. Recently, direct exposure to soil and soil microbes has been reported to have a positive effect on emotional integrity. Among the soil microbes, Streptomyces rimosus is known to produce geosmin, which have a unique odor and positive effects on mental status. In this context, this study aimed to investigate the effects of direct exposure to soil containing S. rimosus on depression-like behavior and depression-related factors in the mouse. To induce depression, the mice were exposed to chronic restraint stress (CRS) for 14 days, and direct soil exposure continued for 17 days from the first day of CRS. The results showed that direct exposure to soil containing S. rimosus alleviated the CRS-induced depression-like behavior. Additionally, S. rimosus-rich soil exposure reduced the activation of microglia and astrocyte in the depression-related brain area, and reduced the mRNA expression levels of cytokines including interleukin (IL)-6, interferon-γ, and IL-17 A. Moreover, S. rimosus-rich soil contact increased synaptic plasticity, which was reduced by CRS. The same effects were not observed in the group exposed to sterilized soil. Collectively, the current study suggests that S. rimosus soil contact can be a beneficial psychological therapeutic strategy for patients with mental illnesses.},
}

Animals
Mice
*Neuronal Plasticity/drug effects
*Depression
*Streptomyces/metabolism
*Soil Microbiology
*Stress, Psychological
Male
*Neuroinflammatory Diseases
Cytokines/metabolism
Behavior, Animal
Microglia/metabolism
Disease Models, Animal
Soil/chemistry
Mice, Inbred C57BL

@article {pmid40750543,
year = {2025},
author = {Wen, Z and Yu, P and Shen, J and Lambers, H},
title = {Do rhizosphere microbiomes match root functional traits?.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2025.07.002},
pmid = {40750543},
issn = {1872-8383},
abstract = {Land plants and microorganisms have developed intricate partnerships during millions of years of coevolution. However, it remains largely unknown how rhizosphere microbiomes align with diverse root functional traits among and within species. We argue that deciphering the bidirectional interactions of root traits with microbial partners is pivotal for understanding rhizosphere processes and belowground ecosystem functioning. We review emerging evidence illustrating how root functional traits shape rhizosphere microbiomes and how rhizosphere microbiomes modulate root-trait expression. We conclude that rhizosphere microbiota and root traits comprise a holistic evolutionary unit that governs plant health and belowground resource acquisition. This knowledge provides valuable insights into the adaptive evolution of plant host-microbe associations and informs strategies to leverage their beneficial interactions for sustainably managed systems.},
}

@article {pmid40750518,
year = {2025},
author = {Li, SJ and Miao, JX and Wang, F and Wang, HY and Ma, YW and Jiang, Y and Xue, X},
title = {Salvia miltiorrhiza components and gut microbiota interactions in Helicobacter pylori infection.},
journal = {Journal of integrative medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joim.2025.07.006},
pmid = {40750518},
issn = {2095-4964},
abstract = {Salvia miltiorrhiza (Danshen) is a traditional Chinese herb that is commonly known for its cardiovascular and hepatoprotective benefits. Recent studies have confirmed that Danshen and its bioactive components can influence gut microbial homeostasis, thereby affecting Helicobacter pylori (HP) colonization in the human stomach. HP is a bacterial pathogen associated with various gastrointestinal diseases. Current HP treatments mainly involve antibiotics and proton pump inhibitors. However, their efficacy is strongly compromised by the rapid emergence of antibiotic resistance in HP and genetic heterogeneity among patients. The interaction between Danshen and gut microbial status provides a novel perspective for HP treatment. Understanding the medical properties of Danshen in altering gut microbiota and eliminating HP, as well as the underlying mechanisms, is important for improving human gastrointestinal healthcare. This review investigates the interaction between Danshen and gut microbiota and its impact on HP infection using databases including Web of Science, PubMed, and Google Scholar. We explored the unconventional intersection between Danshen, gut microbiota, and HP infection, shedding light on their intricate interplay and potential therapeutic implications. A comprehensive understanding of this interaction provides valuable insights into developing novel therapeutic strategies that target the gut microbiota to mitigate HP-associated gastrointestinal disorders. Please cite this article as: Li SJ, Miao JX, Wang F, Wang HY, Ma YW, Jiang Y, Xue X. Salvia miltiorrhiza components and gut microbiota interactions in Helicobacter pylori infection. J Integr Med. 2025; Epub ahead of print.},
}

@article {pmid40750488,
year = {2025},
author = {Lopes, ACA and Martins, LV and Ferreira, GNC and Trivedi, P and Araujo, ASF},
title = {Do plants remember their microbial partners?.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.07.005},
pmid = {40750488},
issn = {1878-4372},
abstract = {Plants host dynamic microbiomes that are critical for stress resilience and productivity. Emerging evidence suggests that 'microbiome memory' enables plants to retain beneficial microbes via epigenetic mechanisms and vertical transmission. Understanding how 'microbiome memory' forms, persists, and influences plant adaptation is crucial for advancing resilient crop systems and sustainable agriculture.},
}

@article {pmid40750120,
year = {2025},
author = {Saisorn, W and Phuengmaung, P and Santiworakul, C and Doi, K and Rianthavorn, P and Leelahavanichkul, A},
title = {Endotoxaemia in childhood-onset systemic lupus erythematosus induces low-density granulocytes and extracellular traps of innate immune cells.},
journal = {Lupus science & medicine},
volume = {12},
number = {2},
pages = {},
doi = {10.1136/lupus-2025-001663},
pmid = {40750120},
issn = {2053-8790},
mesh = {Humans ; *Lupus Erythematosus, Systemic/immunology/complications/blood ; *Endotoxemia/immunology/blood ; *Extracellular Traps/immunology/metabolism ; Female ; *Granulocytes/immunology/metabolism ; Male ; Child ; Immunity, Innate ; Adolescent ; Cytokines/blood ; Neutrophils/immunology ; Leukocytes, Mononuclear/immunology ; },
abstract = {BACKGROUND: Endotoxaemia without infection in lupus is mentioned with the inconclusive clinical importance.

METHODS: With endotoxaemia and lupus activity (Systemic Lupus Erythematosus Disease Activity Index 2000 score), 46 patients with childhood-onset lupus were categorised into active lupus with endotoxaemia (n=14), inactive lupus with endotoxaemia (n=10), active lupus without endotoxaemia (n=10) and inactive lupus without endotoxaemia (n=12). The routine parameters (serum creatinine, urine sediments, proteinuria, complement, haematological aspects and histological activity index) were analysed with lupus activity and other parameters.

RESULTS: Serum cytokines (tumour necrosis factor (TNF)-α, interleukin (IL)-6, IL-8 and IL-10), serum citrullinated histone H3, cell-free DNA and bacterial-free DNA were not different among groups. The extracellular traps (ETs) in the peripheral blood mononuclear cell (PBMC) fraction, measured by immunofluorescence of myeloperoxidase (MPO) and neutrophil elastase (NE), were elevated in endotoxaemia regardless of lupus disease activity. Interestingly, low-density granulocytes (LDGs), the neutrophils in the PBMC fraction after gradient separation, were elevated in active lupus regardless of endotoxaemia but higher in the patients with positive endotoxaemia. Because endotoxaemia might be derived from the gut, the blood microbiome was measured, and the Burkholderia group was the representative bacteria in active lupus with endotoxaemia. The incubation of LPS or bacterial-free DNA with neutrophils from the healthy control altered these regular-density neutrophils to LDGs.

CONCLUSION: Endotoxaemia presented in both active and inactive lupus (possibly correlated with some bacterial groups in the gut) that caused ETs in the PBMC fraction and LDGs. However, elevated LDGs were most prominent in endotoxaemia with active lupus.},
}

Humans
*Lupus Erythematosus, Systemic/immunology/complications/blood
*Endotoxemia/immunology/blood
*Extracellular Traps/immunology/metabolism
Female
*Granulocytes/immunology/metabolism
Male
Child
Immunity, Innate
Adolescent
Cytokines/blood
Neutrophils/immunology
Leukocytes, Mononuclear/immunology

@article {pmid40750089,
year = {2025},
author = {Raza, ML and Ali, SI and Bhojani, A and Zehra, R and Zehra, R},
title = {Microbiome Modulation in Dermatological Disorders: Current Insights and Therapeutic Prospects - A narrative review.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107940},
doi = {10.1016/j.micpath.2025.107940},
pmid = {40750089},
issn = {1096-1208},
abstract = {The human skin microbiome is a complex ecosystem of bacteria, fungi, and viruses that plays a vital role in maintaining skin health and protecting against pathogens. Disruptions in the delicate balance of the skin microbiome have been implicated in various dermatological disorders, including atopic dermatitis, acne, rosacea, and psoriasis. This narrative review explores current insights into microbiome modulation as a therapeutic approach for skin disorders. We further discussed strategies such as probiotics, prebiotics, synbiotics, bacteriophage therapy, and topical formulations designed to restore microbial balance. This narrative review also examines the challenges in translating microbiome research into clinical practice, including individual variability in microbiome composition and regulatory considerations. By synthesizing recent advances in skin microbiome research, this article provides a comprehensive overview of the potential for microbiome-based therapies in dermatology and highlights future directions for this rapidly evolving field.},
}

@article {pmid40750034,
year = {2025},
author = {Wei, M and Zhou, Y and Hu, X and Tie, H and Chen, Q and Yao, W},
title = {In vivo bacterial infection acne treatment of Sapindus saponins: Skin microbiota, network pharmacology, and transcriptomic analysis.},
journal = {Journal of ethnopharmacology},
volume = {353},
number = {Pt A},
pages = {120345},
doi = {10.1016/j.jep.2025.120345},
pmid = {40750034},
issn = {1872-7573},
abstract = {Sapindus mukorossi has been traditionally used in China for skin whitening and acne treatment. Previous studies have confirmed the antibacterial activity of Sapindus saponins against Cutibacterium acnes, which is reportedly the primary factor causing inflamed lesions in acne vulgaris. However, the anti-acne activity in vivo and related cellular targets of Sapindus saponins are still unknown.

AIM OF THE STUDY: This study aimed to investigate the anti-acne effects in vivo and the action mechanism of Sapindus mukorossi saponins fraction (SMSF) by the strategy of network pharmacology, transcriptomic analysis, and microbiome integration.

MATERIALS AND METHODS: The network pharmacology analysis was used to evaluate the cellular targets of SMSF treatment on acne. The transcriptome analysis was utilized to identify the differentially expressed genes (DEGs), and the 16S rDNA sequencing was employed to analyze the composition of skin microbiota.

RESULTS: SMSF was proven to have no acute, continuous skin or eye irritation in New Zealand rabbits when the concentration was below 50 mg/mL. SMSF could greatly reduce the lesion degree of rabbit ear acne and significantly decrease the content of pro-inflammatory factors in the rabbit ear tissue and serum after treatment for 14 days. The contents of dihydrotestosterone and leukotriene were significantly decreased, and the structure of bacterial microbiota was regulated. The network pharmacology analysis showed that the main 79 anti-acne targets of SMSF such as tumor necrosis factor (TNF) and interleukin 10. The transcriptomic analysis confirmed that there were 2084 DEGs between the SMSF-treated group and the model group, of which 870 were up-regulated and 1214 were down-regulated. Correlation analysis between the DEGs and the anti-acne targets predicted by network pharmacology showed that there were 6 overlapping targets, including TNF, vitamin D receptor, androgen receptor, prostaglandin endoperoxide synthase 2, peroxisome proliferator activated receptor gamma, and nuclear receptor subfamily 3, group C, member 1. Moreover, SMSF achieved anti-acne activities by maintaining normal cellular protein synthesis, regulating cytokine production as well as regulating cancer-related genes and the mitogen-activated protein kinase signaling pathway.

CONCLUSION: SMSF exerted anti-acne activities via multiple targets and signaling pathways. This study provided a theoretical basis for the utilization of Sapindus saponins in the fields of medicine and cosmetics, and supplied a guiding significance for the development of natural anti-acne drugs.},
}

@article {pmid40749888,
year = {2025},
author = {Carella, F and Correggia, M and Cordone, A and Iacovino, O and Maresca, F and Villari, G and Roque, A and Vico, G},
title = {The bald disease in the natural population of the purple sea urchin Paracentrotus lividus of the Mediterranean Sea: From spines to tissues.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108415},
doi = {10.1016/j.jip.2025.108415},
pmid = {40749888},
issn = {1096-0805},
abstract = {Recently, unusual mortality outbreaks have been reported in the echinoderm populations over broad geographic regions. The present work use different diagnostic approaches to unravel the Bald Sea Urchin Disease (BSUD) causes in a natural population of P. lividus from the Gulf of Naples sampled in 2021. Symptomatic individuals displayed the typical signs such as test discoloration and ulceration, loss of spines and pedicellariae and visceral hyperpigmentation. Scanning Electron Microscopy of diseased individuals (stage 2 and stage 3) revealed a bare exoskeleton with multiplying bacteria penetrating the damaged test, and histopathology revealed inflammatory lesions and phagocytosis only in the stages 2 and 3, with Gram negative and positive bacteria at stage 3. Metagenomic revealed an increase in DNA virus and Proteobacteria during disease progression. Microbial community analyses failed to reveal a single putative pathogen associated with symptomatic, but microbiome showed higher diversity in asymptomatic individuals compared to the asymptomatic. Different Vibrio spp. belonging to Splendidus clade were also isolated, with V. crassostreae as the most represented in advanced stages of disease. We cannot confirm that the observed microorganisms were associated with tissue damage and their contribution to the disease outcome remains unclear as they could be just opportunistic in the lesions. This preliminary study on wild population highlights the importance of morphological analysis (histopathology and SEM) coupled with microbiome and metagenome in sea urchin disease investigations. Moreover, we suggest also performing Transmission Electron Microscopy (TEM), experimental challenges and in situ hybridization methods (ISH) to provide morphological evidence of potential infective agents. Future studies should also include histopathology of the test.},
}

@article {pmid40749856,
year = {2025},
author = {Gao, J and Lee, AA and Abtahi, S and Turner, JR and Grover, M and Schmidt, A and Schmidt, TM and Nee, JW and Iturrino, J and Lembo, A and Chey, WD and Wiley, JW and Singh, P},
title = {Low FODMAP diet improves colonic barrier function and mast cell activation in patients with IBS-D: A mechanistic trial.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.07.016},
pmid = {40749856},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: A diet low in fermentable oligo-, di-, monosaccharides and polyols (FODMAP) (LFD) is the most efficacious dietary therapy for irritable bowel syndrome (IBS). However, the mechanisms by which FODMAPs drive IBS pathophysiology are unclear.

METHODS: Patients with Rome IV diarrhea-predominant IBS (IBS-D) underwent barrier function evaluation pre- and post-LFD along with assessment of mast cell number and activation profile. Finally, fecal supernatants (FS) were administered intracolonically to wildtype mice with/without pharmacological inhibition, tlr4[-/-] mice and mast cell-deficient mice with/without mast cell reconstitution.

RESULTS: Of 42 patients, 34 responded to LFD and 8 did not. IBS-D patients had a significant improvement in colonic barrier structure and function, mast cell number, and levels of mast cell mediators post-LFD. The magnitude of physiological changes did not correlate with the magnitude of clinical response. Humanization of germ-free mice with pre-LFD feces caused barrier dysfunction while post-LFD feces did not. Similarly, pre-LFD FS caused barrier dysfunction in wildtype mice, whereas post-LFD FS did not. LPS removal and TLR4 antagonism reversed pre-LFD IBS FS-induced barrier dysfunction. Barrier dysfunction was absent in tlr4[-/-] mice treated with pre-LFD FS. Similarly, pre-LFD IBS FS did not cause barrier dysfunction in wildtype mice treated with mast cell stabilizer, or in mast cell-deficient mice. However, barrier dysfunction was inducible in mast cell-deficient mice upon reconstitution with wildtype mast cells but not tlr4[-/-] mast cells.

CONCLUSIONS: IBS-D patients exhibited improvement in colonic barrier dysfunction, mast cell recruitment, and activation post-LFD. FODMAP-mediated barrier dysfunction in IBS-D is mediated by direct activation of the TLR4 receptor on colonic mast cells by fecal LPS.

CLINICALTRIALS: gov (NCT04542018).},
}

@article {pmid40749830,
year = {2025},
author = {Morrison, KM and Agarwal, R and Stubbs, HE and Yu, H and Ruhl, S and Chen, X and Sullam, PM and Bensing, BA and Smith, JC and Iverson, TM},
title = {Sialic Acid Identity Modulates Host Tropism of Sialoglycan-binding Viridans Group Streptococci.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {110540},
doi = {10.1016/j.jbc.2025.110540},
pmid = {40749830},
issn = {1083-351X},
abstract = {Microbial interactions with multiple species may expand the range of potential hosts, supporting both pathogen reservoirs and zoonotic spillover. Viridans group streptococci interact with host cells by engaging protein-attached glycosylations capped with terminal sialic acids (sialoglycans). One potential origin for host tropism of these streptococci arises because humans exclusively synthesize the N-acetylneuraminic acid (Neu5Ac) form of sialic acid, while non-human mammals synthesize both Neu5Ac and a hydroxylated N-glycolylneuraminic acid (Neu5Gc). However, the link between binding preference for these sialic acids and preference for host has not been tested experimentally. Here, we investigate sialoglycan-binding by Neu5Ac/Neu5Gc cross-reactive Siglec-like binding regions (SLBRs) from two strains of streptococci, Streptococcus gordonii strain Challis (SLBRHsa) and Streptococcus sanguinis strain SK36 (SLBRSrpA). Structural and computational analyses of SLBRHsa identified molecular details for the binding of disaccharides capped in Neu5Ac or Neu5Gc. Engineering SLBRHsa and SLBRSrpA for narrow selectivity to synthetic Neu5Gc-terminated glycans shifted the binding preference from authentic human plasma receptors to plasma receptors from rat sources. However, host receptor preference did not fully recapitulate purified Neu5Ac/Neu5Gc-capped sialoglycan preference. These findings suggest that sialic acid identity modulates, but does not uniquely determine, host preference by these streptococci. This work refines our understanding of host specificity and challenges prevailing assumptions about the relative role of sialic acids in host tropism.},
}

@article {pmid40749821,
year = {2025},
author = {Tian, Y and Jin, W and Jin, X and Wang, Y and Wu, R and Yu, R and Jiang, J and Zhu, M},
title = {Fecal microbiota transplantation promotes hair growth through gut microbiome and metabolic regulation.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123887},
doi = {10.1016/j.lfs.2025.123887},
pmid = {40749821},
issn = {1879-0631},
abstract = {BACKGROUND: Gut microbiota plays a role in the etiology of a number of skin illnesses. In this study, we aimed to determine the relationship between intestinal flora (and related metabolites) and Androgenetic Alopecia (AGA).

METHODS: Mendelian randomization (MR) analysis was used to explore the causal relationship between gut microbiota and AGA. Gut microbiota was detected by fecal 16S rRNA sequencing, and fecal metabolites were analyzed by non-targeted metabolomics. Senescence and inflammation levels in the colon and hair follicles of mice were detected by β-galactosidase assay kits and other staining methods. Hair growth was assessed by dermoscopy and hair growth scoring.

RESULTS: Mendelian randomization analysis revealed a significant correlation between Lactobacillaceae (OR = 0.981, 95 % CI: 0.969-0.992, p = 0.001) and Lactobacillus (OR = 0.985, 95 % CI: 0.973-0.997, p = 0.018) with AGA. A similar reduction in Lactobacillaceae and Lactobacillus was observed in the feces of AGA mice (p < 0.05). Fecal microbiota transplantation (FMT) increased Lactobacillaceae and Lactobacillus levels (p < 0.05), and Lactobacillus rhamnosus GG (LGG) reversed aging and inflammation in the gut and hair follicles, promoting hair growth.

CONCLUSION: There is an intestinal-skin axis regulation pattern in the pathological process of AGA, and the aging of intestinal tissues and the alteration of bacterial flora and related metabolites can affect hair follicle aging and inflammation.},
}

@article {pmid40749791,
year = {2025},
author = {Li, M and Zhao, G and Li, MM},
title = {Regulatory mechanisms of quorum sensing in microbial communities and their potential applications in ruminant livestock production.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.055},
pmid = {40749791},
issn = {2090-1224},
abstract = {BACKGROUND: Quorum sensing (QS) is a cell-to-cell communication system that enables microbial communities to dynamically regulate their metabolism and physiological activities according to the surrounding cell density. The rumen's diverse microbial ecosystem represents a classic example of host-microbiome symbiosis. Despite significant progress in understanding the composition and function of ruminal microbial communities, the underlying communication mechanisms in the rumen ecosystem remain largely enigmatic. Gaining insight into these regulatory mechanisms is crucial for developing knowledge-based strategies to improve animal productivity, health, and sustainability in ruminant livestock production.

AIM OF REVIEW: This review aims to provide an overview of microbial QS communication systems mediated by diverse signaling molecules, including bacterial intraspecies and interspecies QS, fungal QS, and archaeal QS. We conducted a structured review by searching multiple scientific databases, synthesizing data from relevant studies, and critically evaluating the roles of QS systems in microbial communities. This approach ensures a comprehensive analysis of the current understanding of QS mechanisms and their implications for ruminant livestock. Specifically, we elucidate the identification and potential mechanisms of the QS system facilitated by three prevalent signaling molecules (N-acyl homoserine lactones, autoinducing peptides, and autoinducer 2) in ruminants. Recent advances in understanding the effects of QS on microbial fermentation, immune function, biofilm formation, and virulence factor production are summarized in detail, providing a scientific basis for applying QS in ruminant livestock production.

The rumen harbors various QS signaling molecules that modulate microbial community dynamics, impacting composition, structure, and function. The versatility of QS allows it to regulate ruminal fermentation and inhibit pathogen growth, thereby improving productivity and reducing disease risk in ruminants. This review synthesizes recent advances in QS mechanisms, crucial for disease prevention, combating antibiotic resistance, and promoting sustainable livestock production. Future research should investigate QS pathways and networks in the rumen microbiome through in vivo experiments and multi-omics analyses to gain a deeper understanding of microbial community regulation.},
}

@article {pmid40749788,
year = {2025},
author = {Uthoff, C and Yakovlyeva, Y and Engelmann, B and Rolle-Kampczyk, U and Haange, SB and Alkassab, AT and Pistorius, J and Brix, F and Waschina, S and Thum, AS and Jehmlich, N and von Bergen, M},
title = {Comprehension of the age-dependent gut and brain interaction of honey bee workers by integration of multi omics approaches.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.045},
pmid = {40749788},
issn = {2090-1224},
abstract = {INTRODUCTION: In honey bees, division of labour is a key feature, with age-related behavioural transitions being closely associated with molecular changes in the brain, gut, and microbiota. Despite evidence of both microbiome and brain changes in honey bees, most studies focus on either aspect or a single method of investigation, limiting our understanding of their interconnected roles in development and task differentiation.

OBJECTIVES: In this study, we investigated the molecular changes in the gut and brain in honey bee workers of different ages using (meta-)proteomics and metabolomics to better understand their contribution to behavioural responses and modulation.

METHODS: Workers were sampled at seven timepoints throughout their life. Mass spectrometry for (meta-) proteomic and metabolomic of the guts and brains allowed insights into the global structural and functional dynamics of the microbiota, as well as the functional and metabolic alterations in the host gut and brain, and their interactions.

RESULTS: Our results indicate the transport of amino acids between the gut and brain, potentially influencing functional pathways and behavioural phenotypes. We observed a correlation between concentrations of tryptophan and its metabolic products between honey bee brain and gut. This provides evidence regarding gut-brain axis as a way of internal communication for different host mechanisms in honey bees. Microbiota composition changed significantly, with protein numbers increasing significantly in the establishment phase. Proteomic results from both the host and the microbiota reveal that altered metabolic and functional pathway abundances may be due to energy expenditure, task differentiation, and age of onset of foraging.

CONCLUSION: Overall, our findings are the first to describe the global (meta-)proteomic and metabolomic changes in the honeybee gut and brain throughout a worker's life. This provides new insights toward developing potential biomarkers for evaluation of different functional changes related to various environmental stressors.},
}

@article {pmid40749768,
year = {2025},
author = {Lu, S and Brown, RW and Li, M and Chen, M and Huang, C and Lian, J and Wu, D and Jones, DL},
title = {Soil application of PE and PLA microplastics alter earthworm (Eisenia nordenskioldi) gut bacterial community and soil microbiome-metabolome dynamics.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126895},
doi = {10.1016/j.envpol.2025.126895},
pmid = {40749768},
issn = {1873-6424},
abstract = {Non-biodegradable polyethylene (PE) and biodegradable polylactic acid (PLA)pose potential risks to soil ecosystems. However, there is a lack of in-depth studies to fully understand the ecological toxicity of these two types of microplastics (MPs) on soil microbiomes and their underlying mechanisms. Therefore, this study investigated the ecological risks of PE and PLA at environmentally relevant concentrations over a 120-day microcosm experiment, utilizing 16S rRNA high-throughput sequencing and untargeted soil metabolomics analysis. The results suggest that, compared to PLA, PE had a more significant impact on both earthworm gut and soil bacteria. PE significantly reduced the Shannon diversity index of the earthworm gut microbiome and decreased the relative abundance of Actinomycetota in soil by 5.79% compared to control, while PLA exhibited a more pronounced interaction with soil metabolites. The introduction of MPs disrupted multiple metabolic pathways, significantly reducing the abundance of lipids, carbohydrates, and amino acids-key components closely associated with the multifunctionality of soil ecosystems. These metabolites were significantly negatively correlated with soil dissolved organic carbon levels. Two genera involved in the degradation of MPs, Paenibacillus and Acinetobacter, were identified in the earthworm gut after MPs exposure. Partial least squares path modeling analysis revealed that MPs addition was negatively correlated with the levels of lipids, carbohydrates, and amino acids. Overall, this study may provide valuable insights into assessing the impact of pollutants on soil health and offers important evidence for evaluating the ecological risks to soil ecosystems.},
}

@article {pmid40749692,
year = {2025},
author = {Tomezsko, PJ and Wynn, J and Ostrinskaya, A and Hendricks, J and Vian, T},
title = {Multi-modal breath measurements for biomarker discovery.},
journal = {Journal of breath research},
volume = {},
number = {},
pages = {},
doi = {10.1088/1752-7163/adf6cd},
pmid = {40749692},
issn = {1752-7163},
abstract = {Breath contains numerous classes of compounds and biomolecules that could potentially be used as biomarkers for infectious disease as well as a range of other respiratory conditions or states. The goal of this work was to develop a testbed for simultaneous, multi-modal breath measurements. To validate the capabilities of this testbed, a pilot human-subjects research study was conducted to gather a wide range of correlated breath measurements. Seventeen healthy subjects provided breath samples at baseline respiratory rate for particle size, lipid composition and bacterial nucleic acid composition analysis. The majority of the particles the participants exhaled at baseline were smaller than 5 μm, consistent with previous literature. A deviation from baseline was detected in one participant immediately prior to COVID-19 symptom onset. This feature persisted for weeks after infection. The exhaled breath particulate contained lipids found in lung surfactant, indicating origin in the lung. Although bacterial DNA was not significantly higher in the exhaled breath particulate than in the environmental background, the metagenome of the breath was distinct from the environment, oral cavity and nasal passages of the participants. The low abundance of the breath microbiome limited analysis. No assertions of statistical significance are offered due to the limited nature of the study scope, The multi-modal breath testbed has promise for discovery of breath biomarkers and as a reference for biomarkers of different classes that are currently being used. .},
}

@article {pmid40749656,
year = {2025},
author = {Asghar, MU and Zhai, Y and Liu, T and Fan, P and Ain, NU and Zaidi, AH and Tariq, M and Mainar-Jaime, RC and Jeong, KC},
title = {A metagenomics-based approach to understanding the transmission of healthcare-associated antimicrobial resistance in Pakistan.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139384},
doi = {10.1016/j.jhazmat.2025.139384},
pmid = {40749656},
issn = {1873-3336},
abstract = {Hospital environments are critical yet underexamined reservoirs for hazardous antimicrobial resistance (AMR), particularly in lower-middle-income countries (LMICs) where resource constraints often hinder comprehensive surveillance. In this study, we employed 16S rRNA gene sequencing and shotgun metagenomics to characterize the microbiome, resistome, and potential transmission routes across five clinical environments within a hospital in Pakistan: the intensive care unit (ICU), surgical ward (SW), cardiac surgery ward (CSW), cardiac ward (CW), and operating theater (OT). Microbial community analysis revealed compositional similarities among the ICU, SW, and OT, with the ICU emerging as a primary source of microbial dissemination. Species-level profiling identified hospital-associated pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, and Enterobacter cloacae, and metagenome-assembled genome (MAG) analysis enabled the linkage of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) to specific bacterial hosts. ARGs and MGEs displayed setting-specific patterns, with the SW harboring the highest abundance of ARGs, particularly those conferring resistance to β-lactams and biocides. Insertion sequences were the most prevalent MGEs and were commonly linked to ARGs, indicating potential horizontal gene transfer. Co-occurrence network analysis identified Staphylococcus, Enterococcus, and Escherichia as central hub taxa within the microbial communities of the ICU, SW, and OT, indicating their critical roles in potential ARG transmission. These findings provide critical insights into the environmental transmission dynamics of AMR in LMIC healthcare settings and underscore the urgent need for metagenomics-informed infection control strategies.},
}

@article {pmid40749165,
year = {2025},
author = {McManus, D and Copsel, SN and Pfeiffer, BJ and Wolf, D and Barreras, H and Ma, S and Khodor, A and Komai, S and Burgos da Silva, M and Hazime, H and Gallardo, M and Lime, SGR and van den Brink, MRM and Park, JH and Abreu, MT and Hill, GR and Perez, VL and Levy, RB},
title = {Pretransplant targeting of TNFRSF25 and CD25 stimulates recipient Tregs in target tissues, ameliorating GVHD post-HSCT.},
journal = {Blood},
volume = {},
number = {},
pages = {},
doi = {10.1182/blood.2025028418},
pmid = {40749165},
issn = {1528-0020},
abstract = {The current approach to minimize transplant-associated complications, including graft-versus-host disease (GVHD) includes long-term pharmacological immune suppression frequently accompanied by unwanted side effects. Advances in targeted immunotherapies regulating alloantigen responses in the recipient continue to reduce the need for pan-immunosuppression. Here, in vivo targeting of the TNF superfamily receptor TNFRSF25 and the high affinity IL-2 receptor with a TL1A-Ig fusion protein and low dose IL-2, respectively was used to pre-treat recipient mice prior to allogeneic-HSCT (aHSCT). Pre-treatment induced Treg expansion persisting 1-2 weeks post-HSCT leading to diminished GVHD and improved transplant outcomes. Expansion was accompanied by an increase in the frequency of stable and active Tregs creating a suppressive tissue environment in the colon, liver and eye. Importantly, pre-treatment supported epithelial cell function/integrity, a diverse microbiome including reduction of pathologic bacteria outgrowth and promotion of butyrate producing bacteria, while maintaining physiologic levels of obligate/facultative anaerobes. Notably, using a sphingosine 1-phosphate receptor agonist to sequester T cells in lymphoid tissues, it was found that the increased tissue Treg frequency included resident CD69+CD103+FoxP3+ hepatic Tregs. In contrast to infusion of donor Treg cells, the strategy developed here resulted in the presence of immunosuppressive target tissue environments in the recipient prior to the receipt of donor allo-reactive T cells and successful perseveration of GVL responses. We posit strategies that circumvent the need of producing large numbers of Tregs ex-vivo through manipulating this recipient compartment in vivo, can provide translational approaches to improve aHSCT outcomes.},
}

@article {pmid40748490,
year = {2025},
author = {He, T and Wang, Y and Zhao, L and Che, Y and Zhang, L and Zeng, Y and Shen, H and Hao, H and Cao, L},
title = {Integrated Microbiota-Bile Acid Analysis as Potential NonInvasive Biomarkers for Ulcerative Colitis Staging Diagnose.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {15},
pages = {e70859},
doi = {10.1096/fj.202501078R},
pmid = {40748490},
issn = {1530-6860},
support = {2021YFA1301300//the National Key Research and Development Program of China/ ; 2022YFF1100601//the National Key Research and Development Program of China/ ; 82173886//the National Natural Science Foundation of China/ ; 82373886//the National Natural Science Foundation of China/ ; 82404997//the National Natural Science Foundation of China/ ; G20582017001//111 Plan | Overseas Expertise Introduction Project for Discipline Innovation/ ; SKLNMZZ202402//the Project of State Key Laboratory of Natural Medicines, China Pharmaceutical University/ ; },
mesh = {Humans ; *Colitis, Ulcerative/diagnosis/microbiology/metabolism/blood ; *Bile Acids and Salts/metabolism/blood/analysis ; Male ; Biomarkers/metabolism/blood ; Adult ; Female ; Feces/microbiology/chemistry ; Middle Aged ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Clinical staging diagnosis and progression tracking for ulcerative colitis (UC) is as challenging as poor patient compliance with endoscopic biopsy. We perform a study that integrates metabolomic profiling, 16S rRNA, and metagenomic sequencing on serum and fecal samples from 23 active state UC patients, 24 remission state UC patients, and 20 healthy volunteers from China, aiming to explore a non-invasive integrative biochemical index to quantitatively track and monitor pathological activity of UC. Besides the known associations of microbes such as Fusobacterium nucleatum and Clostridium symbiosum with UC, we found several bile acid-transforming species, including 7α-dehydroxygenase and 7α/β-dehydrogenase expressing microbiota, were significantly correlated with UC pathological activity. We identified 2 bacterial gene markers related to secondary bile acid synthesis besides Clostridium scindens that differentiated active and remission stage UC and healthy control microbiomes. Relevantly, reduced serum deoxycholic acid (DCA)/cholic acid (CA) species ratio and increased fecal ursodeoxycholic acid (UDCA)/chenodeoxycholic acid (CDCA) ratio were associated with the pathological activity of UC. Moreover, receiver operating characteristic analysis based on serum/fecal bile acid ratios was much more accurate in the prediction of active and remission stage outcomes. This species-specific temporal change and bile acid dysregulation pattern linked to disease severity indicate that integrated microbiome-bile acid profiles may be implied for disease activity prediction and that targeting microbiome-mediated gut flora and bile acid homeostasis may be implicative of therapy efficacy. These insights will help improve clinical diagnosis and optimize existing medical treatments.},
}

Humans
*Colitis, Ulcerative/diagnosis/microbiology/metabolism/blood
*Bile Acids and Salts/metabolism/blood/analysis
Male
Biomarkers/metabolism/blood
Adult
Female
Feces/microbiology/chemistry
Middle Aged
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics

@article {pmid40748243,
year = {2025},
author = {Portal-Gonzalez, N and Wang, W and He, W and Santos-Bermudez, R},
title = {Engineering Plant Holobionts for Climate-Resilient Agriculture.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf158},
pmid = {40748243},
issn = {1751-7370},
abstract = {The plant holobiont-an integrated unit of the host and its microbiome-has co-evolved through ecological and genetic interactions. Microbiome engineering offers a promising route to enhance resilience in response to climate stress, soil degradation, and yield stagnation. This review presents an integrated framework combining microbial ecology, synthetic biology, and computational modeling to rationally design synthetic microbial communities (SynComs) for agriculture. We outline ecological principles-priority effects, keystone taxa, and functional redundancy-that shape microbiome assembly and guide SynCom design. Strategies like CRISPR interference, biosensor circuits, and quorum-sensing modules enable programmable microbial functions. We also highlight the predictive potential of in silico modeling-including genome-scale metabolic models, dynamic flux balance analysis, and machine learning-to simulate interactions, optimize SynCom composition, and enhance design accuracy. To bridge lab and field, we discuss native microbial chassis, encapsulation, and precision delivery as tools for scalable, ecosystem-integrated deployment. We introduce the concept of the programmable holobiont: an engineered plant-microbe partnership capable of dynamic feedback, interkingdom signaling, and ecological memory. This systems-level perspective reframes plants as designable ecosystems. By synthesizing cross-disciplinary advances, we offer a roadmap for climate-resilient agriculture, where engineered microbiomes improve sustainability, yield stability, and environmental adaptation.},
}

@article {pmid40748242,
year = {2025},
author = {Causevic, S and Tackmann, J and Sentchilo, V and Malfertheiner, L and von Mering, C and van der Meer, JR},
title = {Habitat filtering more than microbiota origin controls microbiome transplant outcomes in soil.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf162},
pmid = {40748242},
issn = {1751-7370},
abstract = {Human activities cause a global loss of soil microbiome diversity and functionality. One way to reverse this trend is through microbiota transplants, but the processes determining merger outcomes are not well understood. Here, we investigated the roles of habitat filtering and microbiota origin on microbiome development upon mergers, with the hypothesis that native strains are better adapted to their own habitat and will outcompete non-native ones in niche colonization. To test this, we contrasted community development in soil microcosms between two taxa-diverse microbiota originating from either topsoil (SoilCom) or freshwater lake (LakeCom), and a defined mixture of 21 soil bacteria (SynCom). When inoculated separately, SoilCom and LakeCom showed similar taxa and colonization patterns contributing to community growth and decline within the soil microcosms. SynCom transplants to either SoilCom or LakeCom under renewed growth conditions permanently altered their community trajectories, and slightly further converged their taxa compositions. Levels of SynCom members in both resident backgrounds decreased from initial 50-80% to below 1% within two months. Merged as well as non-merged communities resembled natural soils in comparison to over 81,000 publicly available soil, sediment, and lake microbiomes. Our results show that habitat filtering is dominant over microbiota taxa origin in determining transplant outcomes. Even though the proliferation of SynCom transplants remained limited, their capacity to influence community merger trajectories long term opens new paths for soil microbiome engineering.},
}

@article {pmid40748072,
year = {2025},
author = {Bedree, JK and Bourgeois, J and Balani, P and Cen, L and Hendrickson, EL and Kerns, KA and Camilli, A and McLean, JS and Shi, W and He, X},
title = {Identifying essential genes in Schaalia odontolytica using a saturated transposon library.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0016425},
doi = {10.1128/jb.00164-25},
pmid = {40748072},
issn = {1098-5530},
abstract = {The unique epibiotic-parasitic relationship between Nanosynbacter lyticus type strain TM7x, a member of the newly identified candidate phyla radiation, now referred to as Patescibacteria, and its basibiont, Schaalia odontolytica strain XH001 (formerly Actinomyces odontolyticus), requires more powerful genetic tools for a deeper understanding of the genetic underpinnings that mediate their obligate relationship. Previous studies have mainly characterized the genomic landscape of XH001 during or post-TM7x infection through comparative genomic or transcriptomic analyses, followed by phenotypic analysis. Comprehensive genetic dissection of the pair is currently cumbersome due to the lack of robust genetic tools in TM7x. However, basic genetic tools are available for XH001, and this study expands the current genetic toolset by developing high-throughput transposon insertion sequencing (Tn-seq). Tn-seq was employed to screen for essential genes in XH001 under laboratory conditions. A highly saturated Tn-seq library was generated with nearly 660,000 unique insertion mutations, averaging one insertion every two-three nucleotides. A total of 203 genes comprising 10.5% of the XH001 genome were identified as putatively essential.IMPORTANCESchaalia odontolytica strain XH001, an early colonizer of the oral multispecies biofilm (dental plaque), forms a unique epibiotic-parasitic relationship with Nanosynbacter lyticus type strain TM7x, a member of the newly identified Patescibacteria (formerly candidate phyla radiation). Achieving a mechanistic understanding of their relationship requires practical genetic tools for dissecting the roles played by different genetic mediators and shedding light on how their interspecies interaction may affect dynamics in the oral microbiome. In this study, we developed a high-throughput mutagenesis technique, Tn-seq, in XH001. The constructed Tn-seq library enabled the identification of putatively essential genes in XH001, revealing growth requirements under laboratory conditions. This library can be leveraged in future studies to elucidate TM7x's dependence on XH001 at the molecular level.},
}

@article {pmid40748062,
year = {2025},
author = {Vives, MJ},
title = {Decoding the human phageome helps to unravel microbial dynamics in health and disease.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0091925},
doi = {10.1128/aem.00919-25},
pmid = {40748062},
issn = {1098-5336},
abstract = {Bacteriophages are the most abundant biological entities on Earth-equally abundant within the human body. Their potential impacts on host function and homeostasis are becoming increasingly important in biomedical and microbiological research. Phage abundance and diversity often signal changes in the resident bacterial microbiome, but they can also regulate microbiome dysbiosis, help identify pathogenic bacterial candidates, and provide clues to understand the disease-related microbiome changes and the role of the phageomes in health and disease contexts. In a recent minireview, Rybicka and Kaźmierczak (Appl Environ Microbiol 91:e01788-24, 2025, https://doi.org/10.1128/aem.01788-24) synthesize the current understanding of phage communities across the human gut, oral cavity, skin, respiratory, and urogenital tracts, seeking connections with health and disease status.},
}

@article {pmid40748061,
year = {2025},
author = {Sommer, AJ and Worley, TK and Sapountzis, P and Coon, KL},
title = {Phylogenetic intermixing reveals stable fly-mediated circulation of mastitis-associated bacteria in dairy settings.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021525},
doi = {10.1128/msystems.00215-25},
pmid = {40748061},
issn = {2379-5077},
abstract = {Stomoxys flies are common blood-feeding pests on dairy farms and are suspected carriers of pathogenic bacteria due to their close association with manure and cattle hosts. While prior studies have used amplicon sequencing and culture-dependent methodologies to characterize the composition of the Stomoxys microbiota, little is known about strain-level acquisition of mastitis-causing bacteria from manure by Stomoxys or the functional diversity of Stomoxys-associated taxa. In this study, we address these key knowledge gaps by using whole genome sequencing to provide the first comparative genomic analysis of Stomoxys-derived Escherichia coli, Klebsiella pneumoniae, and Staphylococcaceae isolates. Our results show that fly and manure isolates collected from the same farm system are phylogenetically interspersed, with subsequent pairwise genome alignments revealing near-identical strains and plasmids shared between the two sources. We further identify a phylogenetic clade of Mammaliicoccus sciuri containing known mastitis agents associated with both flies and manure. Functional analysis reveals that this clade is highly enriched in xylose metabolism genes that are rare across other M. sciuri lineages, suggesting potential niche differentiation within the genus. Collectively, our results provide strong evidence for the acquisition of fecal-associated bacteria by adult Stomoxys flies, confirming the link between biting muscid flies and manure habitats. The intermixing of fly and manure isolates in clinically relevant taxonomic groups strongly suggests that flies serve as carriers of opportunistic mastitis-causing or other fecal-borne pathogens and may serve as important vehicles of pathogen dissemination across the dairy farm environment.IMPORTANCEBovine mastitis causes up to $32 billion dollars in losses annually in the global dairy industry. Opportunistic intramammary pathogens can be transmitted through incidental contact with bacteria in environmental reservoirs like manure. However, factors affecting the abundance, persistence, and spread of these bacteria are not well understood. Our research shows that mastitis pathogens are present in the guts of blood-feeding Stomoxys (stable) flies, which develop in cow feces and bite cows. Genomic analysis of isolates from flies, manure, and mastitis cases reveals that strains and antimicrobial resistance genes are shared between these sources. Further analysis of fly gut isolates shows virulence factors and possible niche specialization, identifying fly-associated clades with known mastitis agents from mastitic cows. This strongly suggests that Stomoxys flies play a role in the carriage and circulation of bovine mastitis pathogens from manure in dairy settings.},
}

@article {pmid40747954,
year = {2025},
author = {Shawer, R and Solomon, A},
title = {Unraveling the immune axis of ocular surface microbiota in keratoconus.},
journal = {Current opinion in allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ACI.0000000000001098},
pmid = {40747954},
issn = {1473-6322},
abstract = {PURPOSE OF REVIEW: This review's objective is to give readers an update on recent and developing information about the function of the ocular surface microbiome in keratoconus.

RECENT FINDINGS: The microbiome's function in the pathogenesis of keratoconus is supported by recent research. Numerous metabolites that are produced by the ocular surface bacteria can affect the host tissue. A shift in the microbiota may influence the composition of these metabolites, which could have an effect on keratoconus by altering the cornea's metabolic environment.

SUMMARY: Gaining insight into the function of the ocular surface microbiota in keratoconus could open up new avenues for the creation of new therapeutic modalities.},
}

@article {pmid40747645,
year = {2025},
author = {Deng, Y and Xia, P and Chen, H and Tan, H and Wang, Q and Chen, W and Chen, D},
title = {Unraveling Persistent Health Impacts in Mice Following Cessation of Microplastic Exposure: Insights beyond the Surface.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c08357},
pmid = {40747645},
issn = {1936-086X},
abstract = {The ability of organisms to recover from microplastic (MP) exposure is critical for forming global strategies for MP regulation, risk mitigation, and health protection. However, the recovery dynamics following chronic exposure to environmentally relevant concentrations (ERCs) of MPs remains poorly understood. Here, we present a comprehensive investigation into postexposure recovery following long-term ingestion of polystyrene MPs (40-100 μm) in mice. Animals were fed MPs at either an ERC (approximately 512-2060 particles/day) or a high-dose level (ten times ERC) for 21 weeks, followed by a 4 week recovery period without exposure. Despite cessation of exposure, disruptions in lipid metabolism and gut microbiota persisted in dose- and size-dependent manners, with high-dose groups showing markedly limited recovery. Mechanistic in vitro studies using Caco-2 cells further revealed that MPs impair lipid metabolic homeostasis via sustained suppression of the AMP-activated protein kinase (AMPK) signaling pathway. Together, our findings provide crucial in vivo evidence via a mammalian model that chronic exposure to ERCs of MPs can lead to long-lasting metabolic and microbiome disturbances postexposure. These results underscore the urgency of reassessing the long-term health risks of MPs and developing strategies that address both exposure and postexposure recovery.},
}

@article {pmid40747614,
year = {2025},
author = {Zhang, X and Zhang, X and Wang, X and Tang, X and Xu, H and Zhang, N and Zhao, S and Yang, H and He, Q},
title = {Mannose-binding lectin insufficiency is associated with airway Haemophilus colonization and a higher risk of post-RSV bronchiolitis recurrent wheezing.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {8},
pages = {e70158},
doi = {10.1111/pai.70158},
pmid = {40747614},
issn = {1399-3038},
support = {//Beijing Natural Science Foundation-Daxing Innovation Joint Fund [L246038]/ ; },
mesh = {Humans ; *Respiratory Sounds/etiology ; Infant ; Male ; Female ; *Mannose-Binding Lectin/deficiency/blood ; *Respiratory Syncytial Virus Infections/immunology/complications ; Recurrence ; Child, Preschool ; *Bronchiolitis ; *Haemophilus ; Sputum/microbiology ; Follow-Up Studies ; *Metabolism, Inborn Errors ; *Haemophilus Infections/immunology ; Cytokines/metabolism ; Microbiota ; Risk Factors ; Infant, Newborn ; },
abstract = {OBJECTIVE: To investigate whether mannose-binding lectin (MBL) insufficiency influences the airway microbiota composition and development of subsequent recurrent wheezing in infants with severe respiratory syncytial virus (RSV) bronchiolitis.

METHODS: Sixty-seven infants who were hospitalized during an initial episode of severe RSV bronchiolitis at 6 months of age or less were included in the study and followed up until the age of 3 years. Serum and sputum samples were collected. The serum MBL concentrations were determined by ELISA; the sputum microbiota and cytokines were analyzed by 16S rRNA-based sequencing and multiplex immunoassay, respectively.

RESULTS: Twenty-six infants developed recurrent wheezing by the age of 3 years, and 41 did not. The rate of MBL insufficiency was significantly higher among infants who developed recurrent wheezing compared to those who did not [50.0% (13/26) vs. 24.4% (10/41), (p = .031)]. MBL insufficiency was independently associated with a higher risk of subsequent development of recurrent wheezing (adjusted Odds Ratio: 3.5, 95% CI 1.1-12.3, p = .035). Haemophilus was found to be the most discriminative genus between infants with and without MBL insufficiency (LDA >4.0). The level of INF-γ (p = .019) in infants with MBL insufficiency was significantly lower than that among infants with normal MBL.

CONCLUSION: During the first episode of severe RSV bronchiolitis in infants <6 months of age, MBL insufficiency was associated with a higher risk of developing subsequent recurrent wheezing by age three. Infants with MBL insufficiency were more likely to be colonized with Haemophilus and have weaker airway IFN-γ response.},
}

Humans
*Respiratory Sounds/etiology
Infant
Male
Female
*Mannose-Binding Lectin/deficiency/blood
*Respiratory Syncytial Virus Infections/immunology/complications
Recurrence
Child, Preschool
*Bronchiolitis
*Haemophilus
Sputum/microbiology
Follow-Up Studies
*Metabolism, Inborn Errors
*Haemophilus Infections/immunology
Cytokines/metabolism
Microbiota
Risk Factors
Infant, Newborn

@article {pmid40747609,
year = {2025},
author = {Avellán-Llaguno, RD and Xie, A and Obeten, AU and Pan, Z and Zhang, Y and Ye, G and Sun, X and Huang, Q},
title = {Composition, Antibiotic Resistance, and Functionality of the Gut Microbiome in Urban Cats.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05156},
pmid = {40747609},
issn = {1520-5851},
abstract = {This study examined the gut microbiota of urban cats: household (D), free-roaming (FR), and free-range domestic (FRD) groups. Taxonomic analysis revealed that the FRD group had the highest microbial diversity and the widest distribution of microbial classes, while the D group showed lower diversity with more concentrated classes. FRD cats possessed the highest number of exclusive classes and species. Across all groups, 890 antibiotic resistance genes (ARGs) were identified, with FRD exhibiting the most diverse ARG profile. Functional profiling indicated unique metabolic pathways in FRD cats. The FRD group also displayed the highest abundance of virulence factors (VFs) encoding genes. Candidate probiotics were identified, particularly in FRD. These findings demonstrate the complex interplay between cats' urbanization, lifestyle, and gut microbiota composition. The results highlight significant public health concerns regarding the dissemination of diverse ARGs and VFs, especially in FRD cats, indicating potential risks to animal and human health. This necessitates targeted surveillance and management strategies. Understanding urban feline microbial diversity and its functional implications is crucial for informing public health interventions and enhancing feline health.},
}

@article {pmid40747461,
year = {2025},
author = {Zhu, Z and Zhu, Y and Sun, Q and Xue, J and Xie, M and Yu, Y and Wang, B and Shangguan, W and Feng, Z and Wu, P},
title = {Pentosan polysulfate alleviates interstitial cystitis/bladder pain syndrome by modulating bile acid metabolism and activating the TGR5 receptor through gut microbiota regulation.},
journal = {Bladder (San Francisco, Calif.)},
volume = {12},
number = {2},
pages = {e21200036},
pmid = {40747461},
issn = {2327-2120},
abstract = {BACKGROUND: The disrupted gut microbiome has been found to be implicated in the development of interstitial cystitis/bladder pain syndrome (IC/BPS). Pentosan polysulfate (PPS) is an oral medication used for treating IC/BPS, acting as both an anti-inflammatory agent and a bladder barrier protector. However, the precise mechanisms by which the PPS-mediated modulation of the gut microbiome alleviates IC/BPS are not fully understood.

OBJECTIVE: This study aimed to identify the key gut microbiota species and metabolites involved in PPS's protective effects against IC/BPS.

METHODS: We employed a multifaceted approach, including 16S rDNA gene sequencing, antibiotic treatment, and fecal microbiota transplantation, to validate the dependency of PPS's protective effects on the gut microbiome. Furthermore, we performed a comprehensive metabolomic profiling using non-targeted metabolomics and liquid chromatography-tandem mass spectrometry.

RESULTS: PPS significantly elevated the abundance of the xylan-degrading bacteria, Eubacterium xylanophilum group, which, through its interaction with the gut microbiome, markedly reduced inflammation and barrier damage induced by cyclophosphamide in IC/BPS. In addition, PPS significantly increased the level of ursodeoxycholic acid (UDCA), a secondary bile acid, demonstrating a strong correlation with the abundance of the E. xylanophilum group. Ex vivo supplementation with UDCA mitigated lipopolysaccharide-induced inflammation and barrier disruption in SV-HUC-1 cells by activating the TGR5 receptor.

CONCLUSION: PPS exerts its protective effects against IC/BPS by modulating the gut microbiome and its metabolites.},
}

@article {pmid40747428,
year = {2025},
author = {Rodrigues, RR and Karumuru, V and Nuss, S and Elliott, M and Shriver, I and Chao, CM and Doyle, HA and Tripp, C and Mamula, MJ and Dzutsev, A and Morgun, A and Shulzhenko, N},
title = {Gut microbiota of dogs with cancer receiving anti-EGFR/HER2 immunization reveals potential biomarkers of patient survival.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.13.663784},
pmid = {40747428},
issn = {2692-8205},
abstract = {BACKGROUND: Canine cancer remains a leading cause of death in dogs, yet advances in veterinary oncology lag behind human medicine, particularly in immunotherapy. While immune checkpoint inhibitors are just entering clinical trials in dogs, other immunotherapies, such as anti-EGFR/HER2 vaccines, have shown promise. In parallel, mounting evidence in human oncology links gut microbiota composition to immunotherapy response. However, this relationship remains unexplored in canine patients. In this pilot study, we analyzed the gut microbiome of dogs enrolled in a clinical trial of anti-EGFR/HER2 immunotherapy to identify microbial biomarkers associated with survival outcomes.

METHODS: Rectal swab samples of 51 dogs were collected at the time of first vaccine administration (baseline microbiota) and underwent 16S rRNA gene sequencing according to standard protocols.

RESULTS: Microbiome composition showed no significant differences by cancer type, sex, or breed, suggesting no inherent microbiome bias in the cohort. However, Cox regression analysis revealed 11 bacterial taxa whose abundances were significantly associated with overall survival (FDR < 0.1), independently of cancer type. Seven taxa were linked to increased mortality risk, while four were associated with prolonged survival. These associations remained significant after adjusting for confounders such as hemangiosarcoma diagnosis and advanced age.

CONCLUSIONS: To our knowledge, this is the first study to identify gut microbial signatures associated with survival in dogs undergoing cancer immunotherapy. These findings suggest that specific bacterial taxa may serve as prognostic biomarkers for immunotherapy outcomes in canine cancer, laying the groundwork for microbiota-targeted strategies to improve therapeutic efficacy in veterinary oncology.},
}

@article {pmid40747416,
year = {2025},
author = {Sarwal, R and Tarca, V and Dubin, C and Kalavros, N and Bhatti, G and Bhattacharya, S and Butte, A and Romero, R and Stolovitzky, G and Oskotsky, TT and Tarca, AL and Sirota, M},
title = {Benchmarking Large Language Models for Predictive Modeling in Biomedical Research With a Focus on Reproductive Health.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.07.663529},
pmid = {40747416},
issn = {2692-8205},
abstract = {Generative AI, particularly large language models (LLMs), is increasingly being used in computational biology to support code generation for data analysis. In this study, we evaluated the ability of LLMs to generate functional R and Python code for predictive modeling tasks, leveraging standardized molecular datasets from several recent DREAM (Dialogue for Reverse Engineering Assessments and Methods) Challenges focused on reproductive health. We assessed LLM performance across four predictive tasks derived from three DREAM challenges: gestational age regression from gene expression, gestational age regression from DNA methylation profiles, and classification of preterm birth and early preterm birth from microbiome data. LLMs were prompted with task descriptions, data locations, and target outcomes. LLM-generated code was then run to fit and apply prediction models and generate graphics, and they were ranked based on their success in completing the tasks and achieving strong test set performance. Among the eight LLMs tested, o3-mini-high, 4o, DeepseekR1 and Gemini 2.0 completed at least one task without error. Overall, R code generation was more successful (14/16 tasks) than Python (7/16), attributed to the utility of Bioconductor packages for querying Gene Expression Omnibus data. OpenAI's o3-mini-high outperformed others, completing 7/8 tasks. Test set performance of the top LLM matched or exceeded top-performing teams from the original DREAM challenges. These findings underscore the potential of LLMs to enhance exploratory analysis and democratize access to predictive modeling in omics by automating key components of analysis pipelines, and highlight the potential to increase research output when conducting analyses of standardized datasets from public repositories.},
}

@article {pmid40747333,
year = {2025},
author = {Pattapulavar, V and Ramanujam, S and Kini, B and Christopher, JG},
title = {Probiotic-derived postbiotics: a perspective on next-generation therapeutics.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1624539},
pmid = {40747333},
issn = {2296-861X},
abstract = {The gut microbiome plays a fundamental role in regulating host immunity, metabolism, and overall health. Disruptions to this microbial ecosystem, known as dysbiosis, have been implicated in various conditions such as colorectal cancer, inflammatory bowel diseases, and metabolic syndromes. Although probiotics are widely used to restore microbial balance, their efficacy is often inconsistent due to variable colonization and concerns over antimicrobial resistance gene transfer. This review explores the growing body of literature surrounding postbiotics-bioactive metabolites produced by probiotics-as a promising alternative to live microbial therapy. We focus on key classes of postbiotics including exopolysaccharides, cell-free supernatants, short-chain fatty acids, and bacteriocins, summarizing their reported immunomodulatory, antimicrobial, antioxidant, and anti-cancer properties. We also highlight recent developments in formulation techniques, such as encapsulation, which enhance their stability and bioavailability. While current findings are promising, limitations persist, including variability in postbiotic composition and a lack of standardized clinical evaluations. Future research should aim to clarify their mechanisms of action, define optimal delivery strategies, and assess long-term safety. Overall, postbiotics present a sustainable, non-viable, and functionally rich alternative to probiotics, aligning with global health goals-Sustainable Development Goal 3 (Good Health and Well-being) and Sustainable Development Goal 9 (Industry, Innovation, and Infrastructure)-by offering safer, scalable, and effective therapeutic solutions.},
}

@article {pmid40747223,
year = {2025},
author = {Mitchell, NE and Chan, SY and Jerez Diaz, D and Ansari, N and Lee, J and Twohig, P},
title = {Evolving therapeutic landscape of primary biliary cholangitis: A review.},
journal = {World journal of hepatology},
volume = {17},
number = {7},
pages = {107223},
pmid = {40747223},
issn = {1948-5182},
abstract = {Primary biliary cholangitis (PBC) is a chronic autoimmune cholestatic liver disease characterized by progressive bile duct destruction, leading to fibrosis, cirrhosis, and eventual liver failure. Over the past two decades, significant advancements have paved the way for novel therapeutic strategies. Ursodeoxycholic acid (UDCA) has been the cornerstone of PBC management, improving survival and delaying disease progression in most patients. However, up to 40% of patients demonstrate an inadequate response to UDCA, necessitating additional treatment options. Obeticholic acid (OCA), a farnesoid X receptor agonist, has emerged as a second-line therapy, showing efficacy in reducing alkaline phosphatase levels and improving liver biochemistry. Beyond UDCA and OCA, a new wave of therapeutic agents are reshaping the PBC landscape. These include fibrates, peroxisome proliferator-activated receptor agonists and novel immunomodulatory drugs aimed at reducing autoimmune-mediated liver injury. Bile acid transport inhibitors, anti-fibrotic agents, and gut microbiome-targeted therapies are also under investigation, offering hope for personalized treatment approaches. This review highlights the evolution of PBC therapy, emphasizing the unmet needs of patients with refractory disease and the potential of emerging therapies to improve outcomes. As the therapeutic landscape continues to expand, optimizing treatment strategies through precision medicine holds the promise of transforming the management of PBC.},
}

@article {pmid40747222,
year = {2025},
author = {Pamungkas, KMN and Lesmana Dewi, PIS and Alamsyah, AZ and Dewi, NLPY and Dewi, NNGK and Mariadi, IK and Sindhughosa, DA},
title = {Microbiome dysbiosis and immune checkpoint inhibitors: Dual targets in Hepatocellular carcinoma management.},
journal = {World journal of hepatology},
volume = {17},
number = {7},
pages = {106810},
pmid = {40747222},
issn = {1948-5182},
abstract = {Hepatocellular carcinoma (HCC), a primary malignancy of the liver and leading cause of cancer-related mortality worldwide, poses substantial therapeutic challenges, particularly in advanced and unresectable stages. Immune checkpoint inhibitors (ICIs) have emerged as critical therapeutic agents, targeting immune checkpoint pathways to restore antitumor immune responses. Combinations such as atezolizumab (anti-programmed cell death ligand 1 with bevacizumab (anti-vascular endothelial growth factor), as well as antibodies directed against cytotoxic T-lymphocyte associated protein 4 and programmed cell death protein 1 (e.g., ipilimumab and nivolumab), have demonstrated improved clinical outcome in selected patients. However, the overall efficacy of ICIs remains hindered by variable response rate and primary or acquired resistance. Recent evidence suggests that the gut microbiome plays a pivotal role in modulating host immune responses and may significantly influence the therapeutic efficacy of ICIs. Dysbiosis within the gut-liver axis has been implicated not only in pathogenesis and progression of HCC but also diminishing immunotherapy effectiveness. Emerging studies highlight the potential of microbiome-targeted interventions including dietary modulation, prebiotics, probiotics, and fecal microbiota transplantation to enhance ICIs responsiveness. This review explores the evolving interplay between the gut microbiota and immunotherapy in HCC, with a focus on microbiome-based strategies aimed at optimizing clinical outcomes.},
}

@article {pmid40746321,
year = {2025},
author = {Li, C and Chen, Y and Yao, W and Zhang, P and Wang, X and Qu, G and Ren, Z and Wang, J},
title = {Gut microbiome and serum metabolome alterations in osteosarcoma patients.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1616603},
pmid = {40746321},
issn = {1664-302X},
abstract = {BACKGROUND: Gut microbiota has been shown to initiate tumorigenesis and cancer metastasis in multiple cancer types. However, the functional alterations of gut microbiota and their association with metabolism in osteosarcoma patients remain largely unexplored. This study aimed to characterize the gut microbiota and serum metabolite profiles in osteosarcoma patients, evaluate the diagnostic potential of gut microbiota and serum metabolites for osteosarcoma, and explore their correlations.

METHODS: We collected 128 fecal and 181 serum samples from osteosarcoma patients, paired with matched healthy controls. 16S rRNA sequencing and untargeted metabolomics were applied to analyze gut microbiota and serum metabolism with significantly altered abundance in patients with osteosarcoma. Models based on gut microbiome or serum metabolites were established and evaluated in an independent validation cohort.

RESULTS: The gut microbial diversity decreased in osteosarcoma patients compared to healthy individuals. Principal component analysis identified 33 microbial species that exhibited significant changes in osteosarcoma patients. Of note, the relative abundance of Alloprevotella and Prevotella increased in these patients. This distinct alteration in gut microbiota was accompanied by functional changes in pathways related to glycan degradation, pentose and glucuronate interconversions, the citrate cycle, and fructose and mannose metabolism during osteosarcoma progression. Furthermore, metabolomic analyses revealed a distinct distribution of serum metabolites in osteosarcoma patients compared to healthy controls. These metabolites were correlated with cancer's carbon metabolism, glucagon signaling, and the citrate cycle pathways. Combined with the enrichment analysis results, gut microbiota and serum metabolites were associated with carbohydrate-related metabolism in osteosarcoma patients. Importantly, classifiers utilizing 3 optimal microbial markers (6 serum metabolites) demonstrated strong diagnostic efficiency in distinguishing osteosarcoma patients from healthy controls across various cohorts.

CONCLUSION: This study thoroughly analyzed gut microbiota and serum metabolites in osteosarcoma patients, exploring their correlations and facilitating the establishment of a diagnostic model.},
}

@article {pmid40746318,
year = {2025},
author = {Ma, H and Fang, J and Li, M and Qin, Y and Wang, Y and Kang, SG and Huang, K and Tong, T},
title = {Characteristic alterations of gut microbiota and metabolites in patients with perianal abscess: a multi-omics analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1557972},
pmid = {40746318},
issn = {1664-302X},
abstract = {BACKGROUND/OBJECTIVES: Various studies have highlighted the important associations between perianal abscess (PA) and gut microbiota and related metabolites. Nevertheless, the establishment of causal relationships between these associations remains to be determined. This study aimed to provide direct evidence and a comprehensive understanding of gut microbiota disturbance in children with PA through combined 16S rRNA sequencing and untargeted metabolomic analysis.

METHODS: Thirty three children with PA and 16 healthy controls (HC) were continuously enrolled, and the demographic and clinical characteristics of the subjects were collected. First, 16S rRNA sequencing was used to evaluate differences in the gut microbiota between children with PA and the HC group, and 10 children with PA and 10 children in the HC group were randomly selected for non-targeted metabolomic analysis.

RESULTS: There were significant differences in the gut microbiota diversity and composition between children with PA and HC. Comprehensive analyses revealed an elevation of the genus Enterococcus and a depletion of the phylum Firmicutes as well as Eubacterium_hallii_group, Faecalibacterium, Blautia, and Fusicatenibacter at the genus level in children with PA. Non-targeted metabolomics detected 1168 different metabolites between children with PA and HC. Functional analysis of the gut microbiota and KEGG pathway enrichment analysis of differential metabolites between the PA and HC groups corroborated that the pathways of phenylalanine, tyrosine and tryptophan biosynthesis, valine, leucine and isoleucine biosynthesis, and pantothenate and CoA biosynthesis were down-regulated in children with PA, while the pathways of ubiquinone and other terpenoid-quinone biosynthesis, tyrosine metabolism, and tryptophan metabolism were up-regulated in children with PA. The correlation analysis highlighted meaningful associations between the altered microbiota and specific metabolic profiles, further underscoring the complex interplay between microbial composition and metabolic function in the pathogenesis of PA in children.

CONCLUSIONS: This study provides new evidence of the pathogenesis of PA. There are significant differences in the gut microbiota, metabolites, and metabolic pathways between HC and children with PA, and the differences in metabolites are related to specific changes in bacterial abundance. These findings provide a foundation for future studies aimed at exploring targeted microbiome-based therapeutic strategies for managing PA in pediatric populations.},
}

@article {pmid40746172,
year = {2025},
author = {Fan, Y and Pu, Y and Xu, X and Yang, J},
title = {Benefit of Lycium barbarum polysaccharide supplementation in patients with nonalcoholic fatty liver disease: A pre-post study.},
journal = {Nutrition and health},
volume = {},
number = {},
pages = {2601060251357979},
doi = {10.1177/02601060251357979},
pmid = {40746172},
issn = {0260-1060},
abstract = {Background: Nonalcoholic fatty liver disease (NAFLD) is characterized by an abnormal accumulation of lipids in the liver tissue. Aim: This study aims to evaluate the potential therapeutic effect of oral Lycium barbarum polysaccharide (LBP) capsules in patients with NAFLD. Methods: A pre-post-intervention clinical trial involving 13 participants, aged 28-50 years, was conducted at a community health center. Participants underwent abdominal ultrasound and laboratory tests, including alanine aminotransferase level measurements. During the 12-week intervention period, participants received a daily oral LBP supplement capsule (300 mg). We collected blood and stool samples at baseline and postintervention, which were for 16S rRNA gene sequencing and metabolomics analysis. Results: Postintervention, significant reductions (p < 0.05) were observed in gamma-glutamyltransferase (GGT), ALB, TP, and D-BIL levels. There were 125 upregulated and 65 downregulated metabolites. LBP supplementation increased Gemmiger abundance. Microbiota diversity, analyzed through 16S rRNA sequencing, showed altered phylum distribution in fecal samples, with PICRUSt2 indicating effects on linoleic acid metabolism. Changes in negative correlations between specific lipid metabolites, such as Her2Cer(d14:0_22:6), and enzyme activities like GGT, were also noted. Conclusion: Lycium barbarum polysaccharide intervention may enhance GGT, ALB, TP, and D-BIL levels, demonstrating beneficial effects on critical biochemical parameters in NAFLD patients. Correlation analysis showed LBP alters the relationship between specific lipid metabolites and enzyme activity, notably between GGT and Her2Cer(d14:0_22:6), laying groundwork for further research on LBP's impact on NAFLD. Trial registration: Chinese Clinical Trial Registry, ChiCTR2000034740, and Institutional Ethics Committee of Ningxia Medical University, 2019-329.},
}

@article {pmid40746157,
year = {2025},
author = {Hubert, J and Sopko, B and Głowska-Patyniak, E},
title = {Environmental Microbiome of Tyrophagus Putrescentiae Culture and Its Changes in Manipulative Experiments.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70142},
doi = {10.1111/1758-2229.70142},
pmid = {40746157},
issn = {1758-2229},
support = {UMO-2021/03/Y/NZ8/00060//National Science Centre, Poland/ ; GF22-15841K//Grantová Agentura České Republiky/ ; //Czech Science Foundation/ ; },
mesh = {Animals ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Acaridae/microbiology/growth & development ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Environmental Microbiology ; },
abstract = {Storage mites consume stored products in interaction with environmental microorganisms, resulting in the destruction of infested food and providing specific odours. Here we simulated the effect of mite grazing on oat flakes. Spent growth medium (SPGM) was obtained from seven mite cultures and mixed with oat flakes as the source of faeces and microbes. SPGM-treated diets were offered to 4 mite cultures. The microbiomes were analysed using sequencing of V4_16S_DNA. Mite growth tests, food preferences, and microbiome changes were observed in correlation with SPGM type and mite cultures. The microbiome consisted of 41 OTUs belonging to mite-associated bacteria and faeces bacteria. The composition of the microbiome depends more on the source of SPGM than on mite culture. The SPGM diet accelerated mite population growth and influenced mite food choice, although the effect was dependent on both types of SPGM and mite culture. Kocuria, Brevibacterium, Virgibacillus, and Staphylococcus profiles in SPGM added into diets showed positive correlations to mite population growth. The Kocuria profile in the bodies of mites was positively correlated with mite population growth. The results showed that mites are influenced by SPGM-treated diets, and mite feeding influences the environmental microbiome. The most beneficial was the mite interaction with Kocuria.},
}

Animals
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Acaridae/microbiology/growth & development
Feces/microbiology
RNA, Ribosomal, 16S/genetics
*Environmental Microbiology

@article {pmid40745659,
year = {2025},
author = {Karimi, M and Rabiei, R and Kazemi, K and Motlagh, RB and Asbaghi, O},
title = {Effects of probiotics and synbiotics oral supplementation on thyroid function in adults: a grade-assessed systematic review and meta-analysis.},
journal = {Thyroid research},
volume = {18},
number = {1},
pages = {39},
pmid = {40745659},
issn = {1756-6614},
abstract = {BACKGROUND AND AIM: Evidence suggests that the gut microbiota may have a potential impact on thyroid function, given the gut-thyroid axis and the microbiome's involvement in nutrient absorption, immune modulation, and hormone metabolism. Emerging research highlighted that probiotics and synbiotics may influence thyroid hormone regulation, although findings in original studies are inconsistent. Therefore, this meta-analysis aims to evaluate the effects of probiotics and synbiotics oral supplementation on thyroid hormones in adults.

METHODS: A systematic search was conducted across major online databases until April 2025. Studies were selected, relevant data extracted, and statistically analyzed using standard mean differences (SMD) and 95% confidence intervals (CI).

RESULTS: The pooled analysis of nine clinical trials showed that probiotics and synbiotics oral supplementation led to a significant reduction in thyroid-stimulating hormone (TSH) (SMD: -1.10, 95%CI: [-1.96, -0.23], p = 0.013), and significantly increase free triiodothyronine (T3) (SMD: 0.98, 95% CI: [0.10, 1.85], p = 0.029) and free thyroxine (T4) (SMD: 1.04, 95%CI: [0.04, 2.05], p = 0.042). Subgroup analyses indicated that supplementation lasting ≤ 8 weeks showed a stronger effect. Additionally, patients with thyroid disorders show higher responsiveness.

CONCLUSION: Probiotics and synbiotics supplementation may beneficially modulate thyroid function, demonstrated by a significant reduction in TSH levels and increases in free T3 and free T4, particularly among individuals with thyroid disorders. These findings support the potential role of microbiome-targeted interventions as adjunctive strategies in managing thyroid dysfunction. However, further large-scale, long-term RCTs are needed to confirm their clinical efficacy and to establish standardized protocols for their use in routine care.},
}

@article {pmid40745634,
year = {2025},
author = {Tao, YX and Zhang, ED and Yue, JX and Wan, ZL and Fan, JW and Li, Y and Fan, Y and Yan, L},
title = {2bRAD-M reveals circulating microbiome in chronic antibody-mediated rejection (CAMR) and IgA nephropathy (IgAN) after kidney transplantation.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {468},
pmid = {40745634},
issn = {1471-2180},
support = {2024NSFSC1540//Sichuan Provincial Youth Science and Technology Foundation/ ; 82102466//National Natural Youth Science Foundation of China/ ; 2023YFS0108//Sichuan Provincial Science and Technology Support Program/ ; HXQMX0089//"Qimingxing" Research Fund for Young Talents/ ; },
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Glomerulonephritis, IGA/microbiology/blood/immunology ; Male ; Female ; Adult ; *Graft Rejection/microbiology/immunology/blood ; Middle Aged ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Kidney transplantation is currently the most effective method for treating end-stage renal disease. However, postoperative-related rejection and IgA nephropathy remains a serious obstacle to the long-term survival of kidney transplant patients. Its pathogenesis is not fully understood, and potential causative factors remain to be explored. In this study, we used 2bRAD-M to analyze differences in the peripheral blood microbiome of renal transplant recipients who were stable postoperatively (STABLE) and those who developed chronic antibody-mediated rejection (CAMR) or IgA nephropathy (IgAN) recurrence.

METHOD: Thirty one renal transplant patients were recruited, including 12 STABLE, 8 CAMR and 11 IgAN patients after kidney transplantation. 2bRAD-M was used to characterize the microbiota in peripheral blood to explore the presence of microbial differences.

RESULTS: Differences in microbial community composition were observed between CAMR, IgAN and STABLE. The alpha diversity of CAMR and IgAN was all higher than STABLE, there are also differences in beta diversity. LEfSe was performed to identify different abundance taxa, 21 discriminative features between CAMR and STABLE, 39 discriminative features between IgAN and STABLE. The mean decrease Gini index and random forest analysis indicated that Staphylococcus_epidermidis might serve as indicator bacteria for CAMR, Kocuria_palustris might serve as indicator bacteria for IgAN. ROC analysis was performed to assess the performance of some optimal marker models, and the average AUC value achieved 89.6% between CAMR and STABLE, 67.4% between IgAN and STABLE. Functional annotation analysis showed 4353 different COGs and 378 related signaling pathways between CAMR and STABLE, 4396 different COGs and 384 related signaling pathways between CAMR and STABLE.

CONCLUSION: The first 2bRAD-M microbiome study of CAMR and IgAN after renal transplantation showed a potential association between the circulating microbiome and the disease, and provided a possible target and basis for subsequent studies of the mechanisms underlying the development and progression of CAMR and IgAN after renal transplantation.},
}

Humans
*Kidney Transplantation/adverse effects
*Glomerulonephritis, IGA/microbiology/blood/immunology
Male
Female
Adult
*Graft Rejection/microbiology/immunology/blood
Middle Aged
*Microbiota
*Bacteria/classification/genetics/isolation & purification

@article {pmid40745568,
year = {2025},
author = {Hornung, F and SureshKumar, HK and Klement, L and Reisser, Y and Wernike, C and Nischang, V and Jordan, PM and Werz, O and Hoffmann, C and Löffler, B and Deinhardt-Emmer, S},
title = {High-fat diet impairs microbial metabolite production and aggravates influenza A infection.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {359},
pmid = {40745568},
issn = {1478-811X},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; Humans ; *Influenza A virus/physiology ; Mice ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; *Orthomyxoviridae Infections/metabolism/microbiology ; Mice, Inbred C57BL ; Male ; *Influenza, Human/metabolism/microbiology ; Lung/virology/pathology/metabolism ; Acetates/pharmacology ; },
abstract = {BACKGROUND: Alterations in the gut microbiom can significantly impact various regions in the human body, including the pulmonary tract. This study investigates alterations in the gut microbiome during a high-fat diet (HFD), particularly short-chain fatty acids (SCFAs), and how these metabolites affect lung infection caused by Influenza A virus (IAV).

METHODS: We used a HFD-mouse model to evaluate gut microbiota composition, SCFA levels, and pulmonary outcomes following IAV infection. Microbial changes were analyzed via taxonomic and functional profiling and SCFA levels were measured from non-obese and obese serum donors. Ultimately, acetate's effects were tested ex vivo in human precision-cut lung slices (PCLS) and in vitro in pulmonary epithelial cells. Mechanistic studies investigated the involvement of the SCFA receptor free fatty acid receptor 2 (FFAR2) and intracellular antiviral pathways.

RESULTS: Our data indicates an increased Firmicutes/Bacteroidetes ratio of the gut microbiome and an altered carbohydrate metabolism, leading to reduced SCFA production. Infected HFD mice showed increased IAV titers and sustained microbial alterations. Interestingly, acetate demonstrated antiviral effects in both the human PCLS model and pulmonary cells with an reduced viral replication. These effects depended on FFAR2, which also acts as an IAV co-receptor, as acetate treatment led to FFAR2 internalization and influenced host cell metabolism in our in vitro data.

CONCLUSION: HFD alters the SCFA production, reducing acetate levels in the gut microbiome. This reduction may lead to higher viral loads and worsened disease in HFD mice infected with IAV. Our findings indicate that acetate has antiviral effects during IAV infection in both a human ex vivo lung model and pulmonary epithelial cells. Here, acetate prevents viral entry and affects the cellular metabolic state and antiviral response. Understanding these mechanisms could provide new targets for preventing and treating viral infections in individuals with diet-related health issues.},
}

Animals
*Diet, High-Fat/adverse effects
Humans
*Influenza A virus/physiology
Mice
Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome
*Orthomyxoviridae Infections/metabolism/microbiology
Mice, Inbred C57BL
Male
*Influenza, Human/metabolism/microbiology
Lung/virology/pathology/metabolism
Acetates/pharmacology

@article {pmid40745546,
year = {2025},
author = {Chung, S and Shin, JH and Kim, JH and Kim, KB and Nam, YD and Lim, MY},
title = {Association between a low-carbohydrate diet and macronutrient intake with the gut microbiome, and their interaction with dyslipidemia among Korean adults.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {121},
pmid = {40745546},
issn = {1475-2891},
support = {E0252500-01//Ministry of Science and ICT, South Korea/ ; E0252500-01//Ministry of Science and ICT, South Korea/ ; E0252500-01//Ministry of Science and ICT, South Korea/ ; E0170600-09//Ministry of Science and ICT, South Korea/ ; E0252500-01//Ministry of Science and ICT, South Korea/ ; E0252500-01//Ministry of Science and ICT, South Korea/ ; },
}

@article {pmid40745494,
year = {2025},
author = {Rupp, M and Ferry, T and Khan Mirzaei, M and Alt, V and Deng, L and Walter, N},
title = {[Bacteriophages for the treatment of musculoskeletal infections-An overview of clinical use, open questions, and legal framework].},
journal = {Orthopadie (Heidelberg, Germany)},
volume = {},
number = {},
pages = {},
pmid = {40745494},
issn = {2731-7153},
abstract = {BACKGROUND: Bacteriophages, or simply phages, are viruses that specifically infect and lyse bacteria. As antibiotic resistance becomes a growing global concern, phage therapy is gaining renewed attention as a targeted and effective treatment option. In orthopedics and trauma surgery-disciplines characterized by high rates of chronic and implant-associated infections-phages offer promising new therapeutic avenues, particularly in cases involving multidrug-resistant pathogens or when conventional surgery is limited.

CURRENT DEVELOPMENTS: Originally developed in the early 20th century, phage therapy lost prominence with the rise of antibiotics. Today, case studies and emerging clinical protocols-especially in the context of periprosthetic joint infections-demonstrate the potential of personalized phage cocktails and advanced delivery systems, such as hydrogels or intra-articular injections. Their specificity enables bacterial eradication while sparing the host microbiome.

REGULATORY SITUATION: However, the regulatory landscape in the European Union poses significant challenges. Phages are classified as biological medicinal products, requiring comprehensive preclinical and clinical evaluation. While magistral production and compassionate use permit individual applications, broad clinical integration demands standardized protocols, accessible phage libraries, and robust quality control. Furthermore, safety concerns, including immunogenicity and systemic distribution, must be addressed through structured research.

CONCLUSION: To fully realize the potential of phage therapy in orthopaedic infection management, interdisciplinary collaboration, targeted funding, and clinical trials are essential. Responsible implementation within expert centers can ensure efficacy and safety, paving the way for a controlled and evidence-based adoption of phages as a complementary strategy alongside traditional surgical and antibiotic treatments.},
}

@article {pmid40745489,
year = {2025},
author = {Caminero, A and Tropini, C and Valles-Colomer, M and Shung, DL and Gibbons, SM and Surette, MG and Sokol, H and Tomeo, NJ and , and Tarr, PI and Verdu, EF},
title = {Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41575-025-01100-9},
pmid = {40745489},
issn = {1759-5053},
abstract = {The microbiome has critical roles in human health and disease. Advances in high-throughput sequencing and metabolomics have revolutionized our understanding of human gut microbial communities and identified plausible associations with a variety of disorders. However, microbiome research remains constrained by challenges in establishing causality, an over-reliance on correlative studies, and methodological and analytical limitations. Artificial intelligence (AI) has emerged as a powerful tool to address these challenges; however, the seamless integration of preclinical models and clinical trials is crucial to maximizing the translational impact of microbiome studies. This manuscript critically evaluates best methodological practices and limitations in the field, focusing on how emerging AI tools can bridge the gap between microbial insights and clinical applications. Specifically, we emphasize the necessity of rigorous, reproducible methodologies that integrate multiomics approaches, preclinical models and clinical trials in the AI-driven era. We propose a practical framework for applying AI to microbiome studies, alongside strategic recommendations for clinical trial design, regulatory pathways, and best practices for microbiome-based informed diagnostics, AI training and clinical interventions. By establishing these guidelines, we aim to accelerate the translation of microbiome research into clinical practice, enabling precision medicine approaches informed by the human microbiome.},
}

@article {pmid40745465,
year = {2025},
author = {Popova, A and Rācenis, K and Brīvība, M and Saksis, R and Saulīte, M and Šlisere, B and Berga-Švītiņa, E and Oļeiņika, K and Saulīte, AJ and Seilis, J and Kroiča, J and Čerņevskis, H and Pētersons, A and Kloviņš, J and Lejnieks, A and Kuzema, V},
title = {Reduced butyrate-producing bacteria and altered metabolic pathways in the gut microbiome of immunoglobulin A nephropathy patients.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28011},
pmid = {40745465},
issn = {2045-2322},
support = {lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/metabolism/pathology ; Female ; *Butyrates/metabolism ; Male ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; *Metabolic Networks and Pathways ; Cross-Sectional Studies ; Feces/microbiology ; *Bacteria/metabolism/genetics/classification ; Prospective Studies ; Immunoglobulin A/metabolism ; Case-Control Studies ; },
abstract = {Gut-associated lymphoid tissue is central to the production of galactose-deficient IgA1 (Gd-IgA1), a key factor in immunoglobulin A nephropathy (IgAN). Although no major differences in gut microbiome diversity have been reported across IgAN cohorts, functional alterations in microbial composition may contribute to disease pathogenesis. The study was designed as a cross-sectional study with an embedded prospective cohort component. Forty-eight adults with biopsy-confirmed IgAN-categorized as progressors (eGFR decline > 5 ml/min/1.73 m[2]/year, n = 23) or nonprogressors (n = 23)-and 23 healthy controls (HC) were recruited. Stool samples underwent metagenomic and functional profiling. Alpha diversity did not differ significantly between IgAN patients and HC. However, butyrate-producing bacteria (Butyrococcus, Agathobacter rectalis) were less abundant in IgAN patients. The sulfoquinovose degradation I pathway, associated with these bacteria, was also reduced. Nucleotide- and nucleoside-biosynthesis pathways were elevated in IgAN. Gd-IgA1 levels correlated with variations in metabolic pathways. Progressors demonstrated enhanced activity in isopropanol biosynthesis, biotin biosynthesis II, and phospholipid biosynthesis pathways. IgAN patients show reduced butyrate-producing bacteria and distinct functional changes in the gut microbiome suggestive of immune activation and inflammation. Progressors exhibit additional metabolic shifts linked to bacterial membrane stabilization.},
}

Humans
*Glomerulonephritis, IGA/microbiology/metabolism/pathology
Female
*Butyrates/metabolism
Male
Adult
*Gastrointestinal Microbiome
Middle Aged
*Metabolic Networks and Pathways
Cross-Sectional Studies
Feces/microbiology
*Bacteria/metabolism/genetics/classification
Prospective Studies
Immunoglobulin A/metabolism
Case-Control Studies

@article {pmid40745404,
year = {2025},
author = {Carletti, M and Pandit, J and Gadaleta, M and Chiang, D and Delgado, F and Quartuccio, K and Fernandez, B and Raygoza Garay, JA and Torkamani, A and Miotto, R and Rossman, H and Berk, B and Baca-Motes, K and Kheterpal, V and Segal, E and Topol, EJ and Ramos, E and Quer, G},
title = {Multimodal AI correlates of glucose spikes in people with normal glucose regulation, pre-diabetes and type 2 diabetes.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-025-03849-7},
pmid = {40745404},
issn = {1546-170X},
support = {UM1TR004407//U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; },
abstract = {Type 2 diabetes (T2D) is a multifaceted disease associated with several factors, including diet, genetics, exercise, sleep and gut microbiome. Current diagnostic and monitoring methods based on episodic assays like glycated hemoglobin (HbA1c) fail to capture its full complexity. Here, in a prospective cohort of 1,137 participants in the United States, we analyzed multimodal data from 347 deeply phenotyped individuals (174 normoglycemic, 79 prediabetic and 94 T2D). We found significant differences in the distribution of glucose spike metrics among different diabetes states, with longer expected time for spike resolution and higher values of nocturnal hypoglycemia in T2D. We identified significant correlations between mean glucose level and gut microbiome diversity, and between expected time for spike resolution and resting heart rate. Our multimodal glycemic risk profiles, validated in 1,955 normoglycemic and 114 prediabetic individuals from an independent cohort, improved risk stratification by highlighting substantial variability among individuals with the same value of HbA1c. Such a multimodal approach provides a detailed phenotype that can potentially improve T2D prevention, diagnosis and treatment, and is more informative than HbA1c.},
}

@article {pmid40745139,
year = {2025},
author = {Soteriou, E and Apidianakis, Y and Pitsouli, C},
title = {Host-Microbe Interactions in Drosophila Cancer.},
journal = {Advances in experimental medicine and biology},
volume = {1482},
number = {},
pages = {119-133},
doi = {10.1007/978-3-031-97035-1_7},
pmid = {40745139},
issn = {0065-2598},
mesh = {Animals ; *Neoplasms/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Drosophila melanogaster/microbiology ; *Host Microbial Interactions ; *Drosophila/microbiology ; Carcinogenesis ; },
abstract = {Dysbiosis, the imbalance of an organism's commensal microbiota, may drive dysplasia and tumorigenesis via aberrant immune response, increased inflammation, and stem cell overactivation. The Drosophila gut is a useful model to study host-microbiota interactions leading to tumorigenesis due to its molecular, cellular, and physiological similarity with the human gut and its simplicity at the host and microbiome levels. A primary lesson learned from Drosophila gut studies is that microbiota and pathogenic microbes, such as bacteria and viruses, induce multiple innate immune and stress signaling pathways in enterocytes and other gut cells that, in turn, activate mitogens driving regenerative stem cell proliferation. A second important lesson learned from Drosophila gut studies is that wild-type and genetically predisposed intestinal epithelial cells are more likely to initiate tumorigenesis and tissue invasion upon interaction with intestinal microbes. Lastly, microbial nutrients may directly affect intestinal stem cell proliferation and tissue regeneration. This review discusses the mechanisms by which the microbiome influences directly and indirectly stem cell proliferation, tumorigenesis, and tumor cell dissemination, shedding light on microbiota-mediated cancer predisposition.},
}

Animals
*Neoplasms/microbiology/pathology
Humans
*Gastrointestinal Microbiome
*Drosophila melanogaster/microbiology
*Host Microbial Interactions
*Drosophila/microbiology
Carcinogenesis

@article {pmid40745072,
year = {2025},
author = {Adeyemo, AA and Daodu, AO and Opowoye, IO and Adewole, FA and Sogunle, OM},
title = {Gut microbiome and antibacterial activities of Bryophyllum pinnatum (Life plant) blend on gut of broiler chickens.},
journal = {Tropical animal health and production},
volume = {57},
number = {7},
pages = {331},
pmid = {40745072},
issn = {1573-7438},
}

@article {pmid40745056,
year = {2025},
author = {Kuhn, KA and Yomogida, K and Knoop, K and Wu, HJ and Zaiss, MM},
title = {More than a leaky gut: how gut priming shapes arthritis.},
journal = {Nature reviews. Rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41584-025-01282-1},
pmid = {40745056},
issn = {1759-4804},
abstract = {The gut microbiome forms an ecosystem that provides the host with numerous benefits such as digestion with nutrient generation, protection from pathogens and immune system maturation. Alterations in the microbial ecosystem associated with rheumatoid arthritis and spondyloarthritis have led to the gut-joint hypothesis, which postulates that these ecological changes cause immune dysfunction that contributes to the development of arthritis. Mechanisms by which dysbiosis might trigger arthritis include molecular mimicry, dysregulation of mucosal immunity, microbial translocation, production of immunomodulatory metabolites and immune cell trafficking. We discuss the data supporting each of these mechanisms, and highlight misconceptions, limitations and gaps in knowledge. In particular, we advise against the term 'leaky-gut' as the mechanisms and effects on the immune system of intestinal permeability and bacterial translocation are distinct. Nevertheless, rheumatoid arthritis and spondyloarthritis possibly result from the convergence of multiple pathways that could be unique to subgroups of individuals within these diseases. To move the field forward, each mechanism needs to be considered through the use of model organisms and interventional trials, individually and in concert.},
}

@article {pmid40745023,
year = {2025},
author = {Figuerola, B and Capdevila, P and Cerdà-Domènech, M and Garrabou, J and Mirasole, A and Bassols, P and Del Campo, J and Teixidó, N},
title = {Interactive effects of ocean acidification and warming disrupt calcification and microbiome composition in bryozoans.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1135},
pmid = {40745023},
issn = {2399-3642},
mesh = {Animals ; *Bryozoa/microbiology/physiology ; *Microbiota ; *Seawater/chemistry ; *Calcification, Physiologic ; Hydrogen-Ion Concentration ; Oceans and Seas ; Carbon Dioxide ; *Global Warming ; Ecosystem ; Climate Change ; Ocean Acidification ; },
abstract = {Marine habitat-forming species provide crucial ecosystem functions and services worldwide. Still, the individual and combined long-term effects of ocean acidification and warming on bryozoan populations, structures, and microbiomes remain unexplored. Here, we investigate the skeletal properties, microbiome shifts, and population trends of two bryozoan species living inside and outside a volcanic CO2 vent, a natural analog to future ocean acidification conditions. We show that bryozoans can acclimatize to acidification by adjusting skeletal properties and maintaining stable microbiomes. However, we document a decrease in microbial genera playing essential functions under acidified conditions. Moreover, we show that ocean acidification exacerbates bryozoan cover loss and mortality caused by ocean warming. The observed shifts in the microbiome and cover suggest that, despite their morphological plasticity, bryozoan species will be heavily impacted by future ocean conditions, posing a threat to many benthic ecosystems in which they play a pivotal role.},
}

Animals
*Bryozoa/microbiology/physiology
*Microbiota
*Seawater/chemistry
*Calcification, Physiologic
Hydrogen-Ion Concentration
Oceans and Seas
Carbon Dioxide
*Global Warming
Ecosystem
Climate Change
Ocean Acidification

@article {pmid40744977,
year = {2025},
author = {Leelahavanichkul, A and Phuengmaung, P and Bhunyakarnjanarat, T and Kaewduangduen, W and Boonnaj, P and Tengamnuay, P and Chancharoenthana, W and Tungsanga, S and Udomkarnjananun, S and Tumwasorn, S},
title = {Lacticaseibacillus rhamnosus attenuates uremic toxins in patients with nondialysis chronic kidney disease through the anti-inflammatory molecules.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27990},
doi = {10.1038/s41598-025-12768-z},
pmid = {40744977},
issn = {2045-2322},
support = {C02F660002//the NSRF through the Program Management Unit for Competitiveness/ ; C02F660002//the NSRF through the Program Management Unit for Competitiveness/ ; },
mesh = {Humans ; *Renal Insufficiency, Chronic/therapy/microbiology ; *Lacticaseibacillus rhamnosus/physiology ; Male ; *Uremic Toxins/metabolism ; Middle Aged ; Female ; *Probiotics/therapeutic use/administration & dosage ; *Anti-Inflammatory Agents/pharmacology ; Indican ; Gastrointestinal Microbiome ; Caco-2 Cells ; Aged ; Adult ; Inflammation ; Dysbiosis ; Neutrophils/metabolism ; },
abstract = {Because of the strain-dependent effect and the lack of simultaneous in vitro test with limited clinical data on Lacticaseibacillus rhamnosus L34 (L34) isolated from the Thai population, L34 was tested and compared with L. rhamnosus GG (LGG). The before and after test using L34 and a randomized placebo-controlled trial using placebo, L34, and LGG, for 4 weeks in patients with non-dialysis chronic kidney disease stage 3-5 (CKD) together with the in vitro experiments using indoxyl sulfate (IS, a representative uremic toxin) were performed. In comparison with the baseline, 4-week-L34 administration reduced gut-derived uremic toxins (GDUTs), except total IS, and attenuated several biomarkers, including i) systemic inflammation, as measured by cytokines and neutrophil extracellular traps using citrullinated histone 3, cell-free DNA, and fluorescent-stained nuclear morphology; ii) gut permeability defect (beta-D-glucan but not by endotoxemia); and iii) gut dysbiosis (fecal microbiome analysis). Additionally, L34-conditioned media attenuated IS-induced injuries on Caco-2 enterocytes, THP-1-derived-macrophages, and isolated neutrophils. Despite the possible different active compounds, both probiotics similarly attenuated IS-induced inflammation in vitro and in patients when compared with the placebo. In conclusion, L34 and LGG similarly attenuated systemic inflammation in patients with CKD, through the improved gut dysbiosis and anti-inflammation.},
}

Humans
*Renal Insufficiency, Chronic/therapy/microbiology
*Lacticaseibacillus rhamnosus/physiology
Male
*Uremic Toxins/metabolism
Middle Aged
Female
*Probiotics/therapeutic use/administration & dosage
*Anti-Inflammatory Agents/pharmacology
Indican
Gastrointestinal Microbiome
Caco-2 Cells
Aged
Adult
Inflammation
Dysbiosis
Neutrophils/metabolism

@article {pmid40747296,
year = {2023},
author = {Ma, J and Zhang, J and Kuang, Z},
title = {A microbiota-epigenetic circuit controls systematic circadian programs in the gut epithelium.},
journal = {Frontiers in systems biology},
volume = {3},
number = {},
pages = {},
pmid = {40747296},
issn = {2674-0702},
abstract = {The intestinal microbiota is an important factor that regulates mammalian circadian rhythms and health. We previously reported that the microbiota synchronizes lipid uptake and metabolism in the intestinal epithelium through histone deacetylase 3 (HDAC3). However, the breadth and significance of microbiota-circadian crosstalk in the intestine are not well understood. Here, we show that the gut microbiota programs the rhythmic expression of a broad range of biological processes, and temporally orchestrates epithelial functions and physiology in accordance with the rhythmic gut environment. Protein synthesis, cell proliferation, and metabolic and immune activities are differentially expressed in the daytime and nighttime respectively, indicating a daily alternation of "working" and "recharging" themes in the gut. The rhythms of gene expression are dampened or altered in germ-free mice, suggesting that the microbiota helps to structure the timing of host gene expression. Further analysis showed that HDAC3 drives a vast majority of these microbiota-dependent circadian programs, likely through rhythmic deacetylation of histones. Motif enrichment analysis revealed that HDAC3 could differentially control distinct rhythmic pathways, most likely by recruiting different transcription factors. These findings provide a systematic view of how the commensal microbiota exploits an epigenetic factor to program just-in-time functions in the intestinal epithelium and maintain host homeostasis.},
}

@article {pmid40744840,
year = {2025},
author = {Zhan, J and Cheng, B and Guo, K and Tao, X and Cai, X and Li, Z and Tang, Z and Zhan, J and Wu, C},
title = {Absolute quantitative metagenomic analysis reveals unique gut bacteria underlying berberine and metformin's anti-metabolic disorders effects.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0008425},
doi = {10.1128/spectrum.00084-25},
pmid = {40744840},
issn = {2165-0497},
abstract = {This study aimed to evaluate the potential functional bacteria in the efficacy of two drugs in ameliorating diet-induced metabolic disorder model using absolute and relative quantification methods and to evaluate the benefit of absolute quantification compared with relative quantification. The gut microbiota is implicated in the pathogenesis of various chronic diseases, including diet-induced metabolic disorder model. Berberine (BBR) and metformin (MET) are commonly used in the clinical management of metabolic disorder, yet their effects on gut microbiota regulation differ. This study employs both relative and absolute quantitative methods to assess the differential impacts of these drugs on the modulation of gut microbiota in metabolic disorder mice. Both BBR and MET effectively ameliorate the condition of metabolic disorder. While some relative quantitative sequencing results contradicted the absolute sequencing data, the latter was more consistent with the actual microbial community composition. Absolute quantitative sequencing provides a more accurate reflection of the drug's effects. Notably, both absolute and relative quantitative sequencing demonstrated an upregulation of Akkermansia.IMPORTANCEOur study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.},
}

@article {pmid40744839,
year = {2025},
author = {Hardman, M and Higgi, S and Hanson, L and Schutz, K and Wargo, MJ and Teneback, CC and Daniels, TWV and van der Gast, C and Rivett, DW},
title = {Nontuberculous mycobacteria remodel lung microbiota in cystic fibrosis-associated respiratory infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0038225},
doi = {10.1128/spectrum.00382-25},
pmid = {40744839},
issn = {2165-0497},
abstract = {Nontuberculous mycobacterial (NTM) infections in people with cystic fibrosis (pwCF) can have detrimental effects on prognosis and pose significant challenges to treatment. However, there are still questions regarding the contribution and influence of NTMs on the respiratory microbiome and the mechanisms by which NTMs cause infections. Here, we investigate the impact of NTM infection on microbiome composition and lung function (percent predicted forced expiratory volume in 1 second). Primary comparisons were between culture-positive cohorts for Mycobacterium avium complex and Mycobacterium abscessus complex and those who were culture-negative for NTMs and attending outpatient clinics. Additionally, the consequence of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy status and positive NTM culture was assessed in terms of microbiome change. Our data suggest that the presence of NTM significantly alters the diversity and the composition of the lung microbiota in pwCF, including those receiving CFTR modulator therapies. Importantly, significant associations were detected between NTM presence and changes in abundance of Pseudomonas aeruginosa and Burkholderia cepacia complex members, inferring modulatory effects of NTMs on respiratory microbiomes. This study contributes to the understanding of NTM infection and these organisms' interaction with the respiratory microbiome and CFTR modulator therapy, highlighting the need for further research in this area.IMPORTANCEThe influence of NTM infection in pwCF is still debated, and the extent of their contribution to mortality and morbidity is still questioned. Findings in this study highlight a link between the presence of NTMs and significant alterations in the composition of the respiratory microbiome, particularly with respect to some of the canonical CF pathogens, especially Pseudomonas aeruginosa and members of the Burkholderia cepacia complex. This indicates that complex relationships are occurring within the microbiome. This study further contributes to the understanding of NTM infection in pwCF, with and without CFTR modulator therapy, and highlights the need for further research in this area. The knowledge gained from this study has implications for treatment strategies and management, ultimately aiming to improve and prolong the lives of pwCF.},
}

@article {pmid40744696,
year = {2025},
author = {Lee, HJ},
title = {Effects of Particulate Matter on Obstructive Sleep Apnea and Obesity.},
journal = {Journal of rhinology : official journal of the Korean Rhinologic Society},
volume = {32},
number = {2},
pages = {67-75},
doi = {10.18787/jr.2025.00016},
pmid = {40744696},
issn = {2384-4361},
support = {//Chung-Ang University/ ; },
abstract = {With accelerated global urbanization, understanding the impact of pollutant emissions and air pollution on obstructive sleep apnea (OSA) and obesity has become increasingly important. Particulate matter (PM) is a major component of air pollution. Recent studies have reported that PM influences OSA, obesity, and obesity-related metabolic disorders. The primary mechanisms proposed to underlie the effects of PM on OSA involve chronic inflammation and oxidative stress in the nasal epithelia. Regarding obesity, PM induces chronic inflammation in the hypothalamus, adipose tissue, skeletal muscle, and mitochondria; oxidative stress in white adipose tissue, the lungs, and the thyroid; activation of lipogenesis genes; changes in adipose tissue distribution; dysbiosis of the intestinal microbiome; and disruption of circadian rhythms. Therefore, reducing air pollution, including PM concentrations, represents a potential strategy for treating OSA and obesity and preventing related complications. Further prospective longitudinal studies in human participants are needed to clarify the effects of PM on the risk of OSA and obesity and to elucidate the underlying mechanisms.},
}

@article {pmid40744347,
year = {2025},
author = {Jacobs, JP and Labus, JS and Dong, TS and Shin, AS and , and Mayer, EA and Chang, L},
title = {Extraintestinal symptoms in irritable bowel syndrome are associated with stress reactivity and the gut microbiome in a sex-dependent manner.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2025.07.026},
pmid = {40744347},
issn = {1542-7714},
}

@article {pmid40744021,
year = {2025},
author = {Komaroff, AL and Dantzer, R},
title = {Causes of symptoms and symptom persistence in long COVID and myalgic encephalomyelitis/chronic fatigue syndrome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102259},
doi = {10.1016/j.xcrm.2025.102259},
pmid = {40744021},
issn = {2666-3791},
abstract = {Debilitating symptoms for many years can follow acute COVID-19 ("long COVID"), myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), and various post-acute infection syndromes (PAISs). Together, long COVID and ME/CFS affect 60-400 million individuals, globally. Many similar underlying biological abnormalities have been identified in both conditions including autoantibodies against neural targets, endothelial dysfunction, acquired mitochondrial dysfunction, and a pro-inflammatory gut microbiome. Each of these abnormalities may directly cause some of the symptoms. In addition, the symptoms also may be caused by ancient, evolutionarily conserved symptomatic and metabolic responses to vital threats-sickness behavior and torpor-responses mediated by specific, recently discovered neural circuits. These neural circuits constitute a symptom-generating pathway, activated by neuroinflammation, which may be targeted by therapeutics to quell neuroinflammation. Many factors cause the symptoms to become chronic, including persistent infectious agents (and/or their nucleic acids and antigens) and the fact that many of the underlying biological abnormalities reinforce each other, creating ongoing physiological vicious cycles.},
}

@article {pmid40744013,
year = {2025},
author = {Arnoldini, M and Sharma, R and Moresi, C and Chure, G and Chabbey, J and Slack, E and Cremer, J},
title = {Quantifying the varying harvest of fermentation products from the human gut microbiota.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.07.005},
pmid = {40744013},
issn = {1097-4172},
abstract = {Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2%-5% of human energy demand for Western diets and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiota's mechanistic functions in health and disease.},
}

@article {pmid40743743,
year = {2025},
author = {Liu, S and Dong, H and Lu, H and Li, Y and Zhang, G and Mi, Y and Wang, X},
title = {Dynamic changes in composition during processing of Lonicerae japonicae flos black tea.},
journal = {Food chemistry},
volume = {493},
number = {Pt 1},
pages = {145684},
doi = {10.1016/j.foodchem.2025.145684},
pmid = {40743743},
issn = {1873-7072},
abstract = {Lonicerae japonicae flos (LJF) black tea is a fermented tea and it is hypothesized that microbial communities have an important role in shaping the functional and aroma components during processing. This study investigated dynamic compositional changes during LJF black tea processing using GC-IMS, LC MS, and microbiome analysis. Chemical analysis showed that processing was associated with increased content of functional components such as quinic acid, kaempferol, and luteolin, as well as aroma components such as acetic acid ethyl ester, 1-hexanol, and nonanal. These changes collectively contributed to the distinct functional chemical profiles and aroma characteristic of LJF black tea. Also, microbial sequencing analysis revealed that bacterial communities, including Bacillus, Staphylococcus and Chryseobacterium spp., were associated with the formation of these chemical profiles, probably via hydrolysis of glycosidic bonds and formation of amino acids or their derivatives, thereby accelerating synthesis of featured volatile components.},
}

@article {pmid40743285,
year = {2025},
author = {Herman, C and Bolyen, E and Simard, A and Gehret, L and Caporaso, JG},
title = {Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013299},
doi = {10.1371/journal.pcbi.1013299},
pmid = {40743285},
issn = {1553-7358},
abstract = {We present q2-fmt, a QIIME 2 plugin that provides diverse methods for assessing the extent of microbiome engraftment following fecal microbiota transplant. The methods implemented here were informed by a recent literature review on approaches for assessing FMT engraftment, and cover aspects of engraftment including Community Coalescence, Indicator Features, and Resilience. q2-fmt is free for all use, and detailed documentation illustrating worked examples on a real-world data set are provided in the project's documentation.},
}

@article {pmid40742986,
year = {2025},
author = {Manica-Cattani, MF and Mânica da Cruz, IB and Sato-Miyata, Y and Trindade, LS and Rogalski, F and Ribeiro, EE and Tsuda, M and Aigaki, T},
title = {Characterization of a Drosophila model to study functions of guarana seeds.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0328985},
doi = {10.1371/journal.pone.0328985},
pmid = {40742986},
issn = {1932-6203},
mesh = {Animals ; *Drosophila melanogaster/physiology/genetics/drug effects/metabolism ; Longevity/drug effects ; Oxidative Stress/drug effects ; *Seeds/chemistry ; *Paullinia/chemistry ; Transcriptome ; Female ; Fertility/drug effects ; Feces/microbiology ; Male ; Metabolomics ; },
abstract = {The seeds of the Amazonian fruit, guarana (Paullinia cupana), have been used as traditional medicine and, in recent years, as an ingredient in commercial energy beverages. However, mechanisms underlying the beneficial effects of guarana are not well understood. To establish a model system to study molecular mechanisms underlying the beneficial effects of guarana, we investigated how its ingestion affects physiology in the fruit fly, Drosophila melanogaster. We found that guarana enhanced oxidative stress resistance, longevity, physical activity, and fecundity of flies. To deepen our understanding of guarana function, we performed transcriptomic, metabolomic, and fecal microbiome analyses. Transcriptomic analysis identified 58 upregulated and eight downregulated genes in guarana-fed flies. Highly upregulated genes included those encoding detoxification enzymes, such as cytochromes P450 (CYPs), glutathione S-transferases (GSTs), and Juvenile hormone epoxide hydrolase 1 (Jheh1). Metabolomic analysis identified glutathione metabolism, an antioxidant system, as being promoted by guarana ingestion. These findings likely represent the molecular basis for enhanced oxidative stress resistance and longevity in guarana-fed flies. We also analyzed fecal microbiota composition and found significant changes: guarana increased the proportion of probiotic Lactobacillus species, some species known to extend longevity. At the same time, it decreased the proportion of Enterococcus faecalis, a species known to reduce longevity. These changes might have contributed to the beneficial effects of dietary guarana. Thus, we demonstrate that guarana exerts beneficial effects in flies and provide fundamental data for further investigation of its biological mechanisms in Drosophila.},
}

Animals
*Drosophila melanogaster/physiology/genetics/drug effects/metabolism
Longevity/drug effects
Oxidative Stress/drug effects
*Seeds/chemistry
*Paullinia/chemistry
Transcriptome
Female
Fertility/drug effects
Feces/microbiology
Male
Metabolomics

@article {pmid40742978,
year = {2025},
author = {Reig, A},
title = {Chronic endometritis, chronic questions: a narrative review of current practices.},
journal = {Current opinion in obstetrics & gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1097/GCO.0000000000001053},
pmid = {40742978},
issn = {1473-656X},
abstract = {PURPOSE OF REVIEW: Chronic endometritis is a condition that may affect reproductive outcomes, particularly in patients with unexplained infertility, recurrent implantation failure, or recurrent pregnancy loss. This review concisely summarizes the available literature, highlighting some of the controversies on this topic.

RECENT FINDINGS: Although embryo selection through preimplantation genetic testing for aneuploidy has improved, many euploid embryo transfers still fail, prompting interest in endometrial factors such as chronic endometritis. Chronic endometritis is typically asymptomatic and diagnosed by identifying plasma cells in endometrial biopsy specimens; however, diagnostic criteria vary widely regarding biopsy timing, staining techniques, and threshold definitions, contributing to inconsistent prevalence and outcomes across studies. It is often attributed to chronic infection and is treated with empirical or culture-guided antibiotics, though reported cure rates vary significantly. While some studies suggest that treating chronic endometritis improves reproductive outcomes, evidence is limited by methodological heterogeneity. Meta-analyses support treatment, yet diagnostic inconsistencies and potential effects of antibiotics on the microbiome remain concerns.

SUMMARY: While frequently diagnosed in the infertility setting, the true prevalence and impact of chronic endometritis remain unclear. The heterogeneity of the existing literature and the lack of large prospective cohort studies remain challenges to fully understanding the condition, particularly regarding the general infertile population.},
}

@article {pmid40742751,
year = {2025},
author = {Fischer, MT and Xue, KS and Costello, EK and Dvorak, M and Raboisson, G and Robaczewska, A and Caty, SN and Relman, DA and O'Connell, LA},
title = {Effects of parental care on skin microbial community composition in poison frogs.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.103331},
pmid = {40742751},
issn = {2050-084X},
support = {DP2HD102042/NH/NIH HHS/United States ; Erwin Schroedinger Stipend J-4526B//Austrian Science Fund/ ; },
mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Anura/microbiology/physiology ; Larva/microbiology ; Female ; Male ; *Bacteria/classification/isolation & purification/genetics ; Poison Frogs ; },
abstract = {Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects and shaping host health and disease. Microbe acquisition during parental care is well studied in humans and agriculturally relevant species but remains poorly understood in other vertebrate groups, such as amphibians. Here, we investigate vertical transmission of skin microbiota in poison frogs (Dendrobatidae), where fathers transport tadpoles piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of embryos begins after hatching, suggesting that the vitelline envelope acts as a microbial barrier. A cross-foster experiment demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts skin communities of tadpoles in an ecologically relevant setting, we sampled sympatric species that do or do not exhibit tadpole transport in their natural habitat. We did not find a higher degree of similarity between microbial communities of tadpoles and adults in species that transport their offspring compared to those that do not. Similarly, communities of tadpoles were no more similar to their caregiver than to unrelated adults, indicating that most caregiver-associated microbes do not remain in tadpole communities long-term. Nonetheless, some taxa persisted on tadpoles over development. This study is the first to demonstrate that offspring transport facilitates transmission of parental skin microbes in anurans.},
}

Animals
*Skin/microbiology
*Microbiota
*Anura/microbiology/physiology
Larva/microbiology
Female
Male
*Bacteria/classification/isolation & purification/genetics
Poison Frogs

@article {pmid40742547,
year = {2025},
author = {Shedaliya, U and Adwani, G and Anju, TR and Krishnakumar, A and Kumar, A},
title = {Role of the microbiome in diabetic wound healing: implications for new therapeutic approaches.},
journal = {Archives of microbiology},
volume = {207},
number = {9},
pages = {208},
pmid = {40742547},
issn = {1432-072X},
mesh = {Humans ; *Wound Healing ; *Microbiota ; *Skin/microbiology ; Animals ; Probiotics/therapeutic use ; *Diabetes Complications/microbiology/therapy ; Dysbiosis/microbiology ; *Diabetes Mellitus/microbiology ; },
abstract = {Diabetic wounds present a persistent clinical challenge due to delayed healing and an increased risk of infection and complications. The rising global prevalence of diabetes and the associated burden of chronic, non-healing wounds highlight the urgent need for innovative and effective therapeutic strategies. Recent research has underscored the critical yet often overlooked role of the skin microbiome in modulating wound healing outcomes. This review explores the complex interactions between the skin microbiome and diabetic wound healing, aiming to inform the development of microbiome-based interventions. The review begins by outlining the composition and physiological functions of the skin microbiome, emphasizing its roles in maintaining cutaneous homeostasis, immune regulation, and barrier integrity. It then examines how diabetes-induced hyperglycemia disrupts microbial balance, leading to dysbiosis, impaired immune responses, and increased colonization by opportunistic pathogens. These alterations contribute to the formation of persistent biofilms, chronic inflammation, impaired angiogenesis, and ultimately, delayed wound repair. Mechanisms by which the microbiome exacerbates wound pathology are discussed, alongside emerging therapeutic strategies targeting the wound microbiota. These include probiotics, prebiotics, bacteriophage therapy, antimicrobial peptides, and microbiome-responsive dressings. Innovative approaches such as photoimmuno-antimicrobial therapies and advanced drug delivery systems are also considered for their potential to enhance treatment efficacy. Despite these promising developments, significant challenges remain in deciphering the full complexity of microbiome-host interactions and translating this knowledge into clinical practice. The review emphasizes the future potential of personalized, microbiome-based therapies tailored to individual microbial profiles and advocates for a precision medicine approach to diabetic wound care. Additionally, it highlights the need for further research into non-bacterial components of the microbiome and the integration of multi-omics technologies with advanced wound management strategies.},
}

Humans
*Wound Healing
*Microbiota
*Skin/microbiology
Animals
Probiotics/therapeutic use
*Diabetes Complications/microbiology/therapy
Dysbiosis/microbiology
*Diabetes Mellitus/microbiology

@article {pmid40742521,
year = {2025},
author = {Shen, Y and Meng, L and Li, Y and Yang, J},
title = {Bacteroides ovatus Has the Potential to Be a Next-Generation Probiotic Strain.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40742521},
issn = {1867-1314},
support = {(CX (24) 1020)//the Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund Project/ ; No. BK20233003//the Jiangsu Basic Research Center for Synthetic Biology Grant/ ; No. 32200154//National Natural Science Foundation of China/ ; },
abstract = {Bacteroides ovatus (B. ovatus), a key member of the gut microbiota, is strongly associated with host health, thereby emerging as a promising candidate for the development of next-generation probiotics. This bacterium is linked to various pathophysiological conditions and shows potential probiotic biological activity, particularly in modulating metabolism and treating certain diseases. In the present review, we aim to provide a comprehensive synthesis of the established biological attributes of B. ovatus, while also elucidating the patterns and characteristics of its abundance fluctuations across diverse clinical indications. We also investigate the influence of probiotics, prebiotics, natural products, dietary patterns, and other extrinsic factors on the dynamic changes in B. ovatus abundance. Additionally, an evaluative and prospective analysis of the potential applications of B. ovatus in the realms of functional nutrition and specialized medical foods is presented. Finally, we highlight the transformative potential of B. ovatus in functional nutrition and specialized medical foods, providing a basis for the development of novel microbiome preparations.},
}

@article {pmid40742509,
year = {2025},
author = {Aziz, T and Shabbir, MA and Sarwar, A and Yang, Z and Lin, L and Al-Megrin, WAI and Shami, A and Alwethaynani, MS and Alhhazmi, AA and Al-Asmari, F and Al-Joufi, FA and Fallatah, D},
title = {Revealing Lactiplantibacillus Plantarum K25 Derived (Z)-18-Octadec-9-Enolide in Modulating Aquaporin-8 in Colorectal Cancer by Bridging the Gut Microbiome and Membrane Biology.},
journal = {Cell biochemistry and biophysics},
volume = {},
number = {},
pages = {},
pmid = {40742509},
issn = {1559-0283},
}

@article {pmid40742382,
year = {2025},
author = {Hutchings, B and López-Legentil, S and Stefaniak, LM and Nydam, ML and Erwin, PM},
title = {Depuration of a solitary ascidian depletes transient bacteria without altering microbiome alpha-diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf078},
pmid = {40742382},
issn = {1574-6941},
abstract = {Depuration, or the process of clearing impurities from the gut, is commonly applied to marine food products due to its efficacy at removing human pathogens from shellfish and edible ascidians. Recent studies also reported applications to gut microbiome studies, where depuration of filter-feeding animals helped reduce transient bacteria and identify resident symbionts. Here, we examined the impact of depuration on bacteria in the branchial sac, gut, and hepatic gland of the solitary ascidian Pyura vittata. Replicates were kept in filtered seawater for four days prior to dissection ("aquaria-depuration") and compared to samples that were immediately processed following collection ("wild-no depuration") and replicates kept in unfiltered seawater for four days ("aquaria-control"). 16S rRNA gene sequence analysis revealed no significant differences among ascidian sources for microbial alpha-diversity but significant shifts in beta-diversity. Depuration reduced the number of core bacteria markedly (66-84%) across all body regions, and bacteria that remained post-depuration consisted of genera associated with enhanced host health and resilience within other marine symbioses. Our results suggest that microbial profiles obtained following depuration do not substantially differ from those of non-depurated animals, but depuration can help differentiate transient from core and resident taxa in complex host-microbiome symbioses.},
}

@article {pmid40742353,
year = {2025},
author = {Yang, Y and Duan, Y and Su, C and Sheng, J and Zhu, L and Xie, Y and Liu, H and Tang, N and Qiu, Y and Lu, C and Chen, C and Mao, L and Fu, X},
title = {The impact of preoperative biliary drainage on bile colonization of patients undergoing pancreaticoduodenectomy.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2540024},
doi = {10.1080/07853890.2025.2540024},
pmid = {40742353},
issn = {1365-2060},
mesh = {Humans ; *Pancreaticoduodenectomy/adverse effects/methods ; Female ; Male ; *Drainage/methods/adverse effects ; Retrospective Studies ; Middle Aged ; *Bile/microbiology ; Aged ; *Surgical Wound Infection/epidemiology/microbiology/etiology/prevention & control ; *Preoperative Care/methods/adverse effects ; Risk Factors ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Preoperative biliary drainage (PBD) may be performed for jaundiced patients with periampullary tumors. This study aimed to evaluate the impact of PBD on biliary microbiome and perioperative complications in patients undergoing pancreaticoduodenectomy (PD).

METHODS: This retrospective study enrolled 323 patients who underwent PD between March 2018 and March 2024. Intraoperative bile specimens were obtained for microbiological analysis of species identification and antimicrobial resistance patterns..

RESULTS: PBD was performed in 191 (59.1%) of the 323 patients. Organ/space surgical site infection (SSI) (51.8% vs 37.9%, p < 0.001) and bacterial colonization of bile (90.6% vs 28.0%, p < 0.001) were significantly more frequent in patients with PBD. PBD was identified as an independent risk factor of organ/space SSI (OR = 1.837, 95% CI: 1.158-2.916, p = 0.010) and associated with increased contamination with polymicrobial mixed flora (47.1% vs 4.5%, p < 0.001), K. pneumoniae (23.6% vs 0.8%, p < 0.001), E. faecalis (14.1% vs 1.5%, p < 0.001), E. faecium (6.8% vs 0.8%, p = 0.009). This shift corresponded to higher resistance to piperacillin-tazobactam (23.1% vs 0.0%, p = 0.038), cefoperazone-sulbactam (25.3% vs 0.0%, p = 0.021), ciprofloxacin (36.1% vs 6.3%, p = 0.006), and levofloxacin (47.4% vs 4.8%, p < 0.001). Patients with positive bile culture had a significantly higher occurrence of organ/space SSI than the negative group (53.3% vs 32.7%, p < 0.001). K. pneumoniae was identified as an independent risk factor for organ/space SSI (OR = 2.636, 95% CI: 1.353-5.137, p = 0.004).

CONCLUSIONS: There were fundamental differences in the bile microbiome profile and antibiotic resistance of patients with/without PBD. These findings suggest that adjusting perioperative antibiotic regimens based on biliary culture may be warranted.},
}

Humans
*Pancreaticoduodenectomy/adverse effects/methods
Female
Male
*Drainage/methods/adverse effects
Retrospective Studies
Middle Aged
*Bile/microbiology
Aged
*Surgical Wound Infection/epidemiology/microbiology/etiology/prevention & control
*Preoperative Care/methods/adverse effects
Risk Factors
Anti-Bacterial Agents/therapeutic use

@article {pmid40742298,
year = {2025},
author = {Morder, KM and Nguyen, M and Wilfahrt, DN and Dahmani, ZL and Burr, AB and Xie, B and Morikone, M and Nieves-Rosado, H and Gunn, WG and Hurd, DE and Wang, H and Mullett, SJ and Bossong, K and Gelhaus, SL and Rajasundaram, D and Kane, LP and Delgoffe, GM and Das, J and Davar, D and Overacre-Delgoffe, AE},
title = {Sucralose consumption ablates cancer immunotherapy response through microbiome disruption.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-25-0247},
pmid = {40742298},
issn = {2159-8290},
abstract = {Gut microbiota composition is directly associated with response to immunotherapies in cancer. How the diet impacts the gut microbiota and downstream immune responses to cancer remains unclear. Here, we show that consumption of a common non-nutritive sweetener, sucralose, modifies microbiome composition, restricts T cell metabolism and function, and limits immunotherapy response in preclinical models of cancer and advanced cancer patients treated with anti-PD-1 based immune checkpoint inhibitors (ICIs). Sucralose consumption is associated with a reduction in microbiota-accessible arginine, and amino acid supplementation or fecal microbiome transfer (FMT) from anti-PD-1 responder mice completely restores T cell function and immunotherapy response. Overall, sucralose consumption destabilizes the gut microbiota, resulting in compromised T cell function and ablated ICI response in cancer.},
}

@article {pmid40742180,
year = {2025},
author = {Tang, G and Carr, AV and Perez, C and Ramos Sarmiento, K and Levy, L and Lampe, JW and Diener, C and Gibbons, SM},
title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0098425},
doi = {10.1128/msystems.00984-25},
pmid = {40742180},
issn = {2379-5077},
abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, quantitative polymerase chain reaction (qPCR), or spike-ins, can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read count ratios. We compared B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. B:H ratios in stool were correlated with bacterial-to-diet (B:D) read count ratios, but B:D ratios exhibited a substantial number of outlier points. Host read depletion methods reduced the total number of human reads in a given sample, but B:H ratios were strongly correlated before and after host read depletion, indicating that host read depletion did not reduce the utility of B:H ratios. B:H ratios showed expected variation between health and disease states and were generally stable in healthy individuals over time. Finally, we showed how B:H and B:D ratios can be used to track antibiotic treatment response and recovery. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning, enabling robust absolute biomass estimates directly from stool metagenomic data.IMPORTANCEIn this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, additional experimental biomass measurements, or training data. The approach assumes that the contribution of host DNA to stool is more constant or stable than biologically relevant fluctuations in bacterial biomass. We find that host read normalization is an effective method for detecting variation in gut bacterial biomass. Absolute bacterial biomass is a key metric that often gets left out of gut microbiome studies, and empowering researchers to include this measure more broadly in their metagenomic analyses should serve to improve our understanding of host-microbiota interactions.},
}

@article {pmid40742109,
year = {2025},
author = {Jones, KR and Song, Y and Rinaldi, SS and Moran, NA},
title = {Effects of priority on strain-level composition of the honey bee gut community.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0082825},
doi = {10.1128/aem.00828-25},
pmid = {40742109},
issn = {1098-5336},
abstract = {Host-associated microbiomes are complex communities shaped by interactions between members. The type VI secretion system (T6SS), among other bacterial weapons, allows gram-negative bacteria to deliver toxic effectors into competitors. In this study, we investigated the impact of differential colonization timing on the competitive advantage associated with T6SS possession using Snodgrassella alvi, a core symbiont of the honey bee gut microbiome. Following a timeline based on the natural establishment window of the gut microbiome, we sequentially inoculated newly emerged bees with fluorescently labeled strains that differed in presence of the T6SS-1. When inoculated simultaneously, the T6SS-1-possessing strain (wkB2) consistently excluded the T6SS-1-lacking strain (wkB332); however, when given a 5-day advantage, the second strain was consistently excluded regardless of strain identities. With a 1-day advantage, the effect of priority was weakened, but wkB332 was able to persist following introduction of wkB2. Utilizing a wkB2 T6SS-1 knockout strain, we repeated our 24 hour priority experiments and found that the T6SS-1 contributes to invasion outcomes along with other mechanisms of competition. Through fluorescent microscopy, we explored how coexisting strains in these experimental scenarios organize spatially within the bee ileum. Our results demonstrate that colonization timing can have lasting consequences for strain composition of the established microbiome. These findings illustrate the influence of stochastic processes in microbial community assembly and emphasize that differences in colonization timing may alter competitive outcomes between taxa, impacting taxon coexistence.IMPORTANCEThe bacterial gut communities of honey bees possess considerable strain-level diversity between hives, between individual bees, and within individual bees. However, the factors underlying strain coexistence are unclear. Here, we provide support for timing of colonization, or priority effects, as one factor driving this strain-level diversity. Our results show that priority inoculation can prevent colonization by subsequent competing bacterial strains and mitigate advantages conferred through bacterial weaponry. Further, a brief window of priority can facilitate the coexistence of strongly and weakly competitive strains within single bees. These results add to our understanding of the impacts of priority effects in host-associated microbial communities. Such an understanding can aid the development of future probiotic strategies aimed at improving honey bee health.},
}

@article {pmid40742104,
year = {2025},
author = {Vieira, FC and Mandadi, KK and Ramasamy, M and de Souza, A and Callahan, K and Fyle, C and Kamemoto, A and Koontz, AG and Yang, C and Crowley, R and Kou, KGM and Maloney, KN and Roper, MC},
title = {Amicoumacins produced by the native citrus microbiome isolate Bacillus safensis inhibit the Huanglongbing-associated bacterial pathogen "Candidatus Liberibacter asiaticus".},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0086925},
doi = {10.1128/aem.00869-25},
pmid = {40742104},
issn = {1098-5336},
abstract = {Huanglongbing (HLB) is a devastating citrus disease associated with the gram-negative, phloem-limited, and unculturable bacterium "Candidatus Liberibacter asiaticus (CLas)," which is transmitted by the Asian citrus psyllid Diaphorina citri. Despite extensive research, effective, long-term, and sustainable solutions for managing HLB remain elusive. Oxytetracycline (OTC) is currently used as an emergency measure, but there is an urgent need for alternative compounds to complement or replace OTC. In this study, we identified amicoumacins, a class of antimicrobial compounds produced by the bacterium Bacillus safensis CB729 isolated from the citrus microbiome, and demonstrated their ability to suppress CLas. Genome mining of B. safensis CB729, combined with metabolomic analysis and bioassay-guided fractionation, revealed the presence of amicoumacins and related derivatives in fractions inhibitory to Liberibacter crescens, a culturable surrogate for CLas. We tested commercially available synthetic amicoumacins A and B, along with a B. safensis-derived amicoumacin mixture, against L. crescens and CLas. We determined the MICs of amicoumacin A (1.25 µg/mL) and amicoumacin B (10 µg/mL) against L. crescens. Furthermore, amicoumacin B and the amicoumacin mixture significantly reduced CLas populations in ex vivo citrus hairy root assays. This study highlights the potential of amicoumacins as a promising group of natural products for the management of HLB, offering valuable insights for the development of novel and sustainable disease control strategies.IMPORTANCEFor two decades, the citrus industry has been severely impacted by Huanglongbing (HLB), a devastating disease caused by "Candidatus Liberibacter asiaticus (CLas)" and transmitted by the Asian citrus psyllid (Diaphorina citri). Despite extensive research, effective, long-term, and sustainable solutions remain unavailable for growers. Currently, medically relevant antibiotics, such as oxytetracycline (OTC), are used as an emergency response to combat HLB in Florida, the most affected citrus-producing state in the U.S. This underscores the urgent need for alternative treatments that can be used in rotation or as replacements for OTC. Here, we present amicoumacins, a group of bioactive secondary metabolites with antibiotic properties. We identified amicoumacin B and its derivatives from the culture broth of a Bacillus safensis isolate, native to citrus, and demonstrated their ability to inhibit Liberibacter spp. and reduce CLas populations in citrus tissue. This study highlights how microbial discovery can lead to the identification of antimicrobial compounds with potential applications in plant disease management.},
}

@article {pmid40742099,
year = {2025},
author = {Skupa, SA and Cooper, KM and Smith, AL and Drengler, EM and Eiken, AP and Schmitz, E and Waldron, GM and Mathew, G and Primeaux, M and Dhawan, P and Talmon, GA and D'Angelo, CR and El-Gamal, D},
title = {Gut microbiome profiling in Eµ-TCL1 mice reveals intestinal changes and a dysbiotic signature specific to chronic lymphocytic leukemia.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-25-0022},
pmid = {40742099},
issn = {2767-9764},
abstract = {The gut microbiome's role in the pathogenesis of hematological malignancies is actively being explored; yet studies in chronic lymphocytic leukemia (CLL) are limited. Using the Eµ-TCL1 murine model of CLL, we identify a unique and dysbiotic disease-associated gut microbiome that develops in mice over time. Leukemic mice show an increase in abundance of pathogenic bacteria, specifically members of the Proteobacteria phylum. We found that this dysbiotic microenvironment is associated with CLL involvement within the intestinal tract and high levels of markers indicative of altered tight junction permeability (e.g., CLDN2, sCD14, zonulin). Moreover, utilizing the syngeneic model of CLL in tandem with a microflora antibiotic-ablation approach, we found that leukemic mice receiving microflora-ablating antibiotics show marked changes to the gut microbiome and a delayed disease onset compared to mice receiving antibiotics-free water. Immunophenotyping of murine spleens showed that this delay in disease was accompanied by more tumor-reactive CD8+ T cells that co-expressed fewer inhibitory receptors (e.g., PD-1, LAG3, TIM3). These findings confirm a dysbiotic gut microbiome develops during CLL disease and demonstrate unique intestinal involvement and potential immune dysregulation occurring during CLL progression that may be influencing the overall microbial signature.},
}